Publications

Publications

2018

*
Protein inference using PIA workflows and PSI standard file formats
Uszkoreit J, Perez-Riverol Y, Eggers B, Marcus K, Eisenacher M. Preprint DOI: 10.1101/424473
ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature.
Dalkiran A, Rifaioglu AS, Martin MJ, Cetin-Atalay R, Atalay V, Doğan T. BMC bioinformatics Volume 19 (2018) p.334 DOI: 10.1186/s12859-018-2368-y
*
VEP-G2P: A Tool for Efficient, Flexible and Scalable Diagnostic Filtering of Genomic Variants
Thormann A, Halachev M, McLaren W, Moore DJ, Svinti V, Campbell A, Kerr SM, Hunt S, Dunlop MG, Hurles ME, Wright CF, Firth HV, Cunningham F, FitzPatrick D. Preprint DOI: 10.1101/416552
IQSEC2-related encephalopathy in males and females: a comparative study including 37 novel patients.
Mignot C, McMahon AC, Bar C, Campeau PM, Davidson C, Buratti J, Nava C, Jacquemont ML, Tallot M, Milh M, Edery P, Marzin P, Barcia G, Barnerias C, Besmond C, Bienvenu T, Bruel AL, Brunga L, Ceulemans B, Coubes C, Cristancho AG, Cunningham F, Dehouck MB, Donner EJ, Duban-Bedu B, Dubourg C, Gardella E, Gauthier J, Geneviève D, Gobin-Limballe S, Goldberg EM, Hagebeuk E, Hamdan FF, Hančárová M, Hubert L, Ioos C, Ichikawa S, Janssens S, Journel H, Kaminska A, Keren B, Koopmans M, Lacoste C, Laššuthová P, Lederer D, Lehalle D, Marjanovic D, Métreau J, Michaud JL, Miller K, Minassian BA, Morales J, Moutard ML, Munnich A, Ortiz-Gonzalez XR, Pinard JM, Prchalová D, Putoux A, Quelin C, Rosen AR, Roume J, Rossignol E, Simon MEH, Smol T, Shur N, Shelihan I, Štěrbová K, Vyhnálková E, Vilain C, Soblet J, Smits G, Yang SP, van der Smagt JJ, van Hasselt PM, van Kempen M, Weckhuysen S, Helbig I, Villard L, Héron D, Koeleman B, Møller RS, Lesca G, Helbig KL, Nabbout R, Verbeek NE, Depienne C. Genetics in medicine : official journal of the American College of Medical Genetics (2018) DOI: 10.1038/s41436-018-0268-1
An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures.
Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Young MD, Berna J, Tubio JMC, McMurran CE, Young AMH, Sanders M, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson MD, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott MW, Kirollos RW, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U. Scientific reports Volume 8 (2018) p.13537 DOI: 10.1038/s41598-018-31659-0
*
Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants
McCarthy DJ, Rostom R, Huang Y, Kunz DJ, Danecek P, Bonder MJ, Hagai T, Wang W, Gaffney DJ, Simons BD, Stegle O, Teichmann SA, HipSci Consortium. Preprint DOI: 10.1101/413047
*
In silico Prioritization of Transporter–Drug Relationships From Drug Sensitivity Screens.
César-Razquin A, Girardi E, Yang M, Brehme M, Saez-Rodriguez J, Superti-Furga G. Frontiers in pharmacology Volume 9 (2018) DOI: 10.3389/fphar.2018.01011
Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils.
Grassi L, Pourfarzad F, Ullrich S, Merkel A, Were F, Carrillo-de-Santa-Pau E, Yi G, Hiemstra IH, Tool ATJ, Mul E, Perner J, Janssen-Megens E, Berentsen K, Kerstens H, Habibi E, Gut M, Yaspo ML, Linser M, Lowy E, Datta A, Clarke L, Flicek P, Vingron M, Roos D, van den Berg TK, Heath S, Rico D, Frontini M, Kostadima M, Gut I, Valencia A, Ouwehand WH, Stunnenberg HG, Martens JHA, Kuijpers TW. Cell reports Volume 24 (2018) p.2784-2794 DOI: 10.1016/j.celrep.2018.08.018
Mass spectrometry evaluation of a neuroblastoma SH-SY5Y cell culture protocol.
Murillo JR, Pla I, Goto-Silva L, Nogueira FCS, Domont GB, Perez-Riverol Y, Sánchez A, Junqueira M. Analytical biochemistry Volume 559 (2018) p.51-54 DOI: 10.1016/j.ab.2018.08.013
The germline genetic component of drug sensitivity in cancer cell lines.
Menden MP, Casale FP, Stephan J, Bignell GR, Iorio F, McDermott U, Garnett MJ, Saez-Rodriguez J, Stegle O. Nature communications Volume 9 (2018) p.3385 DOI: 10.1038/s41467-018-05811-3
The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for bluetongue virus.
Morales-Hojas R, Hinsley M, Armean IM, Silk R, Harrup LE, Gonzalez-Uriarte A, Veronesi E, Campbell L, Nayduch D, Saski C, Tabachnick WJ, Kersey P, Carpenter S, Fife M. BMC genomics Volume 19 (2018) p.624 DOI: 10.1186/s12864-018-5014-1
*
Fast Batch Alignment of Single Cell Transcriptomes Unifies Multiple Mouse Cell Atlases into an Integrated Landscape
Park J, Polanski K, Meyer K, Teichmann SA. Preprint DOI: 10.1101/397042
Scaling up data curation using deep learning: An application to literature triage in genomic variation resources.
Lee K, Famiglietti ML, McMahon A, Wei CH, MacArthur JAL, Poux S, Breuza L, Bridge A, Cunningham F, Xenarios I, Lu Z. PLoS computational biology Volume 14 (2018) p.e1006390 DOI: 10.1371/journal.pcbi.1006390
Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting.
Iorio F, Behan FM, Gonçalves E, Bhosle SG, Chen E, Shepherd R, Beaver C, Ansari R, Pooley R, Wilkinson P, Harper S, Butler AP, Stronach EA, Saez-Rodriguez J, Yusa K, Garnett MJ. BMC genomics Volume 19 (2018) p.604 DOI: 10.1186/s12864-018-4989-y
Terminal uridylyltransferases target RNA viruses as part of the innate immune system.
Le Pen J, Jiang H, Di Domenico T, Kneuss E, Kosałka J, Leung C, Morgan M, Much C, Rudolph KLM, Enright AJ, O'Carroll D, Wang D, Miska EA. Nature structural & molecular biology Volume 25 (2018) p.778-786 DOI: 10.1038/s41594-018-0106-9
CTCF maintains regulatory homeostasis of cancer pathways.
Aitken SJ, Ibarra-Soria X, Kentepozidou E, Flicek P, Feig C, Marioni JC, Odom DT. Genome biology Volume 19 (2018) p.106 DOI: 10.1186/s13059-018-1484-3
*
Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development
Boroviak T, Stirparo GG, Dietmann S, Herraez IH, Mohammed H, Reik W, Smith A, Sasaki E, Nichols J, Bertone P. Preprint DOI: 10.1101/385815
*
Common ELIXIR Service for Researcher Authentication and Authorisation
Linden M, Prochazka M, Lappalainen I, Bucik D, Vyskocil P, Kuba M, Silén S, Belmann P, Sczyrba A, Newhouse S, Matyska L, Nyrönen T. Preprint DOI: 10.12688/f1000research.15161.1
Registered access: authorizing data access.
Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, Flicek P. European journal of human genetics : EJHG (2018) DOI: 10.1038/s41431-018-0219-y
*
The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform
Matthews TC, Bristow FR, Griffiths EJ, Petkau A, Adam J, Dooley D, Kruczkiewicz P, Curatcha J, Cabral J, Fornika D, Winsor GL, Courtot M, Bertelli C, Roudgar A, Feijao P, Mabon P, Enns E, Thiessen J, Keddy A, Isaac-Renton J, Gardy JL, Tang P, Carrico JA, Chindelevitch L, Chauve C, Graham MR, McArthur AG, Taboada EN, Beiko RG, Brinkman FS, Hsiao WW, Van Domselaar G, The IRIDA Consortium. Preprint DOI: 10.1101/381830
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases.
Rifaioglu AS, Atas H, Martin MJ, Cetin-Atalay R, Atalay V, Dogan T. Briefings in bioinformatics (2018) DOI: 10.1093/bib/bby061
*
In silico prioritization of transporter-drug relationships from drug sensitivity screens
Cesar-Razquin A, Girardi E, Yang M, Brehme M, Saez-Rodriguez J, Superti-Furga G. Preprint DOI: 10.1101/381335
*
Microarray-Based quality assessment as a supporting criterion for de novo transcriptome assembly selection.
Carvajal-Lopez P, Von Borstel FD, Torres A, Rustici G, Gutierrez J, Romero-Vivas E. IEEE/ACM transactions on computational biology and bioinformatics (2018) DOI: 10.1109/tcbb.2018.2860997
The Standard Output: A Tool-Agnostic Modeling Storage Format.
Terranova N, Smith MK, Nordgren R, Comets E, Lavielle M, Harling K, Hooker AC, Sarr C, Mentré F, Yvon F, Swat MJ. CPT: pharmacometrics & systems pharmacology (2018) DOI: 10.1002/psp4.12339
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations.
Tang H, Finn RD, Thomas PD. Bioinformatics (Oxford, England) (2018) DOI: 10.1093/bioinformatics/bty625
SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation.
Jankauskaite J, Jiménez-García B, Dapkunas J, Fernández-Recio J, Moal IH. Bioinformatics (Oxford, England) (2018) DOI: 10.1093/bioinformatics/bty635
A High-Resolution Genetic Map for the Laboratory Rat.
Littrell J, Tsaih SW, Baud A, Rastas P, Solberg-Woods L, Flister MJ. G3 (Bethesda, Md.) Volume 8 (2018) p.2241-2248 DOI: 10.1534/g3.118.200187
Alignment Modulates Ancestral Sequence Reconstruction Accuracy.
Vialle RA, Tamuri AU, Goldman N. Molecular biology and evolution Volume 35 (2018) p.1783-1797 DOI: 10.1093/molbev/msy055
Future Prospects of Spectral Clustering Approaches in Proteomics.
Perez-Riverol Y, Vizcaíno JA, Griss J. Proteomics Volume 18 (2018) p.e1700454 DOI: 10.1002/pmic.201700454
HMMER web server: 2018 update.
Potter SC, Luciani A, Eddy SR, Park Y, Lopez R, Finn RD. Nucleic acids research Volume 46 (2018) p.W200-W204 DOI: 10.1093/nar/gky448
Gene expression-based drug repurposing to target aging.
Dönertaş HM, Fuentealba Valenzuela M, Partridge L, Thornton JM. Aging cell (2018) p.e12819 DOI: 10.1111/acel.12819
The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis.
Melamed A, Yaguchi H, Miura M, Witkover A, Fitzgerald TW, Birney E, Bangham CR. eLife Volume 7 (2018) DOI: 10.7554/eLife.36245
*
Spatial Organization of Rho GTPase signaling by RhoGEF/RhoGAP proteins
Mueller PM, Rademacher J, Bagshaw RD, Alp KM, Giudice G, Heinrich LE, Barth C, Eccles RL, Sanchez-Castro M, Brandenburg L, Mbamalu G, Tucholska M, Spatt L, Wortmann C, Czajkowski MT, Welke RW, Zhang S, Nguyen V, Rrustemi T, Trnka P, Freitag K, Larsen B, Popp O, Mertins P, Bakal C, Gingras A, Pertz O, Roth FP, Colwill K, Pawson T, Petsalaki E, Rocks O. Preprint DOI: 10.1101/354316
A microfluidics platform for combinatorial drug screening on cancer biopsies.
Eduati F, Utharala R, Madhavan D, Neumann UP, Longerich T, Cramer T, Saez-Rodriguez J, Merten CA. Nature communications Volume 9 (2018) p.2434 DOI: 10.1038/s41467-018-04919-w
ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data.
Lee JY, Choi H, Colangelo CM, Davis D, Hoopmann MR, Käll L, Lam H, Payne SH, Perez-Riverol Y, The M, Wilson R, Weintraub ST, Palmblad M. Journal of biomolecular techniques : JBT Volume 29 (2018) p.39-45 DOI: 10.7171/jbt.18-2902-003
Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.
Argelaguet R, Velten B, Arnol D, Dietrich S, Zenz T, Marioni JC, Buettner F, Huber W, Stegle O. Molecular systems biology Volume 14 (2018) p.e8124 DOI: 10.15252/msb.20178124
*
Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis
Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC, Odom DT. Preprint DOI: 10.1101/350868
htsget: a protocol for securely streaming genomic data.
Kelleher J, Lin M, Albach CH, Birney E, Davies R, Gourtovaia M, Glazer D, Gonzalez CY, Jackson DK, Kemp A, Marshall J, Nowak A, Senf A, Tovar-Corona JM, Vikhorev A, Keane TM, GA4GH Streaming Task Team. Bioinformatics (Oxford, England) (2018) DOI: 10.1093/bioinformatics/bty492
3DPatch: fast 3D structure visualization with residue conservation.
Jakubec D, Vondrášek J, Finn RD. Bioinformatics (Oxford, England) (2018) DOI: 10.1093/bioinformatics/bty464
*
Capturing variation impact on molecular interactions: the IMEx Consortium mutations data set
The IMEx Consortium curators, del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Pinero J, Kotlyar M, Chiara P, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras Millan P. Preprint DOI: 10.1101/346833
*
Understanding trivial challenges of microbial genomics: An assembly example
Lariviere D, Mei H, Freeberg M, Taylor J, Nekrutenko A. Preprint DOI: 10.1101/347625
*
Recommendations for the packaging and containerizing of bioinformatics software
Gruening B, Sallou O, Moreno P, da Veiga Leprevost F, Ménager H, Søndergaard D, Röst H, Sachsenberg T, O'Connor B, Madeira F, Dominguez Del Angel V, Crusoe MR, Varma S, Blankenberg D, Jimenez RC, Perez-Riverol Y, BioContainers Community. Preprint DOI: 10.12688/f1000research.15140.1
*
SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation
Jankauskaite J, Jimenez-Garcia B, Dapkunas J, Fernandez-Recio J, Moal IH. Preprint DOI: 10.1101/341735
*
Single-cell transcriptomics identifies CD44 as a new marker and regulator of haematopoietic stem cells development
Oatley M, Vargel Bolukbasi O, Svensson V, Shvartsman M, Ganter K, Zirngibl K, Pavlovich PV, Milchevskaya V, Foteva V, Natarajan KN, Baying B, Benes V, Patil KR, Teichmann SA, Lancrin C. Preprint DOI: 10.1101/338178
Expanding the horizons of microRNA bioinformatics.
Huntley RP, Kramarz B, Sawford T, Umrao Z, Kalea A, Acquaah V, Martin MJ, Mayr M, Lovering RC. RNA (New York, N.Y.) Volume 24 (2018) p.1005-1017 DOI: 10.1261/rna.065565.118
Non-Coding RNA Analysis Using the Rfam Database.
Kalvari I, Nawrocki EP, Argasinska J, Quinones-Olvera N, Finn RD, Bateman A, Petrov AI. Current protocols in bioinformatics Volume 62 (2018) p.e51 DOI: 10.1002/cpbi.51
*
Best practice data life cycle approaches for the life sciences
Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WW, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. Preprint DOI: 10.12688/f1000research.12344.2
*
Benchmark and integration of resources for the estimation of human transcription factor activities
Garcia-Alonso L, Ibrahim MM, Turei D, Saez-Rodriguez J. Preprint DOI: 10.1101/337915
High-throughput mouse phenomics for characterizing mammalian gene function.
Brown SDM, Holmes CC, Mallon AM, Meehan TF, Smedley D, Wells S. Nature reviews. Genetics Volume 19 (2018) p.357-370 DOI: 10.1038/s41576-018-0005-2
Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE).
Lill JR, van Veelen PA, Tenzer S, Admon A, Caron E, Elias JE, Heck AJR, Marcilla M, Marino F, Müller M, Peters B, Purcell A, Sette A, Sturm T, Ternette N, Vizcaíno JA, Bassani-Sternberg M. Proteomics Volume 18 (2018) p.e1800110 DOI: 10.1002/pmic.201800110
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi.
Keilwagen J, Hartung F, Paulini M, Twardziok SO, Grau J. BMC bioinformatics Volume 19 (2018) p.189 DOI: 10.1186/s12859-018-2203-5
Structural biology data archiving - where we are and what lies ahead.
Kleywegt GJ, Velankar S, Patwardhan A. FEBS letters Volume 592 (2018) p.2153-2167 DOI: 10.1002/1873-3468.13086
SPIN: Submitting Sequences Determined at Protein Level to UniProt.
Pichler K, Warner K, Magrane M, UniProt Consortium. Current protocols in bioinformatics Volume 62 (2018) p.e52 DOI: 10.1002/cpbi.52
*
Tandem duplications lead to loss of fitness effects in CRISPR-Cas9 data
Goncalves E, Behan FM, Louzada S, Arnol D, Stronach E, Yang F, Yusa K, Stegle O, Iorio F, Garnett MJ. Preprint DOI: 10.1101/325076
Combined HAT/EZH2 modulation leads to cancer-selective cell death.
Petraglia F, Singh AA, Carafa V, Nebbioso A, Conte M, Scisciola L, Valente S, Baldi A, Mandoli A, Petrizzi VB, Ingenito C, De Falco S, Cicatiello V, Apicella I, Janssen-Megens EM, Kim B, Yi G, Logie C, Heath S, Ruvo M, Wierenga ATJ, Flicek P, Yaspo ML, Della Valle V, Bernard O, Tomassi S, Novellino E, Feoli A, Sbardella G, Gut I, Vellenga E, Stunnenberg HG, Mai A, Martens JHA, Altucci L. Oncotarget Volume 9 (2018) p.25630-25646 DOI: 10.18632/oncotarget.25428
*
Combined single cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity
Linker SM, Urban L, Clark S, Chhatriwala M, Amatya S, McCarthy D, Ebersberger I, Vallier L, Reik W, Stegle O, Bonder MJ. Preprint DOI: 10.1101/328138
Multi-omics profiling reveals a distinctive epigenome signature for high-risk acute promyelocytic leukemia.
Singh AA, Petraglia F, Nebbioso A, Yi G, Conte M, Valente S, Mandoli A, Scisciola L, Lindeboom R, Kerstens H, Janssen-Megens EM, Pourfarzad F, Habibi E, Berentsen K, Kim B, Logie C, Heath S, Wierenga ATJ, Clarke L, Flicek P, Jansen JH, Kuijpers T, Yaspo ML, Valle VD, Bernard O, Gut I, Vellenga E, Stunnenberg HG, Mai A, Altucci L, Martens JHA. Oncotarget Volume 9 (2018) p.25647-25660 DOI: 10.18632/oncotarget.25429
The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia.
Beekman R, Chapaprieta V, Russiñol N, Vilarrasa-Blasi R, Verdaguer-Dot N, Martens JHA, Duran-Ferrer M, Kulis M, Serra F, Javierre BM, Wingett SW, Clot G, Queirós AC, Castellano G, Blanc J, Gut M, Merkel A, Heath S, Vlasova A, Ullrich S, Palumbo E, Enjuanes A, Martín-García D, Beà S, Pinyol M, Aymerich M, Royo R, Puiggros M, Torrents D, Datta A, Lowy E, Kostadima M, Roller M, Clarke L, Flicek P, Agirre X, Prosper F, Baumann T, Delgado J, López-Guillermo A, Fraser P, Yaspo ML, Guigó R, Siebert R, Martí-Renom MA, Puente XS, López-Otín C, Gut I, Stunnenberg HG, Campo E, Martin-Subero JI. Nature medicine Volume 24 (2018) p.868-880 DOI: 10.1038/s41591-018-0028-4
The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation.
Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Brown SDM, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Hrabě de Angelis M, Kim JK, Lloyd KCK, McKerlie C, Morgan H, Murray SA, Nutter LMJ, Reilly PT, Seavitt JR, Seong JK, Simon M, Wardle-Jones H, Mallon AM, Smedley D, Parkinson HE, IMPC consortium. Conservation genetics. Volume 19 (2018) p.995-1005 DOI: 10.1007/s10592-018-1072-9
Uniform resolution of compact identifiers for biomedical data.
Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T. Scientific data Volume 5 (2018) p.180029 DOI: 10.1038/sdata.2018.29
*
Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression
Lun X, Szklarczyk D, Gabor A, Dobberstein N, Zanotelli VRT, Saez-Rodriguez J, von Mering C, Bodenmiller B. Preprint DOI: 10.1101/314716
Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body.
Achim K, Eling N, Vergara HM, Bertucci PY, Musser J, Vopalensky P, Brunet T, Collier P, Benes V, Marioni JC, Arendt D. Molecular biology and evolution Volume 35 (2018) p.1047-1062 DOI: 10.1093/molbev/msx336
Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments.
Almeida A, Mitchell AL, Tarkowska A, Finn RD. GigaScience Volume 7 (2018) DOI: 10.1093/gigascience/giy054
*
In vivo and in vitro identification of Z-BOX C - a new bilirubin oxidation end product.
Ritter M, Neupane S, Seidel RA, Steinbeck C, Pohnert G. Organic & biomolecular chemistry Volume 16 (2018) p.3553-3555 DOI: 10.1039/c8ob00164b
Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich.
Iorio F, Garcia-Alonso L, Brammeld JS, Martincorena I, Wille DR, McDermott U, Saez-Rodriguez J. Scientific reports Volume 8 (2018) p.6713 DOI: 10.1038/s41598-018-25076-6
Defective germline reprogramming rewires the spermatogonial transcriptome.
Vasiliauskaitė L, Berrens RV, Ivanova I, Carrieri C, Reik W, Enright AJ, O'Carroll D. Nature structural & molecular biology Volume 25 (2018) p.394-404 DOI: 10.1038/s41594-018-0058-0
*
Genomic, Proteomic and Phenotypic Heterogeneity in HeLa Cells across Laboratories: Implications for Reproducibility of Research Results
Liu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Germain P, Frank M, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, Bena FS, Zhou H, Dehio C, Testa G, Saez-Rodriguez J, Antonarakis SE, Hardt W, Aebersold R. Preprint DOI: 10.1101/307421
*
A rapid and robust method for single cell chromatin accessibility profiling
Chen X, Natarajan KN, Teichmann SA. Preprint DOI: 10.1101/309831
Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.
Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TMF, Bacanu SA, Bækvad-Hansen M, Beekman AFT, Bigdeli TB, Binder EB, Blackwood DRH, Bryois J, Buttenschøn HN, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen JH, Clarke TK, Coleman JIR, Colodro-Conde L, Couvy-Duchesne B, Craddock N, Crawford GE, Crowley CA, Dashti HS, Davies G, Deary IJ, Degenhardt F, Derks EM, Direk N, Dolan CV, Dunn EC, Eley TC, Eriksson N, Escott-Price V, Kiadeh FHF, Finucane HK, Forstner AJ, Frank J, Gaspar HA, Gill M, Giusti-Rodríguez P, Goes FS, Gordon SD, Grove J, Hall LS, Hannon E, Hansen CS, Hansen TF, Herms S, Hickie IB, Hoffmann P, Homuth G, Horn C, Hottenga JJ, Hougaard DM, Hu M, Hyde CL, Ising M, Jansen R, Jin F, Jorgenson E, Knowles JA, Kohane IS, Kraft J, Kretzschmar WW, Krogh J, Kutalik Z, Lane JM, Li Y, Li Y, Lind PA, Liu X, Lu L, MacIntyre DJ, MacKinnon DF, Maier RM, Maier W, Marchini J, Mbarek H, McGrath P, McGuffin P, Medland SE, Mehta D, Middeldorp CM, Mihailov E, Milaneschi Y, Milani L, Mill J, Mondimore FM, Montgomery GW, Mostafavi S, Mullins N, Nauck M, Ng B, Nivard MG, Nyholt DR, O'Reilly PF, Oskarsson H, Owen MJ, Painter JN, Pedersen CB, Pedersen MG, Peterson RE, Pettersson E, Peyrot WJ, Pistis G, Posthuma D, Purcell SM, Quiroz JA, Qvist P, Rice JP, Riley BP, Rivera M, Saeed Mirza S, Saxena R, Schoevers R, Schulte EC, Shen L, Shi J, Shyn SI, Sigurdsson E, Sinnamon GBC, Smit JH, Smith DJ, Stefansson H, Steinberg S, Stockmeier CA, Streit F, Strohmaier J, Tansey KE, Teismann H, Teumer A, Thompson W, Thomson PA, Thorgeirsson TE, Tian C, Traylor M, Treutlein J, Trubetskoy V, Uitterlinden AG, Umbricht D, Van der Auwera S, van Hemert AM, Viktorin A, Visscher PM, Wang Y, Webb BT, Weinsheimer SM, Wellmann J, Willemsen G, Witt SH, Wu Y, Xi HS, Yang J, Zhang F, eQTLGen, 23andMe, Arolt V, Baune BT, Berger K, Boomsma DI, Cichon S, Dannlowski U, de Geus ECJ, DePaulo JR, Domenici E, Domschke K, Esko T, Grabe HJ, Hamilton SP, Hayward C, Heath AC, Hinds DA, Kendler KS, Kloiber S, Lewis G, Li QS, Lucae S, Madden PFA, Magnusson PK, Martin NG, McIntosh AM, Metspalu A, Mors O, Mortensen PB, Müller-Myhsok B, Nordentoft M, Nöthen MM, O'Donovan MC, Paciga SA, Pedersen NL, Penninx BWJH, Perlis RH, Porteous DJ, Potash JB, Preisig M, Rietschel M, Schaefer C, Schulze TG, Smoller JW, Stefansson K, Tiemeier H, Uher R, Völzke H, Weissman MM, Werge T, Winslow AR, Lewis CM, Levinson DF, Breen G, Børglum AD, Sullivan PF, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium. Nature genetics Volume 50 (2018) p.668-681 DOI: 10.1038/s41588-018-0090-3
Response to "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra".
Griss J, Perez-Riverol Y, The M, Käll L, Vizcaíno JA. Journal of proteome research Volume 17 (2018) p.1993-1996 DOI: 10.1021/acs.jproteome.7b00824
Using single-cell genomics to understand developmental processes and cell fate decisions.
Griffiths JA, Scialdone A, Marioni JC. Molecular systems biology Volume 14 (2018) p.e8046 DOI: 10.15252/msb.20178046
Interactions between genetic variation and cellular environment in skeletal muscle gene expression.
Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Casale FP, Wolford BN, Guan L, Varshney A, Albanus RD, Parker SCJ, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS. PloS one Volume 13 (2018) p.e0195788 DOI: 10.1371/journal.pone.0195788
A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms.
The M, Edfors F, Perez-Riverol Y, Payne SH, Hoopmann MR, Palmblad M, Forsström B, Käll L. Journal of proteome research Volume 17 (2018) p.1879-1886 DOI: 10.1021/acs.jproteome.7b00899
The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies.
Angers-Loustau A, Petrillo M, Bengtsson-Palme J, Berendonk T, Blais B, Chan KG, Coque TM, Hammer P, Heß S, Kagkli DM, Krumbiegel C, Lanza VF, Madec JY, Naas T, O'Grady J, Paracchini V, Rossen JWA, Ruppé E, Vamathevan J, Venturi V, Van den Eede G. F1000Research Volume 7 (2018) p.459 DOI: 10.12688/f1000research.14509.1
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.
Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S. BMC bioinformatics Volume 19 (2018) p.134 DOI: 10.1186/s12859-018-2118-1
*
JACKS: joint analysis of CRISPR/Cas9 knock-out screens
Allen F, Behan F, Iorio F, Yusa K, Garnett M, Parts L. Preprint DOI: 10.1101/285114
JAMI: a Java library for molecular interactions and data interoperability.
Sivade Dumousseau M, Koch M, Shrivastava A, Alonso-López D, De Las Rivas J, Del-Toro N, Combe CW, Meldal BHM, Heimbach J, Rappsilber J, Sullivan J, Yehudi Y, Orchard S. BMC bioinformatics Volume 19 (2018) p.133 DOI: 10.1186/s12859-018-2119-0
Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers.
Meier B, Volkova NV, Hong Y, Schofield P, Campbell PJ, Gerstung M, Gartner A. Genome research Volume 28 (2018) p.666-675 DOI: 10.1101/gr.226845.117
*
Epigenomic and functional dynamics of human bone marrow myeloid differentiation to mature blood neutrophils
Grassi L, Pourfarzad F, Ullrich S, Merkel A, Were F, Carrillo de Santa Pau E, Yi G, Hiemstra IH, Tool AT, Mul E, Perner J, Janssen-Megens E, Berentsen K, Kerstens H, Habibi E, Gut M, Yaspo ML, Linser M, Lowy E, Datta A, Clarke L, Flicek P, Vingron M, Roos D, van den Berg TK, Heath S, Rico D, Frontini M, Kostadima M, Gut I, Valencia A, Ouwehand WH, Stunnenberg HG, Martens JH, Kuijpers TW. Preprint DOI: 10.1101/295014
*
Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
Lun A, Riesenfeld S, Andrews T, Dao TP, Gomes T, Marioni J, participants in the 1st Human Cell Atlas Jamboree. Preprint DOI: 10.1101/234872
*
Circadian protein regulation in the green lineage I. A phospho-dawn anticipates light onset before proteins peak in daytime.
Noordally ZB, Hindle MM, Martin SF, Seaton DD, Simpson I, Le Bihan T, Millar AJ. Preprint DOI: 10.1101/287862
*
PDX Finder: A Portal for Patient-Derived tumor Xenograft Model Discovery
Conte N, Mason J, Halmagyi C, Neuhauser SB, Mosaku A, Begley DA, Krupke DM, Parkinson H, Meehan T, Bult CJ. Preprint DOI: 10.1101/291443
*
Integrative analysis of pharmacogenomics in major cancer cell line databases using CellMinerCDB
Rajapakse VN, Luna A, Yamade M, Loman L, Varma S, Sunshine M, Iorio F, Sousa FG, Elloumi F, Aladjem MI, Thomas A, Sander C, Kohn K, Benes CH, Garnett M, Reinhold WC, Pommier Y. Preprint DOI: 10.1101/292904
SBML Level 3 package: Render, Version 1, Release 1.
Bergmann FT, Keating SM, Gauges R, Sahle S, Wengler K. Journal of integrative bioinformatics Volume 15 (2018) DOI: 10.1515/jib-2017-0078
Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Haghverdi L, Lun ATL, Morgan MD, Marioni JC. Nature biotechnology Volume 36 (2018) p.421-427 DOI: 10.1038/nbt.4091
GDSCTools for mining pharmacogenomic interactions in cancer.
Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ. Bioinformatics (Oxford, England) Volume 34 (2018) p.1226-1228 DOI: 10.1093/bioinformatics/btx744
Reactome diagram viewer: data structures and strategies to boost performance.
Fabregat A, Sidiropoulos K, Viteri G, Marin-Garcia P, Ping P, Stein L, D'Eustachio P, Hermjakob H. Bioinformatics (Oxford, England) Volume 34 (2018) p.1208-1214 DOI: 10.1093/bioinformatics/btx752
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.
Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D. Journal of integrative bioinformatics Volume 15 (2018) DOI: 10.1515/jib-2018-0013
PhenotypeSimulator: a comprehensive framework for multi-trait, multi-locus phenotype to genotype simulation.
Meyer HV, Birney E. Bioinformatics (Oxford, England) (2018) DOI: 10.1093/bioinformatics/bty197
*
Corrigendum: Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches.
George S, Pankhurst L, Hubbard A, Votintseva A, Stoesser N, Sheppard AE, Mathers A, Norris R, Navickaite I, Eaton C, Iqbal Z, Crook DW, Phan HTT. Microbial genomics Volume 4 (2018) DOI: 10.1099/mgen.0.000130
*
Unexplored therapeutic opportunities in the human genome.
Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma'ayan A, Malovannaya A, Mani S, Mathias SL, McManus MT, Meehan TF, von Mering C, Muthas D, Nguyen DT, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Southall N, Tomita S, Tudose I, Ursu O, Vidovic D, Waller A, Westergaard D, Yang JJ, Zahoránszky-Köhalmi G. Nature reviews. Drug discovery Volume 17 (2018) p.377 DOI: 10.1038/nrd.2018.52
Unexplored therapeutic opportunities in the human genome.
Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma'ayan A, Malovannaya A, Mani S, Mathias SL, McManus MT, Meehan TF, von Mering C, Muthas D, Nguyen DT, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Southall N, Tomita S, Tudose I, Ursu O, Vidovic D, Waller A, Westergaard D, Yang JJ, Zahoránszky-Köhalmi G. Nature reviews. Drug discovery Volume 17 (2018) p.317-332 DOI: 10.1038/nrd.2018.14
Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.
Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P. Genome research Volume 28 (2018) p.448-459 DOI: 10.1101/gr.234096.117
Application of CRISPR-Cas9 Based Genome-Wide Screening Approaches to Study Cellular Signalling Mechanisms.
Sharma S, Petsalaki E. International journal of molecular sciences Volume 19 (2018) DOI: 10.3390/ijms19040933
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.
Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR. Nature microbiology Volume 3 (2018) p.514-522 DOI: 10.1038/s41564-018-0123-9
SpatialDE: identification of spatially variable genes.
Svensson V, Teichmann SA, Stegle O. Nature methods Volume 15 (2018) p.343-346 DOI: 10.1038/nmeth.4636
*
Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits
Gilly A, Suveges D, Kuchenbaecker K, Pollard MO, Southam L, Hatzikotoulas K, Farmaki A, Bjornland T, Waples R, Appel EV, Casalone E, Melloni G, Kilian B, Rayner NW, Ntalla I, Kundu K, Walter K, Danesh J, Butterworth A, Barroso I, Tsafantakis E, Dedoussis G, Moltke I, Zeggini E. Preprint DOI: 10.1101/283481
Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci.
Amaral PP, Leonardi T, Han N, Viré E, Gascoigne DK, Arias-Carrasco R, Büscher M, Pandolfini L, Zhang A, Pluchino S, Maracaja-Coutinho V, Nakaya HI, Hemberg M, Shiekhattar R, Enright AJ, Kouzarides T. Genome biology Volume 19 (2018) p.32 DOI: 10.1186/s13059-018-1405-5
Simplifying research access to genomics and health data with Library Cards.
Cabili MN, Carey K, Dyke SOM, Brookes AJ, Fiume M, Jeanson F, Kerry G, Lash A, Sofia H, Spalding D, Tasse AM, Varma S, Pandya R. Scientific data Volume 5 (2018) p.180039 DOI: 10.1038/sdata.2018.39
*
Quantifying the impact of public omics data
Perez-Riverol Y, Zorin A, Dass G, Glonț M, Vizcaino JA, Jarnuczak A, Petryszak R, Ping P, Hermjakob H. Preprint DOI: 10.1101/282517
ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy.
Barton C, Morganella S, Ødegård-Fougner Ø, Alexander S, Ries J, Fitzgerald T, Ellenberg J, Birney E. PLoS computational biology Volume 14 (2018) p.e1006002 DOI: 10.1371/journal.pcbi.1006002
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.
Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. Journal of integrative bioinformatics Volume 15 (2018) DOI: 10.1515/jib-2017-0081
*
The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis
Melamed A, Yaguchi H, Miura M, Witkover A, Fitzgerald TW, Birney E, Bangham CRM. Preprint DOI: 10.1101/277335
A recombinant Fasciola gigantica 14-3-3 epsilon protein (rFg14-3-3e) modulates various functions of goat peripheral blood mononuclear cells.
Tian AL, Lu M, Calderón-Mantilla G, Petsalaki E, Dottorini T, Tian X, Wang Y, Huang SY, Hou JL, Li X, Elsheikha HM, Zhu XQ. Parasites & vectors Volume 11 (2018) p.152 DOI: 10.1186/s13071-018-2745-4
Convergent genomic signatures of domestication in sheep and goats.
Alberto FJ, Boyer F, Orozco-terWengel P, Streeter I, Servin B, de Villemereuil P, Benjelloun B, Librado P, Biscarini F, Colli L, Barbato M, Zamani W, Alberti A, Engelen S, Stella A, Joost S, Ajmone-Marsan P, Negrini R, Orlando L, Rezaei HR, Naderi S, Clarke L, Flicek P, Wincker P, Coissac E, Kijas J, Tosser-Klopp G, Chikhi A, Bruford MW, Taberlet P, Pompanon F. Nature communications Volume 9 (2018) p.813 DOI: 10.1038/s41467-018-03206-y
*
Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer
Berndt N, Egners A, Mastrobuoni G, Vvedenskaya O, Fragoulis A, Dugourd A, Bulik S, Pietzke M, Bielow C, van Gassel R, Olde Damink S, Erdem M, Saez-Rodriguez J, Holzhuetter H, Kempa S, Cramer T. Preprint DOI: 10.1101/275040
*
CELLector: Genomics Guided Selection of Cancer in vitro Models
Najgebauer H, Yang M, Francies H, Stronach EA, Garnett MJ, Saez-Rodriguez J, Iorio F. Preprint DOI: 10.1101/275032
Gene Unprediction with Spurio: A tool to identify spurious protein sequences.
Höps W, Jeffryes M, Bateman A. F1000Research Volume 7 (2018) p.261 DOI: 10.12688/f1000research.14050.1
Validation of ligands in macromolecular structures determined by X-ray crystallography.
Smart OS, Horský V, Gore S, Svobodová Vařeková R, Bendová V, Kleywegt GJ, Velankar S. Acta crystallographica. Section D, Structural biology Volume 74 (2018) p.228-236 DOI: 10.1107/S2059798318002541
Worldwide Protein Data Bank validation information: usage and trends.
Smart OS, Horský V, Gore S, Svobodová Vařeková R, Bendová V, Kleywegt GJ, Velankar S. Acta crystallographica. Section D, Structural biology Volume 74 (2018) p.237-244 DOI: 10.1107/S2059798318003303
Molecular Genetic Analysis Subdivided by Adversity Exposure Suggests Etiologic Heterogeneity in Major Depression.
Peterson RE, Cai N, Dahl AW, Bigdeli TB, Edwards AC, Webb BT, Bacanu SA, Zaitlen N, Flint J, Kendler KS. The American journal of psychiatry Volume 175 (2018) p.545-554 DOI: 10.1176/appi.ajp.2017.17060621
Whither systems medicine?
Apweiler R, Beissbarth T, Berthold MR, Blüthgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Höfer T, Jansen PL, Kaderali L, Klingmüller U, Koch I, Kohlbacher O, Kuepfer L, Lammert F, Maier D, Pfeifer N, Radde N, Rehm M, Roeder I, Saez-Rodriguez J, Sax U, Schmeck B, Schuppert A, Seilheimer B, Theis FJ, Vera J, Wolkenhauer O. Experimental & molecular medicine Volume 50 (2018) p.e453 DOI: 10.1038/emm.2017.290
ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins.
Pineda SS, Chaumeil PA, Kunert A, Kaas Q, Thang MWC, Le L, Nuhn M, Herzig V, Saez NJ, Cristofori-Armstrong B, Anangi R, Senff S, Gorse D, King GF. Bioinformatics (Oxford, England) Volume 34 (2018) p.1074-1076 DOI: 10.1093/bioinformatics/btx661
UniProt: the universal protein knowledgebase.
UniProt Consortium T. Nucleic acids research Volume 46 (2018) p.2699 DOI: 10.1093/nar/gky092
*
A linear mixed model approach to study multivariate gene-environment interactions
Moore R, Casale FP, Bonder MJ, Horta D, Franke L, Barroso I, Stegle O, BIOS Consortium. Preprint DOI: 10.1101/270611
scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.
Clark SJ, Argelaguet R, Kapourani CA, Stubbs TM, Lee HJ, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W. Nature communications Volume 9 (2018) p.781 DOI: 10.1038/s41467-018-03149-4
*
Rapid proteotyping reveals cancer biology and drug response determinants in the NCI-60 cells
Guo T, Luna A, Koh CC, Rajapakse V, Wu Z, Menden MP, Cheng Y, Calzone L, Martignetti L, Ori A, Iskar M, Gillet L, Zhong Q, Varma S, Schmitt U, Qiu P, Sun Y, zhu Y, Wild P, Mathew G, Bork P, Beck M, Saez-Rodriguez J, Reinhold W, Sander C, Pommier Y, Aebersold R. Preprint DOI: 10.1101/268953
Interleukins and their signaling pathways in the Reactome biological pathway database.
Jupe S, Ray K, Roca CD, Varusai T, Shamovsky V, Stein L, D'Eustachio P, Hermjakob H. The Journal of allergy and clinical immunology Volume 141 (2018) p.1411-1416 DOI: 10.1016/j.jaci.2017.12.992
Exploring autophagy with Gene Ontology.
Denny P, Feuermann M, Hill DP, Lovering RC, Plun-Favreau H, Roncaglia P. Autophagy Volume 14 (2018) p.419-436 DOI: 10.1080/15548627.2017.1415189
*
Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases
Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R, Subramanian A, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D, The DREAM Module Identification Challenge Consortium. Preprint DOI: 10.1101/265553
A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog.
Morales J, Welter D, Bowler EH, Cerezo M, Harris LW, McMahon AC, Hall P, Junkins HA, Milano A, Hastings E, Malangone C, Buniello A, Burdett T, Flicek P, Parkinson H, Cunningham F, Hindorff LA, MacArthur JAL. Genome biology Volume 19 (2018) p.21 DOI: 10.1186/s13059-018-1396-2
*
pyseer: a comprehensive tool for microbial pangenome-wide association studies
Lees J, Galardini M, Bentley SD, Weiser JN, Corander J. Preprint DOI: 10.1101/266312
*
Modelling cell-cell interactions from spatial molecular data with spatial variance component analysis
Arnol D, Schapiro D, Bodenmiller B, Saez-Rodriguez J, Stegle O. Preprint DOI: 10.1101/265256
Using OWL reasoning to support the generation of novel gene sets for enrichment analysis.
Osumi-Sutherland DJ, Ponta E, Courtot M, Parkinson H, Badi L. Journal of biomedical semantics Volume 9 (2018) p.10 DOI: 10.1186/s13326-018-0175-z
*
A functional landscape of chronic kidney disease entities from public transcriptomic data
Tajti F, Antoranz A, Ibrahim MM, Kim H, Ceccarelli F, Kuppe C, Alexopoulos LG, Kramann R, Saez-Rodriguez J. Preprint DOI: 10.1101/265447
ProForma: A Standard Proteoform Notation.
LeDuc RD, Schwämmle V, Shortreed MR, Cesnik AJ, Solntsev SK, Shaw JB, Martin MJ, Vizcaino JA, Alpi E, Danis P, Kelleher NL, Smith LM, Ge Y, Agar JN, Chamot-Rooke J, Loo JA, Pasa-Tolic L, Tsybin YO. Journal of proteome research Volume 17 (2018) p.1321-1325 DOI: 10.1021/acs.jproteome.7b00851
*
Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci
Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Czechanski A, Danecek P, Diekhans M, Dolle D, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Kolmogorov M, Koenig S, Lelliott C, Loveland J, Mott R, Muir P, Navarro F, Odom D, Park N, Pelan S, Phan SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yang F, Adams DJ, Paten B, Keane TM. Preprint DOI: 10.1101/235838
Harmonising phenomics information for a better interoperability in the rare disease field.
Maiella S, Olry A, Hanauer M, Lanneau V, Lourghi H, Donadille B, Rodwell C, Köhler S, Seelow D, Jupp S, Parkinson H, Groza T, Brudno M, Robinson PN, Rath A. European journal of medical genetics (2018) DOI: 10.1016/j.ejmg.2018.01.013
*
Comprehensive and empirical evaluation of machine learning algorithms for LC retention time prediction
Bouwmeester R, Martens L, Degroeve S. Preprint DOI: 10.1101/259168
*
Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Nature biotechnology Volume 36 (2018) p.196 DOI: 10.1038/nbt0218-196a
*
Allele-specific transcription factor binding as a benchmark for assessing variant impact predictors
Wagih O, Merico D, Delong A, Frey BJ. Preprint DOI: 10.1101/253427
NADH Shuttling Couples Cytosolic Reductive Carboxylation of Glutamine with Glycolysis in Cells with Mitochondrial Dysfunction.
Gaude E, Schmidt C, Gammage PA, Dugourd A, Blacker T, Chew SP, Saez-Rodriguez J, O'Neill JS, Szabadkai G, Minczuk M, Frezza C. Molecular cell Volume 69 (2018) p.581-593.e7 DOI: 10.1016/j.molcel.2018.01.034
Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.
Lovering RC, Roncaglia P, Howe DG, Laulederkind SJF, Khodiyar VK, Berardini TZ, Tweedie S, Foulger RE, Osumi-Sutherland D, Campbell NH, Huntley RP, Talmud PJ, Blake JA, Breckenridge R, Riley PR, Lambiase PD, Elliott PM, Clapp L, Tinker A, Hill DP. Circulation. Genomic and precision medicine Volume 11 (2018) p.e001813 DOI: 10.1161/CIRCGEN.117.001813
The development and application of bioinformatics core competencies to improve bioinformatics training and education.
Mulder N, Schwartz R, Brazas MD, Brooksbank C, Gaeta B, Morgan SL, Pauley MA, Rosenwald A, Rustici G, Sierk M, Warnow T, Welch L. PLoS computational biology Volume 14 (2018) p.e1005772 DOI: 10.1371/journal.pcbi.1005772
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.
Menschaert G, Wang X, Jones AR, Ghali F, Fenyö D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaíno JA. Genome biology Volume 19 (2018) p.12 DOI: 10.1186/s13059-017-1377-x
*
LiMMBo: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies
Hannah MV, Casale FP, Stegle O, Birney E. Preprint DOI: 10.1101/255497
Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system.
Pratas MI, Aguiar B, Vieira J, Nunes V, Teixeira V, Fonseca NA, Iezzoni A, van Nocker S, Vieira CP. Scientific reports Volume 8 (2018) p.1717 DOI: 10.1038/s41598-018-19820-1
Reactome graph database: Efficient access to complex pathway data.
Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, Wu G, Stein L, D'Eustachio P, Hermjakob H. PLoS computational biology Volume 14 (2018) p.e1005968 DOI: 10.1371/journal.pcbi.1005968
Recommendations for a nomenclature system for reporting methylation aberrations in imprinted domains.
Monk D, Morales J, den Dunnen JT, Russo S, Court F, Prawitt D, Eggermann T, Beygo J, Buiting K, Tümer Z, Nomenclature group of the European Network for Human Congenital Imprinting Disorders. Epigenetics Volume 13 (2018) p.117-121 DOI: 10.1080/15592294.2016.1264561
*
A SNP panel for identification of DNA and RNA specimens.
Yousefi S, Abbassi-Daloii T, Kraaijenbrink T, Vermaat M, Mei H, van 't Hof P, van Iterson M, Zhernakova DV, Claringbould A, Franke L, 't Hart LM, Slieker RC, van der Heijden A, de Knijff P, BIOS consortium, 't Hoen PAC. BMC genomics Volume 19 (2018) p.90 DOI: 10.1186/s12864-018-4482-7
*
Dawn and photoperiod sensing by phytochrome A
Seaton D, Toledo-Ortiz G, Kubota A, Ganpudi A, Imaizumi T, Halliday K. Preprint DOI: 10.1101/253989
Plant genetic resources for food and agriculture: opportunities and challenges emerging from the science and information technology revolution.
Halewood M, Chiurugwi T, Sackville Hamilton R, Kurtz B, Marden E, Welch E, Michiels F, Mozafari J, Sabran M, Patron N, Kersey P, Bastow R, Dorius S, Dias S, McCouch S, Powell W. The New phytologist Volume 217 (2018) p.1407-1419 DOI: 10.1111/nph.14993
Identification of genetic elements in metabolism by high-throughput mouse phenotyping.
Rozman J, Rathkolb B, Oestereicher MA, Schütt C, Ravindranath AC, Leuchtenberger S, Sharma S, Kistler M, Willershäuser M, Brommage R, Meehan TF, Mason J, Haselimashhadi H, IMPC Consortium, Hough T, Mallon AM, Wells S, Santos L, Lelliott CJ, White JK, Sorg T, Champy MF, Bower LR, Reynolds CL, Flenniken AM, Murray SA, Nutter LMJ, Svenson KL, West D, Tocchini-Valentini GP, Beaudet AL, Bosch F, Braun RB, Dobbie MS, Gao X, Herault Y, Moshiri A, Moore BA, Kent Lloyd KC, McKerlie C, Masuya H, Tanaka N, Flicek P, Parkinson HE, Sedlacek R, Seong JK, Wang CL, Moore M, Brown SD, Tschöp MH, Wurst W, Klingenspor M, Wolf E, Beckers J, Machicao F, Peter A, Staiger H, Häring HU, Grallert H, Campillos M, Maier H, Fuchs H, Gailus-Durner V, Werner T, Hrabe de Angelis M. Nature communications Volume 9 (2018) p.288 DOI: 10.1038/s41467-017-01995-2
Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells.
Kolluri KK, Alifrangis C, Kumar N, Ishii Y, Price S, Michaut M, Williams S, Barthorpe S, Lightfoot H, Busacca S, Sharkey A, Yuan Z, Sage EK, Vallath S, Le Quesne J, Tice DA, Alrifai D, von Karstedt S, Montinaro A, Guppy N, Waller DA, Nakas A, Good R, Holmes A, Walczak H, Fennell DA, Garnett M, Iorio F, Wessels L, McDermott U, Janes SM. eLife Volume 7 (2018) DOI: 10.7554/eLife.30224
*
The genome of the biting midgeCulicoides sonorensisand gene expression analyses of vector competence for Bluetongue virus
Morales Hojas R, Hinsley M, Armean IM, Silk R, Harrup LE, Gonzalez-Uriarte A, Veronesi E, Campbell L, Nayduch D, Saski C, Tabachnick WJ, Kersey P, Carpenter S, Fife M. Preprint DOI: 10.1101/249482
*
Mutation accumulation differentially impacts ageing in mammalian tissues
Turan ZG, Parvizi P, Donertas HM, Tung J, Khaitovich P, Somel M. Preprint DOI: 10.1101/247700
*
Beyond the ribosome: proteome-wide secretability studies using SECRiFY
Boone M, Ramasamy P, Maddelein D, Turan D, Vandermarliere E, Vranken W, Callewaert N. Preprint DOI: 10.1101/241349
Single-cell RNA-sequencing resolves self-antigen expression during mTEC development.
Miragaia RJ, Zhang X, Gomes T, Svensson V, Ilicic T, Henriksson J, Kar G, Lönnberg T. Scientific reports Volume 8 (2018) p.685 DOI: 10.1038/s41598-017-19100-4
Designing an intuitive web application for drug discovery scientists.
Karamanis N, Pignatelli M, Carvalho-Silva D, Rowland F, Cham JA, Dunham I. Drug discovery today Volume 23 (2018) p.1169-1174 DOI: 10.1016/j.drudis.2018.01.032
Improving communication for interdisciplinary teams working on storage of digital information in DNA.
Hesketh EE, Sayir J, Goldman N. F1000Research Volume 7 (2018) p.39 DOI: 10.12688/f1000research.13482.1
Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.
Ibarra-Soria X, Jawaid W, Pijuan-Sala B, Ladopoulos V, Scialdone A, Jörg DJ, Tyser RCV, Calero-Nieto FJ, Mulas C, Nichols J, Vallier L, Srinivas S, Simons BD, Göttgens B, Marioni JC. Nature cell biology Volume 20 (2018) p.127-134 DOI: 10.1038/s41556-017-0013-z
Evolution, dynamics and dysregulation of kinase signalling.
Ochoa D, Bradley D, Beltrao P. Current opinion in structural biology Volume 48 (2018) p.133-140 DOI: 10.1016/j.sbi.2017.12.008
Perturbation-response genes reveal signaling footprints in cancer gene expression.
Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Blüthgen N, Saez-Rodriguez J. Nature communications Volume 9 (2018) p.20 DOI: 10.1038/s41467-017-02391-6
*
Biotea: semantics for Pubmed Central.
Garcia A, Lopez F, Garcia L, Giraldo O, Bucheli V, Dumontier M. PeerJ Volume 6 (2018) p.e4201 DOI: 10.7717/peerj.4201
The European Bioinformatics Institute in 2017: data coordination and integration.
Cook CE, Bergman MT, Cochrane G, Apweiler R, Birney E. Nucleic acids research Volume 46 (2018) p.D21-D29 DOI: 10.1093/nar/gkx1154
Europe PMC in 2017.
Levchenko M, Gou Y, Graef F, Hamelers A, Huang Z, Ide-Smith M, Iyer A, Kilian O, Katuri J, Kim JH, Marinos N, Nambiar R, Parkin M, Pi X, Rogers F, Talo F, Vartak V, Venkatesan A, McEntyre J. Nucleic acids research Volume 46 (2018) p.D1254-D1260 DOI: 10.1093/nar/gkx1005
The BioStudies database-one stop shop for all data supporting a life sciences study.
Sarkans U, Gostev M, Athar A, Behrangi E, Melnichuk O, Ali A, Minguet J, Rada JC, Snow C, Tikhonov A, Brazma A, McEntyre J. Nucleic acids research Volume 46 (2018) p.D1266-D1270 DOI: 10.1093/nar/gkx965
*
Three-dimensional cardiovascular imaging-genetics: a mass univariate framework.
Biffi C, de Marvao A, Attard MI, Dawes TJW, Whiffin N, Bai W, Shi W, Francis C, Meyer H, Buchan R, Cook SA, Rueckert D, O'Regan DP. Bioinformatics (Oxford, England) Volume 34 (2018) p.97-103 DOI: 10.1093/bioinformatics/btx552
Using WormBase ParaSite: An Integrated Platform for Exploring Helminth Genomic Data.
Bolt BJ, Rodgers FH, Shafie M, Kersey PJ, Berriman M, Howe KL. Methods in molecular biology (Clifton, N.J.) Volume 1757 (2018) p.471-491 DOI: 10.1007/978-1-4939-7737-6_15
Gramene 2018: unifying comparative genomics and pathway resources for plant research.
Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D'Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D. Nucleic acids research Volume 46 (2018) p.D1181-D1189 DOI: 10.1093/nar/gkx1111
The European Nucleotide Archive in 2017.
Silvester N, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Harrison PW, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Menchi M, Reddy K, Pakseresht N, Rajan J, Rossello M, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Nucleic acids research Volume 46 (2018) p.D36-D40 DOI: 10.1093/nar/gkx1125
A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.
Kurtz A, Seltmann S, Bairoch A, Bittner MS, Bruce K, Capes-Davis A, Clarke L, Crook JM, Daheron L, Dewender J, Faulconbridge A, Fujibuchi W, Gutteridge A, Hei DJ, Kim YO, Kim JH, Kokocinski AK, Lekschas F, Lomax GP, Loring JF, Ludwig T, Mah N, Matsui T, Müller R, Parkinson H, Sheldon M, Smith K, Stachelscheid H, Stacey G, Streeter I, Veiga A, Xu RH. Stem cell reports Volume 10 (2018) p.1-6 DOI: 10.1016/j.stemcr.2017.12.002
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.
Ribeiro AJM, Holliday GL, Furnham N, Tyzack JD, Ferris K, Thornton JM. Nucleic acids research Volume 46 (2018) p.D618-D623 DOI: 10.1093/nar/gkx1012
Antibody-mediated modulation of cytokinins in tobacco: organ-specific changes in cytokinin homeostasis.
Gelová Z, Ten Hoopen P, Novák O, Motyka V, Pernisová M, Dabravolski S, Didi V, Tillack I, Okleštková J, Strnad M, Hause B, Haruštiaková D, Conrad U, Janda L, Hejátko J. Journal of experimental botany Volume 69 (2018) p.441-454 DOI: 10.1093/jxb/erx426
BioModels: expanding horizons to include more modelling approaches and formats.
Glont M, Nguyen TVN, Graesslin M, Hälke R, Ali R, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat MJ, Eils J, Eils R, Laibe C, Malik-Sheriff RS, Chelliah V, Le Novère N, Hermjakob H. Nucleic acids research Volume 46 (2018) p.D1248-D1253 DOI: 10.1093/nar/gkx1023
Expression Atlas: gene and protein expression across multiple studies and organisms.
Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AM, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R. Nucleic acids research Volume 46 (2018) p.D246-D251 DOI: 10.1093/nar/gkx1158
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.
Young JY, Westbrook JD, Feng Z, Peisach E, Persikova I, Sala R, Sen S, Berrisford JM, Swaminathan GJ, Oldfield TJ, Gutmanas A, Igarashi R, Armstrong DR, Baskaran K, Chen L, Chen M, Clark AR, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Ikegawa Y, Kengaku Y, Lawson CL, Liang Y, Mak L, Mukhopadhyay A, Narayanan B, Nishiyama K, Patwardhan A, Sahni G, Sanz-García E, Sato J, Sekharan MR, Shao C, Smart OS, Tan L, van Ginkel G, Yang H, Zhuravleva MA, Markley JL, Nakamura H, Kurisu G, Kleywegt GJ, Velankar S, Berman HM, Burley SK. Database : the journal of biological databases and curation Volume 2018 (2018) DOI: 10.1093/database/bay002
The international nucleotide sequence database collaboration.
Karsch-Mizrachi I, Takagi T, Cochrane G, International Nucleotide Sequence Database Collaboration. Nucleic acids research Volume 46 (2018) p.D48-D51 DOI: 10.1093/nar/gkx1097
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes.
Grove C, Cain S, Chen WJ, Davis P, Harris T, Howe KL, Kishore R, Lee R, Paulini M, Raciti D, Tuli MA, Van Auken K, Williams G, WormBase Consortium. Methods in molecular biology (Clifton, N.J.) Volume 1757 (2018) p.399-470 DOI: 10.1007/978-1-4939-7737-6_14
WormBase 2017: molting into a new stage.
Lee RYN, Howe KL, Harris TW, Arnaboldi V, Cain S, Chan J, Chen WJ, Davis P, Gao S, Grove C, Kishore R, Muller HM, Nakamura C, Nuin P, Paulini M, Raciti D, Rodgers F, Russell M, Schindelman G, Tuli MA, Van Auken K, Wang Q, Williams G, Wright A, Yook K, Berriman M, Kersey P, Schedl T, Stein L, Sternberg PW. Nucleic acids research Volume 46 (2018) p.D869-D874 DOI: 10.1093/nar/gkx998
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.
Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI. Nucleic acids research Volume 46 (2018) p.D335-D342 DOI: 10.1093/nar/gkx1038
Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.
Pujar S, O'Leary NA, Farrell CM, Loveland JE, Mudge JM, Wallin C, Girón CG, Diekhans M, Barnes I, Bennett R, Berry AE, Cox E, Davidson C, Goldfarb T, Gonzalez JM, Hunt T, Jackson J, Joardar V, Kay MP, Kodali VK, Martin FJ, McAndrews M, McGarvey KM, Murphy M, Rajput B, Rangwala SH, Riddick LD, Seal RL, Suner MM, Webb D, Zhu S, Aken BL, Bruford EA, Bult CJ, Frankish A, Murphy T, Pruitt KD. Nucleic acids research Volume 46 (2018) p.D221-D228 DOI: 10.1093/nar/gkx1031
Ensembl 2018.
Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Girón CG, Gil L, Gordon L, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, To JK, Laird MR, Lavidas I, Liu Z, Loveland JE, Maurel T, McLaren W, Moore B, Mudge J, Murphy DN, Newman V, Nuhn M, Ogeh D, Ong CK, Parker A, Patricio M, Riat HS, Schuilenburg H, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Zadissa A, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Cunningham F, Yates A, Flicek P. Nucleic acids research Volume 46 (2018) p.D754-D761 DOI: 10.1093/nar/gkx1098
Searching and Extracting Data from the EMBL-EBI Complex Portal.
Meldal BHM, Orchard S. Methods in molecular biology (Clifton, N.J.) Volume 1764 (2018) p.377-390 DOI: 10.1007/978-1-4939-7759-8_24
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.
Mitchell AL, Scheremetjew M, Denise H, Potter S, Tarkowska A, Qureshi M, Salazar GA, Pesseat S, Boland MA, Hunter FMI, Ten Hoopen P, Alako B, Amid C, Wilkinson DJ, Curtis TP, Cochrane G, Finn RD. Nucleic acids research Volume 46 (2018) p.D726-D735 DOI: 10.1093/nar/gkx967
AmyPro: a database of proteins with validated amyloidogenic regions.
Varadi M, De Baets G, Vranken WF, Tompa P, Pancsa R. Nucleic acids research Volume 46 (2018) p.D387-D392 DOI: 10.1093/nar/gkx950
The Ensembl Genome Browser: Strategies for Accessing Eukaryotic Genome Data.
Newman V, Moore B, Sparrow H, Perry E. Methods in molecular biology (Clifton, N.J.) Volume 1757 (2018) p.115-139 DOI: 10.1007/978-1-4939-7737-6_6
The eukaryotic linear motif resource - 2018 update.
Gouw M, Michael S, Sámano-Sánchez H, Kumar M, Zeke A, Lang B, Bely B, Chemes LB, Davey NE, Deng Z, Diella F, Gürth CM, Huber AK, Kleinsorg S, Schlegel LS, Palopoli N, Roey KV, Altenberg B, Reményi A, Dinkel H, Gibson TJ. Nucleic acids research Volume 46 (2018) p.D428-D434 DOI: 10.1093/nar/gkx1077
The SysteMHC Atlas project.
Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E. Nucleic acids research Volume 46 (2018) p.D1237-D1247 DOI: 10.1093/nar/gkx664
The Reactome Pathway Knowledgebase.
Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B, Milacic M, Roca CD, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Viteri G, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. Nucleic acids research Volume 46 (2018) p.D649-D655 DOI: 10.1093/nar/gkx1132
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
Kersey PJ, Allen JE, Allot A, Barba M, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Grabmueller C, Kumar N, Liu Z, Maurel T, Moore B, McDowall MD, Maheswari U, Naamati G, Newman V, Ong CK, Paulini M, Pedro H, Perry E, Russell M, Sparrow H, Tapanari E, Taylor K, Vullo A, Williams G, Zadissia A, Olson A, Stein J, Wei S, Tello-Ruiz M, Ware D, Luciani A, Potter S, Finn RD, Urban M, Hammond-Kosack KE, Bolser DM, De Silva N, Howe KL, Langridge N, Maslen G, Staines DM, Yates A. Nucleic acids research Volume 46 (2018) p.D802-D808 DOI: 10.1093/nar/gkx1011
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.
Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD. Nucleic acids research Volume 46 (2018) p.D624-D632 DOI: 10.1093/nar/gkx1134
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.
Mir S, Alhroub Y, Anyango S, Armstrong DR, Berrisford JM, Clark AR, Conroy MJ, Dana JM, Deshpande M, Gupta D, Gutmanas A, Haslam P, Mak L, Mukhopadhyay A, Nadzirin N, Paysan-Lafosse T, Sehnal D, Sen S, Smart OS, Varadi M, Kleywegt GJ, Velankar S. Nucleic acids research Volume 46 (2018) p.D486-D492 DOI: 10.1093/nar/gkx1070

2017

Phenotype inference in an Escherichia coli strain panel.
Galardini M, Koumoutsi A, Herrera-Dominguez L, Cordero Varela JA, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P. eLife Volume 6 (2017) DOI: 10.7554/eLife.31035
A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it.
Spicer RA, Steinbeck C. Metabolomics : Official journal of the Metabolomic Society Volume 14 (2018) p.16 DOI: 10.1007/s11306-017-1309-5
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat.
Martín-Gálvez D, Dunoyer de Segonzac D, Ma MCJ, Kwitek AE, Thybert D, Flicek P. BMC genomics Volume 18 (2017) p.986 DOI: 10.1186/s12864-017-4351-9
*
Comparative analysis of neutrophil and monocyte epigenomes
Rico D, Martens JH, Downes K, Carrillo-de-Santa-Pau E, Pancaldi V, Breschi A, Richardson D, Heath S, Saeed S, Frontini M, Chen L, Watt S, Muller F, Clarke L, Kerstens HH, Wilder SP, Palumbo E, Djebali S, Rainieri E, Merkel A, Esteve-Codina A, Sultan M, van Bommel A, Gut M, Yaspo M, Rubio M, Fernandez JM, Attwood A, de la Torre V, Royo R, Fragkogianni S, Gelpi JL, Torrents D, Iotchkova V, Logie C, Aghajanirefah A, Singh AA, Janssen-Megens EM, Berentsen K, Erber W, Rendon A, Kostadima M, Loos R, van der Ent MA, Kaan A, Sharifi N, Paul DS, Ifrim DC, Quintin J, Love MI, Pisano DG, Burden F, Foad N, Farrow S, Zerbino DR, Dunham I, Kuijpers T, Lehrach H, Lengauer T, Bertone P, Netea MG, Vnigron M, Beck S, Flicek P, Gut I, Ouwehand WH, Bock C, Soranzo N, Guigo R, Valencia A, Stunnenberg H. Preprint DOI: 10.1101/237784
Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions.
Tang J, Tanoli ZU, Ravikumar B, Alam Z, Rebane A, Vähä-Koskela M, Peddinti G, van Adrichem AJ, Wakkinen J, Jaiswal A, Karjalainen E, Gautam P, He L, Parri E, Khan S, Gupta A, Ali M, Yetukuri L, Gustavsson AL, Seashore-Ludlow B, Hersey A, Leach AR, Overington JP, Repasky G, Wennerberg K, Aittokallio T. Cell chemical biology Volume 25 (2018) p.224-229.e2 DOI: 10.1016/j.chembiol.2017.11.009
Usage of cell nomenclature in biomedical literature.
Kafkas Ş, Sarntivijai S, Hoehndorf R. BMC bioinformatics Volume 18 (2017) p.561 DOI: 10.1186/s12859-017-1978-0
Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge.
Sarntivijai S, Diehl AD, He Y. BMC bioinformatics Volume 18 (2017) p.560 DOI: 10.1186/s12859-017-1976-2
Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses.
Ong E, Xie J, Ni Z, Liu Q, Sarntivijai S, Lin Y, Cooper D, Terryn R, Stathias V, Chung C, Schürer S, He Y. BMC bioinformatics Volume 18 (2017) p.556 DOI: 10.1186/s12859-017-1981-5
Comparison, alignment, and synchronization of cell line information between CLO and EFO.
Ong E, Sarntivijai S, Jupp S, Parkinson H, He Y. BMC bioinformatics Volume 18 (2017) p.557 DOI: 10.1186/s12859-017-1979-z
Accurate and fast feature selection workflow for high-dimensional omics data.
Perez-Riverol Y, Kuhn M, Vizcaíno JA, Hitz MP, Audain E. PloS one Volume 12 (2017) p.e0189875 DOI: 10.1371/journal.pone.0189875
*
A protein standard that emulates homology for the characterization of protein inference algorithms
The M, Edfors F, Perez-Riverol Y, Payne SH, Hoopmann MR, Palmblad M, Forsström B, Käll L. Preprint DOI: 10.1101/236471
*
Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.
Flannick J, Fuchsberger C, Mahajan A, Teslovich TM, Agarwala V, Gaulton KJ, Caulkins L, Koesterer R, Ma C, Moutsianas L, McCarthy DJ, Rivas MA, Perry JRB, Sim X, Blackwell TW, Robertson NR, Rayner NW, Cingolani P, Locke AE, Tajes JF, Highland HM, Dupuis J, Chines PS, Lindgren CM, Hartl C, Jackson AU, Chen H, Huyghe JR, van de Bunt M, Pearson RD, Kumar A, Müller-Nurasyid M, Müller-Nurasyid M, Grarup N, Stringham HM, Gamazon ER, Lee J, Chen Y, Scott RA, Below JE, Chen P, Huang J, Go MJ, Stitzel ML, Pasko D, Parker SCJ, Varga TV, Green T, Beer NL, Day-Williams AG, Ferreira T, Fingerlin T, Horikoshi M, Hu C, Huh I, Ikram MK, Kim BJ, Kim Y, Kim YJ, Kwon MS, Lee J, Lee S, Lin KH, Maxwell TJ, Nagai Y, Wang X, Welch RP, Yoon J, Zhang W, Barzilai N, Voight BF, Han BG, Jenkinson CP, Kuulasmaa T, Kuusisto J, Manning A, Ng MCY, Palmer ND, Balkau B, Stančáková A, Abboud HE, Boeing H, Giedraitis V, Prabhakaran D, Gottesman O, Scott J, Carey J, Kwan P, Grant G, Smith JD, Neale BM, Purcell S, Butterworth AS, Howson JMM, Lee HM, Lu Y, Kwak SH, Zhao W, Danesh J, Lam VKL, Park KS, Saleheen D, So WY, Tam CHT, Afzal U, Aguilar D, Arya R, Aung T, Chan E, Navarro C, Cheng CY, Palli D, Correa A, Curran JE, Rybin D, Farook VS, Fowler SP, Freedman BI, Griswold M, Hale DE, Hicks PJ, Khor CC, Kumar S, Lehne B, Thuillier D, Lim WY, Liu J, Loh M, Musani SK, Puppala S, Scott WR, Yengo L, Tan ST, Taylor HA, Thameem F, Wilson G, Wong TY, Njølstad PR, Levy JC, Mangino M, Bonnycastle LL, Schwarzmayr T, Fadista J, Surdulescu GL, Herder C, Groves CJ, Wieland T, Bork-Jensen J, Brandslund I, Christensen C, Koistinen HA, Doney ASF, Kinnunen L, Esko T, Farmer AJ, Hakaste L, Hodgkiss D, Kravic J, Lyssenko V, Hollensted M, Jørgensen ME, Jørgensen T, Ladenvall C, Justesen JM, Käräjämäki A, Kriebel J, Rathmann W, Lannfelt L, Lauritzen T, Narisu N, Linneberg A, Melander O, Milani L, Neville M, Orho-Melander M, Qi L, Qi Q, Roden M, Rolandsson O, Swift A, Rosengren AH, Stirrups K, Wood AR, Mihailov E, Blancher C, Carneiro MO, Maguire J, Poplin R, Shakir K, Fennell T, DePristo M, de Angelis MH, Deloukas P, Gjesing AP, Jun G, Nilsson P, Murphy J, Onofrio R, Thorand B, Hansen T, Meisinger C, Hu FB, Isomaa B, Karpe F, Liang L, Peters A, Huth C, O'Rahilly SP, Palmer CNA, Pedersen O, Rauramaa R, Tuomilehto J, Salomaa V, Watanabe RM, Syvänen AC, Bergman RN, Bharadwaj D, Bottinger EP, Cho YS, Chandak GR, Chan JC, Chia KS, Daly MJ, Ebrahim SB, Langenberg C, Elliott P, Jablonski KA, Lehman DM, Jia W, Ma RCW, Pollin TI, Sandhu M, Tandon N, Froguel P, Barroso I, Teo YY, Zeggini E, Loos RJF, Small KS, Ried JS, DeFronzo RA, Grallert H, Glaser B, Metspalu A, Wareham NJ, Walker M, Banks E, Gieger C, Ingelsson E, Im HK, Illig T, Franks PW, Buck G, Trakalo J, Buck D, Prokopenko I, Mägi R, Lind L, Farjoun Y, Owen KR, Gloyn AL, Strauch K, Tuomi T, Kooner JS, Lee JY, Park T, Donnelly P, Morris AD, Hattersley AT, Bowden DW, Collins FS, Atzmon G, Chambers JC, Spector TD, Laakso M, Strom TM, Bell GI, Blangero J, Duggirala R, Tai ES, McVean G, Hanis CL, Wilson JG, Seielstad M, Frayling TM, Meigs JB, Cox NJ, Sladek R, Lander ES, Gabriel S, Mohlke KL, Meitinger T, Groop L, Abecasis G, Scott LJ, Morris AP, Kang HM, Altshuler D, Burtt NP, Florez JC, Boehnke M, McCarthy MI. Scientific data Volume 4 (2017) p.170179 DOI: 10.1038/sdata.2017.179
Open Targets: Mining gene and disease associations for improved drug target identification
Carvalho-Silva D. DOI: 10.6019/tol.opentargets-w.2017.00001.1
GWAS Catalog: Exploring SNP-trait associations
Emery L, MacArthur J. DOI: 10.6019/tol.gwas-t.2017.00001.1
Finding the best data for your needs in the PDB archive
Conroy M. DOI: 10.6019/tol.pdbenov17-w.2017.00001.1
*
Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis
Stojic L, Lun A, Mangei J, Mascalchi P, Quarantotti V, Barr A, Bakal C, Marioni J, Gergely F, Odom D. Preprint DOI: 10.1101/234930
*
Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging
Severo MS, Landry JJ, Lindquist RL, Goosmann C, Brinkmann V, Collier P, Hauser AE, Benes V, Henriksson J, Teichmann SA, Levashina EA. Preprint DOI: 10.1101/234492
*
The IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation
Pramanik J, Chen X, Kar G, Gomes T, Henriksson J, Miao Z, Natarajan K, McKenzie ANJ, Mahata B, Teichmann SA. Preprint DOI: 10.1101/235010
*
Real-time search of all bacterial and viral genomic data
Bradley P, den Bakker H, Rocha E, McVean G, Iqbal Z. Preprint DOI: 10.1101/234955
Condensed tannins affect bacterial and fungal microbiomes and mycotoxin production during ensiling and upon aerobic exposure.
Peng K, Jin L, Niu YD, Huang Q, McAllister TA, Yang HE, Denise H, Xu Z, Acharya S, Wang S, Wang Y. Applied and environmental microbiology (2017) DOI: 10.1128/AEM.02274-17
Sharing and reuse of individual participant data from clinical trials: principles and recommendations.
Ohmann C, Banzi R, Canham S, Battaglia S, Matei M, Ariyo C, Becnel L, Bierer B, Bowers S, Clivio L, Dias M, Druml C, Faure H, Fenner M, Galvez J, Ghersi D, Gluud C, Groves T, Houston P, Karam G, Kalra D, Knowles RL, Krleža-Jerić K, Kubiak C, Kuchinke W, Kush R, Lukkarinen A, Marques PS, Newbigging A, O'Callaghan J, Ravaud P, Schlünder I, Shanahan D, Sitter H, Spalding D, Tudur-Smith C, van Reusel P, van Veen EB, Visser GR, Wilson J, Demotes-Mainard J. BMJ open Volume 7 (2017) p.e018647 DOI: 10.1136/bmjopen-2017-018647
nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.
Schober D, Jacob D, Wilson M, Cruz JA, Marcu A, Grant JR, Moing A, Deborde C, de Figueiredo LF, Haug K, Rocca-Serra P, Easton J, Ebbels TMD, Hao J, Ludwig C, Günther UL, Rosato A, Klein MS, Lewis IA, Luchinat C, Jones AR, Grauslys A, Larralde M, Yokochi M, Kobayashi N, Porzel A, Griffin JL, Viant MR, Wishart DS, Steinbeck C, Salek RM, Neumann S. Analytical chemistry Volume 90 (2018) p.649-656 DOI: 10.1021/acs.analchem.7b02795
In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering.
Wu Q, Ferry QRV, Baeumler TA, Michaels YS, Vitsios DM, Habib O, Arnold R, Jiang X, Maio S, Steinkraus BR, Tapia M, Piazza P, Xu N, Holländer GA, Milne TA, Kim JS, Enright AJ, Bassett AR, Fulga TA. Nature communications Volume 8 (2017) p.2109 DOI: 10.1038/s41467-017-00686-2
Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling.
Tresadern G, Trabanco AA, Pérez-Benito L, Overington JP, van Vlijmen HWT, van Westen GJP. Journal of chemical information and modeling Volume 57 (2017) p.2976-2985 DOI: 10.1021/acs.jcim.7b00338
Molecular and functional variation in iPSC-derived sensory neurons.
Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, Patel M, Goncalves A, Ferreira R, Benn CL, Wilbrey A, Bictash M, Impey E, Cao L, Lainez S, Loucif AJ, Whiting PJ, Gutteridge A, Gaffney DJ, HIPSCI Consortium. Nature genetics Volume 50 (2018) p.54-61 DOI: 10.1038/s41588-017-0005-8
Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.
Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Peat G, Pignatelli M, Falcone F, Benes CH, Dunham I, Bignell G, McDade SS, Garnett MJ, Saez-Rodriguez J. Cancer research Volume 78 (2018) p.769-780 DOI: 10.1158/0008-5472.can-17-1679
The HMMER Web Server for Protein Sequence Similarity Search.
Prakash A, Jeffryes M, Bateman A, Finn RD. Current protocols in bioinformatics Volume 60 (2017) p.3.15.1-3.15.23 DOI: 10.1002/cpbi.40
Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines.
Blattmann P, Henriques D, Zimmermann M, Frommelt F, Sauer U, Saez-Rodriguez J, Aebersold R. Cell systems Volume 5 (2017) p.604-619.e7 DOI: 10.1016/j.cels.2017.11.002
Immuno-oncology from the perspective of somatic evolution.
González S, Volkova N, Beer P, Gerstung M. Seminars in cancer biology Volume 52 (2018) p.75-85 DOI: 10.1016/j.semcancer.2017.12.001
Analysis of the genomic landscape of multiple myeloma highlights novel prognostic markers and disease subgroups.
Bolli N, Biancon G, Moarii M, Gimondi S, Li Y, de Philippis C, Maura F, Sathiaseelan V, Tai YT, Mudie L, O'Meara S, Raine K, Teague JW, Butler AP, Carniti C, Gerstung M, Bagratuni T, Kastritis E, Dimopoulos M, Corradini P, Anderson K, Moreau P, Minvielle S, Campbell PJ, Papaemmanuil E, Avet-Loiseau H, Munshi NC. Leukemia (2017) DOI: 10.1038/leu.2017.344
The Human Cell Atlas.
Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N, Human Cell Atlas Meeting Participants. eLife Volume 6 (2017) DOI: 10.7554/eLife.27041
Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the "Gene-Battery" Model.
Sundaram V, Wang T. BioEssays : news and reviews in molecular, cellular and developmental biology Volume 40 (2018) DOI: 10.1002/bies.201700155
*
Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting
Iorio F, Behan FM, Goncalves E, Bhosle S, Chen E, Shepherd R, Beaver C, Ansari R, Pooley R, Wilkinson P, Harper S, Butler AP, Stronach E, Saez-Rodriguez J, Yusa K, Garnett MJ. Preprint DOI: 10.1101/228189
Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.
Vitsios DM, Kentepozidou E, Quintais L, Benito-Gutiérrez E, van Dongen S, Davis MP, Enright AJ. Nucleic acids research Volume 45 (2017) p.e177 DOI: 10.1093/nar/gkx836
*
Variation and Functional Impact of Neanderthal Ancestry in Western Asia.
Taskent RO, Alioglu ND, Fer E, Melike Donertas H, Somel M, Gokcumen O. Genome biology and evolution Volume 9 (2017) p.3516-3524 DOI: 10.1093/gbe/evx216
clustComp, a bioconductor package for the comparison of clustering results.
Torrente A, Brazma A. Bioinformatics (Oxford, England) Volume 33 (2017) p.4001-4003 DOI: 10.1093/bioinformatics/btx532
Editorial overview: Catalysis and regulation.
Thornton J, Orengo C. Current opinion in structural biology Volume 47 (2017) p.vi-viii DOI: 10.1016/j.sbi.2017.11.005
*
DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation.
Richard MA, Huan T, Ligthart S, Gondalia R, Jhun MA, Brody JA, Irvin MR, Marioni R, Shen J, Tsai PC, Montasser ME, Jia Y, Syme C, Salfati EL, Boerwinkle E, Guan W, Mosley TH, Bressler J, Morrison AC, Liu C, Mendelson MM, Uitterlinden AG, van Meurs JB, BIOS Consortium, Franco OH, Zhang G, Li Y, Stewart JD, Bis JC, Psaty BM, Chen YI, Kardia SLR, Zhao W, Turner ST, Absher D, Aslibekyan S, Starr JM, McRae AF, Hou L, Just AC, Schwartz JD, Vokonas PS, Menni C, Spector TD, Shuldiner A, Damcott CM, Rotter JI, Palmas W, Liu Y, Paus T, Horvath S, O'Connell JR, Guo X, Pausova Z, Assimes TL, Sotoodehnia N, Smith JA, Arnett DK, Deary IJ, Baccarelli AA, Bell JT, Whitsel E, Dehghan A, Levy D, Fornage M. American journal of human genetics Volume 101 (2017) p.888-902 DOI: 10.1016/j.ajhg.2017.09.028
Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.
Shahbazi MN, Scialdone A, Skorupska N, Weberling A, Recher G, Zhu M, Jedrusik A, Devito LG, Noli L, Macaulay IC, Buecker C, Khalaf Y, Ilic D, Voet T, Marioni JC, Zernicka-Goetz M. Nature Volume 552 (2017) p.239-243 DOI: 10.1038/nature24675
*
Genetic diversity of the African malaria vector Anopheles gambiae.
Anopheles gambiae 1000 Genomes Consortium, Data analysis group, Partner working group, Sample collections—Angola:, Burkina Faso:, Cameroon:, Gabon:, Guinea:, Guinea-Bissau:, Kenya:, Uganda:, Crosses:, Sequencing and data production, Web application development, Project coordination. Nature Volume 552 (2017) p.96-100 DOI: 10.1038/nature24995
Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants.
Rifaioglu AS, Doğan T, Saraç ÖS, Ersahin T, Saidi R, Atalay MV, Martin MJ, Cetin-Atalay R. Proteins Volume 86 (2018) p.135-151 DOI: 10.1002/prot.25416
*
Assessing the Gene Regulatory Landscape in 1,188 Human Tumors
Calabrese C, Lehmann K, Urban L, Liu F, Erkek S, Fonseca N, Kahles A, Kilpinen-Barrett LH, Markowski J, Waszak S, Korbel J, Zhang Z, Brazma A, Raetsch G, Schwarz R, Stegle O, PCAWG-3. Preprint DOI: 10.1101/225441
Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells.
Gonçalves E, Sciacovelli M, Costa ASH, Tran MGB, Johnson TI, Machado D, Frezza C, Saez-Rodriguez J. Metabolic engineering Volume 45 (2018) p.149-157 DOI: 10.1016/j.ymben.2017.11.011
Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression.
Berthelot C, Villar D, Horvath JE, Odom DT, Flicek P. Nature ecology & evolution Volume 2 (2018) p.152-163 DOI: 10.1038/s41559-017-0377-2
The challenge of modeling protein assemblies: the CASP12-CAPRI experiment.
Lensink MF, Velankar S, Baek M, Heo L, Seok C, Wodak SJ. Proteins Volume 86 Suppl 1 (2018) p.257-273 DOI: 10.1002/prot.25419
Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.
Griffiths JA, Scialdone A, Marioni JC. BMC genomics Volume 18 (2017) p.904 DOI: 10.1186/s12864-017-4253-x
*
5-Formylcytosine controls nucleosome positioning through covalent histone-DNA interaction
Raiber E, Portella G, Martinez Cuesta S, Hardisty R, Murat P, Li Z, Iurlaro M, Dean W, Spindel J, Beraldi D, Dawson M, Reik W, Balasubramanian S. Preprint DOI: 10.1101/224444
Validation of Structures in the Protein Data Bank.
Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ. Structure (London, England : 1993) Volume 25 (2017) p.1916-1927 DOI: 10.1016/j.str.2017.10.009
*
Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast
Stirparo GG, Boroviak T, Guo G, Nichols J, Smith A, Bertone P. Preprint DOI: 10.1101/222760
*
The global distribution and spread of the mobilized colistin resistance gene mcr-1
Wang R, van Dorp L, Shaw L, Bradley P, Wang Q, Wang X, Jin L, Zhang Q, Liu Y, Rieux A, Dorai-Schneiders T, Weinert LA, Iqbal Z, Didelot X, Wang H, Balloux F. Preprint DOI: 10.1101/220921
A high-resolution mRNA expression time course of embryonic development in zebrafish.
White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Billis K, Hourlier T, Füllgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. eLife Volume 6 (2017) DOI: 10.7554/eLife.30860
Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.
Welby E, Lakowski J, Di Foggia V, Budinger D, Gonzalez-Cordero A, Lun ATL, Epstein M, Patel A, Cuevas E, Kruczek K, Naeem A, Minneci F, Hubank M, Jones DT, Marioni JC, Ali RR, Sowden JC. Stem cell reports Volume 9 (2017) p.1898-1915 DOI: 10.1016/j.stemcr.2017.10.018
DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.
Kraiczy J, Nayak KM, Howell KJ, Ross A, Forbester J, Salvestrini C, Mustata R, Perkins S, Andersson-Rolf A, Leenen E, Liebert A, Vallier L, Rosenstiel PC, Stegle O, Dougan G, Heuschkel R, Koo BK, Zilbauer M. Gut (2017) DOI: 10.1136/gutjnl-2017-314817
Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus.
Schulz H, Ruppert AK, Herms S, Wolf C, Mirza-Schreiber N, Stegle O, Czamara D, Forstner AJ, Sivalingam S, Schoch S, Moebus S, Pütz B, Hillmer A, Fricker N, Vatter H, Müller-Myhsok B, Nöthen MM, Becker AJ, Hoffmann P, Sander T, Cichon S. Nature communications Volume 8 (2017) p.1511 DOI: 10.1038/s41467-017-01818-4
*
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi
Keilwagen J, Hartung F, Paulini M, Twardziok SO, Grau J. Preprint DOI: 10.1101/219287
*
Corrigendum: High-throughput discovery of novel developmental phenotypes.
Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie Helmut Fuchs SM, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Nutter SNLMJ, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, International Mouse Phenotyping Consortium, Wurst W, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SDM, Adams DJ, Lloyd KCK, McKerlie C, Beaudet AL, Murray MBSA. Nature Volume 551 (2017) p.398 DOI: 10.1038/nature24643
To what extent do structural changes in catalytic metal sites affect enzyme function?
Valasatava Y, Rosato A, Furnham N, Thornton JM, Andreini C. Journal of inorganic biochemistry Volume 179 (2018) p.40-53 DOI: 10.1016/j.jinorgbio.2017.11.002
f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.
Buettner F, Pratanwanich N, McCarthy DJ, Marioni JC, Stegle O. Genome biology Volume 18 (2017) p.212 DOI: 10.1186/s13059-017-1334-8
*
A novel multi SNP based method for the identification of subspecies and associated lineages and sub-lineages of the Mycobacterium tuberculosis complex by whole genome sequencing
Lipworth SIW, Jajou R, de Neeling H, Bradley P, van der Hoek W, Maphalala G, Bonnet M, Sanchez-Padilla E, Diel R, Niemann S, Iqbal Z, Smith G, Peto T, Crook D, Walker TM, van Soolingen D. Preprint DOI: 10.1101/213850
*
Interoperable and scalable data analysis with microservices: Applications in Metabolomics
Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran A, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone S, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O. Preprint DOI: 10.1101/213603
PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.
Meehan TF, Conte N, Goldstein T, Inghirami G, Murakami MA, Brabetz S, Gu Z, Wiser JA, Dunn P, Begley DA, Krupke DM, Bertotti A, Bruna A, Brush MH, Byrne AT, Caldas C, Christie AL, Clark DA, Dowst H, Dry JR, Doroshow JH, Duchamp O, Evrard YA, Ferretti S, Frese KK, Goodwin NC, Greenawalt D, Haendel MA, Hermans E, Houghton PJ, Jonkers J, Kemper K, Khor TO, Lewis MT, Lloyd KCK, Mason J, Medico E, Neuhauser SB, Olson JM, Peeper DS, Rueda OM, Seong JK, Trusolino L, Vinolo E, Wechsler-Reya RJ, Weinstock DM, Welm A, Weroha SJ, Amant F, Pfister SM, Kool M, Parkinson H, Butte AJ, Bult CJ. Cancer research Volume 77 (2017) p.e62-e66 DOI: 10.1158/0008-5472.can-17-0582
*
Genomic Research Data Generation, Analysis and Sharing - Challenges in the African Setting
Mulder N, Adebamowo CA, Adebamowo SN, Adebayo O, Adeleye O, Alibi M, Baichoo S, Benkahla A, Fadlelmola FM, Ghazal H, Ghedira K, Matimba A, Moussa A, Mungloo-Dilmohamud Z, Owolabi MO, Radouani F, Rotimi CN, Stein DJ, Souiai O. Data Science Journal Volume 16 (2017) p.49 DOI: 10.5334/dsj-2017-049
ComplexViewer: visualization of curated macromolecular complexes.
Combe CW, Sivade MD, Hermjakob H, Heimbach J, Meldal BHM, Micklem G, Orchard S, Rappsilber J. Bioinformatics (Oxford, England) Volume 33 (2017) p.3673-3675 DOI: 10.1093/bioinformatics/btx497
cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.
Martin-Herranz DE, Ribeiro AJM, Krueger F, Thornton JM, Reik W, Stubbs TM. Nucleic acids research Volume 45 (2017) p.11559-11569 DOI: 10.1093/nar/gkx814
Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells.
Faure AJ, Schmiedel JM, Lehner B. Cell systems Volume 5 (2017) p.471-484.e4 DOI: 10.1016/j.cels.2017.10.003
On expert curation and scalability: UniProtKB/Swiss-Prot as a case study.
Poux S, Arighi CN, Magrane M, Bateman A, Wei CH, Lu Z, Boutet E, Bye-A-Jee H, Famiglietti ML, Roechert B, UniProt Consortium T. Bioinformatics (Oxford, England) Volume 33 (2017) p.3454-3460 DOI: 10.1093/bioinformatics/btx439
LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data.
Sehnal D, Deshpande M, Vařeková RS, Mir S, Berka K, Midlik A, Pravda L, Velankar S, Koča J. Nature methods Volume 14 (2017) p.1121-1122 DOI: 10.1038/nmeth.4499
Sub-minute Phosphoregulation of Cell Cycle Systems during Plasmodium Gamete Formation.
Invergo BM, Brochet M, Yu L, Choudhary J, Beltrao P, Billker O. Cell reports Volume 21 (2017) p.2017-2029 DOI: 10.1016/j.celrep.2017.10.071
Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean.
Kılınç GM, Koptekin D, Atakuman Ç, Sümer AP, Dönertaş HM, Yaka R, Bilgin CC, Büyükkarakaya AM, Baird D, Altınışık E, Flegontov P, Götherström A, Togan İ, Somel M. Proceedings. Biological sciences Volume 284 (2017) DOI: 10.1098/rspb.2017.2064
Reactome enhanced pathway visualization.
Sidiropoulos K, Viteri G, Sevilla C, Jupe S, Webber M, Orlic-Milacic M, Jassal B, May B, Shamovsky V, Duenas C, Rothfels K, Matthews L, Song H, Stein L, Haw R, D'Eustachio P, Ping P, Hermjakob H, Fabregat A. Bioinformatics (Oxford, England) Volume 33 (2017) p.3461-3467 DOI: 10.1093/bioinformatics/btx441
*
NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease.
Schwerd T, Bryant RV, Pandey S, Capitani M, Meran L, Cazier JB, Jung J, Mondal K, Parkes M, Mathew CG, Fiedler K, McCarthy DJ, WGS500 Consortium, Oxford IBD cohort study investigators, COLORS in IBD group investigators, UK IBD Genetics Consortium, Sullivan PB, Rodrigues A, Travis SPL, Moore C, Sambrook J, Ouwehand WH, Roberts DJ, Danesh J, INTERVAL Study, Russell RK, Wilson DC, Kelsen JR, Cornall R, Denson LA, Kugathasan S, Knaus UG, Serra EG, Anderson CA, Duerr RH, McGovern DP, Cho J, Powrie F, Li VS, Muise AM, Uhlig HH. Mucosal immunology Volume 11 (2018) p.562-574 DOI: 10.1038/mi.2017.74
ggseqlogo: a versatile R package for drawing sequence logos.
Wagih O. Bioinformatics (Oxford, England) Volume 33 (2017) p.3645-3647 DOI: 10.1093/bioinformatics/btx469
Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.
Jasinska AJ, Zelaya I, Service SK, Peterson CB, Cantor RM, Choi OW, DeYoung J, Eskin E, Fairbanks LA, Fears S, Furterer AE, Huang YS, Ramensky V, Schmitt CA, Svardal H, Jorgensen MJ, Kaplan JR, Villar D, Aken BL, Flicek P, Nag R, Wong ES, Blangero J, Dyer TD, Bogomolov M, Benjamini Y, Weinstock GM, Dewar K, Sabatti C, Wilson RK, Jentsch JD, Warren W, Coppola G, Woods RP, Freimer NB. Nature genetics Volume 49 (2017) p.1714-1721 DOI: 10.1038/ng.3959
PDBsum: Structural summaries of PDB entries.
Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM. Protein science : a publication of the Protein Society Volume 27 (2018) p.129-134 DOI: 10.1002/pro.3289
*
Terminal uridylyltransferases target RNA viruses as part of the innate immune system in animals
Le Pen J, Jiang H, Di Domenico T, Kneuss E, Kosalka J, Morgan M, Much C, Rudolph KLM, Enright AJ, O'Carroll D, Wang D, Miska EA. Preprint DOI: 10.1101/209114
*
Proteomics and phosphoproteomics in precision medicine: applications and challenges.
Giudice G, Petsalaki E. Briefings in bioinformatics (2017) DOI: 10.1093/bib/bbx141
Report of the International Stem Cell Banking Initiative Workshop Activity: Current Hurdles and Progress in Seed-Stock Banking of Human Pluripotent Stem Cells.
Kim JH, Kurtz A, Yuan BZ, Zeng F, Lomax G, Loring JF, Crook J, Ju JH, Clarke L, Inamdar MS, Pera M, Firpo MT, Sheldon M, Rahman N, O'Shea O, Pranke P, Zhou Q, Isasi R, Rungsiwiwut R, Kawamata S, Oh S, Ludwig T, Masui T, Novak TJ, Takahashi T, Fujibuchi W, Koo SK, Stacey GN. Stem cells translational medicine Volume 6 (2017) p.1956-1962 DOI: 10.1002/sctm.17-0144
Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.
Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC, Odom DT, Flicek P. Nature communications Volume 8 (2017) p.1092 DOI: 10.1038/s41467-017-01037-x
Comprehensive Pharmacogenomic Profiling of Malignant Pleural Mesothelioma Identifies a Subgroup Sensitive to FGFR Inhibition.
Quispel-Janssen JM, Badhai J, Schunselaar L, Price S, Brammeld J, Iorio F, Kolluri K, Garnett M, Berns A, Baas P, McDermott U, Neefjes J, Alifrangis C. Clinical cancer research : an official journal of the American Association for Cancer Research Volume 24 (2018) p.84-94 DOI: 10.1158/1078-0432.ccr-17-1172
Universal Patterns of Selection in Cancer and Somatic Tissues.
Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K, Van Loo P, Davies H, Stratton MR, Campbell PJ. Cell Volume 171 (2017) p.1029-1041.e21 DOI: 10.1016/j.cell.2017.09.042
*
Genomics in healthcare: GA4GH looks to 2022
Birney E, Vamathevan J, Goodhand P. Preprint DOI: 10.1101/203554
*
Identifying accurate metagenome and amplicon software via a meta-analysis of benchmarking studies
Gardner PP, Watson RJ, Morgan XC, Draper JL, Finn RD, Morales SE, Stott MB. Preprint DOI: 10.1101/202077
A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction.
Bowl MR, Simon MM, Ingham NJ, Greenaway S, Santos L, Cater H, Taylor S, Mason J, Kurbatova N, Pearson S, Bower LR, Clary DA, Meziane H, Reilly P, Minowa O, Kelsey L, International Mouse Phenotyping Consortium, Tocchini-Valentini GP, Gao X, Bradley A, Skarnes WC, Moore M, Beaudet AL, Justice MJ, Seavitt J, Dickinson ME, Wurst W, de Angelis MH, Herault Y, Wakana S, Nutter LMJ, Flenniken AM, McKerlie C, Murray SA, Svenson KL, Braun RE, West DB, Lloyd KCK, Adams DJ, White J, Karp N, Flicek P, Smedley D, Meehan TF, Parkinson HE, Teboul LM, Wells S, Steel KP, Mallon AM, Brown SDM. Nature communications Volume 8 (2017) p.886 DOI: 10.1038/s41467-017-00595-4
DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.
Howell KJ, Kraiczy J, Nayak KM, Gasparetto M, Ross A, Lee C, Mak TN, Koo BK, Kumar N, Lawley T, Sinha A, Rosenstiel P, Heuschkel R, Stegle O, Zilbauer M. Gastroenterology Volume 154 (2018) p.585-598 DOI: 10.1053/j.gastro.2017.10.007
Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer.
Gonçalves E, Fragoulis A, Garcia-Alonso L, Cramer T, Saez-Rodriguez J, Beltrao P. Cell systems Volume 5 (2017) p.386-398.e4 DOI: 10.1016/j.cels.2017.08.013
Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach.
Guruceaga E, Garin-Muga A, Prieto G, Bejarano B, Marcilla M, Marín-Vicente C, Perez-Riverol Y, Casal JI, Vizcaíno JA, Corrales FJ, Segura V. Journal of proteome research Volume 16 (2017) p.4374-4390 DOI: 10.1021/acs.jproteome.7b00388
*
Co-expression networks reveal the tissue-specific regulation of transcription and splicing.
Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, GTEx Consortium, Engelhardt BE, Battle A. Genome research Volume 27 (2017) p.1843-1858 DOI: 10.1101/gr.216721.116
*
Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis.
Yang F, Wang J, GTEx Consortium, Pierce BL, Chen LS. Genome research Volume 27 (2017) p.1859-1871 DOI: 10.1101/gr.216754.116
*
A cancer pharmacogenomic screen powering crowd-sourced advancement of drug combination prediction
Menden MP, Wang D, Guan Y, Mason M, Szalai B, Bulusu KC, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Chaibub Neto E, Norman T, Tang EK, Garnett MJ, Di Veroli G, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J, AstraZeneca-Sanger Drug Combination DREAM Consorti. Preprint DOI: 10.1101/200451
*
Assessment of batch-correction methods for scRNA-seq data with a new test metric
Buttner M, Miao Z, Wolf A, Teichmann SA, Theis FJ. Preprint DOI: 10.1101/200345
*
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.
Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F, Broad-DREAM Community, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA. Cell systems Volume 5 (2017) p.485-497.e3 DOI: 10.1016/j.cels.2017.09.004
SourceData: a semantic platform for curating and searching figures.
Liechti R, George N, Götz L, El-Gebali S, Chasapi A, Crespo I, Xenarios I, Lemberger T. Nature methods Volume 14 (2017) p.1021-1022 DOI: 10.1038/nmeth.4471
*
The impact of rare variation on gene expression across tissues.
Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Bassik MC, Merker JD, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Hall IM, Battle A, Montgomery SB. Nature Volume 550 (2017) p.239-243 DOI: 10.1038/nature24267
*
Genetic effects on gene expression across human tissues.
GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lead analysts:, Laboratory, Data Analysis &Coordinating Center (LDACC):, NIH program management:, Biospecimen collection:, Pathology:, eQTL manuscript working group:, Battle A, Brown CD, Engelhardt BE, Montgomery SB. Nature Volume 550 (2017) p.204-213 DOI: 10.1038/nature24277
*
Dynamic landscape and regulation of RNA editing in mammals.
Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Chawla A, Del Sal G, Peltz G, Brunet A, Conrad DF, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB. Nature Volume 550 (2017) p.249-254 DOI: 10.1038/nature24041
*
Landscape of X chromosome inactivation across human tissues.
Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG. Nature Volume 550 (2017) p.244-248 DOI: 10.1038/nature24265
Intestinal Fork Head Regulates Nutrient Absorption and Promotes Longevity.
Bolukbasi E, Khericha M, Regan JC, Ivanov DK, Adcott J, Dyson MC, Nespital T, Thornton JM, Alic N, Partridge L. Cell reports Volume 21 (2017) p.641-653 DOI: 10.1016/j.celrep.2017.09.042
*
Corrigendum: A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.
Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, Nik-Zainal S. Nature genetics Volume 49 (2017) p.1661 DOI: 10.1038/ng1117-1661a
Single-cell epigenomics: Recording the past and predicting the future.
Kelsey G, Stegle O, Reik W. Science (New York, N.Y.) Volume 358 (2017) p.69-75 DOI: 10.1126/science.aan6826
OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.
Perez-Riverol Y, Ternent T, Koch M, Barsnes H, Vrousgou O, Jupp S, Vizcaíno JA. Proteomics Volume 17 (2017) DOI: 10.1002/pmic.201700244
*
Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.
Hadinnapola C, Bleda M, Haimel M, Screaton N, Swift A, Dorfmüller P, Preston SD, Southwood M, Hernandez-Sanchez J, Martin J, Treacy C, Yates K, Bogaard H, Church C, Coghlan G, Condliffe R, Corris PA, Gibbs S, Girerd B, Holden S, Humbert M, Kiely DG, Lawrie A, Machado R, MacKenzie Ross R, Moledina S, Montani D, Newnham M, Peacock A, Pepke-Zaba J, Rayner-Matthews P, Shamardina O, Soubrier F, Southgate L, Suntharalingam J, Toshner M, Trembath R, Vonk Noordegraaf A, Wilkins MR, Wort SJ, Wharton J, NIHR BioResource–Rare Diseases Consortium; UK National Cohort Study of Idiopathic and Heritable PAH, Gräf S, Morrell NW. Circulation Volume 136 (2017) p.2022-2033 DOI: 10.1161/circulationaha.117.028351
*
A screen for combination therapies in BRAF/NRAS wild type melanoma identifies nilotinib plus MEK inhibitor as a synergistic combination
Ranzani M, Kemper K, Michaut M, Krijgsman O, Aben N, Iyer V, Wong K, Roumeliotis TI, Del Castillo Velasco-Herrera M, Nsengimana J, Turner G, Thompson N, Shahrabi A, Sjoberg M, Rashid M, Speak AO, Grinkevich V, Behan F, Tamborero D, Iorio F, van Dongen S, Bignell GR, Alsinet C, Chen S, Supper E, Dutton-Regester K, Pritchard A, Wong C, Enright A, Newton-Bishop J, McDermott U, Hayward NK, Choudhary JS, Yusa K, Wessels L, Garnett MJ, Peeper D, Adams DJ. Preprint DOI: 10.1101/195354
Two independent modes of chromatin organization revealed by cohesin removal.
Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, H Haering C, Mirny L, Spitz F. Nature Volume 551 (2017) p.51-56 DOI: 10.1038/nature24281
A decade after the metabolomics standards initiative it's time for a revision.
Spicer RA, Salek R, Steinbeck C. Scientific data Volume 4 (2017) p.170138 DOI: 10.1038/sdata.2017.138
*
A new pan-European Train-the-Trainer programme for bioinformatics: pilot results on feasibility, utility and sustainability of learning.
Via A, Attwood TK, Fernandes PL, Morgan SL, Schneider MV, Palagi PM, Rustici G, Tractenberg RE. Briefings in bioinformatics (2017) DOI: 10.1093/bib/bbx112
Compliance with minimum information guidelines in public metabolomics repositories.
Spicer RA, Salek R, Steinbeck C. Scientific data Volume 4 (2017) p.170137 DOI: 10.1038/sdata.2017.137
*
Multi-platform discovery of haplotype-resolved structural variation in human genomes
Chaisson MJ, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez O, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie A, Antaki D, Audano P, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin C, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin D, Gujral M, Guryev V, Haynes Heaton W, Korlach J, Kumar S, Kwon JY, Lee JE, Lee J, Lee W, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro F, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang A, Qiu Y, Rosanio G, Ryan M, Stutz A, Spierings DC, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok P, Lansdorp PM, Marth G, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski M, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Preprint DOI: 10.1101/193144
*
UniProt Genomic Mapping for Deciphering Functional Effects of Missense Variants
McGarvey P, Nightingale A, Luo J, Huang H, Martin M, Wu C, UniProt Consortium. Preprint DOI: 10.1101/192914
Perspectives from the NanoSafety Modelling Cluster on the validation criteria for (Q)SAR models used in nanotechnology.
Puzyn T, Jeliazkova N, Sarimveis H, Marchese Robinson RL, Lobaskin V, Rallo R, Richarz AN, Gajewicz A, Papadopulos MG, Hastings J, Cronin MTD, Benfenati E, Fernández A. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association Volume 112 (2018) p.478-494 DOI: 10.1016/j.fct.2017.09.037
*
C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis.
Lepik K, Annilo T, Kukuškina V, eQTLGen Consortium, Kisand K, Kutalik Z, Peterson P, Peterson H. PLoS computational biology Volume 13 (2017) p.e1005766 DOI: 10.1371/journal.pcbi.1005766
*
A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy.
Sorzano COS, Vargas J, Otón J, de la Rosa-Trevín JM, Vilas JL, Kazemi M, Melero R, Del Caño L, Cuenca J, Conesa P, Gómez-Blanco J, Marabini R, Carazo JM. BioMed Research International Volume 2017 (2017) p.6482567 DOI: 10.1155/2017/6482567
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.
Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR. Journal of proteome research Volume 16 (2017) p.4288-4298 DOI: 10.1021/acs.jproteome.7b00370
PharmML in Action: an Interoperable Language for Modeling and Simulation.
Bizzotto R, Comets E, Smith G, Yvon F, Kristensen NR, Swat MJ. CPT: pharmacometrics & systems pharmacology Volume 6 (2017) p.651-665 DOI: 10.1002/psp4.12213
Uncovering novel repositioning opportunities using the Open Targets platform.
Khaladkar M, Koscielny G, Hasan S, Agarwal P, Dunham I, Rajpal D, Sanseau P. Drug discovery today Volume 22 (2017) p.1800-1807 DOI: 10.1016/j.drudis.2017.09.007
Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets.
Jarnuczak AF, Vizcaíno JA. Current protocols in bioinformatics Volume 59 (2017) p.13.31.1-13.31.12 DOI: 10.1002/cpbi.30
Understanding enzyme function evolution from a computational perspective.
Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM. Current opinion in structural biology Volume 47 (2017) p.131-139 DOI: 10.1016/j.sbi.2017.08.003
*
BraCeR: Reconstruction of B-cell receptor sequences and clonality inference from single-cell RNA-sequencing
Lindeman I, Emerton G, Sollid LM, Teichmann S, Stubbington MJT. Preprint DOI: 10.1101/185504
The future of metabolomics in ELIXIR.
van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Le Corguillé G, Moreno P, Moschonas NK, Neumann S, O'Donovan C, Reczko M, Rocca-Serra P, Rosato A, Salek RM, Sansone SA, Satagopam V, Schober D, Shimmo R, Spicer RA, Spjuth O, Thévenot EA, Viant MR, Weber RJM, Willighagen EL, Zanetti G, Steinbeck C. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.12342.2
Societal challenges of precision medicine: Bringing order to chaos.
Salgado R, Moore H, Martens JWM, Lively T, Malik S, McDermott U, Michiels S, Moscow JA, Tejpar S, McKee T, Lacombe D, IBCD-Faculty. European journal of cancer (Oxford, England : 1990) Volume 84 (2017) p.325-334 DOI: 10.1016/j.ejca.2017.07.028
*
Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Fonseca NA, He Y, Kahles A, Lehmann K, Liu F, Shiraishi Y, Soulette CM, Urban L, Demircioğlu D, Greger L, Li S, Liu D, Perry MD, Xiang L, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, PCAWG Transcriptome Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/183889
*
Reports from CAGI: The Critical Assessment of Genome Interpretation.
Hoskins RA, Repo S, Barsky D, Andreoletti G, Moult J, Brenner SE. Human mutation Volume 38 (2017) p.1039-1041 DOI: 10.1002/humu.23290
PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models.
Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J. Structure (London, England : 1993) Volume 25 (2017) p.1317-1318 DOI: 10.1016/j.str.2017.08.001
More on the Best Evolutionary Rate for Phylogenetic Analysis.
Klopfstein S, Massingham T, Goldman N. Systematic biology Volume 66 (2017) p.769-785 DOI: 10.1093/sysbio/syx051
Best practice data life cycle approaches for the life sciences.
Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. F1000Research Volume 6 (2017) p.1618 DOI: 10.12688/f1000research.12344.2
*
Best practice data life cycle approaches for the life sciences
Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WW, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. Preprint DOI: 10.12688/f1000research.12344.1
The RNA m6A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence.
Ivanova I, Much C, Di Giacomo M, Azzi C, Morgan M, Moreira PN, Monahan J, Carrieri C, Enright AJ, O'Carroll D. Molecular cell Volume 67 (2017) p.1059-1067.e4 DOI: 10.1016/j.molcel.2017.08.003
Absence of Selection for Quantum Coherence in the Fenna-Matthews-Olson Complex: A Combined Evolutionary and Excitonic Study.
Valleau S, Studer RA, Häse F, Kreisbeck C, Saer RG, Blankenship RE, Shakhnovich EI, Aspuru-Guzik A. ACS central science Volume 3 (2017) p.1086-1095 DOI: 10.1021/acscentsci.7b00269
Gearing up to handle the mosaic nature of life in the quest for orthologs.
Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT, Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S. Bioinformatics (Oxford, England) (2017) DOI: 10.1093/bioinformatics/btx542
*
Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
Seaton D, Graf A, Baerenfaller K, Stitt M, Millar A, Gruissem W. Preprint DOI: 10.1101/182071
A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity.
Kuepfer L, Clayton O, Thiel C, Cordes H, Nudischer R, Blank LM, Baier V, Heymans S, Caiment F, Roth A, Fluri DA, Kelm JM, Castell J, Selevsek N, Schlapbach R, Keun H, Hynes J, Sarkans U, Gmuender H, Herwig R, Niederer S, Schuchhardt J, Segall M, Kleinjans J. Archives of toxicology Volume 92 (2018) p.553-555 DOI: 10.1007/s00204-017-2041-7
In silico prediction of novel therapeutic targets using gene-disease association data.
Ferrero E, Dunham I, Sanseau P. Journal of translational medicine Volume 15 (2017) p.182 DOI: 10.1186/s12967-017-1285-6
The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training.
Morgan SL, Palagi PM, Fernandes PL, Koperlainen E, Dimec J, Marek D, Larcombe L, Rustici G, Attwood TK, Via A. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.12332.1
The application of project-based learning in bioinformatics training.
Emery LR, Morgan SL. PLoS computational biology Volume 13 (2017) p.e1005620 DOI: 10.1371/journal.pcbi.1005620
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data.
Zhang C, Bijlard J, Staiger C, Scollen S, van Enckevort D, Hoogstrate Y, Senf A, Hiltemann S, Repo S, Pipping W, Bierkens M, Payralbe S, Stringer B, Heringa J, Stubbs A, Bonino Da Silva Santos LO, Belien J, Weistra W, Azevedo R, van Bochove K, Meijer G, Boiten JW, Rambla J, Fijneman R, Spalding JD, Abeln S. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.12168.1
*
Detection and removal of barcode swapping in single-cell RNA-seq data
Griffiths JA, Richard AC, Bach K, Lun AT, Marioni JC. Preprint DOI: 10.1101/177048
EMBL-EBI, programmatically: take a REST from manual searches
Burke M, Armstrong D, Carvalho-Silva D, Castro L, Cowley A, Finn R, Foix A, Katuri J, Laird M, Lee J, Levchenko M, Lopez R, Nightingale A, Nowotka M, Perry E, Pichler K, Pundir S, Morgan S, Saunders G, Garcia P, Squizzato S. DOI: 10.6019/tol.ebiprogrammatically-w.2017.00001.1
How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.
Marioni JC, Arendt D. Annual review of cell and developmental biology Volume 33 (2017) p.537-553 DOI: 10.1146/annurev-cellbio-100616-060818
A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology.
Penas DR, Henriques D, González P, Doallo R, Saez-Rodriguez J, Banga JR. PloS one Volume 12 (2017) p.e0182186 DOI: 10.1371/journal.pone.0182186
*
A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters
Demircioğlu D, Kindermans M, Nandi T, Cukuroglu E, Calabrese C, Fonseca NA, Kahles A, Lehmann K, Stegle O, Brazma A, Brooks A, Rätsch G, Tan P, Göke J, PCAWG Transcriptome Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/176487
mRNA 3' uridylation and poly(A) tail length sculpt the mammalian maternal transcriptome.
Morgan M, Much C, DiGiacomo M, Azzi C, Ivanova I, Vitsios DM, Pistolic J, Collier P, Moreira PN, Benes V, Enright AJ, O'Carroll D. Nature Volume 548 (2017) p.347-351 DOI: 10.1038/nature23318
Navigating freely-available software tools for metabolomics analysis.
Spicer R, Salek RM, Moreno P, Cañueto D, Steinbeck C. Metabolomics : Official journal of the Metabolomic Society Volume 13 (2017) p.106 DOI: 10.1007/s11306-017-1242-7
*
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Nature biotechnology Volume 35 (2017) p.725-731 DOI: 10.1038/nbt.3893
BioContainers: an open-source and community-driven framework for software standardization.
da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y. Bioinformatics (Oxford, England) Volume 33 (2017) p.2580-2582 DOI: 10.1093/bioinformatics/btx192
Automated assembly of species metabolomes through data submission into a public repository.
Salek RM, Conesa P, Cochrane K, Haug K, Williams M, Kale N, Moreno P, Jayaseelan KV, Macias JR, Nainala VC, Hall RD, Reed LK, Viant MR, O'Donovan C, Steinbeck C. GigaScience Volume 6 (2017) p.1-4 DOI: 10.1093/gigascience/gix062
Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.
Mohammed H, Hernando-Herraez I, Savino A, Scialdone A, Macaulay I, Mulas C, Chandra T, Voet T, Dean W, Nichols J, Marioni JC, Reik W. Cell reports Volume 20 (2017) p.1215-1228 DOI: 10.1016/j.celrep.2017.07.009
mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.
Larralde M, Lawson TN, Weber RJM, Moreno P, Haug K, Rocca-Serra P, Viant MR, Steinbeck C, Salek RM. Bioinformatics (Oxford, England) Volume 33 (2017) p.2598-2600 DOI: 10.1093/bioinformatics/btx169
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Genoscope Technical Team, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Tara Oceans Consortium Coordinators, Pesant S, Karsenti E, Wincker P. Scientific data Volume 4 (2017) p.170093 DOI: 10.1038/sdata.2017.93
*
A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine.
Vamathevan J, Birney E. Yearbook of medical informatics Volume 26 (2017) p.178-187 DOI: 10.15265/iy-2017-017
BioCIDER: a Contextualisation InDEx for biological Resources discovery.
Horro C, Cook M, Attwood TK, Brazas MD, Hancock JM, Palagi P, Corpas M, Jimenez R. Bioinformatics (Oxford, England) Volume 33 (2017) p.2607-2608 DOI: 10.1093/bioinformatics/btx213
Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS. Cell reports Volume 20 (2017) p.2201-2214 DOI: 10.1016/j.celrep.2017.08.010
The metagenomic data life-cycle: standards and best practices.
Ten Hoopen P, Finn RD, Bongo LA, Corre E, Fosso B, Meyer F, Mitchell A, Pelletier E, Pesole G, Santamaria M, Willassen NP, Cochrane G. GigaScience Volume 6 (2017) p.1-11 DOI: 10.1093/gigascience/gix047
Genomic Evolution of Breast Cancer Metastasis and Relapse.
Yates LR, Knappskog S, Wedge D, Farmery JHR, Gonzalez S, Martincorena I, Alexandrov LB, Van Loo P, Haugland HK, Lilleng PK, Gundem G, Gerstung M, Pappaemmanuil E, Gazinska P, Bhosle SG, Jones D, Raine K, Mudie L, Latimer C, Sawyer E, Desmedt C, Sotiriou C, Stratton MR, Sieuwerts AM, Lynch AG, Martens JW, Richardson AL, Tutt A, Lønning PE, Campbell PJ. Cancer cell Volume 32 (2017) p.169-184.e7 DOI: 10.1016/j.ccell.2017.07.005
Impact of Alternative Splicing on the Human Proteome.
Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. Cell reports Volume 20 (2017) p.1229-1241 DOI: 10.1016/j.celrep.2017.07.025
*
Computational approaches for discovery of mutational signatures in cancer.
Baez-Ortega A, Gori K. Briefings in bioinformatics (2017) DOI: 10.1093/bib/bbx082
Logic Modeling in Quantitative Systems Pharmacology.
Traynard P, Tobalina L, Eduati F, Calzone L, Saez-Rodriguez J. CPT: pharmacometrics & systems pharmacology Volume 6 (2017) p.499-511 DOI: 10.1002/psp4.12225
*
Beyond the Hype: Deep Neural Networks Outperform Established Methods Using A ChEMBL Bioactivity Benchmark Set
Lenselink EB, ten Dijke N, Bongers B, Papadatos G, van Vlijmen HWT, Kowalczyk W, IJzerman AP, van Westen GJP. Preprint DOI: 10.1101/168914
*
Very low depth whole genome sequencing in complex trait association studies
Gilly A, Southam L, Suveges D, Kuchenbaecker K, Moore R, Melloni G, Hatzikotoulas K, Farmaki A, Ritchie G, Schwartzentruber J, Danecek P, Kilian B, Pollard M, Ge X, Tsafantakis E, Dedoussis G, Zeggini E. Preprint DOI: 10.1101/169789
*
Designing an intuitive web application for drug discovery scientists
Karamanis N, Carvalho-Silva D, Cham JA, Fumis L, Hasan S, Hulcoop D, Koscielny G, Maguire M, Newell W, Ong C, Papa E, Pierleoni A, Pignatelli M, Pundir S, Rowland F, Vamathevan J, Watkins X, Barrett JC, Dunham I. Preprint DOI: 10.1101/169193
*
PIsCO: A Performance indicators framework for collection of bioinformatics resource metrics
Artaza H, Hancock JM, Jimenez RC, Corpas M. Preprint DOI: 10.7287/peerj.preprints.3112
*
Best Practice Data Life Cycle Approaches for the Life Sciences
Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. Preprint DOI: 10.1101/167619
*
Whole-body single-cell sequencing of the Platynereis larva reveals a subdivision into apical versus non-apical tissues
Achim K, Eling N, Martinez Vergara H, Bertucci PY, Brunet T, Collier P, Benes V, Marioni JC, Arendt D. Preprint DOI: 10.1101/167742
*
GDSCTools for Mining Pharmacogenomic Interactions in Cancer
Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Mathew GJ. Preprint DOI: 10.1101/166223
Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity.
Dönertaş HM, İzgi H, Kamacıoğlu A, He Z, Khaitovich P, Somel M. Scientific reports Volume 7 (2017) p.5894 DOI: 10.1038/s41598-017-05927-4
*
Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours.
Haghverdi L, Lun ATL, Morgan MD, Marioni JC. Preprint DOI: 10.1101/165118
*
Online resources for PCAWG data exploration, visualization, and discovery
Goldman M, Zhang J, Fonseca NA, Xiang Q, Craft B, Piñeiro-Yáñez E, O'Connor B, Bazant W, Barrera E, Muñoz A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, Haussler D, Weinstein J, Huber W, Valencia A, Papatheodorou I, Zhu J, Ferreti V, Vazquez M, PCAWG-12 Working Group, PCAWG Network. Preprint DOI: 10.1101/163907
*
Correction: Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.
Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C, BEEHIVE collaboration. PLoS biology Volume 15 (2017) p.e1002608 DOI: 10.1371/journal.pbio.1002608
Platelet function is modified by common sequence variation in megakaryocyte super enhancers.
Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts AS, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide ME, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M, Ouwehand WH, Astle WJ, Downes K, Kostadima M, Frontini M. Nature communications Volume 8 (2017) p.16058 DOI: 10.1038/ncomms16058
*
Sequanix: A Dynamic Graphical Interface for Snakemake Workflows
Desvillechabrol D, Legendre R, Rioualen C, Bouchier C, van Helden J, Kennedy S, Cokelaer T. Preprint DOI: 10.1101/162701
The yeast noncoding RNA interaction network.
Panni S, Prakash A, Bateman A, Orchard S. RNA (New York, N.Y.) Volume 23 (2017) p.1479-1492 DOI: 10.1261/rna.060996.117
*
General guidelines for biomedical software development
Silva LB, Jimenez RC, Blomberg N, Luis Oliveira J. Preprint DOI: 10.12688/f1000research.10750.2
Model Description Language (MDL): A Standard for Modeling and Simulation.
Smith MK, Moodie SL, Bizzotto R, Blaudez E, Borella E, Carrara L, Chan P, Chenel M, Comets E, Gieschke R, Harling K, Harnisch L, Hartung N, Hooker AC, Karlsson MO, Kaye R, Kloft C, Kokash N, Lavielle M, Lestini G, Magni P, Mari A, Mentré F, Muselle C, Nordgren R, Nyberg HB, Parra-Guillén ZP, Pasotti L, Rode-Kristensen N, Sardu ML, Smith GR, Swat MJ, Terranova N, Yngman G, Yvon F, Holford N, DDMoRe consortium. CPT: pharmacometrics & systems pharmacology Volume 6 (2017) p.647-650 DOI: 10.1002/psp4.12222
*
The evolutionary history of 2,658 cancers
Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez Rosado S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vazquez-Garcia I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SCC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, PCAWG Evolution and Heterogeneity Working Group, PCAWG network. Preprint DOI: 10.1101/161562
*
Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments
Yung CK, O'Connor BD, Yakneen S, Zhang J, Ellrott K, Kleinheinz K, Miyoshi N, Raine KM, Royo R, Saksena GB, Schlesner M, Shorser SI, Vazquez M, Weischenfeldt J, Yuen D, Butler AP, Davis-Dusenbery BN, Eils R, Ferretti V, Grossman RL, Harismendy O, Kim Y, Nakagawa H, Newhouse SJ, Torrents D, Stein LD, - PCAWG Technical Working Group. Preprint DOI: 10.1101/161638
*
Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.
Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat RR, Li X, Pal LR, Kundu K, Yin Y, Moult J, Jiang Y, Pejaver V, Pagel KA, Li B, Mooney SD, Radivojac P, Shah S, Carraro M, Gasparini A, Leonardi E, Giollo M, Ferrari C, Tosatto SCE, Bachar E, Azaria JR, Ofran Y, Unger R, Niroula A, Vihinen M, Chang B, Wang MH, Franke A, Petersen BS, Pirooznia M, Zandi P, McCombie R, Potash JB, Altman RB, Klein TE, Hoskins RA, Repo S, Brenner SE, Morgan AA. Human mutation Volume 38 (2017) p.1182-1192 DOI: 10.1002/humu.23280
Building bridges between cellular and molecular structural biology.
Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M, Kleywegt GJ. eLife Volume 6 (2017) DOI: 10.7554/eLife.25835
Linking functions: an additional role for an intrinsically disordered linker domain in the transcriptional coactivator CBP.
Contreras-Martos S, Piai A, Kosol S, Varadi M, Bekesi A, Lebrun P, Volkov AN, Gevaert K, Pierattelli R, Felli IC, Tompa P. Scientific reports Volume 7 (2017) p.4676 DOI: 10.1038/s41598-017-04611-x
Extracellular vesicles are independent metabolic units with asparaginase activity.
Iraci N, Gaude E, Leonardi T, Costa ASH, Cossetti C, Peruzzotti-Jametti L, Bernstock JD, Saini HK, Gelati M, Vescovi AL, Bastos C, Faria N, Occhipinti LG, Enright AJ, Frezza C, Pluchino S. Nature chemical biology Volume 13 (2017) p.951-955 DOI: 10.1038/nchembio.2422
*
Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin A, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams D, Brazma A, Gerstein M, Paten B, Pham S, Keane T, Odom DT, Flicek P. Preprint DOI: 10.1101/158659
Single cell transcriptomics of pluripotent stem cells: reprogramming and differentiation.
Natarajan KN, Teichmann SA, Kolodziejczyk AA. Current opinion in genetics & development Volume 46 (2017) p.66-76 DOI: 10.1016/j.gde.2017.06.003
Programmatic access to bioinformatics tools from EMBL-EBI update: 2017.
Chojnacki S, Cowley A, Lee J, Foix A, Lopez R. Nucleic acids research Volume 45 (2017) p.W550-W553 DOI: 10.1093/nar/gkx273
ProtVista: visualization of protein sequence annotations.
Watkins X, Garcia LJ, Pundir S, Martin MJ, UniProt Consortium. Bioinformatics (Oxford, England) Volume 33 (2017) p.2040-2041 DOI: 10.1093/bioinformatics/btx120
Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks.
Raisaro JL, Tramèr F, Ji Z, Bu D, Zhao Y, Carey K, Lloyd D, Sofia H, Baker D, Flicek P, Shringarpure S, Bustamante C, Wang S, Jiang X, Ohno-Machado L, Tang H, Wang X, Hubaux JP. Journal of the American Medical Informatics Association : JAMIA Volume 24 (2017) p.799-805 DOI: 10.1093/jamia/ocw167
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.
Bertelli C, Laird MR, Williams KP, Simon Fraser University Research Computing Group, Lau BY, Hoad G, Winsor GL, Brinkman FSL. Nucleic acids research Volume 45 (2017) p.W30-W35 DOI: 10.1093/nar/gkx343
Alignment of 1000 Genomes Project reads to reference assembly GRCh38.
Zheng-Bradley X, Streeter I, Fairley S, Richardson D, Clarke L, Flicek P, 1000 Genomes Project Consortium. GigaScience Volume 6 (2017) p.1-8 DOI: 10.1093/gigascience/gix038
The Proteins API: accessing key integrated protein and genome information.
Nightingale A, Antunes R, Alpi E, Bursteinas B, Gonzales L, Liu W, Luo J, Qi G, Turner E, Martin M. Nucleic acids research Volume 45 (2017) p.W539-W544 DOI: 10.1093/nar/gkx237
The EBI search engine: EBI search as a service-making biological data accessible for all.
Park YM, Squizzato S, Buso N, Gur T, Lopez R. Nucleic acids research Volume 45 (2017) p.W545-W549 DOI: 10.1093/nar/gkx359
The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.
Petryszak R, Fonseca NA, Füllgrabe A, Huerta L, Keays M, Tang YA, Brazma A. Bioinformatics (Oxford, England) Volume 33 (2017) p.2218-2220 DOI: 10.1093/bioinformatics/btx143
*
Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity.
Hendricks AE, Bochukova EG, Marenne G, Keogh JM, Atanassova N, Bounds R, Wheeler E, Mistry V, Henning E, Körner A, Muddyman D, McCarthy S, Hinney A, Hebebrand J, Scott RA, Langenberg C, Wareham NJ, Surendran P, Howson JM, Butterworth AS, Danesh J, Nordestgaard BG, Nielsen SF, Afzal S, Papadia S, Ashford S, Garg S, Millhauser GL, Palomino RI, Kwasniewska A, Tachmazidou I, O'Rahilly S, Zeggini E, Barroso I, Farooqi IS, Understanding Society Scientific Group, EPIC-CVD Consortium, UK10K Consortium. Scientific reports Volume 7 (2017) p.4394 DOI: 10.1038/s41598-017-03054-8
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.
McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H. PLoS biology Volume 15 (2017) p.e2001414 DOI: 10.1371/journal.pbio.2001414
Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.
Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Torlai Triglia E, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA. Nature communications Volume 8 (2017) p.36 DOI: 10.1038/s41467-017-00052-2
Prevalence of sexual dimorphism in mammalian phenotypic traits.
Karp NA, Mason J, Beaudet AL, Benjamini Y, Bower L, Braun RE, Brown SDM, Chesler EJ, Dickinson ME, Flenniken AM, Fuchs H, Angelis MH, Gao X, Guo S, Greenaway S, Heller R, Herault Y, Justice MJ, Kurbatova N, Lelliott CJ, Lloyd KCK, Mallon AM, Mank JE, Masuya H, McKerlie C, Meehan TF, Mott RF, Murray SA, Parkinson H, Ramirez-Solis R, Santos L, Seavitt JR, Smedley D, Sorg T, Speak AO, Steel KP, Svenson KL, International Mouse Phenotyping Consortium, Wakana S, West D, Wells S, Westerberg H, Yaacoby S, White JK. Nature communications Volume 8 (2017) p.15475 DOI: 10.1038/ncomms15475
Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.
Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P, Karp N, Santos L, Fiegel T, Ring N, Westerberg H, Greenaway S, Sneddon D, Morgan H, Codner GF, Stewart ME, Brown J, Horner N, International Mouse Phenotyping Consortium, Haendel M, Washington N, Mungall CJ, Reynolds CL, Gallegos J, Gailus-Durner V, Sorg T, Pavlovic G, Bower LR, Moore M, Morse I, Gao X, Tocchini-Valentini GP, Obata Y, Cho SY, Seong JK, Seavitt J, Beaudet AL, Dickinson ME, Herault Y, Wurst W, de Angelis MH, Lloyd KCK, Flenniken AM, Nutter LMJ, Newbigging S, McKerlie C, Justice MJ, Murray SA, Svenson KL, Braun RE, White JK, Bradley A, Flicek P, Wells S, Skarnes WC, Adams DJ, Parkinson H, Mallon AM, Brown SDM, Smedley D. Nature genetics Volume 49 (2017) p.1231-1238 DOI: 10.1038/ng.3901
Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1.
Suri M, Evers JMG, Laskowski RA, O'Brien S, Baker K, Clayton-Smith J, Dabir T, Josifova D, Joss S, Kerr B, Kraus A, McEntagart M, Morton J, Smith A, Splitt M, Thornton JM, DDD Study, Wright CF. Molecular genetics & genomic medicine Volume 5 (2017) p.495-507 DOI: 10.1002/mgg3.304
*
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.
Menschaert G, Wang X, Jones AR, Ghali F, Fenyo D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaino JA. Preprint DOI: 10.1101/152579
*
Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.
Cai B, Li B, Kiga N, Thusberg J, Bergquist T, Chen YC, Niknafs N, Carter H, Tokheim C, Beleva-Guthrie V, Douville C, Bhattacharya R, Yeo HTG, Fan J, Sengupta S, Kim D, Cline M, Turner T, Diekhans M, Zaucha J, Pal LR, Cao C, Yu CH, Yin Y, Carraro M, Giollo M, Ferrari C, Leonardi E, Tosatto SCE, Bobe J, Ball M, Hoskins RA, Repo S, Church G, Brenner SE, Moult J, Gough J, Stanke M, Karchin R, Mooney SD. Human mutation Volume 38 (2017) p.1266-1276 DOI: 10.1002/humu.23265
The Image Data Resource: A Bioimage Data Integration and Publication Platform.
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR. Nature methods Volume 14 (2017) p.775-781 DOI: 10.1038/nmeth.4326
Drug repurposing for aging research using model organisms.
Ziehm M, Kaur S, Ivanov DK, Ballester PJ, Marcus D, Partridge L, Thornton JM. Aging Cell Volume 16 (2017) p.1006-1015 DOI: 10.1111/acel.12626
*
Inferring synteny between genome assemblies: a systematic evaluation
Liu D, Hunt M, Tsai IJ. Preprint DOI: 10.1101/149989
*
Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs.
Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Nature Volume 546 (2017) p.686 DOI: 10.1038/nature23012
Four simple recommendations to encourage best practices in research software.
Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.11407.1
*
Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers
Meier B, Volkova N, Hong Y, Schofield P, Campbell PJ, Gerstung M, Gartner A. Preprint DOI: 10.1101/149153
A community proposal to integrate proteomics activities in ELIXIR.
Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.11751.1
*
Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer
Fonseca NA, He Y, Greger L, Brazma A, Zhang Z, - PCAWG-3. Preprint DOI: 10.1101/148684
Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery.
Nowotka MM, Gaulton A, Mendez D, Bento AP, Hersey A, Leach A. Expert opinion on drug discovery Volume 12 (2017) p.757-767 DOI: 10.1080/17460441.2017.1339032
*
Integrating long-range connectivity information into de Bruijn graphs
Turner I, Garimella KV, Iqbal Z, McVean G. Preprint DOI: 10.1101/147777
Literature evidence in open targets - a target validation platform.
Kafkas Ş, Dunham I, McEntyre J. Journal of biomedical semantics Volume 8 (2017) p.20 DOI: 10.1186/s13326-017-0131-3
*
Epigenetic resetting of human pluripotency
Guo G, von Meyenn F, Rostovskaya M, Clarke J, Dietmann S, Baker D, Sahakyan A, Myers S, Bertone P, Reik W, Plath K, Smith A. Preprint DOI: 10.1101/146712
Dead simple OWL design patterns.
Osumi-Sutherland D, Courtot M, Balhoff JP, Mungall C. Journal of biomedical semantics Volume 8 (2017) p.18 DOI: 10.1186/s13326-017-0126-0
*
Accurate And Fast Feature Selection Workflow For High-Dimensional Omics Data
Perez-Riverol Y, Kun M, Vizcaino JA, Hitz M, Audain E. Preprint DOI: 10.1101/144162
Benchmarking substrate-based kinase activity inference using phosphoproteomic data.
Hernandez-Armenta C, Ochoa D, Gonçalves E, Saez-Rodriguez J, Beltrao P. Bioinformatics (Oxford, England) Volume 33 (2017) p.1845-1851 DOI: 10.1093/bioinformatics/btx082
Structural Variation Shapes the Landscape of Recombination in Mouse.
Morgan AP, Gatti DM, Najarian ML, Keane TM, Galante RJ, Pack AI, Mott R, Churchill GA, de Villena FP. Genetics Volume 206 (2017) p.603-619 DOI: 10.1534/genetics.116.197988
*
PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance.
Nadon C, Van Walle I, Gerner-Smidt P, Campos J, Chinen I, Concepcion-Acevedo J, Gilpin B, Smith AM, Man Kam K, Perez E, Trees E, Kubota K, Takkinen J, Nielsen EM, Carleton H, FWD-NEXT Expert Panel. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin Volume 22 (2017) DOI: 10.2807/1560-7917.ES.2017.22.23.30544
*
MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry
Jain M, Tyson JR, Loose M, Ip CL, Eccles DA, O'Grady J, Malla S, Leggett RM, Wallerman O, Jansen HJ, Zalunin V, Birney E, Brown BL, Snutch TP, Olsen HE, MinION Analysis and Reference Consortium. Preprint DOI: 10.12688/f1000research.11354.1
MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry.
Jain M, Tyson JR, Loose M, Ip CLC, Eccles DA, O'Grady J, Malla S, Leggett RM, Wallerman O, Jansen HJ, Zalunin V, Birney E, Brown BL, Snutch TP, Olsen HE, MinION Analysis and Reference Consortium. F1000Research Volume 6 (2017) p.760 DOI: 10.12688/f1000research.11354.1
*
SpatialDE - Identification of spatially variable genes
Svensson V, Teichmann SA, Stegle O. Preprint DOI: 10.1101/143321
OpenMS - A platform for reproducible analysis of mass spectrometry data.
Pfeuffer J, Sachsenberg T, Alka O, Walzer M, Fillbrunn A, Nilse L, Schilling O, Reinert K, Kohlbacher O. Journal of biotechnology Volume 261 (2017) p.142-148 DOI: 10.1016/j.jbiotec.2017.05.016
Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.
Joseph AP, Lagerstedt I, Patwardhan A, Topf M, Winn M. Journal of structural biology Volume 199 (2017) p.12-26 DOI: 10.1016/j.jsb.2017.05.007
Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.
Tachmazidou I, Süveges D, Min JL, Ritchie GRS, Steinberg J, Walter K, Iotchkova V, Schwartzentruber J, Huang J, Memari Y, McCarthy S, Crawford AA, Bombieri C, Cocca M, Farmaki AE, Gaunt TR, Jousilahti P, Kooijman MN, Lehne B, Malerba G, Männistö S, Matchan A, Medina-Gomez C, Metrustry SJ, Nag A, Ntalla I, Paternoster L, Rayner NW, Sala C, Scott WR, Shihab HA, Southam L, St Pourcain B, Traglia M, Trajanoska K, Zaza G, Zhang W, Artigas MS, Bansal N, Benn M, Chen Z, Danecek P, Lin WY, Locke A, Luan J, Manning AK, Mulas A, Sidore C, Tybjaerg-Hansen A, Varbo A, Zoledziewska M, Finan C, Hatzikotoulas K, Hendricks AE, Kemp JP, Moayyeri A, Panoutsopoulou K, Szpak M, Wilson SG, Boehnke M, Cucca F, Di Angelantonio E, Langenberg C, Lindgren C, McCarthy MI, Morris AP, Nordestgaard BG, Scott RA, Tobin MD, Wareham NJ, SpiroMeta Consortium, GoT2D Consortium, Burton P, Chambers JC, Smith GD, Dedoussis G, Felix JF, Franco OH, Gambaro G, Gasparini P, Hammond CJ, Hofman A, Jaddoe VWV, Kleber M, Kooner JS, Perola M, Relton C, Ring SM, Rivadeneira F, Salomaa V, Spector TD, Stegle O, Toniolo D, Uitterlinden AG, arcOGEN Consortium, Understanding Society Scientific Group, UK10K Consortium, Barroso I, Greenwood CMT, Perry JRB, Walker BR, Butterworth AS, Xue Y, Durbin R, Small KS, Soranzo N, Timpson NJ, Zeggini E. American journal of human genetics Volume 100 (2017) p.865-884 DOI: 10.1016/j.ajhg.2017.04.014
*
Phenotype prediction in an Escherichia coli strain panel
Galardini M, Koumoutsi A, Herrera-Dominguez L, Cordero Varela JA, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P. Preprint DOI: 10.1101/141879
MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni.
Protasio AV, van Dongen S, Collins J, Quintais L, Ribeiro DM, Sessler F, Hunt M, Rinaldi G, Collins JJ, Enright AJ, Berriman M. PLoS neglected tropical diseases Volume 11 (2017) p.e0005559 DOI: 10.1371/journal.pntd.0005559
A MILI-independent piRNA biogenesis pathway empowers partial germline reprogramming.
Vasiliauskaitė L, Vitsios D, Berrens RV, Carrieri C, Reik W, Enright AJ, O'Carroll D. Nature structural & molecular biology Volume 24 (2017) p.604-606 DOI: 10.1038/nsmb.3413
*
scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells
Clark SJ, Argelaguet R, Kapourani C, Stubbs TM, Lee HJ, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W. Preprint DOI: 10.1101/138685
The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.
Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR. Molecular & cellular proteomics : MCP Volume 16 (2017) p.1275-1285 DOI: 10.1074/mcp.M117.068429
Whole genome analysis of a schistosomiasis-transmitting freshwater snail.
Adema CM, Hillier LW, Jones CS, Loker ES, Knight M, Minx P, Oliveira G, Raghavan N, Shedlock A, do Amaral LR, Arican-Goktas HD, Assis JG, Baba EH, Baron OL, Bayne CJ, Bickham-Wright U, Biggar KK, Blouin M, Bonning BC, Botka C, Bridger JM, Buckley KM, Buddenborg SK, Lima Caldeira R, Carleton J, Carvalho OS, Castillo MG, Chalmers IW, Christensens M, Clifton S, Cosseau C, Coustau C, Cripps RM, Cuesta-Astroz Y, Cummins SF, di Stephano L, Dinguirard N, Duval D, Emrich S, Feschotte C, Feyereisen R, FitzGerald P, Fronick C, Fulton L, Galinier R, Gava SG, Geusz M, Geyer KK, Giraldo-Calderón GI, de Souza Gomes M, Gordy MA, Gourbal B, Grunau C, Hanington PC, Hoffmann KF, Hughes D, Humphries J, Jackson DJ, Jannotti-Passos LK, de Jesus Jeremias W, Jobling S, Kamel B, Kapusta A, Kaur S, Koene JM, Kohn AB, Lawson D, Lawton SP, Liang D, Limpanont Y, Liu S, Lockyer AE, Lovato TL, Ludolf F, Magrini V, McManus DP, Medina M, Misra M, Mitta G, Mkoji GM, Montague MJ, Montelongo C, Moroz LL, Munoz-Torres MC, Niazi U, Noble LR, Oliveira FS, Pais FS, Papenfuss AT, Peace R, Pena JJ, Pila EA, Quelais T, Raney BJ, Rast JP, Rollinson D, Rosse IC, Rotgans B, Routledge EJ, Ryan KM, Scholte LLS, Storey KB, Swain M, Tennessen JA, Tomlinson C, Trujillo DL, Volpi EV, Walker AJ, Wang T, Wannaporn I, Warren WC, Wu XJ, Yoshino TP, Yusuf M, Zhang SM, Zhao M, Wilson RK. Nature communications Volume 8 (2017) p.15451 DOI: 10.1038/ncomms15451
*
Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.
Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, Gough J, Katsonis P, Leonardi E, Lichtarge O, Menin C, Martelli PL, Niroula A, Pal LR, Repo S, Scaini MC, Vihinen M, Wei Q, Xu Q, Yang Y, Yin Y, Zaucha J, Zhao H, Zhou Y, Brenner SE, Moult J, Tosatto SCE. Human mutation Volume 38 (2017) p.1042-1050 DOI: 10.1002/humu.23235
Normalizing single-cell RNA sequencing data: challenges and opportunities.
Vallejos CA, Risso D, Scialdone A, Dudoit S, Marioni JC. Nature methods Volume 14 (2017) p.565-571 DOI: 10.1038/nmeth.4292
Parotid gland mean dose as a xerostomia predictor in low-dose domains.
Gabryś HS, Buettner F, Sterzing F, Hauswald H, Bangert M. Acta oncologica (Stockholm, Sweden) Volume 56 (2017) p.1197-1203 DOI: 10.1080/0284186x.2017.1324209
Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution.
Davis MP, Carrieri C, Saini HK, van Dongen S, Leonardi T, Bussotti G, Monahan JM, Auchynnikava T, Bitetti A, Rappsilber J, Allshire RC, Shkumatava A, O'Carroll D, Enright AJ. EMBO reports Volume 18 (2017) p.1231-1247 DOI: 10.15252/embr.201744059
Erratum to: DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.
Angermueller C, Lee HJ, Reik W, Stegle O. Genome biology Volume 18 (2017) p.90 DOI: 10.1186/s13059-017-1233-z
Common genetic variation drives molecular heterogeneity in human iPSCs.
Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Nature Volume 546 (2017) p.370-375 DOI: 10.1038/nature22403
Common sequence variants affect molecular function more than rare variants?
Mahlich Y, Reeb J, Hecht M, Schelling M, De Beer TAP, Bromberg Y, Rost B. Scientific reports Volume 7 (2017) p.1608 DOI: 10.1038/s41598-017-01054-2
*
The Human Cell Atlas
Regev A, Teichmann S, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Gottgens B, Hacohen N, Haniffa M, Hemberg M, Kim SK, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundeberg J, Majumder P, Marioni J, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Philipakis A, Ponting CP, Quake SR, Reik W, Rozenblatt-Rosen O, Sanes JR, Satija R, Shumacher T, Shalek AK, Shapiro E, Sharma P, Shin J, Stegle O, Stratton M, Stubbington MJT, van Oudenaarden A, Wagner A, Watt FM, Weissman JS, Wold B, Xavier RJ, Yosef N, Human Cell Atlas Meeting Participants. Preprint DOI: 10.1101/121202
Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.
Cabezas-Wallscheid N, Buettner F, Sommerkamp P, Klimmeck D, Ladel L, Thalheimer FB, Pastor-Flores D, Roma LP, Renders S, Zeisberger P, Przybylla A, Schönberger K, Scognamiglio R, Altamura S, Florian CM, Fawaz M, Vonficht D, Tesio M, Collier P, Pavlinic D, Geiger H, Schroeder T, Benes V, Dick TP, Rieger MA, Stegle O, Trumpp A. Cell Volume 169 (2017) p.807-823.e19 DOI: 10.1016/j.cell.2017.04.018
An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.
Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu FH, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser DM, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Palma FD, Phillips AL, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD. Genome research Volume 27 (2017) p.885-896 DOI: 10.1101/gr.217117.116
Discovering and linking public omics data sets using the Omics Discovery Index.
Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H. Nature biotechnology Volume 35 (2017) p.406-409 DOI: 10.1038/nbt.3790
Anna Tramontano 1957-2017.
Thornton JM, Valencia A, Schwede T. Nature structural & molecular biology Volume 24 (2017) p.431-432 DOI: 10.1038/nsmb.3410
*
Applications of the 1000 Genomes Project resources.
Zheng-Bradley X, Flicek P. Briefings in functional genomics Volume 16 (2017) p.163-170 DOI: 10.1093/bfgp/elw027
*
Universal Patterns Of Selection In Cancer And Somatic Tissues
Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K, Van Loo P, Davies H, Stratton MR, Campbell PJ. Preprint DOI: 10.1101/132324
Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
Beier S, Himmelbach A, Colmsee C, Zhang XQ, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Sampath D, Heavens D, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Houben A, Doležel J, Ayling S, Lonardi S, Langridge P, Muehlbauer GJ, Kersey P, Clark MD, Caccamo M, Schulman AH, Platzer M, Close TJ, Hansson M, Zhang G, Braumann I, Li C, Waugh R, Scholz U, Stein N, Mascher M. Scientific data Volume 4 (2017) p.170044 DOI: 10.1038/sdata.2017.44
Mechanism-based biomarker discovery.
Antoranz A, Sakellaropoulos T, Saez-Rodriguez J, Alexopoulos LG. Drug discovery today Volume 22 (2017) p.1209-1215 DOI: 10.1016/j.drudis.2017.04.013
*
A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog
Morales J, Bowler EH, Buniello A, Cerezo M, Hall P, Harris LW, Hastings E, Junkins HA, Malangone C, McMahon AC, Milano A, Welter D, Burdett T, Cunningham F, Flicek P, Parkinson H, Hindorff L, MacArthur JAL. Preprint DOI: 10.1101/129395
*
Transcription factor activities enhance markers of drug response in cancer
Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Falcone F, Bignell G, McDade SS, Garnett MJ, Saez-Rodriguez J. Preprint DOI: 10.1101/129478
UniEuk: Time to Speak a Common Language in Protistology!
Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C. The Journal of eukaryotic microbiology Volume 64 (2017) p.407-411 DOI: 10.1111/jeu.12414
Trends in the Electron Microscopy Data Bank (EMDB).
Patwardhan A. Acta crystallographica. Section D, Structural biology Volume 73 (2017) p.503-508 DOI: 10.1107/S2059798317004181
Joint genetic analysis using variant sets reveals polygenic gene-context interactions.
Casale FP, Horta D, Rakitsch B, Stegle O. PLoS genetics Volume 13 (2017) p.e1006693 DOI: 10.1371/journal.pgen.1006693
A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining.
Barradas-Bautista D, Moal IH, Fernández-Recio J. Proteins Volume 85 (2017) p.1287-1297 DOI: 10.1002/prot.25289
DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.
Angermueller C, Lee HJ, Reik W, Stegle O, Stegle O. Genome biology Volume 18 (2017) p.67 DOI: 10.1186/s13059-017-1189-z
Multi-tissue DNA methylation age predictor in mouse.
Stubbs TM, Bonder MJ, Stark AK, Krueger F, BI Ageing Clock Team, von Meyenn F, Stegle O, Reik W. Genome biology Volume 18 (2017) p.68 DOI: 10.1186/s13059-017-1203-5
*
Sub-minute phosphoregulation of cell-cycle systems during Plasmodium gamete formation
Invergo B, Brochet M, Yu L, Choudhary J, Beltrao P, Billker O. Preprint DOI: 10.1101/126276
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM. Genome research Volume 27 (2017) p.849-864 DOI: 10.1101/gr.213611.116
*
Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression
Berthelot C, Villar D, Horvath JE, Odom DT, Flicek P. Preprint DOI: 10.1101/125435
*
The Fes tyrosine kinase guides CD19 receptor fate in B-cells by shaping regulatory Src phosphorylation networks
Helbig AO, Kofler M, Petsalaki E, Gish G, Lorenzen K, Tucholska M, Zhang C, Roth FP, Colwill K, Pawson T. Preprint DOI: 10.1101/125088
*
Literature Evidence in Open Targets - a target validation platform
Kafkas S, Dunham I, McEntyre J. Preprint DOI: 10.1101/124719
Short template switch events explain mutation clusters in the human genome.
Löytynoja A, Goldman N. Genome research Volume 27 (2017) p.1039-1049 DOI: 10.1101/gr.214973.116
Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models.
Eduati F, Doldàn-Martelli V, Klinger B, Cokelaer T, Sieber A, Kogera F, Dorel M, Garnett MJ, Blüthgen N, Saez-Rodriguez J. Cancer research Volume 77 (2017) p.3364-3375 DOI: 10.1158/0008-5472.can-17-0078
A chromosome conformation capture ordered sequence of the barley genome.
Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang XQ, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N. Nature Volume 544 (2017) p.427-433 DOI: 10.1038/nature22043
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.
McCarthy DJ, Campbell KR, Lun AT, Wills QF. Bioinformatics (Oxford, England) Volume 33 (2017) p.1179-1186 DOI: 10.1093/bioinformatics/btw777
Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold.
Pearson WR, Li W, Lopez R. Nucleic acids research Volume 45 (2017) p.e46 DOI: 10.1093/nar/gkw1207
Identifying genes for neurobehavioural traits in rodents: progress and pitfalls.
Baud A, Flint J. Disease models & mechanisms Volume 10 (2017) p.373-383 DOI: 10.1242/dmm.027789
Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer.
Zuber V, Bettella F, Witoelar A, PRACTICAL Consortium, CRUK GWAS, BCAC Consortium, TRICL Consortium, Andreassen OA, Mills IG, Urbanucci A. BMC genomics Volume 18 (2017) p.270 DOI: 10.1186/s12864-017-3620-y
Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity.
Thomas DC, Clare S, Sowerby JM, Pardo M, Juss JK, Goulding DA, van der Weyden L, Storisteanu D, Prakash A, Espéli M, Flint S, Lee JC, Hoenderdos K, Kane L, Harcourt K, Mukhopadhyay S, Umrania Y, Antrobus R, Nathan JA, Adams DJ, Bateman A, Choudhary JS, Lyons PA, Condliffe AM, Chilvers ER, Dougan G, Smith KG. The Journal of experimental medicine Volume 214 (2017) p.1111-1128 DOI: 10.1084/jem.20161382
3' Uridylation controls mature microRNA turnover during CD4 T-cell activation.
Gutiérrez-Vázquez C, Enright AJ, Rodríguez-Galán A, Pérez-García A, Collier P, Jones MR, Benes V, Mizgerd JP, Mittelbrunn M, Ramiro AR, Sánchez-Madrid F. RNA (New York, N.Y.) Volume 23 (2017) p.882-891 DOI: 10.1261/rna.060095.116
Microbiology Managers: Managerial Training in the RItrain Project.
Paterson RRM, Lima N, Brooksbank C, Guarini E, Pasterk M, Lavitrano M, RItrain project consortium. Trends in microbiology Volume 25 (2017) p.425-428 DOI: 10.1016/j.tim.2017.03.002
Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma.
Arseneault M, Monlong J, Vasudev NS, Laskar RS, Safisamghabadi M, Harnden P, Egevad L, Nourbehesht N, Panichnantakul P, Holcatova I, Brisuda A, Janout V, Kollarova H, Foretova L, Navratilova M, Mates D, Jinga V, Zaridze D, Mukeria A, Jandaghi P, Brennan P, Brazma A, Tost J, Scelo G, Banks RE, Lathrop M, Bourque G, Riazalhosseini Y. Scientific reports Volume 7 (2017) p.44876 DOI: 10.1038/srep44876
Orchestrating differential data access for translational research: a pilot implementation.
Brandizi M, Melnichuk O, Bild R, Kohlmayer F, Rodriguez-Castro B, Spengler H, Kuhn KA, Kuchinke W, Ohmann C, Mustonen T, Linden M, Nyrönen T, Lappalainen I, Brazma A, Sarkans U. BMC medical informatics and decision making Volume 17 (2017) p.30 DOI: 10.1186/s12911-017-0424-6
Somatic mutations reveal asymmetric cellular dynamics in the early human embryo.
Ju YS, Martincorena I, Gerstung M, Petljak M, Alexandrov LB, Rahbari R, Wedge DC, Davies HR, Ramakrishna M, Fullam A, Martin S, Alder C, Patel N, Gamble S, O'Meara S, Giri DD, Sauer T, Pinder SE, Purdie CA, Borg Å, Stunnenberg H, van de Vijver M, Tan BK, Caldas C, Tutt A, Ueno NT, van 't Veer LJ, Martens JW, Sotiriou C, Knappskog S, Span PN, Lakhani SR, Eyfjörd JE, Børresen-Dale AL, Richardson A, Thompson AM, Viari A, Hurles ME, Nik-Zainal S, Campbell PJ, Stratton MR. Nature Volume 543 (2017) p.714-718 DOI: 10.1038/nature21703
*
Multi-Tissue DNA Methylation Age Predictor In Mouse
Stubbs TM, Bonder MJ, Stark A, Krueger F, von Meyenn F, Stegle O, Reik W, BI Ageing Clock Team. Preprint DOI: 10.1101/119206
Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.
Huang Y, Kim JK, Do DV, Lee C, Penfold CA, Zylicz JJ, Marioni JC, Hackett JA, Surani MA. eLife Volume 6 (2017) DOI: 10.7554/eLife.22345
*
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
McMurry J, Juty N, Blomberg N, Burdett A, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows D, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hermjakob H, Heriche J, Ison J, Jimenez R, Jupp S, Kunze J, Laibe C, Le Novere N, Malone JR, Martin M, McEntyre J, Morris C, Muilu J, Mueller W, Rocca-Serra P, Sansone S, Sariyar M, Snoep J, Stanford NJ, Soiland-Reyes S, Swainston N, Washington N, Williams A, Wimalaratne S, Winfree L, Wolstencroft K, Goble C, Mungall C, Haendel M, Parkinson H. Preprint DOI: 10.1101/117812
*
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, Harris SR. Preprint DOI: 10.1101/118000
Shared Consensus Machine Learning Models for Predicting Blood Stage Malaria Inhibition.
Verras A, Waller CL, Gedeck P, Green DV, Kogej T, Raichurkar A, Panda M, Shelat AA, Clark J, Guy RK, Papadatos G, Burrows J. Journal of chemical information and modeling Volume 57 (2017) p.445-453 DOI: 10.1021/acs.jcim.6b00572
*
Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression
Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Triglia ET, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA. Preprint DOI: 10.1101/117267
Adipocyte Accumulation in the Bone Marrow during Obesity and Aging Impairs Stem Cell-Based Hematopoietic and Bone Regeneration.
Ambrosi TH, Scialdone A, Graja A, Gohlke S, Jank AM, Bocian C, Woelk L, Fan H, Logan DW, Schürmann A, Saraiva LR, Schulz TJ. Cell stem cell Volume 20 (2017) p.771-784.e6 DOI: 10.1016/j.stem.2017.02.009
Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring.
Imamura H, Wagih O, Niinae T, Sugiyama N, Beltrao P, Ishihama Y. Journal of proteome research Volume 16 (2017) p.1825-1830 DOI: 10.1021/acs.jproteome.7b00087
Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions.
Zaman S, Sarntivijai S, Abernethy DR. Gene regulation and systems biology Volume 11 (2017) p.1177625017696075 DOI: 10.1177/1177625017696075
*
Severe infections emerge from the microbiome by adaptive evolution
Young BC, Wu C, Gordon NC, Cole K, Price JR, Liu E, Sheppard A, Perera S, Charlesworth J, Golubchik T, Iqbal Z, Bowden R, Massey R, Paul J, Crook DW, Peto TE, Walker AS, Llewelyn M, Wyllie DH, Wilson D. Preprint DOI: 10.1101/116681
HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
Davies H, Glodzik D, Morganella S, Yates LR, Staaf J, Zou X, Ramakrishna M, Martin S, Boyault S, Sieuwerts AM, Simpson PT, King TA, Raine K, Eyfjord JE, Kong G, Borg Å, Birney E, Stunnenberg HG, van de Vijver MJ, Børresen-Dale AL, Martens JW, Span PN, Lakhani SR, Vincent-Salomon A, Sotiriou C, Tutt A, Thompson AM, Van Laere S, Richardson AL, Viari A, Campbell PJ, Stratton MR, Nik-Zainal S. Nature medicine Volume 23 (2017) p.517-525 DOI: 10.1038/nm.4292
3D structures of individual mammalian genomes studied by single-cell Hi-C.
Stevens TJ, Lando D, Basu S, Atkinson LP, Cao Y, Lee SF, Leeb M, Wohlfahrt KJ, Boucher W, O'Shaughnessy-Kirwan A, Cramard J, Faure AJ, Ralser M, Blanco E, Morey L, Sansó M, Palayret MGS, Lehner B, Di Croce L, Wutz A, Hendrich B, Klenerman D, Laue ED. Nature Volume 544 (2017) p.59-64 DOI: 10.1038/nature21429
Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy.
Tong P, Monahan J, Prendergast JG. PLoS genetics Volume 13 (2017) p.e1006673 DOI: 10.1371/journal.pgen.1006673
Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.
Cheung WA, Shao X, Morin A, Siroux V, Kwan T, Ge B, Aïssi D, Chen L, Vasquez L, Allum F, Guénard F, Bouzigon E, Simon MM, Boulier E, Redensek A, Watt S, Datta A, Clarke L, Flicek P, Mead D, Paul DS, Beck S, Bourque G, Lathrop M, Tchernof A, Vohl MC, Demenais F, Pin I, Downes K, Stunnenberg HG, Soranzo N, Pastinen T, Grundberg E. Genome biology Volume 18 (2017) p.50 DOI: 10.1186/s13059-017-1173-7
*
ChromoTrace: Reconstruction of 3D Chromosome Configurations by Super-Resolution Microscopy
Barton C, Morganella S, Oedegaard O, Alexander S, Ries J, Fitzgerald T, Ellenberg J, Birney E. Preprint DOI: 10.1101/115436
Rapid establishment of the European Bank for induced Pluripotent Stem Cells (EBiSC) - the Hot Start experience.
De Sousa PA, Steeg R, Wachter E, Bruce K, King J, Hoeve M, Khadun S, McConnachie G, Holder J, Kurtz A, Seltmann S, Dewender J, Reimann S, Stacey G, O'Shea O, Chapman C, Healy L, Zimmermann H, Bolton B, Rawat T, Atkin I, Veiga A, Kuebler B, Serano BM, Saric T, Hescheler J, Brüstle O, Peitz M, Thiele C, Geijsen N, Holst B, Clausen C, Lako M, Armstrong L, Gupta SK, Kvist AJ, Hicks R, Jonebring A, Brolén G, Ebneth A, Cabrera-Socorro A, Foerch P, Geraerts M, Stummann TC, Harmon S, George C, Streeter I, Clarke L, Parkinson H, Harrison PW, Faulconbridge A, Cherubin L, Burdett T, Trigueros C, Patel MJ, Lucas C, Hardy B, Predan R, Dokler J, Brajnik M, Keminer O, Pless O, Gribbon P, Claussen C, Ringwald A, Kreisel B, Courtney A, Allsopp TE. Stem cell research Volume 20 (2017) p.105-114 DOI: 10.1016/j.scr.2017.03.002
Power analysis of single-cell RNA-sequencing experiments.
Svensson V, Natarajan KN, Ly LH, Miragaia RJ, Labalette C, Macaulay IC, Cvejic A, Teichmann SA. Nature methods Volume 14 (2017) p.381-387 DOI: 10.1038/nmeth.4220
Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method.
Hayes TW, Moal IH. Journal of chemical theory and computation Volume 13 (2017) p.1401-1410 DOI: 10.1021/acs.jctc.6b01110
Direct Keap1-Nrf2 disruption as a potential therapeutic target for Alzheimer's disease.
Kerr F, Sofola-Adesakin O, Ivanov DK, Gatliff J, Gomez Perez-Nievas B, Bertrand HC, Martinez P, Callard R, Snoeren I, Cochemé HM, Adcott J, Khericha M, Castillo-Quan JI, Wells G, Noble W, Thornton J, Partridge L. PLoS genetics Volume 13 (2017) p.e1006593 DOI: 10.1371/journal.pgen.1006593
Aging increases cell-to-cell transcriptional variability upon immune stimulation.
Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, Stojic L, Rayner TF, Stubbington MJT, Teichmann SA, de la Roche M, Marioni JC, Odom DT. Science (New York, N.Y.) Volume 355 (2017) p.1433-1436 DOI: 10.1126/science.aah4115
An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge.
Pundir S, Onwubiko J, Zaru R, Rosanoff S, Antunes R, Bingley M, Watkins X, O'Donovan C, Martin MJ. Protein engineering, design & selection : PEDS Volume 30 (2017) p.245-251 DOI: 10.1093/protein/gzx008
tranSMART-XNAT Connector tranSMART-XNAT connector-image selection based on clinical phenotypes and genetic profiles.
He S, Yong M, Matthews PM, Guo Y. Bioinformatics (Oxford, England) Volume 33 (2017) p.787-788 DOI: 10.1093/bioinformatics/btw714
*
A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data.
Ogeh D, Badge R. Bioinformatics (Oxford, England) Volume 33 (2017) p.650-653 DOI: 10.1093/bioinformatics/btw687
The druggable genome and support for target identification and validation in drug development.
Finan C, Gaulton A, Kruger FA, Lumbers RT, Shah T, Engmann J, Galver L, Kelley R, Karlsson A, Santos R, Overington JP, Hingorani AD, Casas JP. Science translational medicine Volume 9 (2017) DOI: 10.1126/scitranslmed.aag1166
Data management: A global coalition to sustain core data.
Anderson WP, Global Life Science Data Resources Working Group. Nature Volume 543 (2017) p.179 DOI: 10.1038/543179a
Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.
Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MS, Fogg LG, Nair AS, Liligeto U, Stubbington MJ, Ly LH, Bagger FO, Zwiessele M, Lawrence ND, Souza-Fonseca-Guimaraes F, Bunn PT, Engwerda CR, Heath WR, Billker O, Stegle O, Haque A, Teichmann SA. Science immunology Volume 2 (2017) DOI: 10.1126/sciimmunol.aal2192
*
A global perspective on bioinformatics training needs
Brazas MD, Brooksbank C, Jimenez RC, Blackford S, Palagi PM, De Las Rivas J, Ouellette BF, Kumuthini J, Korpelainen E, Lewitter F, van Gelder CW, Mulder N, Corpas M, Schneider MV, Tan TW, Clements D, Davies A, Attwood TK. Preprint DOI: 10.1101/098996
*
TOWARDS COORDINATED INTERNATIONAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES
Anderson W, Apweiler R, Bateman A, Bauer GA, Berman H, Blake JA, Blomberg N, Burley SK, Cochrane G, Di Francesco V, Donohue T, Durinx C, Game A, Green E, Gojobori T, Goodhand P, Hamosh A, Hermjakob H, Kanehisa M, Kiley R, McEntyre J, McKibbin R, Miyano S, Pauly B, Perrimon N, Ragan MA, Richards G, Teo Y, Westerfield M, Westhof E, Lasko PF. Preprint DOI: 10.1101/110825
Prospective identification of hematopoietic lineage choice by deep learning.
Buggenthin F, Buettner F, Hoppe PS, Endele M, Kroiss M, Strasser M, Schwarzfischer M, Loeffler D, Kokkaliaris KD, Hilsenbeck O, Schroeder T, Theis FJ, Marr C. Nature methods Volume 14 (2017) p.403-406 DOI: 10.1038/nmeth.4182
New drug candidates for liposomal delivery identified by computer modeling of liposomes' remote loading and leakage.
Cern A, Marcus D, Tropsha A, Barenholz Y, Goldblum A. Journal of controlled release : official journal of the Controlled Release Society Volume 252 (2017) p.18-27 DOI: 10.1016/j.jconrel.2017.02.015
The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection.
Hulo C, Masson P, de Castro E, Auchincloss AH, Foulger R, Poux S, Lomax J, Bougueleret L, Xenarios I, Le Mercier P. PloS one Volume 12 (2017) p.e0171746 DOI: 10.1371/journal.pone.0171746
Structure of the Escherichia coli ProQ RNA-binding protein.
Gonzalez GM, Hardwick SW, Maslen SL, Skehel JM, Holmqvist E, Vogel J, Bateman A, Luisi BF, Broadhurst RW. RNA (New York, N.Y.) Volume 23 (2017) p.696-711 DOI: 10.1261/rna.060343.116
Promoter shape varies across populations and affects promoter evolution and expression noise.
Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE. Nature genetics Volume 49 (2017) p.550-558 DOI: 10.1038/ng.3791
*
A high-resolution mRNA expression time course of embryonic development in zebrafish
White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Hourlier T, Fullgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. Preprint DOI: 10.1101/107631
Nuclear RNA Decay Pathways Aid Rapid Remodeling of Gene Expression in Yeast.
Bresson S, Tuck A, Staneva D, Tollervey D. Molecular cell Volume 65 (2017) p.787-800.e5 DOI: 10.1016/j.molcel.2017.01.005
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.
Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK. Structure (London, England : 1993) Volume 25 (2017) p.536-545 DOI: 10.1016/j.str.2017.01.004
Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations.
Brammeld JS, Petljak M, Martincorena I, Williams SP, Alonso LG, Dalmases A, Bellosillo B, Robles-Espinoza CD, Price S, Barthorpe S, Tarpey P, Alifrangis C, Bignell G, Vidal J, Young J, Stebbings L, Beal K, Stratton MR, Saez-Rodriguez J, Garnett M, Montagut C, Iorio F, McDermott U. Genome research Volume 27 (2017) p.613-625 DOI: 10.1101/gr.213546.116
Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.
Koo BM, Kritikos G, Farelli JD, Todor H, Tong K, Kimsey H, Wapinski I, Galardini M, Cabal A, Peters JM, Hachmann AB, Rudner DZ, Allen KN, Typas A, Gross CA. Cell systems Volume 4 (2017) p.291-305.e7 DOI: 10.1016/j.cels.2016.12.013
Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.
Imprialou M, Kahles A, Steffen JG, Osborne EJ, Gan X, Lempe J, Bhomra A, Belfield E, Visscher A, Greenhalgh R, Harberd NP, Goram R, Hein J, Robert-Seilaniantz A, Jones J, Stegle O, Kover P, Tsiantis M, Nordborg M, Rätsch G, Clark RM, Mott R. Genetics Volume 205 (2017) p.1425-1441 DOI: 10.1534/genetics.116.192823
*
Interactions between genetic variation and cellular environment in skeletal muscle gene expression
Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Casale FP, Wolford BN, Guan L, Varshney A, Albanus RD, Parker SC, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS. Preprint DOI: 10.1101/105429
A Comparative Analysis of Drug-Induced Hepatotoxicity in Clinically Relevant Situations.
Thiel C, Cordes H, Fabbri L, Aschmann HE, Baier V, Smit I, Atkinson F, Blank LM, Kuepfer L. PLoS computational biology Volume 13 (2017) p.e1005280 DOI: 10.1371/journal.pcbi.1005280
*
Cell biology: tracking a cell's cycle.
Marx V. Nature methods Volume 14 (2017) p.233-236 DOI: 10.1038/nmeth.4186
The Genetic Architecture of Major Depressive Disorder in Han Chinese Women.
Peterson RE, Cai N, Bigdeli TB, Li Y, Reimers M, Nikulova A, Webb BT, Bacanu SA, Riley BP, Flint J, Kendler KS. JAMA psychiatry Volume 74 (2017) p.162-168 DOI: 10.1001/jamapsychiatry.2016.3578
Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders.
Evers JM, Laskowski RA, Bertolli M, Clayton-Smith J, Deshpande C, Eason J, Elmslie F, Flinter F, Gardiner C, Hurst JA, Kingston H, Kini U, Lampe AK, Lim D, Male A, Naik S, Parker MJ, Price S, Robert L, Sarkar A, Straub V, Woods G, Thornton JM, DDD Study, Wright CF. Human molecular genetics Volume 26 (2017) p.519-526 DOI: 10.1093/hmg/ddw409
Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis.
Vitsios DM, Davis MP, van Dongen S, Enright AJ. Nucleic acids research Volume 45 (2017) p.1079-1090 DOI: 10.1093/nar/gkw1031
*
Postdocs, What Would You Tell Your Younger Self?
Cell Volume 168 (2017) p.745-748 DOI: 10.1016/j.cell.2017.02.016
From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB.
Zaru R, Magrane M, O'Donovan C, UniProt Consortium. The Biochemical journal Volume 474 (2017) p.493-515 DOI: 10.1042/BCJ20160991
Synthetic human proteomes for accelerating protein research.
Perez-Riverol Y, Vizcaíno JA. Nature methods Volume 14 (2017) p.240-242 DOI: 10.1038/nmeth.4191
*
Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration.
Arno G, Carss KJ, Hull S, Zihni C, Robson AG, Fiorentino A, UK Inherited Retinal Disease Consortium, Hardcastle AJ, Holder GE, Cheetham ME, Plagnol V, NIHR Bioresource - Rare Diseases Consortium, Moore AT, Raymond FL, Matter K, Balda MS, Webster AR. American journal of human genetics Volume 100 (2017) p.334-342 DOI: 10.1016/j.ajhg.2016.12.014
Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.
Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP, Sidiropoulos N, Rapin N, Merkel A, BLUEPRINT Consortium, Stunnenberg HG, Stegle O, Frontini M, Downes K, Pastinen T, Kuijpers TW, Rico D, Valencia A, Beck S, Soranzo N, Paul DS. Genome biology Volume 18 (2017) p.18 DOI: 10.1186/s13059-017-1156-8
Genetic Variation in the Social Environment Contributes to Health and Disease.
Baud A, Mulligan MK, Casale FP, Ingels JF, Bohl CJ, Callebert J, Launay JM, Krohn J, Legarra A, Williams RW, Stegle O. PLoS genetics Volume 13 (2017) p.e1006498 DOI: 10.1371/journal.pgen.1006498
*
The Nucleosome Remodelling and Deacetylation complex restricts Mediator access to enhancers to control transcription
Xenophontos M, Reynolds N, Gharbi S, Johnstone E, Signolet J, Floyd R, Ralser M, Borneloev S, Dietmann S, Loos R, Bertone P, Hendrich B. Preprint DOI: 10.1101/103192
ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services.
Robertsen EM, Denise H, Mitchell A, Finn RD, Bongo LA, Willassen NP. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.10443.1
A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.
Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, Nik-Zainal S. Nature genetics Volume 49 (2017) p.341-348 DOI: 10.1038/ng.3771
A Golden Age for Working with Public Proteomics Data.
Martens L, Vizcaíno JA. Trends in biochemical sciences Volume 42 (2017) p.333-341 DOI: 10.1016/j.tibs.2017.01.001
Global open data management in metabolomics.
Haug K, Salek RM, Steinbeck C. Current opinion in chemical biology Volume 36 (2017) p.58-63 DOI: 10.1016/j.cbpa.2016.12.024
Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.
Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJ, Cvejic A, Gfeller D. Genome research Volume 27 (2017) p.451-461 DOI: 10.1101/gr.207704.116
*
Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, Creighton C. Preprint DOI: 10.1101/099861
System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.
Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M, Vaga S, Vitek O, Saez-Rodriguez J, Aebersold R. Journal of proteome research Volume 16 (2017) p.831-841 DOI: 10.1021/acs.jproteome.6b00815
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.
Gonçalves E, Raguz Nakic Z, Zampieri M, Wagih O, Ochoa D, Sauer U, Beltrao P, Saez-Rodriguez J. PLoS computational biology Volume 13 (2017) p.e1005297 DOI: 10.1371/journal.pcbi.1005297
The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying Neurodegeneration: Evolving Dimensions and Future Directions.
Lloret-Villas A, Varusai TM, Juty N, Laibe C, Le NovÈre N, Hermjakob H, Chelliah V. CPT: pharmacometrics & systems pharmacology Volume 6 (2017) p.73-86 DOI: 10.1002/psp4.12155
10th Anniversary Treasure Hunt
Armstrong D, Burke M, Huerta L, Levchenko M, Mitchell A, Morgan S, Mugumbate G, Mutowo P, Orchard S, Perry E, Pundir S, Richardson L, Tang A. DOI: 10.6019/tol.treasure-t.2017.00001.1
Ensembl tools: webinar
Perry E. DOI: 10.6019/tol.ens-too-w.2017.00001.2
Human genetic variation (I): an introduction
Armstrong D, Burke M, Emery L, MacArthur J, Nightingale A, Perry E, Pundir S, Saunders G. DOI: 10.6019/tol.hugenvar_1-t.2017.00001.1
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.
Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. Methods in molecular biology (Clifton, N.J.) Volume 1607 (2017) p.627-641 DOI: 10.1007/978-1-4939-7000-1_26
ODE-Based Modeling of Complex Regulatory Circuits.
Seaton DD. Methods in molecular biology (Clifton, N.J.) Volume 1629 (2017) p.317-330 DOI: 10.1007/978-1-4939-7125-1_20
UniProt Protein Knowledgebase.
Pundir S, Martin MJ, O'Donovan C. Methods in molecular biology (Clifton, N.J.) Volume 1558 (2017) p.41-55 DOI: 10.1007/978-1-4939-6783-4_2
Reactome: Tools for analysis of biological pathways
Jupe S. DOI: 10.6019/tol.reactome_tools-t.2017.00001.1
Reactome: Exploring biological pathways
Jupe S. DOI: 10.6019/tol.reactome_exbp-t.2017.00001.1
EBI Metagenomics: analysing and exploring metagenomic data
Mitchell A. DOI: 10.6019/tol.ebimetagen-w.2017.00001.1
Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data.
Bolser DM, Staines DM, Perry E, Kersey PJ. Methods in molecular biology (Clifton, N.J.) Volume 1533 (2017) p.1-31 DOI: 10.1007/978-1-4939-6658-5_1
Exploring protein interactions with UniProt
Pichler K. DOI: 10.6019/tol.unip-interactions-w.2017.00001.1
Visualising protein structures online
Armstrong A. DOI: 10.6019/tol.pdbe-litemol-w.2017.00001.1
Primer on Ontologies.
Hastings J. Methods in molecular biology (Clifton, N.J.) Volume 1446 (2017) p.3-13 DOI: 10.1007/978-1-4939-3743-1_1
Using the MEROPS Database for Investigation of Lysosomal Peptidases, Their Inhibitors, and Substrates.
Rawlings ND. Methods in molecular biology (Clifton, N.J.) Volume 1594 (2017) p.213-226 DOI: 10.1007/978-1-4939-6934-0_14
Human genetic variation (II): exploring publicly available data
Armstrong D, Burke M, Emery L, MacArthur J, Nightingale A, Perry E, Pundir S, Saunders G. DOI: 10.6019/tol.hugenvar_2-t.2017.00001.1
Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways.
Saidi R, Boudellioua I, Martin MJ, Solovyev V. Methods in molecular biology (Clifton, N.J.) Volume 1613 (2017) p.311-331 DOI: 10.1007/978-1-4939-7027-8_12
The ProFunc Function Prediction Server.
Laskowski RA. Methods in molecular biology (Clifton, N.J.) Volume 1611 (2017) p.75-95 DOI: 10.1007/978-1-4939-7015-5_7
Europe PMC: get the most from literature searches
Parkin M. DOI: 10.6019/tol.epmcsearch-w.2017.00001.1
User experience design for more user-friendly applications
Ide-Smith M, Karamanis N. DOI: 10.6019/tol.uxapp-w.2017.00001.1
EMPIAR: Quick tour
Iudin A, Patwardhan A. DOI: 10.6019/tol.empiar-qt.2017.00001.1
QuickGO - Gene ontology annotation
Georghiou G. DOI: 10.6019/tol.quickgo-w.2017.00001.1
Europe PMC: Quick tour
Parkin M. DOI: 10.6019/tol.epmc-qt.2017.00001.2
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.
Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird M, Longden I, Proctor G, Searle S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P. Database : the journal of biological databases and curation Volume 2017 (2017) DOI: 10.1093/database/bax020
Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149.
Tkavc R, Matrosova VY, Grichenko OE, Gostinčar C, Volpe RP, Klimenkova P, Gaidamakova EK, Zhou CE, Stewart BJ, Lyman MG, Malfatti SA, Rubinfeld B, Courtot M, Singh J, Dalgard CL, Hamilton T, Frey KG, Gunde-Cimerman N, Dugan L, Daly MJ. Frontiers in microbiology Volume 8 (2017) p.2528 DOI: 10.3389/fmicb.2017.02528

2016

*
Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease.
Carss KJ, Arno G, Erwood M, Stephens J, Sanchis-Juan A, Hull S, Megy K, Grozeva D, Dewhurst E, Malka S, Plagnol V, Penkett C, Stirrups K, Rizzo R, Wright G, Josifova D, Bitner-Glindzicz M, Scott RH, Clement E, Allen L, Armstrong R, Brady AF, Carmichael J, Chitre M, Henderson RHH, Hurst J, MacLaren RE, Murphy E, Paterson J, Rosser E, Thompson DA, Wakeling E, Ouwehand WH, Michaelides M, Moore AT, NIHR-BioResource Rare Diseases Consortium, Webster AR, Raymond FL. American journal of human genetics Volume 100 (2017) p.75-90 DOI: 10.1016/j.ajhg.2016.12.003
Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy.
Weber RJM, Lawson TN, Salek RM, Ebbels TMD, Glen RC, Goodacre R, Griffin JL, Haug K, Koulman A, Moreno P, Ralser M, Steinbeck C, Dunn WB, Viant MR. Metabolomics Volume 13 (2017) p.12 DOI: 10.1007/s11306-016-1147-x
Genetic variants regulating expression levels and isoform diversity during embryogenesis.
Cannavò E, Koelling N, Harnett D, Garfield D, Casale FP, Ciglar L, Gustafson HE, Viales RR, Marco-Ferreres R, Degner JF, Zhao B, Stegle O, Birney E, Furlong EE. Nature Volume 541 (2017) p.402-406 DOI: 10.1038/nature20802
Minimizing proteome redundancy in the UniProt Knowledgebase.
Bursteinas B, Britto R, Bely B, Auchincloss A, Rivoire C, Redaschi N, O'Donovan C, Martin MJ. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw139
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.
Singhal A, Leaman R, Catlett N, Lemberger T, McEntyre J, Polson S, Xenarios I, Arighi C, Lu Z. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw161
Efficient randomization of biological networks while preserving functional characterization of individual nodes.
Iorio F, Bernardo-Faura M, Gobbi A, Cokelaer T, Jurman G, Saez-Rodriguez J. BMC bioinformatics Volume 17 (2016) p.542 DOI: 10.1186/s12859-016-1402-1
Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition.
Mateo F, Arenas EJ, Aguilar H, Serra-Musach J, de Garibay GR, Boni J, Maicas M, Du S, Iorio F, Herranz-Ors C, Islam A, Prado X, Llorente A, Petit A, Vidal A, Català I, Soler T, Venturas G, Rojo-Sebastian A, Serra H, Cuadras D, Blanco I, Lozano J, Canals F, Sieuwerts AM, de Weerd V, Look MP, Puertas S, García N, Perkins AS, Bonifaci N, Skowron M, Gómez-Baldó L, Hernández V, Martínez-Aranda A, Martínez-Iniesta M, Serrat X, Cerón J, Brunet J, Barretina MP, Gil M, Falo C, Fernández A, Morilla I, Pernas S, Plà MJ, Andreu X, Seguí MA, Ballester R, Castellà E, Nellist M, Morales S, Valls J, Velasco A, Matias-Guiu X, Figueras A, Sánchez-Mut JV, Sánchez-Céspedes M, Cordero A, Gómez-Miragaya J, Palomero L, Gómez A, Gajewski TF, Cohen EEW, Jesiotr M, Bodnar L, Quintela-Fandino M, López-Bigas N, Valdés-Mas R, Puente XS, Viñals F, Casanovas O, Graupera M, Hernández-Losa J, Ramón Y Cajal S, García-Alonso L, Saez-Rodriguez J, Esteller M, Sierra A, Martín-Martín N, Matheu A, Carracedo A, González-Suárez E, Nanjundan M, Cortés J, Lázaro C, Odero MD, Martens JWM, Moreno-Bueno G, Barcellos-Hoff MH, Villanueva A, Gomis RR, Pujana MA. Oncogene Volume 36 (2017) p.2737-2749 DOI: 10.1038/onc.2016.427
*
Omics Discovery Index - Discovering and Linking Public Omics Datasets
Perez-Riverol Y, Bai M, Leprevost F, Squizzato S, Park YM, et al. DOI: 10.1101/049205
Novel inhibitors of Mycobacterium tuberculosis GuaB2 identified by a target based high-throughput phenotypic screen.
Cox JA, Mugumbate G, Del Peral LV, Jankute M, Abrahams KA, Jervis P, Jackenkroll S, Perez A, Alemparte C, Esquivias J, Lelièvre J, Ramon F, Barros D, Ballell L, Besra GS. Scientific reports Volume 6 (2016) p.38986 DOI: 10.1038/srep38986
*
Rapid identification of optimal drug combinations for personalized cancer therapy using microfluidics
Eduati F, Utharala R, Madhavan D, Neumann UP, Cramer T, Saez-Rodriguez J, Merten CA. Preprint DOI: 10.1101/093906
*
On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study
Poux S, Arighi CN, Magrane M, Bateman A, Wei C, Lu Z, Boutet E, Bye-A-Jee H, Famiglietti ML, Roechert B. Preprint DOI: 10.1101/094011
*
Chromosomal rearrangements are commonly post-transcriptionally attenuated in cancer
Goncalves E, Fragoulis A, Garcia-Alonso L, Cramer T, Saez-Rodriguez J, Beltrao P. Preprint DOI: 10.1101/093369
*
SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data
Venkatesan A, Kim J, Talo F, Ide-Smith M, Gobeill J, Carter J, Batista-Navarro R, Ananiadou S, Ruch P, McEntyre J. Preprint DOI: 10.12688/wellcomeopenres.10210.1
Integration of EGA secure data access into Galaxy.
Hoogstrate Y, Zhang C, Senf A, Bijlard J, Hiltemann S, van Enckevort D, Repo S, Heringa J, Jenster G, J A Fijneman R, Boiten JW, A Meijer G, Stubbs A, Rambla J, Spalding D, Abeln S. F1000Research Volume 5 (2016) DOI: 10.12688/f1000research.10221.1
*
Tracking the embryonic stem cell transition from ground state pluripotency
Kalkan T, Olova N, Roode M, Mulas C, Lee HJ, Nett I, Marks H, Walker R, Stunnenberg HG, Lilley K, Nichols J, Reik W, Bertone P, Smith A. Preprint DOI: 10.1101/092510
*
Protein three-dimensional structure validation
Joosten RP, Chinea G, Kleywegt GJ, Vriend G. Elsevier Reference Module in Chemistry, Molecular Sciences and Chemical Engineering Elsevier, Waltham, MA DOI: 10.1016/b978-0-12-409547-2.02534-8
*
Validation of protein crystal structures
Kleywegt GJ. International Tables for Crystallography, Volume F, Crystallography of biological macromolecules, 2nd edition Wiley DOI: 10.1107/97809553602060000111
EMBO highthrouhput sequencing
Rustici G. DOI: 10.6019/tol.htsembo-v.2011.00001.1
IntAct quick tour
Porras P. DOI: 10.6019/tol.inta-qt.2011.00001.1
Cellular Microscopy Phenotype Ontology (CMPO): Quick tour
Rustici G, Hancocks T. DOI: 10.6019/tol.cmpo-qt.2015.00001.1
Ensembl browser webinar series (2016)
Perry E, Carvalho-Silva D, Moore B, Sparrow H. DOI: 10.6019/tol.ensbrows-w.2016.00001.1
Proteomics: An introduction to EMBL-EBI resources
Orchard S, Charles PD. DOI: 10.6019/tol.pms.2011.00001.1
Reactome: Exploring biological pathways: webinar
Jupe S. DOI: 10.6019/tol.react-w.2015.00001.1
UniProt: Programmatic access to UniProtKB: webinar
Pichler K. DOI: 10.6019/tol.unp-program-w.2015.00001.1
InterPro: functional and structural analysis of protein sequences
Mitchell A, Sangrador-Vegas A, Sehra M. DOI: 10.6019/tol.intp-t.2012.00001.1
Reactome: exploring and analysing biological pathways
Jupe S. DOI: 10.6019/tol.rea-t.2012.00001.2
EMBL-EBI resources: An introduction
Gopalasingam P. DOI: 10.6019/tol.intr-ebi-res-w.2015.00001.1
Protein classification: An introduction to EMBL-EBI resources
Sangrador-Vegas A, Mitchell A. DOI: 10.6019/tol.prc.2011.00001.1
ProteomeXchange submissions via PRIDE
Vizcaino JA, Ternent T, Sehra M, Csordas A. DOI: 10.6019/tol.pxd-t.2014.00001.1
Biomacromolecular structures
Argasinska J, Symmons MF, Gutmanas A, Kleywegt GJ, . DOI: 10.6019/tol.bms.2011.00001.1
BioModels quick tour
Chelliah V. DOI: 10.6019/tol.bm-qt.2012.00001.1
PDBe: quick tour
Velankar S, Battle G. DOI: 10.6019/tol.pdbe-qt.2011.00001.1
PDBe: exploring a Protein Data Bank (PDB) entry
Sen S, Mukhopadhyay A. DOI: 10.6019/tol.pdbe-exp-t.2015.00001.1
PDBe: searching the Protein Data Bank
Sen S, Mukhopadhyay A. DOI: 10.6019/tol.pdbe-sea-t.2015.00001.1
ArrayExpress: Quick tour
Burke M. DOI: 10.6019/tol.arrex-qt.2011.00001.2
IntAct: Molecular Interactions at the EBI
Orchard S. DOI: 10.6019/tol.inta-t.2012.00001.1
Protein interactions and their importance
Porras P, Sehra M. DOI: 10.6019/tol.pro-int.2012.00001.1
Phylogenetics: An introduction
Emery L. DOI: 10.6019/tol.phyl.2015.00001.1
Functional genomics: An introduction to the EMBL-EBI resources
Tang YA, Rustici G. DOI: 10.6019/tol.fng.2014.00001.2
Ensembl: Filmed browser workshop
Perry E, Spudich GM, Carvalho-Silva D. DOI: 10.6019/tol.ensfbw-v.2013.00001.1
Genomics resources: webinar
Emery L. DOI: 10.6019/tol.gen-res-w.2015.00001.1
Network analysis of protein interaction data: an introduction
Porras P. DOI: 10.6019/tol.networks_t.2016.00001.1
Ensembl: Genomic features that regulate genes
Perry E. DOI: 10.6019/tol.ensreg-w.2016.00001.1
Ensembl tools: webinar
Perry E. DOI: 10.6019/tol.ens-too-w.2015.00001.1
Introduction to IntAct - a Protein-Protein Interactions resource
Meldal B, Porras P. DOI: 10.6019/tol.inta-intr-w.2015.00001.1
Ensembl: Filmed API Workshop
Perry E. DOI: 10.6019/tol.ensapi-v.2013.00001.1
Ensembl: Quick tour
Perry E. DOI: 10.6019/tol.ens-qt.2012.00001.1
UniProt: Exploring protein sequence and fucntional information
Magrane M, Pundir S. DOI: 10.6019/tol.unp-t.2014.00001.1
EBI: Next Generation Sequencing Practical Course
Perry E. DOI: 10.6019/tol.ngs-v.2012.00001.1
Array Express: Exploring functional genomics data quickly and easily
Füllgrabe A. DOI: 10.6019/tol.aex-t.2016.00001.2
ChEMBL: Exploring bioactive drug-like molecules
Bellis LJ. DOI: 10.6019/tol.chembl-t.2015.00001.1
EBI Metagenomics portal: Submitting metagenomics data to the European Nucleotide Archive
Denise H. DOI: 10.6019/tol.metagensubm-t.2016.00001.1
EBI Metagenomics resource: Quick tour
Denise H. DOI: 10.6019/tol.mtg-qt.2013.00001.2
UniProt quick tour
Magrane M. DOI: 10.6019/tol.unp-qt.2014.00001.1
Complex Portal: webinar
Meldal BH. DOI: 10.6019/tol.comport-w.2015.00001.1
UniProt: Exploring protein sequence and functional information - webinar
Pundir S. DOI: 10.6019/tol.unp-expl-w.2015.00001.1
PDBe: Searching for biological macromolecular structures
Armstrong DR. DOI: 10.6019/tol.pdbe-intr-w.2015.00001.1
ArrayExpress: why and how to submit your data
Burke M. DOI: 10.6019/tol.aesub-w.2016.00001.1
ChEMBL qt
Bellis LJ. DOI: 10.6019/tol.chembl-qt.2011.00001.1
UniProt peptide search and website updates: webinar
Pichler K. DOI: 10.6019/tol.unp-peptide-pub-w.2016.00001.1
PRIDE: Quick tour
Vizcaino JA. DOI: 10.6019/tol.pride-qt.2014.00001.1
Pfam: Quick tour
El-Gebali S, Richardson L, Finn R. DOI: 10.6019/tol.pfam-qt.2016.00001.1
ChEMBL walkthrough: webinar
Bellis LJ. DOI: 10.6019/tol.chemblwalk-w.2015.00001.1
Europe PMC: Quick tour
Rossiter P. DOI: 10.6019/tol.epmc-qt.2013.00001.2
PRIDE and ProteomeXchange: webinar
Vizcaino JA. DOI: 10.6019/tol.pride-px-w.2015.00001.1
European Nucleotide Archive (ENA) quick tour
Amid C, Cochrane G. DOI: 10.6019/tol.ena-qt.2011.00001.1
Expression Atlas: Quick tour
Keays M. DOI: 10.6019/tol.gea-qt.2013.00001.2
InterPro: quick tour
Mitchell A. DOI: 10.6019/tol.intp-qt.2011.00001.1
BioSamples quick tour
Faulconbridge A. DOI: 10.6019/tol.bsa-qt.2014.00001.1
Bioinformatics for the terrified
Brooksbank C, Cowley A. DOI: 10.6019/tol.bioinfter-c.2016.00001.1
Introduction to training with EMBL-EBI
Brooksbank C. DOI: 10.6019/tol.train-w.2016.00001.1
Biomedical data: Ethical, legal and social implications
Morgan SL, Hancocks T. DOI: 10.6019/tol.elsi-c.2015.00001.1
User experience design
Rowland F, Pundir S, Brooksbank C, Hancocks T. DOI: 10.6019/tol.ux-c.2015.00001.1
SureChEMBL: Accessing chemical patent data: webinar
Papadatos G. DOI: 10.6019/tol.surechembl-w.2015.00001.1
MyChEMBL: webinar
Papadatos G. DOI: 10.6019/tol.mychembl-w.2015.00001.2
Complex Portal: Quick tour
Meldal BH. DOI: 10.6019/tol.compor-qt.2015.00001.1
Ensembl Variant Effect Predictor (VEP): webinar
Moore B. DOI: 10.6019/tol.ensvep-w.2016.00001.1
BioSamples RDF: webinar
Brandizi M, Hancocks T. DOI: 10.6019/tol.bsa-rdf-w.2015.00001.1
Introduction to 1000 Genomes Project and IGSR data resources
Fairley S. DOI: 10.6019/tol.isgr_w.2016.00001.1
Reactome quick tour
Jupe S. DOI: 10.6019/tol.rea-qt.2014.00001.1
PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.
Urban M, Cuzick A, Rutherford K, Irvine A, Pedro H, Pant R, Sadanadan V, Khamari L, Billal S, Mohanty S, Hammond-Kosack KE. Nucleic acids research Volume 45 (2017) p.D604-D610 DOI: 10.1093/nar/gkw1089
Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition.
Lensink MF, Velankar S, Wodak SJ. Proteins Volume 85 (2017) p.359-377 DOI: 10.1002/prot.25215
A comprehensive map of molecular drug targets.
Santos R, Ursu O, Gaulton A, Bento AP, Donadi RS, Bologa CG, Karlsson A, Al-Lazikani B, Hersey A, Oprea TI, Overington JP. Nature reviews. Drug discovery Volume 16 (2017) p.19-34 DOI: 10.1038/nrd.2016.230
An atlas of human kinase regulation.
Ochoa D, Jonikas M, Lawrence RT, El Debs B, Selkrig J, Typas A, Villén J, Santos SD, Beltrao P. Molecular systems biology Volume 12 (2016) p.888 DOI: 10.15252/msb.20167295
*
BiologicalWeb services: Integration, optimization, and reasoning
Benedikt M,  Lopez Serrano R,  Tsamoura E. CEUR workshop proceedings (2016) p.21-27 DOI: https://pdfs.semanticscholar.org/9983/e953294f45436c49f28d173ba078b15e4545.pdf
*
Evidence for mitochondrial genetic control of autosomal gene expression.
Kassam I, Qi T, Lloyd-Jones L, Holloway A, Jan Bonder M, Henders AK, Martin NG, Powell JE, Franke L, Montgomery GW, Visscher PM, McRae AF. Human molecular genetics Volume 25 (2016) p.5332-5338 DOI: 10.1093/hmg/ddw347
Plant specimen contextual data consensus.
Hoopen PT, Walls RL, Cannon EK, Cochrane G, Cole J, Johnston A, Karsch-Mizrachi I, Yilmaz P. GigaScience Volume 5 (2016) p.1-4 DOI: 10.1093/gigascience/giw002
*
Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.
Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Cell Volume 167 (2016) p.1897 DOI: 10.1016/j.cell.2016.11.046
European Nucleotide Archive in 2016.
Toribio AL, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Fairley S, Gibson R, Goodgame N, Ten Hoopen P, Jayathilaka S, Kay S, Leinonen R, Liu X, Martínez-Villacorta J, Pakseresht N, Rajan J, Reddy K, Rosello M, Silvester N, Smirnov D, Vaughan D, Zalunin V, Cochrane G. Nucleic acids research Volume 45 (2017) p.D32-D36 DOI: 10.1093/nar/gkw1106
*
UniProt: the universal protein knowledgebase.
The UniProt Consortium. Nucleic acids research Volume 45 (2017) p.D158-D169 DOI: 10.1093/nar/gkw1099
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog).
MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H. Nucleic acids research Volume 45 (2017) p.D896-D901 DOI: 10.1093/nar/gkw1133
Increased DNA methylation variability in type 1 diabetes across three immune effector cell types.
Paul DS, Teschendorff AE, Dang MA, Lowe R, Hawa MI, Ecker S, Beyan H, Cunningham S, Fouts AR, Ramelius A, Burden F, Farrow S, Rowlston S, Rehnstrom K, Frontini M, Downes K, Busche S, Cheung WA, Ge B, Simon MM, Bujold D, Kwan T, Bourque G, Datta A, Lowy E, Clarke L, Flicek P, Libertini E, Heath S, Gut M, Gut IG, Ouwehand WH, Pastinen T, Soranzo N, Hofer SE, Karges B, Meissner T, Boehm BO, Cilio C, Elding Larsson H, Lernmark Å, Steck AK, Rakyan VK, Beck S, Leslie RD. Nature communications Volume 7 (2016) p.13555 DOI: 10.1038/ncomms13555
Pharos: Collating protein information to shed light on the druggable genome.
Nguyen DT, Mathias S, Bologa C, Brunak S, Fernandez N, Gaulton A, Hersey A, Holmes J, Jensen LJ, Karlsson A, Liu G, Ma'ayan A, Mandava G, Mani S, Mehta S, Overington J, Patel J, Rouillard AD, Schürer S, Sheils T, Simeonov A, Sklar LA, Southall N, Ursu O, Vidovic D, Waller A, Yang J, Jadhav A, Oprea TI, Guha R. Nucleic acids research Volume 45 (2017) p.D995-D1002 DOI: 10.1093/nar/gkw1072
InterPro in 2017-beyond protein family and domain annotations.
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. Nucleic acids research Volume 45 (2017) p.D190-D199 DOI: 10.1093/nar/gkw1107
*
Expansion of the Gene Ontology knowledgebase and resources.
The Gene Ontology Consortium. Nucleic acids research Volume 45 (2017) p.D331-D338 DOI: 10.1093/nar/gkw1108
Open Targets: a platform for therapeutic target identification and validation.
Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I. Nucleic acids research Volume 45 (2017) p.D985-D994 DOI: 10.1093/nar/gkw1055
Uniclust databases of clustered and deeply annotated protein sequences and alignments.
Mirdita M, von den Driesch L, Galiez C, Martin MJ, Söding J, Steinegger M. Nucleic acids research Volume 45 (2017) p.D170-D176 DOI: 10.1093/nar/gkw1081
Ensembl 2017.
Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Juettemann T, Keenan S, Laird MR, Lavidas I, Maurel T, McLaren W, Moore B, Murphy DN, Nag R, Newman V, Nuhn M, Ong CK, Parker A, Patricio M, Riat HS, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Wilder SP, Zadissa A, Kostadima M, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Cunningham F, Yates A, Zerbino DR, Flicek P. Nucleic acids research Volume 45 (2017) p.D635-D642 DOI: 10.1093/nar/gkw1104
The ChEMBL database in 2017.
Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibrián-Uhalte E, Davies M, Dedman N, Karlsson A, Magariños MP, Overington JP, Papadatos G, Smit I, Leach AR. Nucleic acids research Volume 45 (2017) p.D945-D954 DOI: 10.1093/nar/gkw1074
IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex.
Maccari G, Robinson J, Ballingall K, Guethlein LA, Grimholt U, Kaufman J, Ho CS, de Groot NG, Flicek P, Bontrop RE, Hammond JA, Marsh SG. Nucleic acids research Volume 45 (2017) p.D860-D864 DOI: 10.1093/nar/gkw1050
WormBase ParaSite - a comprehensive resource for helminth genomics.
Howe KL, Bolt BJ, Shafie M, Kersey P, Berriman M. Molecular and biochemical parasitology Volume 215 (2017) p.2-10 DOI: 10.1016/j.molbiopara.2016.11.005
*
The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Dissemination
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Carazo-Salas RE, Swedlow JR. Preprint DOI: 10.1101/089359
Towards an open grapevine information system.
Adam-Blondon AF, Alaux M, Pommier C, Cantu D, Cheng ZM, Cramer GR, Davies C, Delrot S, Deluc L, Di Gaspero G, Grimplet J, Fennell A, Londo JP, Kersey P, Mattivi F, Naithani S, Neveu P, Nikolski M, Pezzotti M, Reisch BI, Töpfer R, Vivier MA, Ware D, Quesneville H. Horticulture research Volume 3 (2016) p.16056 DOI: 10.1038/hortres.2016.56
Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.
Knijnenburg TA, Klau GW, Iorio F, Garnett MJ, McDermott U, Shmulevich I, Wessels LF. Scientific reports Volume 6 (2016) p.36812 DOI: 10.1038/srep36812
The genome of Onchocerca volvulus, agent of river blindness.
Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JC, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, Ribeiro JM, Rogers MB, Stanley E, Swapna LS, Tsai IJ, Unnasch TR, Voronin D, Parkinson J, Nutman TB, Ghedin E, Berriman M, Lustigman S. Nature microbiology Volume 2 (2016) p.16216 DOI: 10.1038/nmicrobiol.2016.216
The BLUEPRINT Data Analysis Portal.
Fernández JM, de la Torre V, Richardson D, Royo R, Puiggròs M, Moncunill V, Fragkogianni S, Clarke L, BLUEPRINT Consortium, Flicek P, Rico D, Torrents D, Carrillo de Santa Pau E, Valencia A. Cell systems Volume 3 (2016) p.491-495.e5 DOI: 10.1016/j.cels.2016.10.021
*
Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation
Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird MR, Longden I, Proctor G, Searle S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P. Preprint DOI: 10.1101/087239
Measures for interoperability of phenotypic data: minimum information requirements and formatting.
Ćwiek-Kupczyńska H, Altmann T, Arend D, Arnaud E, Chen D, Cornut G, Fiorani F, Frohmberg W, Junker A, Klukas C, Lange M, Mazurek C, Nafissi A, Neveu P, van Oeveren J, Pommier C, Poorter H, Rocca-Serra P, Sansone SA, Scholz U, van Schriek M, Seren Ü, Usadel B, Weise S, Kersey P, Krajewski P. Plant Methods Volume 12 (2016) p.44 DOI: 10.1186/s13007-016-0144-4
*
GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
Iotchkova V, Ritchie GR, Geihs M, Morganella S, Min JL, Walter K, Timpson NJ, Dunham I, Birney E, Soranzo N, UK10K Consortium. Preprint DOI: 10.1101/085738
Erratum to: Making sense of big data in health research: towards an EU action plan.
Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G. Genome medicine Volume 8 (2016) p.118 DOI: 10.1186/s13073-016-0376-y
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.
Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, Wishart DS. Journal of cheminformatics Volume 8 (2016) p.61 DOI: 10.1186/s13321-016-0174-y
The Mighty Fruit Fly Moves into Outbred Genetics.
Birney E. PLoS genetics Volume 12 (2016) p.e1006388 DOI: 10.1371/journal.pgen.1006388
eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data.
Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JHA, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S. Cell reports Volume 17 (2016) p.2137-2150 DOI: 10.1016/j.celrep.2016.10.059
Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems.
Schuyler RP, Merkel A, Raineri E, Altucci L, Vellenga E, Martens JHA, Pourfarzad F, Kuijpers TW, Burden F, Farrow S, Downes K, Ouwehand WH, Clarke L, Datta A, Lowy E, Flicek P, Frontini M, Stunnenberg HG, Martín-Subero JI, Gut I, Heath S. Cell reports Volume 17 (2016) p.2101-2111 DOI: 10.1016/j.celrep.2016.10.054
OmniPath: guidelines and gateway for literature-curated signaling pathway resources.
Türei D, Korcsmáros T, Saez-Rodriguez J. Nature methods Volume 13 (2016) p.966-967 DOI: 10.1038/nmeth.4077
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.
Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N. Cell Volume 167 (2016) p.1398-1414.e24 DOI: 10.1016/j.cell.2016.10.026
SPLASH, a hashed identifier for mass spectra.
Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O. Nature biotechnology Volume 34 (2016) p.1099-1101 DOI: 10.1038/nbt.3689
*
Genome-wide association analysis of pain severity in dysmenorrhea identifies association at chromosome 1p13.2, near the nerve growth factor locus.
Jones AV, Hockley JR, Hyde C, Gorman D, Sredic-Rhodes A, Bilsland J, McMurray G, Furlotte NA, Hu Y, Hinds DA, Cox PJ, Scollen S. Pain Volume 157 (2016) p.2571-2581 DOI: 10.1097/j.pain.0000000000000678
*
RUNX1 mutations in acute myeloid leukemia are associated with distinct clinico-pathologic and genetic features.
Gaidzik VI, Teleanu V, Papaemmanuil E, Weber D, Paschka P, Hahn J, Wallrabenstein T, Kolbinger B, Köhne CH, Horst HA, Brossart P, Held G, Kündgen A, Ringhoffer M, Götze K, Rummel M, Gerstung M, Campbell P, Kraus JM, Kestler HA, Thol F, Heuser M, Schlegelberger B, Ganser A, Bullinger L, Schlenk RF, Döhner K, Döhner H. Leukemia Volume 30 (2016) p.2282 DOI: 10.1038/leu.2016.207
Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium.
Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP, Moreno P, Verma D, Hill E, Drijkoningen J, Gilligan P, Esther CR, Noone PG, Giddings O, Bell SC, Thomson R, Wainwright CE, Coulter C, Pandey S, Wood ME, Stockwell RE, Ramsay KA, Sherrard LJ, Kidd TJ, Jabbour N, Johnson GR, Knibbs LD, Morawska L, Sly PD, Jones A, Bilton D, Laurenson I, Ruddy M, Bourke S, Bowler IC, Chapman SJ, Clayton A, Cullen M, Daniels T, Dempsey O, Denton M, Desai M, Drew RJ, Edenborough F, Evans J, Folb J, Humphrey H, Isalska B, Jensen-Fangel S, Jönsson B, Jones AM, Katzenstein TL, Lillebaek T, MacGregor G, Mayell S, Millar M, Modha D, Nash EF, O'Brien C, O'Brien D, Ohri C, Pao CS, Peckham D, Perrin F, Perry A, Pressler T, Prtak L, Qvist T, Robb A, Rodgers H, Schaffer K, Shafi N, van Ingen J, Walshaw M, Watson D, West N, Whitehouse J, Haworth CS, Harris SR, Ordway D, Parkhill J, Floto RA. Science (New York, N.Y.) Volume 354 (2016) p.751-757 DOI: 10.1126/science.aaf8156
*
The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.
Stunnenberg HG, International Human Epigenome Consortium, Hirst M. Cell Volume 167 (2016) p.1145-1149 DOI: 10.1016/j.cell.2016.11.007
Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.
Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F, BLUEPRINT Consortium, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P. Cell Volume 167 (2016) p.1369-1384.e19 DOI: 10.1016/j.cell.2016.09.037
Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage.
Queirós AC, Beekman R, Vilarrasa-Blasi R, Duran-Ferrer M, Clot G, Merkel A, Raineri E, Russiñol N, Castellano G, Beà S, Navarro A, Kulis M, Verdaguer-Dot N, Jares P, Enjuanes A, Calasanz MJ, Bergmann A, Vater I, Salaverría I, van de Werken HJG, Wilson WH, Datta A, Flicek P, Royo R, Martens J, Giné E, Lopez-Guillermo A, Stunnenberg HG, Klapper W, Pott C, Heath S, Gut IG, Siebert R, Campo E, Martín-Subero JI. Cancer cell Volume 30 (2016) p.806-821 DOI: 10.1016/j.ccell.2016.09.014
Gramene Database: Navigating Plant Comparative Genomics Resources.
Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P. Current plant biology Volume 7-8 (2016) p.10-15 DOI: 10.1016/j.cpb.2016.12.005
The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.
Astle WJ, Elding H, Jiang T, Allen D, Ruklisa D, Mann AL, Mead D, Bouman H, Riveros-Mckay F, Kostadima MA, Lambourne JJ, Sivapalaratnam S, Downes K, Kundu K, Bomba L, Berentsen K, Bradley JR, Daugherty LC, Delaneau O, Freson K, Garner SF, Grassi L, Guerrero J, Haimel M, Janssen-Megens EM, Kaan A, Kamat M, Kim B, Mandoli A, Marchini J, Martens JHA, Meacham S, Megy K, O'Connell J, Petersen R, Sharifi N, Sheard SM, Staley JR, Tuna S, van der Ent M, Walter K, Wang SY, Wheeler E, Wilder SP, Iotchkova V, Moore C, Sambrook J, Stunnenberg HG, Di Angelantonio E, Kaptoge S, Kuijpers TW, Carrillo-de-Santa-Pau E, Juan D, Rico D, Valencia A, Chen L, Ge B, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yang Y, Guigo R, Beck S, Paul DS, Pastinen T, Bujold D, Bourque G, Frontini M, Danesh J, Roberts DJ, Ouwehand WH, Butterworth AS, Soranzo N. Cell Volume 167 (2016) p.1415-1429.e19 DOI: 10.1016/j.cell.2016.10.042
β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance.
Novakovic B, Habibi E, Wang SY, Arts RJW, Davar R, Megchelenbrink W, Kim B, Kuznetsova T, Kox M, Zwaag J, Matarese F, van Heeringen SJ, Janssen-Megens EM, Sharifi N, Wang C, Keramati F, Schoonenberg V, Flicek P, Clarke L, Pickkers P, Heath S, Gut I, Netea MG, Martens JHA, Logie C, Stunnenberg HG. Cell Volume 167 (2016) p.1354-1368.e14 DOI: 10.1016/j.cell.2016.09.034
Plant Reactome: a resource for plant pathways and comparative analysis.
Naithani S, Preece J, D'Eustachio P, Gupta P, Amarasinghe V, Dharmawardhana PD, Wu G, Fabregat A, Elser JL, Weiser J, Keays M, Fuentes AM, Petryszak R, Stein LD, Ware D, Jaiswal P. Nucleic acids research Volume 45 (2017) p.D1029-D1039 DOI: 10.1093/nar/gkw932
Genenames.org: the HGNC and VGNC resources in 2017.
Yates B, Braschi B, Gray KA, Seal RL, Tweedie S, Bruford EA. Nucleic acids research Volume 45 (2017) p.D619-D625 DOI: 10.1093/nar/gkw1033
*
RNAcentral: a comprehensive database of non-coding RNA sequences.
The RNAcentral Consortium. Nucleic acids research Volume 45 (2017) p.D128-D134 DOI: 10.1093/nar/gkw1008
Resolution of ab initio shapes determined from small-angle scattering.
Tuukkanen AT, Kleywegt GJ, Svergun DI. IUCrJ Volume 3 (2016) p.440-447 DOI: 10.1107/S2052252516016018
Updates in Rhea - an expert curated resource of biochemical reactions.
Morgat A, Lombardot T, Axelsen KB, Aimo L, Niknejad A, Hyka-Nouspikel N, Coudert E, Pozzato M, Pagni M, Moretti S, Rosanoff S, Onwubiko J, Bougueleret L, Xenarios I, Redaschi N, Bridge A. Nucleic acids research Volume 45 (2017) p.D415-D418 DOI: 10.1093/nar/gkw990
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.
Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA. Nucleic acids research Volume 45 (2017) p.D1100-D1106 DOI: 10.1093/nar/gkw936
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.
Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y. Nucleic acids research Volume 45 (2017) p.D347-D352 DOI: 10.1093/nar/gkw918
The human-induced pluripotent stem cell initiative-data resources for cellular genetics.
Streeter I, Harrison PW, Faulconbridge A, The HipSci Consortium, Flicek P, Parkinson H, Clarke L. Nucleic acids research Volume 45 (2017) p.D691-D697 DOI: 10.1093/nar/gkw928
*
Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain AS, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon AF, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C, PANGEA-HIV Consortium. Molecular biology and evolution Volume 34 (2017) p.185-203 DOI: 10.1093/molbev/msw217
A multicenter study benchmarks software tools for label-free proteome quantification.
Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S. Nature biotechnology Volume 34 (2016) p.1130-1136 DOI: 10.1038/nbt.3685
ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions.
Marenco L, Wang R, McDougal R, Olender T, Twik M, Bruford E, Liu X, Zhang J, Lancet D, Shepherd G, Crasto C. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw132
A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia.
Tzelepis K, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, Mupo A, Grinkevich V, Li M, Mazan M, Gozdecka M, Ohnishi S, Cooper J, Patel M, McKerrell T, Chen B, Domingues AF, Gallipoli P, Teichmann S, Ponstingl H, McDermott U, Saez-Rodriguez J, Huntly BJP, Iorio F, Pina C, Vassiliou GS, Yusa K. Cell reports Volume 17 (2016) p.1193-1205 DOI: 10.1016/j.celrep.2016.09.079
Evolution of protein phosphorylation across 18 fungal species.
Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Viéitez C, Solé C, Swaney DL, Stanford LB, Liachko I, Böttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villén J. Science (New York, N.Y.) Volume 354 (2016) p.229-232 DOI: 10.1126/science.aaf2144
Identifying ELIXIR Core Data Resources.
Durinx C, McEntyre J, Appel R, Apweiler R, Barlow M, Blomberg N, Cook C, Gasteiger E, Kim JH, Lopez R, Redaschi N, Stockinger H, Teixeira D, Valencia A. F1000Research Volume 5 (2016) DOI: 10.12688/f1000research.9656.2
2016 update of the PRIDE database and its related tools.
Vizcaíno JA, Csordas A, Del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H. Nucleic acids research Volume 44 (2016) p.11033 DOI: 10.1093/nar/gkw880
A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL.
Mutowo P, Bento AP, Dedman N, Gaulton A, Hersey A, Lomax J, Overington JP. Journal of biomedical semantics Volume 7 (2016) p.59 DOI: 10.1186/s13326-016-0102-0
*
Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich
Iorio F, Garcia-Alonso L, Brammeld JS, Martincorena I, Wille DR, McDermott U, Saez-Rodriguez J. Preprint DOI: 10.1101/077701
Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.
Smid M, Rodríguez-González FG, Sieuwerts AM, Salgado R, Prager-Van der Smissen WJ, Vlugt-Daane MV, van Galen A, Nik-Zainal S, Staaf J, Brinkman AB, van de Vijver MJ, Richardson AL, Fatima A, Berentsen K, Butler A, Martin S, Davies HR, Debets R, Gelder ME, van Deurzen CH, MacGrogan G, Van den Eynden GG, Purdie C, Thompson AM, Caldas C, Span PN, Simpson PT, Lakhani SR, Van Laere S, Desmedt C, Ringnér M, Tommasi S, Eyford J, Broeks A, Vincent-Salomon A, Futreal PA, Knappskog S, King T, Thomas G, Viari A, Langerød A, Børresen-Dale AL, Birney E, Stunnenberg HG, Stratton M, Foekens JA, Martens JW. Nature communications Volume 7 (2016) p.12910 DOI: 10.1038/ncomms12910
Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps.
Iotchkova V, Huang J, Morris JA, Jain D, Barbieri C, Walter K, Min JL, Chen L, Astle W, Cocca M, Deelen P, Elding H, Farmaki AE, Franklin CS, Franberg M, Gaunt TR, Hofman A, Jiang T, Kleber ME, Lachance G, Luan J, Malerba G, Matchan A, Mead D, Memari Y, Ntalla I, Panoutsopoulou K, Pazoki R, Perry JRB, Rivadeneira F, Sabater-Lleal M, Sennblad B, Shin SY, Southam L, Traglia M, van Dijk F, van Leeuwen EM, Zaza G, Zhang W, UK10K Consortium, Amin N, Butterworth A, Chambers JC, Dedoussis G, Dehghan A, Franco OH, Franke L, Frontini M, Gambaro G, Gasparini P, Hamsten A, Issacs A, Kooner JS, Kooperberg C, Langenberg C, Marz W, Scott RA, Swertz MA, Toniolo D, Uitterlinden AG, van Duijn CM, Watkins H, Zeggini E, Maurano MT, Timpson NJ, Reiner AP, Auer PL, Soranzo N. Nature genetics Volume 48 (2016) p.1303-1312 DOI: 10.1038/ng.3668
Selenoprotein Gene Nomenclature.
Gladyshev VN, Arnér ES, Berry MJ, Brigelius-Flohé R, Bruford EA, Burk RF, Carlson BA, Castellano S, Chavatte L, Conrad M, Copeland PR, Diamond AM, Driscoll DM, Ferreiro A, Flohé L, Green FR, Guigó R, Handy DE, Hatfield DL, Hesketh J, Hoffmann PR, Holmgren A, Hondal RJ, Howard MT, Huang K, Kim HY, Kim IY, Köhrle J, Krol A, Kryukov GV, Lee BJ, Lee BC, Lei XG, Liu Q, Lescure A, Lobanov AV, Loscalzo J, Maiorino M, Mariotti M, Sandeep Prabhu K, Rayman MP, Rozovsky S, Salinas G, Schmidt EE, Schomburg L, Schweizer U, Simonović M, Sunde RA, Tsuji PA, Tweedie S, Ursini F, Whanger PD, Zhang Y. The Journal of biological chemistry Volume 291 (2016) p.24036-24040 DOI: 10.1074/jbc.M116.756155
First Draft Genome Sequence of a UK Strain (UK99) of Fusarium culmorum.
Urban M, King R, Andongabo A, Maheswari U, Pedro H, Kersey P, Hammond-Kosack K. Genome announcements Volume 4 (2016) DOI: 10.1128/genomeA.00771-16
Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence.
Garin-Muga A, Odriozola L, Martínez-Val A, Del Toro N, Martínez R, Molina M, Cantero L, Rivera R, Garrido N, Dominguez F, Sanchez Del Pino MM, Vizcaíno JA, Corrales FJ, Segura V. Journal of proteome research Volume 15 (2016) p.4101-4115 DOI: 10.1021/acs.jproteome.6b00437
The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.
Clarke L, Fairley S, Zheng-Bradley X, Streeter I, Perry E, Lowy E, Tassé AM, Flicek P. Nucleic acids research Volume 45 (2017) p.D854-D859 DOI: 10.1093/nar/gkw829
High-throughput discovery of novel developmental phenotypes.
Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie SM, Fuchs H, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Newbigging S, Nutter LM, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, International Mouse Phenotyping Consortium, Jackson Laboratory, Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS), Charles River Laboratories, MRC Harwell, Toronto Centre for Phenogenomics, Wellcome Trust Sanger Institute, RIKEN BioResource Center, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SD, Adams DJ, Lloyd KC, McKerlie C, Beaudet AL, Bućan M, Murray SA. Nature Volume 537 (2016) p.508-514 DOI: 10.1038/nature19356
Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles.
Williamson AE, Ylioja PM, Robertson MN, Antonova-Koch Y, Avery V, Baell JB, Batchu H, Batra S, Burrows JN, Bhattacharyya S, Calderon F, Charman SA, Clark J, Crespo B, Dean M, Debbert SL, Delves M, Dennis AS, Deroose F, Duffy S, Fletcher S, Giaever G, Hallyburton I, Gamo FJ, Gebbia M, Guy RK, Hungerford Z, Kirk K, Lafuente-Monasterio MJ, Lee A, Meister S, Nislow C, Overington JP, Papadatos G, Patiny L, Pham J, Ralph SA, Ruecker A, Ryan E, Southan C, Srivastava K, Swain C, Tarnowski MJ, Thomson P, Turner P, Wallace IM, Wells TN, White K, White L, Willis P, Winzeler EA, Wittlin S, Todd MH. ACS central science Volume 2 (2016) p.687-701 DOI: 10.1021/acscentsci.6b00086
*
Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation
Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MSF, Fogg LG, Stubbington MJT, Otzen Bagger F, Zwiessele M, Lawrence N, Souza-Fonseca- Guimaraes F, Heath WR, Billker O, Stegle O, Haque A, Teichmann SA. Preprint DOI: 10.1101/074971
*
Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.
Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A, GEUVADIS Consortium, Rosenstiel P, Strom TM, Lappalainen T, Guigó R, Sammeth M. Scientific reports Volume 6 (2016) p.32406 DOI: 10.1038/srep32406
Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.
Speranzini V, Rotili D, Ciossani G, Pilotto S, Marrocco B, Forgione M, Lucidi A, Forneris F, Mehdipour P, Velankar S, Mai A, Mattevi A. Science advances Volume 2 (2016) p.e1601017 DOI: 10.1126/sciadv.1601017
*
Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data
Lun AT, Marioni JC. Preprint DOI: 10.1101/073973
*
Power Analysis of Single Cell RNA‐Sequencing Experiments
Svensson V, Natarajan KN, Ly L, Miragaia RJ, Labalette C, Macaulay IC, Cvejic A, Teichmann SA. Preprint DOI: 10.1101/073692
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P. Genome biology Volume 17 (2016) p.184 DOI: 10.1186/s13059-016-1037-6
*
Warped Matrix Factorisation for Multi-view Data Integration
Pratanwanich N, Lió P, Stegle O. Machine Learning and Knowledge Discovery in Databases. ECML PKDD 2016. Springer , Cham (Lecture Notes in Computer Science, vol 9852) DOI: 10.1007/978-3-319-46227-1_49
Overview of the interactive task in BioCreative V.
Wang Q, S Abdul S, Almeida L, Ananiadou S, Balderas-Martínez YI, Batista-Navarro R, Campos D, Chilton L, Chou HJ, Contreras G, Cooper L, Dai HJ, Ferrell B, Fluck J, Gama-Castro S, George N, Gkoutos G, Irin AK, Jensen LJ, Jimenez S, Jue TR, Keseler I, Madan S, Matos S, McQuilton P, Milacic M, Mort M, Natarajan J, Pafilis E, Pereira E, Rao S, Rinaldi F, Rothfels K, Salgado D, Silva RM, Singh O, Stefancsik R, Su CH, Subramani S, Tadepally HD, Tsaprouni L, Vasilevsky N, Wang X, Chatr-Aryamontri A, Laulederkind SJ, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Wu CH, Hirschman L, Arighi CN. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw119
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.
Lun AT, McCarthy DJ, Marioni JC. F1000Research Volume 5 (2016) p.2122 DOI: 10.12688/f1000research.9501.2
Pleiotropic Analysis of Lung Cancer and Blood Triglycerides.
Zuber V, Marconett CN, Shi J, Hua X, Wheeler W, Yang C, Song L, Dale AM, Laplana M, Risch A, Witoelar A, Thompson WK, Schork AJ, Bettella F, Wang Y, Djurovic S, Zhou B, Borok Z, van der Heijden HF, de Graaf J, Swinkels D, Aben KK, McKay J, Hung RJ, Bikeböller H, Stevens VL, Albanes D, Caporaso NE, Han Y, Wei Y, Panadero MA, Mayordomo JI, Christiani DC, Kiemeney L, Andreassen OA, Houlston R, Amos CI, Chatterjee N, Laird-Offringa IA, Mills IG, Landi MT. Journal of the National Cancer Institute Volume 108 (2016) DOI: 10.1093/jnci/djw167
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.
Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS. Journal of proteome research Volume 15 (2016) p.3961-3970 DOI: 10.1021/acs.jproteome.6b00392
The health care and life sciences community profile for dataset descriptions.
Dumontier M, Gray AJG, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall CJ, Rietveld L, Wimalaratne SM, Yamaguchi A. PeerJ Volume 4 (2016) p.e2331 DOI: 10.7717/peerj.2331
Top 10 metrics for life science software good practices.
Artaza H, Chue Hong N, Corpas M, Corpuz A, Hooft R, Jimenez RC, Leskošek B, Olivier BG, Stourac J, Svobodová Vařeková R, Van Parys T, Vaughan D. F1000Research Volume 5 (2016) DOI: 10.12688/f1000research.9206.1
Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design?
Christmann-Franck S, van Westen GJ, Papadatos G, Beltran Escudie F, Roberts A, Overington JP, Domine D. Journal of chemical information and modeling Volume 56 (2016) p.1654-1675 DOI: 10.1021/acs.jcim.6b00122
In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.
Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y. Journal of proteomics Volume 150 (2017) p.170-182 DOI: 10.1016/j.jprot.2016.08.002
Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition.
Sciacovelli M, Gonçalves E, Johnson TI, Zecchini VR, da Costa AS, Gaude E, Drubbel AV, Theobald SJ, Abbo SR, Tran MG, Rajeeve V, Cardaci S, Foster S, Yun H, Cutillas P, Warren A, Gnanapragasam V, Gottlieb E, Franze K, Huntly B, Maher ER, Maxwell PH, Saez-Rodriguez J, Frezza C. Nature Volume 537 (2016) p.544-547 DOI: 10.1038/nature19353
Deep learning for computational biology.
Angermueller C, Pärnamaa T, Parts L, Stegle O. Molecular systems biology Volume 12 (2016) p.878 DOI: 10.15252/msb.20156651
Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond.
Van Voorhis WC, Adams JH, Adelfio R, Ahyong V, Akabas MH, Alano P, Alday A, Alemán Resto Y, Alsibaee A, Alzualde A, Andrews KT, Avery SV, Avery VM, Ayong L, Baker M, Baker S, Ben Mamoun C, Bhatia S, Bickle Q, Bounaadja L, Bowling T, Bosch J, Boucher LE, Boyom FF, Brea J, Brennan M, Burton A, Caffrey CR, Camarda G, Carrasquilla M, Carter D, Belen Cassera M, Chih-Chien Cheng K, Chindaudomsate W, Chubb A, Colon BL, Colón-López DD, Corbett Y, Crowther GJ, Cowan N, D'Alessandro S, Le Dang N, Delves M, DeRisi JL, Du AY, Duffy S, Abd El-Salam El-Sayed S, Ferdig MT, Fernández Robledo JA, Fidock DA, Florent I, Fokou PV, Galstian A, Gamo FJ, Gokool S, Gold B, Golub T, Goldgof GM, Guha R, Guiguemde WA, Gural N, Guy RK, Hansen MA, Hanson KK, Hemphill A, Hooft van Huijsduijnen R, Horii T, Horrocks P, Hughes TB, Huston C, Igarashi I, Ingram-Sieber K, Itoe MA, Jadhav A, Naranuntarat Jensen A, Jensen LT, Jiang RH, Kaiser A, Keiser J, Ketas T, Kicka S, Kim S, Kirk K, Kumar VP, Kyle DE, Lafuente MJ, Landfear S, Lee N, Lee S, Lehane AM, Li F, Little D, Liu L, Llinás M, Loza MI, Lubar A, Lucantoni L, Lucet I, Maes L, Mancama D, Mansour NR, March S, McGowan S, Medina Vera I, Meister S, Mercer L, Mestres J, Mfopa AN, Misra RN, Moon S, Moore JP, Morais Rodrigues da Costa F, Müller J, Muriana A, Nakazawa Hewitt S, Nare B, Nathan C, Narraidoo N, Nawaratna S, Ojo KK, Ortiz D, Panic G, Papadatos G, Parapini S, Patra K, Pham N, Prats S, Plouffe DM, Poulsen SA, Pradhan A, Quevedo C, Quinn RJ, Rice CA, Abdo Rizk M, Ruecker A, St Onge R, Salgado Ferreira R, Samra J, Robinett NG, Schlecht U, Schmitt M, Silva Villela F, Silvestrini F, Sinden R, Smith DA, Soldati T, Spitzmüller A, Stamm SM, Sullivan DJ, Sullivan W, Suresh S, Suzuki BM, Suzuki Y, Swamidass SJ, Taramelli D, Tchokouaha LR, Theron A, Thomas D, Tonissen KF, Townson S, Tripathi AK, Trofimov V, Udenze KO, Ullah I, Vallieres C, Vigil E, Vinetz JM, Voong Vinh P, Vu H, Watanabe NA, Weatherby K, White PM, Wilks AF, Winzeler EA, Wojcik E, Wree M, Wu W, Yokoyama N, Zollo PH, Abla N, Blasco B, Burrows J, Laleu B, Leroy D, Spangenberg T, Wells T, Willis PA. PLoS pathogens Volume 12 (2016) p.e1005763 DOI: 10.1371/journal.ppat.1005763
Sall4 controls differentiation of pluripotent cells independently of the Nucleosome Remodelling and Deacetylation (NuRD) complex.
Miller A, Ralser M, Kloet SL, Loos R, Nishinakamura R, Bertone P, Vermeulen M, Hendrich B. Development (Cambridge, England) Volume 143 (2016) p.3074-3084 DOI: 10.1242/dev.139113
*
Phosphoproteomics-based Profiling of Kinase Activities in Cancer Cells
Wirbel J, Rodriguez Cutillas P, Saez-Rodriguez J. Preprint DOI: 10.1101/066019
GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes.
Tuggle CK, Giuffra E, White SN, Clarke L, Zhou H, Ross PJ, Acloque H, Reecy JM, Archibald A, Bellone RR, Boichard M, Chamberlain A, Cheng H, Crooijmans RP, Delany ME, Finno CJ, Groenen MA, Hayes B, Lunney JK, Petersen JL, Plastow GS, Schmidt CJ, Song J, Watson M. Animal genetics Volume 47 (2016) p.528-533 DOI: 10.1111/age.12466
Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti.
diCenzo GC, Checcucci A, Bazzicalupo M, Mengoni A, Viti C, Dziewit L, Finan TM, Galardini M, Fondi M. Nature communications Volume 7 (2016) p.12219 DOI: 10.1038/ncomms12219
The archiving and dissemination of biological structure data.
Berman HM, Burley SK, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. Current opinion in structural biology Volume 40 (2016) p.17-22 DOI: 10.1016/j.sbi.2016.06.018
Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks.
Muetze T, Goenawan IH, Wiencko HL, Bernal-Llinares M, Bryan K, Lynn DJ. F1000Research Volume 5 (2016) p.1745 DOI: 10.12688/f1000research.9118.2
Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases.
Mascotti ML, Juri Ayub M, Furnham N, Thornton JM, Laskowski RA. Journal of molecular biology Volume 428 (2016) p.3131-3146 DOI: 10.1016/j.jmb.2016.07.003
Ten Simple Rules for Taking Advantage of Git and GitHub.
Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost Fda V, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaíno JA. PLoS computational biology Volume 12 (2016) p.e1004947 DOI: 10.1371/journal.pcbi.1004947
Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana.
Meng D, Dubin M, Zhang P, Osborne EJ, Stegle O, Clark RM, Nordborg M. PLoS genetics Volume 12 (2016) p.e1006141 DOI: 10.1371/journal.pgen.1006141
*
The genetic architecture of type 2 diabetes.
Fuchsberger C, Flannick J, Teslovich TM, Mahajan A, Agarwala V, Gaulton KJ, Ma C, Fontanillas P, Moutsianas L, McCarthy DJ, Rivas MA, Perry JRB, Sim X, Blackwell TW, Robertson NR, Rayner NW, Cingolani P, Locke AE, Tajes JF, Highland HM, Dupuis J, Chines PS, Lindgren CM, Hartl C, Jackson AU, Chen H, Huyghe JR, van de Bunt M, Pearson RD, Kumar A, Müller-Nurasyid M, Grarup N, Stringham HM, Gamazon ER, Lee J, Chen Y, Scott RA, Below JE, Chen P, Huang J, Go MJ, Stitzel ML, Pasko D, Parker SCJ, Varga TV, Green T, Beer NL, Day-Williams AG, Ferreira T, Fingerlin T, Horikoshi M, Hu C, Huh I, Ikram MK, Kim BJ, Kim Y, Kim YJ, Kwon MS, Lee J, Lee S, Lin KH, Maxwell TJ, Nagai Y, Wang X, Welch RP, Yoon J, Zhang W, Barzilai N, Voight BF, Han BG, Jenkinson CP, Kuulasmaa T, Kuusisto J, Manning A, Ng MCY, Palmer ND, Balkau B, Stančáková A, Abboud HE, Boeing H, Giedraitis V, Prabhakaran D, Gottesman O, Scott J, Carey J, Kwan P, Grant G, Smith JD, Neale BM, Purcell S, Butterworth AS, Howson JMM, Lee HM, Lu Y, Kwak SH, Zhao W, Danesh J, Lam VKL, Park KS, Saleheen D, So WY, Tam CHT, Afzal U, Aguilar D, Arya R, Aung T, Chan E, Navarro C, Cheng CY, Palli D, Correa A, Curran JE, Rybin D, Farook VS, Fowler SP, Freedman BI, Griswold M, Hale DE, Hicks PJ, Khor CC, Kumar S, Lehne B, Thuillier D, Lim WY, Liu J, van der Schouw YT, Loh M, Musani SK, Puppala S, Scott WR, Yengo L, Tan ST, Taylor HA, Thameem F, Wilson G, Wong TY, Njølstad PR, Levy JC, Mangino M, Bonnycastle LL, Schwarzmayr T, Fadista J, Surdulescu GL, Herder C, Groves CJ, Wieland T, Bork-Jensen J, Brandslund I, Christensen C, Koistinen HA, Doney ASF, Kinnunen L, Esko T, Farmer AJ, Hakaste L, Hodgkiss D, Kravic J, Lyssenko V, Hollensted M, Jørgensen ME, Jørgensen T, Ladenvall C, Justesen JM, Käräjämäki A, Kriebel J, Rathmann W, Lannfelt L, Lauritzen T, Narisu N, Linneberg A, Melander O, Milani L, Neville M, Orho-Melander M, Qi L, Qi Q, Roden M, Rolandsson O, Swift A, Rosengren AH, Stirrups K, Wood AR, Mihailov E, Blancher C, Carneiro MO, Maguire J, Poplin R, Shakir K, Fennell T, DePristo M, de Angelis MH, Deloukas P, Gjesing AP, Jun G, Nilsson P, Murphy J, Onofrio R, Thorand B, Hansen T, Meisinger C, Hu FB, Isomaa B, Karpe F, Liang L, Peters A, Huth C, O'Rahilly SP, Palmer CNA, Pedersen O, Rauramaa R, Tuomilehto J, Salomaa V, Watanabe RM, Syvänen AC, Bergman RN, Bharadwaj D, Bottinger EP, Cho YS, Chandak GR, Chan JCN, Chia KS, Daly MJ, Ebrahim SB, Langenberg C, Elliott P, Jablonski KA, Lehman DM, Jia W, Ma RCW, Pollin TI, Sandhu M, Tandon N, Froguel P, Barroso I, Teo YY, Zeggini E, Loos RJF, Small KS, Ried JS, DeFronzo RA, Grallert H, Glaser B, Metspalu A, Wareham NJ, Walker M, Banks E, Gieger C, Ingelsson E, Im HK, Illig T, Franks PW, Buck G, Trakalo J, Buck D, Prokopenko I, Mägi R, Lind L, Farjoun Y, Owen KR, Gloyn AL, Strauch K, Tuomi T, Kooner JS, Lee JY, Park T, Donnelly P, Morris AD, Hattersley AT, Bowden DW, Collins FS, Atzmon G, Chambers JC, Spector TD, Laakso M, Strom TM, Bell GI, Blangero J, Duggirala R, Tai ES, McVean G, Hanis CL, Wilson JG, Seielstad M, Frayling TM, Meigs JB, Cox NJ, Sladek R, Lander ES, Gabriel S, Burtt NP, Mohlke KL, Meitinger T, Groop L, Abecasis G, Florez JC, Scott LJ, Morris AP, Kang HM, Boehnke M, Altshuler D, McCarthy MI. Nature Volume 536 (2016) p.41-47 DOI: 10.1038/nature18642
Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining.
Boudellioua I, Saidi R, Hoehndorf R, Martin MJ, Solovyev V. PloS one Volume 11 (2016) p.e0158896 DOI: 10.1371/journal.pone.0158896
A Landscape of Pharmacogenomic Interactions in Cancer.
Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U, Garnett MJ. Cell Volume 166 (2016) p.740-754 DOI: 10.1016/j.cell.2016.06.017
Resolving early mesoderm diversification through single-cell expression profiling.
Scialdone A, Tanaka Y, Jawaid W, Moignard V, Wilson NK, Macaulay IC, Marioni JC, Göttgens B. Nature Volume 535 (2016) p.289-293 DOI: 10.1038/nature18633
Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis.
Jakubec D, Laskowski RA, Vondrasek J. PloS one Volume 11 (2016) p.e0158704 DOI: 10.1371/journal.pone.0158704
Letter to the editor for "Update of the human and mouse Fanconi anemia genes".
Nebert DW, Dong H, Bruford EA, Thompson DC, Joenje H, Vasiliou V. Human genomics Volume 10 (2016) p.25 DOI: 10.1186/s40246-016-0081-3
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ. Journal of biomedical semantics Volume 7 (2016) p.44 DOI: 10.1186/s13326-016-0088-7
The Evolutionary Fates of a Large Segmental Duplication in Mouse.
Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AM, Didion JP, Yadgary L, Thybert D, Odom DT, Flicek P, McMillan L, de Villena FP. Genetics Volume 204 (2016) p.267-285 DOI: 10.1534/genetics.116.191007
Using the Gene Ontology to Annotate Key Players in Parkinson's Disease.
Foulger RE, Denny P, Hardy J, Martin MJ, Sawford T, Lovering RC. Neuroinformatics Volume 14 (2016) p.297-304 DOI: 10.1007/s12021-015-9293-2
EphrinB2 drives perivascular invasion and proliferation of glioblastoma stem-like cells.
Krusche B, Ottone C, Clements MP, Johnstone ER, Goetsch K, Lieven H, Mota SG, Singh P, Khadayate S, Ashraf A, Davies T, Pollard SM, De Paola V, Roncaroli F, Martinez-Torrecuadrada J, Bertone P, Parrinello S. eLife Volume 5 (2016) DOI: 10.7554/eLife.14845
Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.
Griss J, Perez-Riverol Y, Lewis S, Tabb DL, Dianes JA, Del-Toro N, Rurik M, Walzer MW, Kohlbacher O, Hermjakob H, Wang R, Vizcaíno JA. Nature methods Volume 13 (2016) p.651-656 DOI: 10.1038/nmeth.3902
Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data.
Rensch T, Villar D, Horvath J, Odom DT, Flicek P. Genome biology Volume 17 (2016) p.139 DOI: 10.1186/s13059-016-0996-y
GeneCodeq: quality score compression and improved genotyping using a Bayesian framework.
Greenfield DL, Stegle O, Rrustemi A. Bioinformatics (Oxford, England) Volume 32 (2016) p.3124-3132 DOI: 10.1093/bioinformatics/btw385
Task-Related Edge Density (TED)-A New Method for Revealing Dynamic Network Formation in fMRI Data of the Human Brain.
Lohmann G, Stelzer J, Zuber V, Buschmann T, Margulies D, Bartels A, Scheffler K. PloS one Volume 11 (2016) p.e0158185 DOI: 10.1371/journal.pone.0158185
Making sense of big data in health research: Towards an EU action plan.
Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G. Genome medicine Volume 8 (2016) p.71 DOI: 10.1186/s13073-016-0323-y
Epigenome-wide Association Studies and the Interpretation of Disease -Omics.
Birney E, Smith GD, Greally JM. PLoS genetics Volume 12 (2016) p.e1006105 DOI: 10.1371/journal.pgen.1006105
*
Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast
Gonçalves E, Raguz Z, Zampieri M, Wagih O, Ochoa D, Sauer U, Beltrao P, Saez-Rodriguez J. Preprint DOI: 10.1101/057398
The Ensembl gene annotation system.
Aken BL, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S, Fernandez Banet J, Billis K, García Girón C, Hourlier T, Howe K, Kähäri A, Kokocinski F, Martin FJ, Murphy DN, Nag R, Ruffier M, Schuster M, Tang YA, Vogel JH, White S, Zadissa A, Flicek P, Searle SM. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw093
*
Admixture into and within sub-Saharan Africa.
Busby GB, Band G, Si Le Q, Jallow M, Bougama E, Mangano VD, Amenga-Etego LN, Enimil A, Apinjoh T, Ndila CM, Manjurano A, Nyirongo V, Doumba O, Rockett KA, Kwiatkowski DP, Spencer CC, Malaria Genomic Epidemiology Network. eLife Volume 5 (2016) DOI: 10.7554/eLife.15266
*
PASP - a whole-transcriptome poly(A) tail length determination assay for the Illumina platform
Sipos B, Stütz AM, Slodkowicz G, Massingham T, Korbel J, Goldman N. Preprint DOI: 10.1101/060004
Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.
Torrente A, Lukk M, Xue V, Parkinson H, Rung J, Brazma A. PloS one Volume 11 (2016) p.e0157484 DOI: 10.1371/journal.pone.0157484
Promiscuous or discriminating: Has the favored mRNA target of Fragile X Mental Retardation Protein been overlooked?
McMahon AC, Rosbash M. Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.7009-7011 DOI: 10.1073/pnas.1607665113
Databases and Archiving for CryoEM.
Patwardhan A, Lawson CL. Methods in enzymology Volume 579 (2016) p.393-412 DOI: 10.1016/bs.mie.2016.04.015
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.
Cairns J, Freire-Pritchett P, Wingett SW, Várnai C, Dimond A, Plagnol V, Zerbino D, Schoenfelder S, Javierre BM, Osborne C, Fraser P, Spivakov M. Genome biology Volume 17 (2016) p.127 DOI: 10.1186/s13059-016-0992-2
Rising levels of atmospheric oxygen and evolution of Nrf2.
Gacesa R, Dunlap WC, Barlow DJ, Laskowski RA, Long PF. Scientific reports Volume 6 (2016) p.27740 DOI: 10.1038/srep27740
Mixed Nodule Infection in Sinorhizobium meliloti-Medicago sativa Symbiosis Suggest the Presence of Cheating Behavior.
Checcucci A, Azzarello E, Bazzicalupo M, Galardini M, Lagomarsino A, Mancuso S, Marti L, Marzano MC, Mocali S, Squartini A, Zanardo M, Mengoni A. Frontiers in plant science Volume 7 (2016) p.835 DOI: 10.3389/fpls.2016.00835
Strand-specific, high-resolution mapping of modified RNA polymerase II.
Milligan L, Huynh-Thu VA, Delan-Forino C, Tuck A, Petfalski E, Lombraña R, Sanguinetti G, Kudla G, Tollervey D. Molecular systems biology Volume 12 (2016) p.874 DOI: 10.15252/msb.20166869
PhenoImageShare: an image annotation and query infrastructure.
Adebayo S, McLeod K, Tudose I, Osumi-Sutherland D, Burdett T, Baldock R, Burger A, Parkinson H. Journal of biomedical semantics Volume 7 (2016) p.35 DOI: 10.1186/s13326-016-0072-2
HDTD: analyzing multi-tissue gene expression data.
Touloumis A, Marioni JC, Tavaré S. Bioinformatics (Oxford, England) Volume 32 (2016) p.2193-2195 DOI: 10.1093/bioinformatics/btw224
The Ensembl Variant Effect Predictor.
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. Genome biology Volume 17 (2016) p.122 DOI: 10.1186/s13059-016-0974-4
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.
Tripathi S, Vercruysse S, Chawla K, Christie KR, Blake JA, Huntley RP, Orchard S, Hermjakob H, Thommesen L, Lægreid A, Kuiper M. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw088
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS, Harrow J. Nature communications Volume 7 (2016) p.11778 DOI: 10.1038/ncomms11778
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Proteins Volume 84 Suppl 1 (2016) p.323-348 DOI: 10.1002/prot.25007
Advancing vector biology research: a community survey for future directions, research applications and infrastructure requirements.
Kohl A, Pondeville E, Schnettler E, Crisanti A, Supparo C, Christophides GK, Kersey PJ, Maslen GL, Takken W, Koenraadt CJ, Oliva CF, Busquets N, Abad FX, Failloux AB, Levashina EA, Wilson AJ, Veronesi E, Pichard M, Arnaud Marsh S, Simard F, Vernick KD. Pathogens and global health Volume 110 (2016) p.164-172 DOI: 10.1080/20477724.2016.1211475
A rule-based model of insulin signalling pathway.
Di Camillo B, Carlon A, Eduati F, Toffolo GM. BMC systems biology Volume 10 (2016) p.38 DOI: 10.1186/s12918-016-0281-4
*
GENOMICS. A federated ecosystem for sharing genomic, clinical data.
Global Alliance for Genomics and Health. Science (New York, N.Y.) Volume 352 (2016) p.1278-1280 DOI: 10.1126/science.aaf6162
*
ISMB 2016 Proceedings.
Baldi P, Przytycka T. Bioinformatics (Oxford, England) Volume 32 (2016) p.i1-i2 DOI: 10.1093/bioinformatics/btw326
Genomic Classification and Prognosis in Acute Myeloid Leukemia.
Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, Potter NE, Heuser M, Thol F, Bolli N, Gundem G, Van Loo P, Martincorena I, Ganly P, Mudie L, McLaren S, O'Meara S, Raine K, Jones DR, Teague JW, Butler AP, Greaves MF, Ganser A, Döhner K, Schlenk RF, Döhner H, Campbell PJ. The New England journal of medicine Volume 374 (2016) p.2209-2221 DOI: 10.1056/NEJMoa1516192
*
RAFTS3: Rapid Alignment-Free Tool for Sequence Similarity Search
Vialle RA, Pedrosa FO, Weiss VA, Guizelini D, Tibaes JH, Marchaukoski JN, de Souza EM, Raittz RT. Preprint DOI: 10.1101/055269
JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
Roll J, Zirbel CL, Sweeney B, Petrov AI, Leontis N. Nucleic acids research Volume 44 (2016) p.W320-7 DOI: 10.1093/nar/gkw453
*
Common genetic variation drives molecular heterogeneity in human iPSCs
Kilpinen H, Goncalves A, Leha A, Afzal V, Ashford S, Bala S, Bensaddek D, Casale FP, Culley O, Danacek P, Faulconbridge A, Harrison P, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Preprint DOI: 10.1101/055160
*
General control non-derepressible 2 (GCN2) in T cells controls disease progression of autoimmune neuroinflammation.
Keil M, Sonner JK, Lanz TV, Oezen I, Bunse T, Bittner S, Meyer HV, Meuth SG, Wick W, Platten M. Journal of neuroimmunology Volume 297 (2016) p.117-126 DOI: 10.1016/j.jneuroim.2016.05.014
spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.
Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A. Nucleic acids research Volume 44 (2016) p.W176-80 DOI: 10.1093/nar/gkw443
The cellular microscopy phenotype ontology.
Jupp S, Malone J, Burdett T, Heriche JK, Williams E, Ellenberg J, Parkinson H, Rustici G. Journal of biomedical semantics Volume 7 (2016) p.28 DOI: 10.1186/s13326-016-0074-0
HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.
Bryan K, Jarboui MA, Raso C, Bernal-Llinares M, McCann B, Rauch J, Boldt K, Lynn DJ. Journal of proteome research Volume 15 (2016) p.2072-2079 DOI: 10.1021/acs.jproteome.5b01008
Multilevel models improve precision and speed of IC50 estimates.
Vis DJ, Bombardelli L, Lightfoot H, Iorio F, Garnett MJ, Wessels LF. Pharmacogenomics Volume 17 (2016) p.691-700 DOI: 10.2217/pgs.16.15
Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).
Welch L, Brooksbank C, Schwartz R, Morgan SL, Gaeta B, Kilpatrick AM, Mietchen D, Moore BL, Mulder N, Pauley M, Pearson W, Radivojac P, Rosenberg N, Rosenwald A, Rustici G, Warnow T. PLoS computational biology Volume 12 (2016) p.e1004943 DOI: 10.1371/journal.pcbi.1004943
Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns.
Digles D, Zdrazil B, Neefs JM, Van Vlijmen H, Herhaus C, Caracoti A, Brea J, Roibás B, Loza MI, Queralt-Rosinach N, Furlong LI, Gaulton A, Bartek L, Senger S, Chichester C, Engkvist O, Evelo CT, Franklin NI, Marren D, Ecker GF, Jacoby E. MedChemComm Volume 7 (2016) p.1237-1244 DOI: 10.1039/c6md00065g
Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.
Rudolph KL, Schmitt BM, Villar D, White RJ, Marioni JC, Kutter C, Odom DT. PLoS genetics Volume 12 (2016) p.e1006024 DOI: 10.1371/journal.pgen.1006024
Subtype-specific micro-RNA expression signatures in breast cancer progression.
Haakensen VD, Nygaard V, Greger L, Aure MR, Fromm B, Bukholm IR, Lüders T, Chin SF, Git A, Caldas C, Kristensen VN, Brazma A, Børresen-Dale AL, Hovig E, Helland Å. International journal of cancer Volume 139 (2016) p.1117-1128 DOI: 10.1002/ijc.30142
BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.
Ryu J, Lee M, Cha J, Laskowski RA, Ryu SE, Kim DS. Nucleic acids research Volume 44 (2016) p.W416-23 DOI: 10.1093/nar/gkw368
Landscape of somatic mutations in 560 breast cancer whole-genome sequences.
Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GK, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van't Veer L, Tutt A, Knappskog S, Tan BK, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR. Nature Volume 534 (2016) p.47-54 DOI: 10.1038/nature17676
*
Ensembl comparative genomics resources.
Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw053
The topography of mutational processes in breast cancer genomes.
Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H, Staaf J, Sieuwerts AM, Brinkman AB, Martin S, Ramakrishna M, Butler A, Kim HY, Borg Å, Sotiriou C, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Sale J, Rada C, Stratton MR, Birney E, Nik-Zainal S. Nature communications Volume 7 (2016) p.11383 DOI: 10.1038/ncomms11383
Improved definition of the mouse transcriptome via targeted RNA sequencing.
Bussotti G, Leonardi T, Clark MB, Mercer TR, Crawford J, Malquori L, Notredame C, Dinger ME, Mattick JS, Enright AJ. Genome research Volume 26 (2016) p.705-716 DOI: 10.1101/gr.199760.115
*
Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci
Amaral PP, Leonardi T, Han N, Vire E, Gascoigne DK, Arias-Carrasco R, Buscher M, Zhang A, Pluchino S, Maracaja-Coutinho V, Nakaya HI, Hemberg M, Shiekhattar R, Enright AJ, Kouzarides T. Preprint DOI: 10.1101/051052
The Ontology for Biomedical Investigations.
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. PloS one Volume 11 (2016) p.e0154556 DOI: 10.1371/journal.pone.0154556
Structure and evolutionary history of a large family of NLR proteins in the zebrafish.
Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni JC, Soylemez O, Kondrashov F, Leptin M. Open biology Volume 6 (2016) p.160009 DOI: 10.1098/rsob.160009
Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.
Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GR, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich Y, Handsaker RE, 1000 Genomes Project Consortium, Bustamante CD, Tyler-Smith C. Nature genetics Volume 48 (2016) p.593-599 DOI: 10.1038/ng.3559
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.
Kılıç S, Sagitova DM, Wolfish S, Bely B, Courtot M, Ciufo S, Tatusova T, O'Donovan C, Chibucos MC, Martin MJ, Erill I. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw055
Organization, evolution and functions of the human and mouse Ly6/uPAR family genes.
Loughner CL, Bruford EA, McAndrews MS, Delp EE, Swamynathan S, Swamynathan SK. Human genomics Volume 10 (2016) p.10 DOI: 10.1186/s40246-016-0074-2
*
Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.
de la Rosa-Trevín JM, Quintana A, Del Cano L, Zaldívar A, Foche I, Gutiérrez J, Gómez-Blanco J, Burguet-Castell J, Cuenca-Alba J, Abrishami V, Vargas J, Otón J, Sharov G, Vilas JL, Navas J, Conesa P, Kazemi M, Marabini R, Sorzano CO, Carazo JM. Journal of structural biology Volume 195 (2016) p.93-99 DOI: 10.1016/j.jsb.2016.04.010
*
Omics Discovery Index - Discovering and Linking Public Omics Datasets
Perez-Riverol Y, Bai M, Leprevost F, Squizzato S, Mi Park Y, Haug OK, Carroll AJ, Spalding D, Paschall J, Wang M, del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch E, Campbell DS, Beavis RC, Salek R, Nesvizhskii A, Sansone S, Steinbeck C, Lopez R, Vizcaino JA, Ping P, Hermjakob H. Preprint DOI: 10.1101/049205
Beyond comparisons of means: understanding changes in gene expression at the single-cell level.
Vallejos CA, Richardson S, Marioni JC. Genome biology Volume 17 (2016) p.70 DOI: 10.1186/s13059-016-0930-3
*
Ten Simple Rules for Taking Advantage of git and GitHub
Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost F, Fufezan C, Ternent T, Eglen SJ, Katz DSS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaino JA. Preprint DOI: 10.1101/048744
Extending gene ontology in the context of extracellular RNA and vesicle communication.
Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC. Journal of biomedical semantics Volume 7 (2016) p.19 DOI: 10.1186/s13326-016-0061-5
A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.
Patro R, Norel R, Prill RJ, Saez-Rodriguez J, Lorenz P, Steinbeck F, Ziems B, Luštrek M, Barbarini N, Tiengo A, Bellazzi R, Thiesen HJ, Stolovitzky G, Kingsford C. BMC bioinformatics Volume 17 (2016) p.155 DOI: 10.1186/s12859-016-1008-7
*
Genetic and environmental influences interact with age and sex in shaping the human methylome.
van Dongen J, Nivard MG, Willemsen G, Hottenga JJ, Helmer Q, Dolan CV, Ehli EA, Davies GE, van Iterson M, Breeze CE, Beck S, BIOS Consortium, Suchiman HE, Jansen R, van Meurs JB, Heijmans BT, Slagboom PE, Boomsma DI. Nature communications Volume 7 (2016) p.11115 DOI: 10.1038/ncomms11115
Lithium Promotes Longevity through GSK3/NRF2-Dependent Hormesis.
Castillo-Quan JI, Li L, Kinghorn KJ, Ivanov DK, Tain LS, Slack C, Kerr F, Nespital T, Thornton J, Hardy J, Bjedov I, Partridge L. Cell reports Volume 15 (2016) p.638-650 DOI: 10.1016/j.celrep.2016.03.041
Mutational History of a Human Cell Lineage from Somatic to Induced Pluripotent Stem Cells.
Rouhani FJ, Nik-Zainal S, Wuster A, Li Y, Conte N, Koike-Yusa H, Kumasaka N, Vallier L, Yusa K, Bradley A. PLoS genetics Volume 12 (2016) p.e1005932 DOI: 10.1371/journal.pgen.1005932
Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes.
Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB. PLoS computational biology Volume 12 (2016) p.e1004862 DOI: 10.1371/journal.pcbi.1004862
The systems biology format converter.
Rodriguez N, Pettit JB, Dalle Pezze P, Li L, Henry A, van Iersel MP, Jalowicki G, Kutmon M, Natarajan KN, Tolnay D, Stefan MI, Evelo CT, Le Novère N. BMC bioinformatics Volume 17 (2016) p.154 DOI: 10.1186/s12859-016-1000-2
*
Standardized benchmarking in the quest for orthologs.
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M, Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C. Nature methods Volume 13 (2016) p.425-430 DOI: 10.1038/nmeth.3830
ProbOnto: ontology and knowledge base of probability distributions.
Swat MJ, Grenon P, Wimalaratne S. Bioinformatics (Oxford, England) Volume 32 (2016) p.2719-2721 DOI: 10.1093/bioinformatics/btw170
Divergence in gene expression within and between two closely related flycatcher species.
Uebbing S, Künstner A, Mäkinen H, Backström N, Bolivar P, Burri R, Dutoit L, Mugal CF, Nater A, Aken B, Flicek P, Martin FJ, Searle SM, Ellegren H. Molecular ecology Volume 25 (2016) p.2015-2028 DOI: 10.1111/mec.13596
Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.
Jupp S, Burdett T, Welter D, Sarntivijai S, Parkinson H, Malone J. Journal of biomedical semantics Volume 7 (2016) p.17 DOI: 10.1186/s13326-016-0055-3
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J. Structure (London, England : 1993) Volume 24 (2016) p.502-508 DOI: 10.1016/j.str.2016.02.017
MetaboLights: An Open-Access Database Repository for Metabolomics Data.
Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P, Rocca-Serra P, Nainala VC, Spicer RA, Williams M, Li X, Salek RM, Griffin JL, Steinbeck C. Current protocols in bioinformatics Volume 53 (2016) p.14.13.1-18 DOI: 10.1002/0471250953.bi1413s53
UniProt Tools.
Pundir S, Martin MJ, O'Donovan C, UniProt Consortium. Current protocols in bioinformatics Volume 53 (2016) p.1.29.1-15 DOI: 10.1002/0471250953.bi0129s53
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation.
Sarntivijai S, Vasant D, Jupp S, Saunders G, Bento AP, Gonzalez D, Betts J, Hasan S, Koscielny G, Dunham I, Parkinson H, Malone J. Journal of biomedical semantics Volume 7 (2016) p.8 DOI: 10.1186/s13326-016-0051-7
EMPIAR: a public archive for raw electron microscopy image data.
Iudin A, Korir PK, Salavert-Torres J, Kleywegt GJ, Patwardhan A. Nature methods Volume 13 (2016) p.387-388 DOI: 10.1038/nmeth.3806
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations.
Sangrador-Vegas A, Mitchell AL, Chang HY, Yong SY, Finn RD. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw027
Exploring regulatory networks of miR-96 in the developing inner ear.
Lewis MA, Buniello A, Hilton JM, Zhu F, Zhang WI, Evans S, van Dongen S, Enright AJ, Steel KP. Scientific reports Volume 6 (2016) p.23363 DOI: 10.1038/srep23363
Evolutionary diversification of retinoic acid receptor ligand-binding pocket structure by molecular tinkering.
Gutierrez-Mazariegos J, Nadendla EK, Studer RA, Alvarez S, de Lera AR, Kuraku S, Bourguet W, Schubert M, Laudet V. Royal Society open science Volume 3 (2016) p.150484 DOI: 10.1098/rsos.150484
ncRNA orthologies in the vertebrate lineage.
Pignatelli M, Vilella AJ, Muffato M, Gordon L, White S, Flicek P, Herrero J. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/bav127
Transcriptional response networks for elucidating mechanisms of action of multitargeted agents.
Kibble M, Khan SA, Saarinen N, Iorio F, Saez-Rodriguez J, Mäkelä S, Aittokallio T. Drug discovery today Volume 21 (2016) p.1063-1075 DOI: 10.1016/j.drudis.2016.03.001
Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design.
Smith JD, Suresh S, Schlecht U, Wu M, Wagih O, Peltz G, Davis RW, Steinmetz LM, Parts L, St Onge RP. Genome biology Volume 17 (2016) p.45 DOI: 10.1186/s13059-016-0900-9
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB.
Doğan T, MacDougall A, Saidi R, Poggioli D, Bateman A, O'Donovan C, Martin MJ. Bioinformatics (Oxford, England) Volume 32 (2016) p.2264-2271 DOI: 10.1093/bioinformatics/btw114
T cell fate and clonality inference from single-cell transcriptomes.
Stubbington MJT, Lönnberg T, Proserpio V, Clare S, Speak AO, Dougan G, Teichmann SA. Nature methods Volume 13 (2016) p.329-332 DOI: 10.1038/nmeth.3800
*
Genomic epidemiology of artemisinin resistant malaria.
MalariaGEN Plasmodium falciparum Community Project. eLife Volume 5 (2016) DOI: 10.7554/eLife.08714
An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway.
Robertson KA, Hsieh WY, Forster T, Blanc M, Lu H, Crick PJ, Yutuc E, Watterson S, Martin K, Griffiths SJ, Enright AJ, Yamamoto M, Pradeepa MM, Lennox KA, Behlke MA, Talbot S, Haas J, Dölken L, Griffiths WJ, Wang Y, Angulo A, Ghazal P. PLoS biology Volume 14 (2016) p.e1002364 DOI: 10.1371/journal.pbio.1002364
libChEBI: an API for accessing the ChEBI database.
Swainston N, Hastings J, Dekker A, Muthukrishnan V, May J, Steinbeck C, Mendes P. Journal of cheminformatics Volume 8 (2016) p.11 DOI: 10.1186/s13321-016-0123-9
Cutting-edge single-cell genomics and modelling in immunology.
Proserpio V, Lönnberg T. Immunology and cell biology Volume 94 (2016) p.224 DOI: 10.1038/icb.2015.117
*
The ORFeome Collaboration: a genome-scale human ORF-clone resource.
ORFeome Collaboration. Nature methods Volume 13 (2016) p.191-192 DOI: 10.1038/nmeth.3776
Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.
Goolam M, Scialdone A, Graham SJL, Macaulay IC, Jedrusik A, Hupalowska A, Voet T, Marioni JC, Zernicka-Goetz M. Cell Volume 165 (2016) p.61-74 DOI: 10.1016/j.cell.2016.01.047
Old knowledge and new technologies allow rapid development of model organisms.
Cook CE, Chenevert J, Larsson TA, Arendt D, Houliston E, Lénárt P. Molecular biology of the cell Volume 27 (2016) p.882-887 DOI: 10.1091/mbc.E15-10-0682
*
transPLANT Resources for Triticeae Genomic Data.
Spannagl M, Alaux M, Lange M, Bolser DM, Bader KC, Letellier T, Kimmel E, Flores R, Pommier C, Kerhornou A, Walts B, Nussbaumer T, Grabmuller C, Chen J, Colmsee C, Beier S, Mascher M, Schmutzer T, Arend D, Thanki A, Ramirez-Gonzalez R, Ayling M, Ayling S, Caccamo M, Mayer KF, Scholz U, Steinbach D, Quesneville H, Kersey PJ. The plant genome Volume 9 (2016) DOI: 10.3835/plantgenome2015.06.0038
Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells.
Kulbe H, Iorio F, Chakravarty P, Milagre CS, Moore R, Thompson RG, Everitt G, Canosa M, Montoya A, Drygin D, Braicu I, Sehouli J, Saez-Rodriguez J, Cutillas PR, Balkwill FR. Oncotarget Volume 7 (2016) p.15648-15661 DOI: 10.18632/oncotarget.7255
LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order.
Fontanesi L, Di Palma F, Flicek P, Smith AT, Thulin CG, Alves PC, Lagomorph Genomics Consortium. The Journal of heredity Volume 107 (2016) p.295-308 DOI: 10.1093/jhered/esw010
*
Computational clustering for viral reference proteomes.
Chen C, Huang H, Mazumder R, Natale DA, McGarvey PB, Zhang J, Polson SW, Wang Y, Wu CH, UniProt Consortium. Bioinformatics (Oxford, England) Volume 32 (2016) p.2041-2043 DOI: 10.1093/bioinformatics/btw110
Guidelines for the functional annotation of microRNAs using the Gene Ontology.
Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC. RNA (New York, N.Y.) Volume 22 (2016) p.667-676 DOI: 10.1261/rna.055301.115
*
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes.
Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R. Genome biology Volume 17 (2016) p.32 DOI: 10.1186/s13059-016-0883-6
Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression.
Rakitsch B, Stegle O. Genome biology Volume 17 (2016) p.33 DOI: 10.1186/s13059-016-0895-2
*
Inferring causal molecular networks: empirical assessment through a community-based effort.
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ, HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S. Nature methods Volume 13 (2016) p.310-318 DOI: 10.1038/nmeth.3773
A multiple-phenotype imputation method for genetic studies.
Dahl A, Iotchkova V, Baud A, Johansson Å, Gyllensten U, Soranzo N, Mott R, Kranis A, Marchini J. Nature genetics Volume 48 (2016) p.466-472 DOI: 10.1038/ng.3513
Reaction Decoder Tool (RDT): extracting features from chemical reactions.
Rahman SA, Torrance G, Baldacci L, Martínez Cuesta S, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM. Bioinformatics (Oxford, England) Volume 32 (2016) p.2065-2066 DOI: 10.1093/bioinformatics/btw096
The UniProtKB guide to the human proteome.
Breuza L, Poux S, Estreicher A, Famiglietti ML, Magrane M, Tognolli M, Bridge A, Baratin D, Redaschi N, UniProt Consortium. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/bav120
Ensembl comparative genomics resources.
Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/bav096
Activation of the TGFβ pathway impairs endothelial to haematopoietic transition.
Vargel Ö, Zhang Y, Kosim K, Ganter K, Foehr S, Mardenborough Y, Shvartsman M, Enright AJ, Krijgsveld J, Lancrin C. Scientific reports Volume 6 (2016) p.21518 DOI: 10.1038/srep21518
*
Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs.
Ricaño-Ponce I, Zhernakova DV, Deelen P, Luo O, Li X, Isaacs A, Karjalainen J, Di Tommaso J, Borek ZA, Zorro MM, Gutierrez-Achury J, Uitterlinden AG, Hofman A, van Meurs J, BIOS Consortium, Lifelines Cohort Study, Netea MG, Jonkers IH, Withoff S, van Duijn CM, Li Y, Ruan Y, Franke L, Wijmenga C, Kumar V. Journal of autoimmunity Volume 68 (2016) p.62-74 DOI: 10.1016/j.jaut.2016.01.002
Ensembl regulation resources.
Zerbino DR, Johnson N, Juetteman T, Sheppard D, Wilder SP, Lavidas I, Nuhn M, Perry E, Raffaillac-Desfosses Q, Sobral D, Keefe D, Gräf S, Ahmed I, Kinsella R, Pritchard B, Brent S, Amode R, Parker A, Trevanion S, Birney E, Dunham I, Flicek P. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/bav119
Clustering Genes of Common Evolutionary History.
Gori K, Suchan T, Alvarez N, Goldman N, Dessimoz C. Molecular biology and evolution Volume 33 (2016) p.1590-1605 DOI: 10.1093/molbev/msw038
The Time Is Right to Focus on Model Organism Metabolomes.
Edison AS, Hall RD, Junot C, Karp PD, Kurland IJ, Mistrik R, Reed LK, Saito K, Salek RM, Steinbeck C, Sumner LW, Viant MR. Metabolites Volume 6 (2016) DOI: 10.3390/metabo6010008
Ten Simple Rules for Selecting a Bio-ontology.
Malone J, Stevens R, Jupp S, Hancocks T, Parkinson H, Brooksbank C. PLoS computational biology Volume 12 (2016) p.e1004743 DOI: 10.1371/journal.pcbi.1004743
Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources.
Bousfield D, McEntyre J, Velankar S, Papadatos G, Bateman A, Cochrane G, Kim JH, Graef F, Vartak V, Alako B, Blomberg N. F1000Research Volume 5 (2016) DOI: 10.12688/f1000research.7911.1
Web-based volume slicer for 3D electron-microscopy data from EMDB.
Salavert-Torres J, Iudin A, Lagerstedt I, Sanz-García E, Kleywegt GJ, Patwardhan A. Journal of structural biology Volume 194 (2016) p.164-170 DOI: 10.1016/j.jsb.2016.02.012
MOCCASIN: converting MATLAB ODE models to SBML.
Gómez HF, Hucka M, Keating SM, Nudelman G, Iber D, Sealfon SC. Bioinformatics (Oxford, England) Volume 32 (2016) p.1905-1906 DOI: 10.1093/bioinformatics/btw056
The Electron Microscopy eXchange (EMX) initiative.
Marabini R, Ludtke SJ, Murray SC, Chiu W, de la Rosa-Trevín JM, Patwardhan A, Heymann JB, Carazo JM. Journal of structural biology Volume 194 (2016) p.156-163 DOI: 10.1016/j.jsb.2016.02.008
Reporting phenotypes in mouse models when considering body size as a potential confounder.
Oellrich A, Meehan TF, Parkinson H, Sarntivijai S, White JK, Karp NA. Journal of biomedical semantics Volume 7 (2016) p.2 DOI: 10.1186/s13326-016-0050-8
Value, but high costs in post-deposition data curation.
ten Hoopen P, Amid C, Buttigieg PL, Pafilis E, Bravakos P, Cerdeño-Tárraga AM, Gibson R, Kahlke T, Legaki A, Narayana Murthy K, Papastefanou G, Pereira E, Rossello M, Luisa Toribio A, Cochrane G. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/bav126
Genomic insights into the Ixodes scapularis tick vector of Lyme disease.
Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayllón N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calderón GI, Grabowski JM, Jiang D, Khalil SM, Kim D, Kocan KM, Koči J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, Sánchez-Gracia A, Severo MS, Silverman N, Šimo L, Tojo M, Tornador C, Van Zee JP, Vázquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio PV, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJ, Park Y, Rozas J, Benton R, Pedra JH, Nelson DR, Unger MF, Tubio JM, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, Nelson KE, Caler E, Hill CA. Nature communications Volume 7 (2016) p.10507 DOI: 10.1038/ncomms10507
Focus on Extracellular Vesicles: Physiological Role and Signalling Properties of Extracellular Membrane Vesicles.
Iraci N, Leonardi T, Gessler F, Vega B, Pluchino S. International journal of molecular sciences Volume 17 (2016) p.171 DOI: 10.3390/ijms17020171
A review of the new HGNC gene family resource.
Gray KA, Seal RL, Tweedie S, Wright MW, Bruford EA. Human genomics Volume 10 (2016) p.6 DOI: 10.1186/s40246-016-0062-6
Exploring the chemistry and evolution of the isomerases.
Martínez Cuesta S, Rahman SA, Thornton JM. Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.1796-1801 DOI: 10.1073/pnas.1509494113
Characterising Complex Enzyme Reaction Data.
Dönertaş HM, Martínez Cuesta S, Rahman SA, Thornton JM. PloS one Volume 11 (2016) p.e0147952 DOI: 10.1371/journal.pone.0147952
Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause.
Scognamiglio R, Cabezas-Wallscheid N, Thier MC, Altamura S, Reyes A, Prendergast ÁM, Baumgärtner D, Carnevalli LS, Atzberger A, Haas S, von Paleske L, Boroviak T, Wörsdörfer P, Essers MA, Kloz U, Eisenman RN, Edenhofer F, Bertone P, Huber W, van der Hoeven F, Smith A, Trumpp A. Cell Volume 164 (2016) p.668-680 DOI: 10.1016/j.cell.2015.12.033
*
Short template switch events explain mutation clusters in the human genome
Löytynoja A, Goldman N. Preprint DOI: 10.1101/038380
The metabolic background is a global player in Saccharomyces gene expression epistasis.
Alam MT, Zelezniak A, Mülleder M, Shliaha P, Schwarz R, Capuano F, Vowinckel J, Radmanesfahar E, Krüger A, Calvani E, Michel S, Börno S, Christen S, Patil KR, Timmermann B, Lilley KS, Ralser M. Nature microbiology Volume 1 (2016) p.15030 DOI: 10.1038/nmicrobiol.2015.30
HMGB1 binds to the rs7903146 locus in TCF7L2 in human pancreatic islets.
Zhou Y, Oskolkov N, Shcherbina L, Ratti J, Kock KH, Su J, Martin B, Oskolkova MZ, Göransson O, Bacon J, Li W, Bucciarelli S, Cilio C, Brazma A, Thatcher B, Rung J, Wierup N, Renström E, Groop L, Hansson O. Molecular and cellular endocrinology Volume 430 (2016) p.138-145 DOI: 10.1016/j.mce.2016.01.027
Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A.
Rohwer N, Bindel F, Grimm C, Lin SJ, Wappler J, Klinger B, Blüthgen N, Du Bois I, Schmeck B, Lehrach H, de Graauw M, Goncalves E, Saez-Rodriguez J, Tan P, Grabsch HI, Prigione A, Kempa S, Cramer T. Oncotarget Volume 7 (2016) p.6693-6710 DOI: 10.18632/oncotarget.6793
*
Tobacco smoking is associated with DNA methylation of diabetes susceptibility genes.
Ligthart S, Steenaard RV, Peters MJ, van Meurs JB, Sijbrands EJ, Uitterlinden AG, Bonder MJ, BIOS consortium, Hofman A, Franco OH, Dehghan A. Diabetologia Volume 59 (2016) p.998-1006 DOI: 10.1007/s00125-016-3872-0
Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs.
Juan D, Perner J, Carrillo de Santa Pau E, Marsili S, Ochoa D, Chung HR, Vingron M, Rico D, Valencia A. Cell reports Volume 14 (2016) p.1246-1257 DOI: 10.1016/j.celrep.2016.01.008
*
Genome wide association analysis of the heart using high-resolution 3D cardiac MRI identifies new genetic loci underlying cardiac structure and function.
Marvao Ad, Meyer HV, Dawes TJ, Shi W, Bai W, Rueckert D, Birney E, O'Regan DP, Cook S. Journal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance Volume 18 (2016) DOI: 10.1186/1532-429X-18-S1-Q63
Consolidating and Exploring Antibiotic Resistance Gene Data Resources.
Xavier BB, Das AJ, Cochrane G, De Ganck S, Kumar-Singh S, Aarestrup FM, Goossens H, Malhotra-Kumar S. Journal of clinical microbiology Volume 54 (2016) p.851-859 DOI: 10.1128/JCM.02717-15
ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.
Schwarz RF, Tamuri AU, Kultys M, King J, Godwin J, Florescu AM, Schultz J, Goldman N. Nucleic acids research Volume 44 (2016) p.e77 DOI: 10.1093/nar/gkw022
Structure of bacterial respiratory complex I.
Berrisford JM, Baradaran R, Sazanov LA. Biochimica et biophysica acta Volume 1857 (2016) p.892-901 DOI: 10.1016/j.bbabio.2016.01.012
Consent Codes: Upholding Standard Data Use Conditions.
Dyke SO, Philippakis AA, Rambla De Argila J, Paltoo DN, Luetkemeier ES, Knoppers BM, Brookes AJ, Spalding JD, Thompson M, Roos M, Boycott KM, Brudno M, Hurles M, Rehm HL, Matern A, Fiume M, Sherry ST. PLoS genetics Volume 12 (2016) p.e1005772 DOI: 10.1371/journal.pgen.1005772
Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis.
Emwas AH, Roy R, McKay RT, Ryan D, Brennan L, Tenori L, Luchinat C, Gao X, Zeri AC, Gowda GA, Raftery D, Steinbeck C, Salek RM, Wishart DS. Journal of proteome research Volume 15 (2016) p.360-373 DOI: 10.1021/acs.jproteome.5b00885
*
SC3 - consensus clustering of single-cell RNA-Seq data
Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR, Hemberg M. Preprint DOI: 10.1101/036558
The EMBL-EBI channel.
McEntyre J, Birney E. F1000Research Volume 5 (2016) p.52 DOI: 10.12688/f1000research.7764.1
Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.
Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood S, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W. Nature methods Volume 13 (2016) p.229-232 DOI: 10.1038/nmeth.3728
*
Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC. Nature communications Volume 7 (2016) p.10415 DOI: 10.1038/ncomms10415
*
BioJS-HGV Viewer: Genetic Variation Visualizer
Choudhary S, Garcia L, Nightingale A, Martin M. DOI: 10.1101/032573
Modelling-based experiment retrieval: a case study with gene expression clustering.
Blomstedt P, Dutta R, Seth S, Brazma A, Kaski S. Bioinformatics (Oxford, England) Volume 32 (2016) p.1388-1394 DOI: 10.1093/bioinformatics/btv762
*
Beyond comparisons of means: understanding changes in gene expression at the single-cell level
Vallejos CA, Richardson S, Marioni JC. Preprint DOI: 10.1101/035949
Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain.
Laskowski RA, Tyagi N, Johnson D, Joss S, Kinning E, McWilliam C, Splitt M, Thornton JM, Firth HV, DDD Study, Wright CF. Human molecular genetics Volume 25 (2016) p.927-935 DOI: 10.1093/hmg/ddv625
Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.
Bolser D, Staines DM, Pritchard E, Kersey P. Methods in molecular biology (Clifton, N.J.) Volume 1374 (2016) p.115-140 DOI: 10.1007/978-1-4939-3167-5_6
The MIntAct Project and Molecular Interaction Databases.
Licata L, Orchard S. Methods in molecular biology (Clifton, N.J.) Volume 1415 (2016) p.55-69 DOI: 10.1007/978-1-4939-3572-7_3
SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data.
Venkatesan A, Kim JH, Talo F, Ide-Smith M, Gobeill J, Carter J, Batista-Navarro R, Ananiadou S, Ruch P, McEntyre J. Wellcome open research Volume 1 (2016) p.25 DOI: 10.12688/wellcomeopenres.10210.2
Protein Structure Databases.
Laskowski RA. Methods in molecular biology (Clifton, N.J.) Volume 1415 (2016) p.31-53 DOI: 10.1007/978-1-4939-3572-7_2

2015

Applying extracellular vesicles based therapeutics in clinical trials - an ISEV position paper.
Lener T, Gimona M, Aigner L, Börger V, Buzas E, Camussi G, Chaput N, Chatterjee D, Court FA, Del Portillo HA, O'Driscoll L, Fais S, Falcon-Perez JM, Felderhoff-Mueser U, Fraile L, Gho YS, Görgens A, Gupta RC, Hendrix A, Hermann DM, Hill AF, Hochberg F, Horn PA, de Kleijn D, Kordelas L, Kramer BW, Krämer-Albers EM, Laner-Plamberger S, Laitinen S, Leonardi T, Lorenowicz MJ, Lim SK, Lötvall J, Maguire CA, Marcilla A, Nazarenko I, Ochiya T, Patel T, Pedersen S, Pocsfalvi G, Pluchino S, Quesenberry P, Reischl IG, Rivera FJ, Sanzenbacher R, Schallmoser K, Slaper-Cortenbach I, Strunk D, Tonn T, Vader P, van Balkom BW, Wauben M, Andaloussi SE, Théry C, Rohde E, Giebel B. Journal of extracellular vesicles Volume 4 (2015) p.30087 DOI: 10.3402/jev.v4.30087
Progress in Medicine: Experts Take Stock.
PLOS Medicine Editors, Beck A, Birney E, Graeber M, Tumwine J, Hay P, Ahn HS, Patel A, du Cros P, von Seidlein L, Wareham N, Low N. PLoS medicine Volume 12 (2015) p.e1001933 DOI: 10.1371/journal.pmed.1001933
Single-cell technologies to study the immune system.
Proserpio V, Mahata B. Immunology Volume 147 (2016) p.133-140 DOI: 10.1111/imm.12553
Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program.
Foti R, Gnan S, Cornacchia D, Dileep V, Bulut-Karslioglu A, Diehl S, Buness A, Klein FA, Huber W, Johnstone E, Loos R, Bertone P, Gilbert DM, Manke T, Jenuwein T, Buonomo SC. Molecular cell Volume 61 (2016) p.260-273 DOI: 10.1016/j.molcel.2015.12.001
The BioStudies database.
McEntyre J, Sarkans U, Brazma A. Molecular systems biology Volume 11 (2015) p.847 DOI: 10.15252/msb.20156658
The evolution of standards and data management practices in systems biology.
Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novère N, Mueller W, Snoep J, Goble C. Molecular systems biology Volume 11 (2015) p.851 DOI: 10.15252/msb.20156053
Ensembl 2016.
Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, Flicek P. Nucleic acids research Volume 44 (2016) p.D710-6 DOI: 10.1093/nar/gkv1157
*
The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.
Hurst LD, Ghanbarian AT, Forrest AR, FANTOM consortium, Huminiecki L. PLoS biology Volume 13 (2015) p.e1002315 DOI: 10.1371/journal.pbio.1002315
Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq.
Saraiva LR, Ibarra-Soria X, Khan M, Omura M, Scialdone A, Mombaerts P, Marioni JC, Logan DW. Scientific reports Volume 5 (2015) p.18178 DOI: 10.1038/srep18178
Exploring the potential of public proteomics data.
Vaudel M, Verheggen K, Csordas A, Raeder H, Berven FS, Martens L, Vizcaíno JA, Barsnes H. Proteomics Volume 16 (2016) p.214-225 DOI: 10.1002/pmic.201500295
The European Bioinformatics Institute in 2016: Data growth and integration.
Cook CE, Cook CE, Bergman MT, Finn RD, Cochrane G, Birney E, Apweiler R. Nucleic acids research Volume 44 (2016) p.D20-6 DOI: 10.1093/nar/gkv1352
The Pfam protein families database: towards a more sustainable future.
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A. Nucleic acids research Volume 44 (2016) p.D279-85 DOI: 10.1093/nar/gkv1344
*
Timing, rates and spectra of human germline mutation.
Rahbari R, Wuster A, Lindsay SJ, Hardwick RJ, Alexandrov LB, Turki SA, Dominiczak A, Morris A, Porteous D, Smith B, Stratton MR, UK10K Consortium, Hurles ME. Nature genetics Volume 48 (2016) p.126-133 DOI: 10.1038/ng.3469
*
Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage.
Carbajo D, Magi S, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest AR, Carninci P, Hayashizaki Y, Daub CO, FANTOM consortium, Okada-Hatakeyama M, Mar JC. PloS one Volume 10 (2015) p.e0144176 DOI: 10.1371/journal.pone.0144176
The International Nucleotide Sequence Database Collaboration.
Cochrane G, Karsch-Mizrachi I, Takagi T, International Nucleotide Sequence Database Collaboration. Nucleic acids research Volume 44 (2016) p.D48-50 DOI: 10.1093/nar/gkv1323
Synthesis of empty african horse sickness virus particles.
Maree S, Maree FF, Putterill JF, de Beer TAP, Huismans H, Theron J. Virus research Volume 213 (2016) p.184-194 DOI: 10.1016/j.virusres.2015.12.006
The Reactome pathway Knowledgebase.
Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, Jassal B, Jupe S, Korninger F, McKay S, Matthews L, May B, Milacic M, Rothfels K, Shamovsky V, Webber M, Weiser J, Williams M, Wu G, Stein L, Hermjakob H, D'Eustachio P. Nucleic acids research Volume 44 (2016) p.D481-7 DOI: 10.1093/nar/gkv1351
Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery.
Rebollo-Lopez MJ, Lelièvre J, Alvarez-Gomez D, Castro-Pichel J, Martínez-Jiménez F, Papadatos G, Kumar V, Colmenarejo G, Mugumbate G, Hurle M, Barroso V, Young RJ, Martinez-Hoyos M, González del Río R, Bates RH, Lopez-Roman EM, Mendoza-Losana A, Brown JR, Alvarez-Ruiz E, Marti-Renom MA, Overington JP, Cammack N, Ballell L, Barros-Aguire D. PloS one Volume 10 (2015) p.e0142293 DOI: 10.1371/journal.pone.0142293
Acellular approaches for regenerative medicine: on the verge of clinical trials with extracellular membrane vesicles?
Fuster-Matanzo A, Gessler F, Leonardi T, Iraci N, Pluchino S. Stem cell research & therapy Volume 6 (2015) p.227 DOI: 10.1186/s13287-015-0232-9
*
H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa.
Mulder NJ, Adebiyi E, Alami R, Benkahla A, Brandful J, Doumbia S, Everett D, Fadlelmola FM, Gaboun F, Gaseitsiwe S, Ghazal H, Hazelhurst S, Hide W, Ibrahimi A, Jaufeerally Fakim Y, Jongeneel CV, Joubert F, Kassim S, Kayondo J, Kumuthini J, Lyantagaye S, Makani J, Mansour Alzohairy A, Masiga D, Moussa A, Nash O, Ouwe Missi Oukem-Boyer O, Owusu-Dabo E, Panji S, Patterton H, Radouani F, Sadki K, Seghrouchni F, Tastan Bishop Ö, Tiffin N, Ulenga N, H3ABioNet Consortium. Genome research Volume 26 (2016) p.271-277 DOI: 10.1101/gr.196295.115
Principles of assembly reveal a periodic table of protein complexes.
Ahnert SE, Marsh JA, Hernández H, Robinson CV, Teichmann SA. Science (New York, N.Y.) Volume 350 (2015) p.aaa2245 DOI: 10.1126/science.aaa2245
The orchestra of lipid-transfer proteins at the crossroads between metabolism and signaling.
Chiapparino A, Maeda K, Turei D, Saez-Rodriguez J, Gavin AC. Progress in lipid research Volume 61 (2016) p.30-39 DOI: 10.1016/j.plipres.2015.10.004
Biocuration of functional annotation at the European nucleotide archive.
Gibson R, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Goodgame N, Ten Hoopen P, Jayathilaka S, Kay S, Leinonen R, Liu X, Pallreddy S, Pakseresht N, Rajan J, Rosselló M, Silvester N, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Nucleic acids research Volume 44 (2016) p.D58-66 DOI: 10.1093/nar/gkv1311
Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps.
Truszkowski J, Goldman N. Systematic biology Volume 65 (2016) p.328-333 DOI: 10.1093/sysbio/syv089
*
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.
SIB Swiss Institute of Bioinformatics Members. Nucleic acids research Volume 44 (2016) p.D27-37 DOI: 10.1093/nar/gkv1310
*
Multiple sequence alignment modeling: methods and applications.
Chatzou M, Magis C, Chang JM, Kemena C, Bussotti G, Erb I, Notredame C. Briefings in bioinformatics Volume 17 (2016) p.1009-1023 DOI: 10.1093/bib/bbv099
The Dfam database of repetitive DNA families.
Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AF, Wheeler TJ. Nucleic acids research Volume 44 (2016) p.D81-9 DOI: 10.1093/nar/gkv1272
A high-content platform to characterise human induced pluripotent stem cell lines.
Leha A, Moens N, Meleckyte R, Culley OJ, Gervasio MK, Kerz M, Reimer A, Cain SA, Streeter I, Folarin A, Stegle O, Kielty CM, HipSci Consortium, Durbin R, Watt FM, Danovi D. Methods (San Diego, Calif.) Volume 96 (2016) p.85-96 DOI: 10.1016/j.ymeth.2015.11.012
Update of the human and mouse Fanconi anemia genes.
Dong H, Nebert DW, Bruford EA, Thompson DC, Joenje H, Vasiliou V. Human genomics Volume 9 (2015) p.32 DOI: 10.1186/s40246-015-0054-y
Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.
Zepeda-Mendoza CJ, Mukhopadhyay S, Wong ES, Harder N, Splinter E, de Wit E, Eckersley-Maslin MA, Ried T, Eils R, Rohr K, Mills A, de Laat W, Flicek P, Sengupta AM, Spector DL. BMC genomics Volume 16 (2015) p.982 DOI: 10.1186/s12864-015-2137-5
Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting.
Kalman LV, Agúndez J, Appell ML, Black JL, Bell GC, Boukouvala S, Bruckner C, Bruford E, Caudle K, Coulthard SA, Daly AK, Del Tredici A, den Dunnen JT, Drozda K, Everts RE, Flockhart D, Freimuth RR, Gaedigk A, Hachad H, Hartshorne T, Ingelman-Sundberg M, Klein TE, Lauschke VM, Maglott DR, McLeod HL, McMillin GA, Meyer UA, Müller DJ, Nickerson DA, Oetting WS, Pacanowski M, Pratt VM, Relling MV, Roberts A, Rubinstein WS, Sangkuhl K, Schwab M, Scott SA, Sim SC, Thirumaran RK, Toji LH, Tyndale RF, van Schaik R, Whirl-Carrillo M, Yeo K, Zanger UM. Clinical pharmacology and therapeutics Volume 99 (2016) p.172-185 DOI: 10.1002/cpt.280
COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses.
Moretto M, Sonego P, Dierckxsens N, Brilli M, Bianco L, Ledezma-Tejeida D, Gama-Castro S, Galardini M, Romualdi C, Laukens K, Collado-Vides J, Meysman P, Engelen K. Nucleic acids research Volume 44 (2016) p.D620-3 DOI: 10.1093/nar/gkv1251
EBI metagenomics in 2016--an expanding and evolving resource for the analysis and archiving of metagenomic data.
Mitchell A, Bucchini F, Cochrane G, Denise H, ten Hoopen P, Fraser M, Pesseat S, Potter S, Scheremetjew M, Sterk P, Finn RD. Nucleic acids research Volume 44 (2016) p.D595-603 DOI: 10.1093/nar/gkv1195
Ensembl Genomes 2016: more genomes, more complexity.
Kersey PJ, Allen JE, Armean I, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Falin LJ, Grabmueller C, Humphrey J, Kerhornou A, Khobova J, Aranganathan NK, Langridge N, Lowy E, McDowall MD, Maheswari U, Nuhn M, Ong CK, Overduin B, Paulini M, Paulini M, Pedro H, Perry E, Spudich G, Tapanari E, Walts B, Williams G, Tello-Ruiz M, Stein J, Wei S, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Maslen G, Staines DM. Nucleic acids research Volume 44 (2016) p.D574-80 DOI: 10.1093/nar/gkv1209
Data standards can boost metabolomics research, and if there is a will, there is a way.
Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A, Ebbels T, Goodacre R, Hastings J, Haug K, Koulman A, Nikolski M, Oresic M, Sansone SA, Schober D, Smith J, Steinbeck C, Viant MR, Neumann S. Metabolomics Volume 12 (2016) p.14 DOI: 10.1007/s11306-015-0879-3
EMDataBank unified data resource for 3DEM.
Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W. Nucleic acids research Volume 44 (2016) p.D396-403 DOI: 10.1093/nar/gkv1126
WormBase 2016: expanding to enable helminth genomic research.
Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, Done J, Down T, Gao S, Grove C, Harris TW, Kishore R, Lee R, Lomax J, Li Y, Muller HM, Nakamura C, Nuin P, Paulini M, Paulini M, Raciti D, Schindelman G, Stanley E, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wright A, Yook K, Berriman M, Kersey P, Schedl T, Stein L, Sternberg PW. Nucleic acids research Volume 44 (2016) p.D774-80 DOI: 10.1093/nar/gkv1217
SureChEMBL: a large-scale, chemically annotated patent document database.
Papadatos G, Davies M, Dedman N, Chambers J, Gaulton A, Siddle J, Koks R, Irvine SA, Pettersson J, Goncharoff N, Hersey A, Overington JP. Nucleic acids research Volume 44 (2016) p.D1220-8 DOI: 10.1093/nar/gkv1253
HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.
Forster SC, Browne HP, Kumar N, Hunt M, Denise H, Mitchell A, Finn RD, Lawley TD. Nucleic acids research Volume 44 (2016) p.D604-9 DOI: 10.1093/nar/gkv1216
*
Pharmacogenomic agreement between two cancer cell line data sets.
Cancer Cell Line Encyclopedia Consortium, Genomics of Drug Sensitivity in Cancer Consortium. Nature Volume 528 (2015) p.84-87 DOI: 10.1038/nature15736
Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.
Mesquita RD, Vionette-Amaral RJ, Lowenberger C, Rivera-Pomar R, Monteiro FA, Minx P, Spieth J, Carvalho AB, Panzera F, Lawson D, Torres AQ, Ribeiro JM, Sorgine MH, Waterhouse RM, Montague MJ, Abad-Franch F, Alves-Bezerra M, Amaral LR, Araujo HM, Araujo RN, Aravind L, Atella GC, Azambuja P, Berni M, Bittencourt-Cunha PR, Braz GR, Calderón-Fernández G, Carareto CM, Christensen MB, Costa IR, Costa SG, Dansa M, Daumas-Filho CR, De-Paula IF, Dias FA, Dimopoulos G, Emrich SJ, Esponda-Behrens N, Fampa P, Fernandez-Medina RD, da Fonseca RN, Fontenele M, Fronick C, Fulton LA, Gandara AC, Garcia ES, Genta FA, Giraldo-Calderón GI, Gomes B, Gondim KC, Granzotto A, Guarneri AA, Guigó R, Harry M, Hughes DS, Jablonka W, Jacquin-Joly E, Juárez MP, Koerich LB, Lange AB, Latorre-Estivalis JM, Lavore A, Lawrence GG, Lazoski C, Lazzari CR, Lopes RR, Lorenzo MG, Lugon MD, Majerowicz D, Marcet PL, Mariotti M, Masuda H, Megy K, Melo AC, Melo AC, Missirlis F, Mota T, Noriega FG, Nouzova M, Nunes RD, Oliveira RL, Oliveira-Silveira G, Ons S, Orchard I, Pagola L, Paiva-Silva GO, Pascual A, Pavan MG, Pedrini N, Peixoto AA, Pereira MH, Pike A, Polycarpo C, Prosdocimi F, Ribeiro-Rodrigues R, Robertson HM, Salerno AP, Salmon D, Santesmasses D, Schama R, Seabra-Junior ES, Silva-Cardoso L, Silva-Neto MA, Souza-Gomes M, Sterkel M, Taracena ML, Tojo M, Tu ZJ, Tubio JM, Ursic-Bedoya R, Venancio TM, Walter-Nuno AB, Wilson D, Warren WC, Wilson RK, Huebner E, Dotson EM, Oliveira PL. Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.14936-14941 DOI: 10.1073/pnas.1506226112
Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks.
Wagih O, Sugiyama N, Ishihama Y, Beltrao P. Molecular & cellular proteomics : MCP Volume 15 (2016) p.236-245 DOI: 10.1074/mcp.M115.052357
Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.
Furnham N, Dawson NL, Rahman SA, Thornton JM, Orengo CA. Journal of molecular biology Volume 428 (2016) p.253-267 DOI: 10.1016/j.jmb.2015.11.010
Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences.
Audain E, Ramos Y, Hermjakob H, Flower DR, Perez-Riverol Y. Bioinformatics (Oxford, England) Volume 32 (2016) p.821-827 DOI: 10.1093/bioinformatics/btv674
The pig X and Y Chromosomes: structure, sequence, and evolution.
Skinner BM, Sargent CA, Churcher C, Hunt T, Herrero J, Loveland JE, Dunn M, Louzada S, Fu B, Chow W, Gilbert J, Austin-Guest S, Beal K, Carvalho-Silva D, Cheng W, Gordon D, Grafham D, Hardy M, Harley J, Hauser H, Howden P, Howe K, Lachani K, Ellis PJ, Kelly D, Kerry G, Kerwin J, Ng BL, Threadgold G, Wileman T, Wood JM, Yang F, Harrow J, Affara NA, Tyler-Smith C. Genome research Volume 26 (2016) p.130-139 DOI: 10.1101/gr.188839.114
A Loss-of-Function Variant in a Minor Isoform of ANK3 Protects Against Bipolar Disorder and Schizophrenia.
Hughes T, Hansson L, Sønderby IE, Athanasiu L, Zuber V, Tesli M, Song J, Hultman CM, Bergen SE, Landén M, Melle I, Andreassen OA, Djurovic S. Biological psychiatry Volume 80 (2016) p.323-330 DOI: 10.1016/j.biopsych.2015.09.021
Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.
Gaulton KJ, Ferreira T, Lee Y, Raimondo A, Mägi R, Reschen ME, Mahajan A, Locke A, Rayner NW, Robertson N, Scott RA, Prokopenko I, Scott LJ, Green T, Sparso T, Thuillier D, Yengo L, Grallert H, Wahl S, Frånberg M, Strawbridge RJ, Kestler H, Chheda H, Eisele L, Gustafsson S, Steinthorsdottir V, Thorleifsson G, Qi L, Karssen LC, van Leeuwen EM, Willems SM, Li M, Chen H, Fuchsberger C, Kwan P, Ma C, Linderman M, Lu Y, Thomsen SK, Rundle JK, Beer NL, van de Bunt M, Chalisey A, Kang HM, Voight BF, Abecasis GR, Almgren P, Baldassarre D, Balkau B, Benediktsson R, Blüher M, Boeing H, Bonnycastle LL, Bottinger EP, Burtt NP, Carey J, Charpentier G, Chines PS, Cornelis MC, Couper DJ, Crenshaw AT, van Dam RM, Doney AS, Dorkhan M, Edkins S, Eriksson JG, Esko T, Eury E, Fadista J, Flannick J, Fontanillas P, Fox C, Franks PW, Gertow K, Gieger C, Gigante B, Gottesman O, Grant GB, Grarup N, Groves CJ, Hassinen M, Have CT, Herder C, Holmen OL, Hreidarsson AB, Humphries SE, Hunter DJ, Jackson AU, Jonsson A, Jørgensen ME, Jørgensen T, Kao WH, Kerrison ND, Kinnunen L, Klopp N, Kong A, Kovacs P, Kraft P, Kravic J, Langford C, Leander K, Liang L, Lichtner P, Lindgren CM, Lindholm E, Linneberg A, Liu CT, Lobbens S, Luan J, Lyssenko V, Männistö S, McLeod O, Meyer J, Mihailov E, Mirza G, Mühleisen TW, Müller-Nurasyid M, Navarro C, Nöthen MM, Oskolkov NN, Owen KR, Palli D, Pechlivanis S, Peltonen L, Perry JR, Platou CG, Roden M, Ruderfer D, Rybin D, van der Schouw YT, Sennblad B, Sigurðsson G, Stančáková A, Steinbach G, Storm P, Strauch K, Stringham HM, Sun Q, Thorand B, Tikkanen E, Tonjes A, Trakalo J, Tremoli E, Tuomi T, Wennauer R, Wiltshire S, Wood AR, Zeggini E, Dunham I, Birney E, Pasquali L, Ferrer J, Loos RJ, Dupuis J, Florez JC, Boerwinkle E, Pankow JS, van Duijn C, Sijbrands E, Meigs JB, Hu FB, Thorsteinsdottir U, Stefansson K, Lakka TA, Rauramaa R, Stumvoll M, Pedersen NL, Lind L, Keinanen-Kiukaanniemi SM, Korpi-Hyövälti E, Saaristo TE, Saltevo J, Kuusisto J, Laakso M, Metspalu A, Erbel R, Jöcke KH, Moebus S, Ripatti S, Salomaa V, Ingelsson E, Boehm BO, Bergman RN, Collins FS, Mohlke KL, Koistinen H, Tuomilehto J, Hveem K, Njølstad I, Deloukas P, Donnelly PJ, Frayling TM, Hattersley AT, de Faire U, Hamsten A, Illig T, Peters A, Cauchi S, Sladek R, Froguel P, Hansen T, Pedersen O, Morris AD, Palmer CN, Kathiresan S, Melander O, Nilsson PM, Groop LC, Barroso I, Langenberg C, Wareham NJ, O'Callaghan CA, Gloyn AL, Altshuler D, Boehnke M, Teslovich TM, McCarthy MI, Morris AP, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium. Nature genetics Volume 47 (2015) p.1415-1425 DOI: 10.1038/ng.3437
Gramene 2016: comparative plant genomics and pathway resources.
Tello-Ruiz MK, Stein J, Wei S, Preece J, Olson A, Naithani S, Amarasinghe V, Dharmawardhana P, Jiao Y, Mulvaney J, Kumari S, Chougule K, Elser J, Wang B, Thomason J, Bolser DM, Kerhornou A, Walts B, Fonseca NA, Huerta L, Keays M, Tang YA, Parkinson H, Fabregat A, McKay S, Weiser J, D'Eustachio P, Stein L, Petryszak R, Kersey PJ, Jaiswal P, Ware D. Nucleic acids research Volume 44 (2016) p.D1133-40 DOI: 10.1093/nar/gkv1179
High-density P300 enhancers control cell state transitions.
Witte S, Bradley A, Enright AJ, Muljo SA. BMC genomics Volume 16 (2015) p.903 DOI: 10.1186/s12864-015-1905-6
PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.
Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA. Molecular & cellular proteomics : MCP Volume 15 (2016) p.305-317 DOI: 10.1074/mcp.O115.050229
Tools and data services registry: a community effort to document bioinformatics resources.
Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S. Nucleic acids research Volume 44 (2016) p.D38-47 DOI: 10.1093/nar/gkv1116
2016 update of the PRIDE database and its related tools.
Vizcaíno JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H. Nucleic acids research Volume 44 (2016) p.D447-56 DOI: 10.1093/nar/gkv1145
Bacterial calpains and the evolution of the calpain (C2) family of peptidases.
Rawlings ND. Biology direct Volume 10 (2015) p.66 DOI: 10.1186/s13062-015-0095-0
Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Barrett AJ, Finn R. Nucleic acids research Volume 44 (2016) p.D343-50 DOI: 10.1093/nar/gkv1118
Glioblastoma Stem Cells Respond to Differentiation Cues but Fail to Undergo Commitment and Terminal Cell-Cycle Arrest.
Carén H, Stricker SH, Bulstrode H, Gagrica S, Johnstone E, Bartlett TE, Feber A, Wilson G, Teschendorff AE, Bertone P, Beck S, Pollard SM. Stem cell reports Volume 5 (2015) p.829-842 DOI: 10.1016/j.stemcr.2015.09.014
Computational proteomics: Integrating mass spectral data into a biological context.
Carvalho PC, Padron G, Calvete JJ, Perez-Riverol Y. Journal of proteomics Volume 129 (2015) p.1-2 DOI: 10.1016/j.jprot.2015.10.013
Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis.
Boroviak T, Loos R, Lombard P, Okahara J, Behr R, Sasaki E, Nichols J, Smith A, Bertone P. Developmental cell Volume 35 (2015) p.366-382 DOI: 10.1016/j.devcel.2015.10.011
*
Corrigendum: The promise and peril of chemical probes.
Arrowsmith CH, Audia JE, Austin C, Baell J, Bennett J, Blagg J, Bountra C, Brennan PE, Brown PJ, Bunnage ME, Buser-Doepner C, Campbell RM, Carter AJ, Cohen P, Copeland RA, Cravatt B, Dahlin JL, Dhanak D, Edwards AM, Frederiksen M, Frye SV, Gray N, Grimshaw CE, Hepworth D, Howe T, Huber KV, Jin J, Knapp S, Kotz JD, Kruger RG, Lowe D, Mader MM, Marsden B, Mueller-Fahrnow A, Müller S, O'Hagan RC, Overington JP, Owen DR, Rosenberg SH, Ross R, Roth B, Schapira M, Schreiber SL, Shoichet B, Sundström M, Superti-Furga G, Taunton J, Toledo-Sherman L, Walpole C, Walters MA, Willson TM, Workman P, Young RN, Zuercher WJ. Nature chemical biology Volume 11 (2015) p.887 DOI: 10.1038/nchembio1115-887c
Proteins: interaction at a distance.
Laskowski RA, Thornton JM. IUCrJ Volume 2 (2015) p.609-610 DOI: 10.1107/S2052252515020217
Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity.
Tyagi N, Farnell EJ, Fitzsimmons CM, Ryan S, Tukahebwa E, Maizels RM, Dunne DW, Thornton JM, Furnham N. PLoS computational biology Volume 11 (2015) p.e1004546 DOI: 10.1371/journal.pcbi.1004546
Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients.
Calligaris R, Banica M, Roncaglia P, Robotti E, Finaurini S, Vlachouli C, Antonutti L, Iorio F, Carissimo A, Cattaruzza T, Ceiner A, Lazarevic D, Cucca A, Pangher N, Marengo E, di Bernardo D, Pizzolato G, Gustincich S. BMC genomics Volume 16 (2015) p.876 DOI: 10.1186/s12864-015-2058-3
Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.
Thiele S, Cerone L, Saez-Rodriguez J, Siegel A, Guziołowski C, Klamt S. BMC bioinformatics Volume 16 (2015) p.345 DOI: 10.1186/s12859-015-0733-7
PhenoMiner: from text to a database of phenotypes associated with OMIM diseases.
Collier N, Groza T, Smedley D, Robinson PN, Oellrich A, Rebholz-Schuhmann D. Database : the journal of biological databases and curation Volume 2015 (2015) DOI: 10.1093/database/bav104
Comprehensive characterization of the Published Kinase Inhibitor Set.
Elkins JM, Fedele V, Szklarz M, Abdul Azeez KR, Salah E, Mikolajczyk J, Romanov S, Sepetov N, Huang XP, Roth BL, Al Haj Zen A, Fourches D, Muratov E, Tropsha A, Morris J, Teicher BA, Kunkel M, Polley E, Lackey KE, Atkinson FL, Overington JP, Bamborough P, Müller S, Price DJ, Willson TM, Drewry DH, Knapp S, Zuercher WJ. Nature biotechnology Volume 34 (2016) p.95-103 DOI: 10.1038/nbt.3374
*
Evolutionary conserved gene co-expression drives generation of self-antigen diversity in medullary thymic epithelial cells.
Rattay K, Meyer HV, Herrmann C, Brors B, Kyewski B. Journal of autoimmunity Volume 67 (2016) p.65-75 DOI: 10.1016/j.jaut.2015.10.001
Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC. Nature communications Volume 6 (2015) p.8687 DOI: 10.1038/ncomms9687
Genetic Markers of Human Evolution Are Enriched in Schizophrenia.
Srinivasan S, Bettella F, Mattingsdal M, Wang Y, Witoelar A, Schork AJ, Thompson WK, Zuber V, Schizophrenia Working Group of the Psychiatric Genomics Consortium, The International Headache Genetics Consortium, Winsvold BS, Zwart JA, Collier DA, Desikan RS, Melle I, Werge T, Dale AM, Djurovic S, Andreassen OA. Biological psychiatry Volume 80 (2016) p.284-292 DOI: 10.1016/j.biopsych.2015.10.009
Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation.
Rawlings ND. Biochimie Volume 122 (2016) p.5-30 DOI: 10.1016/j.biochi.2015.10.003
Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.
Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM, Jupp S, Koskinen S, Mannion O, Huerta L, Megy K, Snow C, Williams E, Barzine M, Hastings E, Weisser H, Wright J, Jaiswal P, Huber W, Choudhary J, Parkinson HE, Brazma A. Nucleic acids research Volume 44 (2016) p.D746-52 DOI: 10.1093/nar/gkv1045
*
Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies.
Patalano S, Vlasova A, Wyatt C, Ewels P, Camara F, Ferreira PG, Asher CL, Jurkowski TP, Segonds-Pichon A, Bachman M, González-Navarrete I, Minoche AE, Krueger F, Lowy E, Marcet-Houben M, Rodriguez-Ales JL, Nascimento FS, Balasubramanian S, Gabaldon T, Tarver JE, Andrews S, Himmelbauer H, Hughes WO, Guigó R, Reik W, Sumner S. Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.13970-13975 DOI: 10.1073/pnas.1515937112
PhytoPath: an integrative resource for plant pathogen genomics.
Pedro H, Maheswari U, Urban M, Urban M, Irvine AG, Cuzick A, McDowall MD, Staines DM, Kulesha E, Hammond-Kosack KE, Kersey PJ. Nucleic acids research Volume 44 (2016) p.D688-93 DOI: 10.1093/nar/gkv1052
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.
Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Lagerstedt I, Mir S, Fernandez Montecelo MA, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Sanz-García E, Sen S, Slowley RA, Wainwright ME, Deshpande MS, Iudin A, Sahni G, Salavert Torres J, Hirshberg M, Mak L, Nadzirin N, Armstrong DR, Clark AR, Smart OS, Korir PK, Kleywegt GJ. Nucleic acids research Volume 44 (2016) p.D385-95 DOI: 10.1093/nar/gkv1047
MinION Analysis and Reference Consortium: Phase 1 data release and analysis.
Ip CLC, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, Simpson JT, Snutch TP, Birney E, Buck D, Goodwin S, Jansen HJ, O'Grady J, Olsen HE, MinION Analysis and Reference Consortium. F1000Research Volume 4 (2015) p.1075 DOI: 10.12688/f1000research.7201.1
ChEBI in 2016: Improved services and an expanding collection of metabolites.
Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. Nucleic acids research Volume 44 (2016) p.D1214-9 DOI: 10.1093/nar/gkv1031
A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions.
Iorio F, Shrestha RL, Levin N, Boilot V, Garnett MJ, Saez-Rodriguez J, Draviam VM. PloS one Volume 10 (2015) p.e0139446 DOI: 10.1371/journal.pone.0139446
A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging.
Su J, Ekman C, Oskolkov N, Lahti L, Ström K, Brazma A, Groop L, Rung J, Hansson O. Skeletal muscle Volume 5 (2015) p.35 DOI: 10.1186/s13395-015-0059-1
DREAMTools: a Python package for scoring collaborative challenges.
Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, de la Fuente A, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G, Saez-Rodriguez J. F1000Research Volume 4 (2015) p.1030 DOI: 10.12688/f1000research.7118.2
Open and closed states of Candida antarctica lipase B: protonation and the mechanism of interfacial activation.
Stauch B, Fisher SJ, Cianci M. Journal of lipid research Volume 56 (2015) p.2348-2358 DOI: 10.1194/jlr.M063388
Devising a Consensus Framework for Validation of Novel Human Coding Loci.
Bruford EA, Lane L, Harrow J. Journal of proteome research Volume 14 (2015) p.4945-4948 DOI: 10.1021/acs.jproteome.5b00688
The genome as a record of environmental exposure.
Nik-Zainal S, Kucab JE, Morganella S, Glodzik D, Alexandrov LB, Arlt VM, Weninger A, Hollstein M, Stratton MR, Phillips DH. Mutagenesis Volume 30 (2015) p.763-770 DOI: 10.1093/mutage/gev073
Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.
Senger S, Bartek L, Papadatos G, Gaulton A. Journal of cheminformatics Volume 7 (2015) p.49 DOI: 10.1186/s13321-015-0097-z
*
Characterising Complex Enzyme Reaction Data
Dönertaş HM, Martínez Cuesta S, Rahman SA, Thornton JM. Preprint DOI: 10.1101/028142
Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.
Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J, Natarajan KN, Tuck AC, Gao X, Bühler M, Liu P, Marioni JC, Teichmann SA. Cell stem cell Volume 17 (2015) p.471-485 DOI: 10.1016/j.stem.2015.09.011
An integrated map of structural variation in 2,504 human genomes.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. Nature Volume 526 (2015) p.75-81 DOI: 10.1038/nature15394
*
A global reference for human genetic variation.
1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. Nature Volume 526 (2015) p.68-74 DOI: 10.1038/nature15393
Human genomics: The end of the start for population sequencing.
Birney E, Soranzo N. Nature Volume 526 (2015) p.52-53 DOI: 10.1038/526052a
Mondo-Mlx Mediates Organismal Sugar Sensing through the Gli-Similar Transcription Factor Sugarbabe.
Mattila J, Havula E, Suominen E, Teesalu M, Surakka I, Hynynen R, Kilpinen H, Väänänen J, Hovatta I, Käkelä R, Ripatti S, Sandmann T, Hietakangas V. Cell reports Volume 13 (2015) p.350-364 DOI: 10.1016/j.celrep.2015.08.081
*
The digital revolution in phenotyping.
Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. Briefings in bioinformatics Volume 17 (2016) p.819-830 DOI: 10.1093/bib/bbv083
VEGAWES: variational segmentation on whole exome sequencing for copy number detection.
Anjum S, Morganella S, D'Angelo F, Iavarone A, Ceccarelli M. BMC bioinformatics Volume 16 (2015) p.315 DOI: 10.1186/s12859-015-0748-0
*
Comprehensive Analysis of Pan-African Mitochondrial DNA Variation Provides New Insights into Continental Variation and Demography.
Cerezo M, Gusmão L, Černý V, Uddin N, Syndercombe-Court D, Gómez-Carballa A, Göbel T, Schneider PM, Salas A. Journal of genetics and genomics = Yi chuan xue bao Volume 43 (2016) p.133-143 DOI: 10.1016/j.jgg.2015.09.005
AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators.
Sousa FL, Parente DJ, Shis DL, Hessman JA, Chazelle A, Bennett MR, Teichmann SA, Swint-Kruse L. Journal of molecular biology Volume 428 (2016) p.671-678 DOI: 10.1016/j.jmb.2015.09.015
Eyeing the Cyr61/CTGF/NOV (CCN) group of genes in development and diseases: highlights of their structural likenesses and functional dissimilarities.
Krupska I, Bruford EA, Chaqour B. Human genomics Volume 9 (2015) p.24 DOI: 10.1186/s40246-015-0046-y
*
Glucose-6-phosphate dehydrogenase deficiency and the risk of malaria and other diseases in children in Kenya: a case-control and a cohort study.
Uyoga S, Ndila CM, Macharia AW, Nyutu G, Shah S, Peshu N, Clarke GM, Kwiatkowski DP, Rockett KA, Williams TN, MalariaGEN Consortium. The Lancet. Haematology Volume 2 (2015) p.e437-44 DOI: 10.1016/S2352-3026(15)00152-0
Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength.
Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR. Genome biology Volume 16 (2015) p.201 DOI: 10.1186/s13059-015-0749-3
Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.
Tsang JC, Yu Y, Burke S, Buettner F, Wang C, Kolodziejczyk AA, Teichmann SA, Lu L, Liu P. Genome biology Volume 16 (2015) p.178 DOI: 10.1186/s13059-015-0739-5
The genome of the vervet (Chlorocebus aethiops sabaeus).
Warren WC, Jasinska AJ, García-Pérez R, Svardal H, Tomlinson C, Rocchi M, Archidiacono N, Capozzi O, Minx P, Montague MJ, Kyung K, Hillier LW, Kremitzki M, Graves T, Chiang C, Hughes J, Tran N, Huang Y, Ramensky V, Choi OW, Jung YJ, Schmitt CA, Juretic N, Wasserscheid J, Turner TR, Wiseman RW, Tuscher JJ, Karl JA, Schmitz JE, Zahn R, O'Connor DH, Redmond E, Nisbett A, Jacquelin B, Müller-Trutwin MC, Brenchley JM, Dione M, Antonio M, Schroth GP, Kaplan JR, Jorgensen MJ, Thomas GW, Hahn MW, Raney BJ, Aken B, Nag R, Schmitz J, Churakov G, Noll A, Stanyon R, Webb D, Thibaud-Nissen F, Nordborg M, Marques-Bonet T, Dewar K, Weinstock GM, Wilson RK, Freimer NB. Genome research Volume 25 (2015) p.1921-1933 DOI: 10.1101/gr.192922.115
Using human genetics to make new medicines.
Barrett JC, Dunham I, Birney E. Nature reviews. Genetics Volume 16 (2015) p.561-562 DOI: 10.1038/nrg3998
*
Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.
Huang J, Howie B, McCarthy S, Memari Y, Walter K, Min JL, Danecek P, Malerba G, Trabetti E, Zheng HF, UK10K Consortium, Gambaro G, Richards JB, Durbin R, Timpson NJ, Marchini J, Soranzo N. Nature communications Volume 6 (2015) p.8111 DOI: 10.1038/ncomms9111
*
The UK10K project identifies rare variants in health and disease.
UK10K Consortium, Walter K, Min JL, Huang J, Crooks L, Memari Y, McCarthy S, Perry JR, Xu C, Futema M, Lawson D, Iotchkova V, Schiffels S, Hendricks AE, Danecek P, Li R, Floyd J, Wain LV, Barroso I, Humphries SE, Hurles ME, Zeggini E, Barrett JC, Plagnol V, Richards JB, Greenwood CM, Timpson NJ, Durbin R, Soranzo N. Nature Volume 526 (2015) p.82-90 DOI: 10.1038/nature14962
Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data.
Terfve CD, Wilkes EH, Casado P, Cutillas PR, Saez-Rodriguez J. Nature communications Volume 6 (2015) p.8033 DOI: 10.1038/ncomms9033
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel.
Cortés-Ciriano I, van Westen GJ, Bouvier G, Nilges M, Overington JP, Bender A, Malliavin TE. Bioinformatics (Oxford, England) Volume 32 (2016) p.85-95 DOI: 10.1093/bioinformatics/btv529
Estimation of Free-Living Energy Expenditure by Heart Rate and Movement Sensing: A Doubly-Labelled Water Study.
Brage S, Westgate K, Franks PW, Stegle O, Wright A, Ekelund U, Wareham NJ. PloS one Volume 10 (2015) p.e0137206 DOI: 10.1371/journal.pone.0137206
*
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.
Hucka M, Bergmann FT, Hoops S, Keating SM, Sahle S, Schaff JC, Smith LP, Wilkinson DJ. Journal of integrative bioinformatics Volume 12 (2015) p.266 DOI: 10.2390/biecoll-jib-2015-266
Designing Experiments to Discriminate Families of Logic Models.
Videla S, Konokotina I, Alexopoulos LG, Saez-Rodriguez J, Schaub T, Siegel A, Guziolowski C. Frontiers in bioengineering and biotechnology Volume 3 (2015) p.131 DOI: 10.3389/fbioe.2015.00131
*
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.
Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. Journal of integrative bioinformatics Volume 12 (2015) p.271 DOI: 10.2390/biecoll-jib-2015-271
Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.
Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC, Odom DT. PloS one Volume 10 (2015) p.e0137367 DOI: 10.1371/journal.pone.0137367
*
The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.
Chaouiya C, Keating SM, Berenguier D, Naldi A, Thieffry D, van Iersel MP, Le Novère N, Helikar T. Journal of integrative bioinformatics Volume 12 (2015) p.270 DOI: 10.2390/biecoll-jib-2015-270
*
Prediction of Metabolic Pathways Involvement in Prokaryotic UniProtKB Data by Association Rule Mining
Boudellioua I, Saidi R, Martin M, Hoehndorf R, Solovyev V.
*
Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability.
Twigg SR, Forecki J, Goos JA, Richardson IC, Hoogeboom AJ, van den Ouweland AM, Swagemakers SM, Lequin MH, Van Antwerp D, McGowan SJ, Westbury I, Miller KA, Wall SA, WGS500 Consortium, van der Spek PJ, Mathijssen IM, Pauws E, Merzdorf CS, Wilkie AO. American journal of human genetics Volume 97 (2015) p.378-388 DOI: 10.1016/j.ajhg.2015.07.007
*
The new science of ageing.
Partridge L, Thornton J, Bates G. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 370 (2015) DOI: 10.1098/rstb.2015.0249
A mouse informatics platform for phenotypic and translational discovery.
Ring N, Meehan TF, Blake A, Brown J, Chen CK, Conte N, Di Fenza A, Fiegel T, Horner N, Jacobsen JO, Karp N, Lawson T, Mason JC, Matthews P, Morgan H, Relac M, Santos L, Smedley D, Sneddon D, Pengelly A, Tudose I, Warren JW, Westerberg H, Yaikhom G, Parkinson H, Mallon AM. Mammalian genome : official journal of the International Mammalian Genome Society Volume 26 (2015) p.413-421 DOI: 10.1007/s00335-015-9599-2
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules.
Murrell DS, Cortes-Ciriano I, van Westen GJP, Stott IP, Bender A, Malliavin TE, Glen RC. Journal of cheminformatics Volume 7 (2015) p.45 DOI: 10.1186/s13321-015-0086-2
*
Simultaneously inferring T cell fate and clonality from single cell transcriptomes
Stubbington MJ, Lönnberg T, Proserpio V, Clare S, Speak AO, Dougan G, Teichmann SA. Preprint DOI: 10.1101/025676
Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.
Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P. PLoS computational biology Volume 11 (2015) p.e1004362 DOI: 10.1371/journal.pcbi.1004362
Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research.
Spjuth O, Krestyaninova M, Hastings J, Shen HY, Heikkinen J, Waldenberger M, Langhammer A, Ladenvall C, Esko T, Persson MÅ, Heggland J, Dietrich J, Ose S, Gieger C, Ried JS, Peters A, Fortier I, de Geus EJ, Klovins J, Zaharenko L, Willemsen G, Hottenga JJ, Litton JE, Karvanen J, Boomsma DI, Groop L, Rung J, Palmgren J, Pedersen NL, McCarthy MI, van Duijn CM, Hveem K, Metspalu A, Ripatti S, Prokopenko I, Harris JR. European journal of human genetics : EJHG Volume 24 (2016) p.521-528 DOI: 10.1038/ejhg.2015.165
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.
Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright AJ, Iliopoulos I. GigaScience Volume 4 (2015) p.38 DOI: 10.1186/s13742-015-0077-2
Changes in Postural Syntax Characterize Sensory Modulation and Natural Variation of C. elegans Locomotion.
Schwarz RF, Branicky R, Grundy LJ, Schafer WR, Brown AE. PLoS computational biology Volume 11 (2015) p.e1004322 DOI: 10.1371/journal.pcbi.1004322
*
A gene expression resource generated by genome-wide lacZ profiling in the mouse.
Tuck E, Estabel J, Oellrich A, Maguire AK, Adissu HA, Souter L, Siragher E, Lillistone C, Green AL, Wardle-Jones H, Carragher DM, Karp NA, Smedley D, Adams NC, Sanger Institute Mouse Genetics Project, Bussell JN, Adams DJ, Ramírez-Solis R, Steel KP, Galli A, White JK. Disease models & mechanisms Volume 8 (2015) p.1467-1478 DOI: 10.1242/dmm.021238
Modeling Signaling Networks to Advance New Cancer Therapies.
Saez-Rodriguez J, MacNamara A, Cook S. Annual review of biomedical engineering Volume 17 (2015) p.143-163 DOI: 10.1146/annurev-bioeng-071813-104927
Prediction of human population responses to toxic compounds by a collaborative competition.
Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O, NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J. Nature biotechnology Volume 33 (2015) p.933-940 DOI: 10.1038/nbt.3299
*
Introduction to the Biomedical Linked Annotation Hackathon (BLAH) 2015 Symposium.
Kim J, Cohen KB, Collier N, Lu Z, Stenetorp P. BMC proceedings Volume 9 (2015) p.A1-A1 DOI: 10.1186/1753-6561-9-S5-A1
SurvCurv database and online survival analysis platform update.
Ziehm M, Ivanov DK, Bhat A, Partridge L, Thornton JM. Bioinformatics (Oxford, England) Volume 31 (2015) p.3878-3880 DOI: 10.1093/bioinformatics/btv463
Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems.
Hostaš J, Jakubec D, Laskowski RA, Gnanasekaran R, Řezáč J, Vondrášek J, Hobza P. Journal of chemical theory and computation Volume 11 (2015) p.4086-4092 DOI: 10.1021/acs.jctc.5b00398
DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug-Drug Interactions and Their Mechanisms.
Herrero-Zazo M, Segura-Bedmar I, Hastings J, Martínez P. Journal of chemical information and modeling Volume 55 (2015) p.1698-1707 DOI: 10.1021/acs.jcim.5b00119
Molecular disease presentation in diabetic nephropathy.
Heinzel A, Mühlberger I, Stelzer G, Lancet D, Oberbauer R, Martin M, Perco P. Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association Volume 30 Suppl 4 (2015) p.iv17-25 DOI: 10.1093/ndt/gfv267
*
Biology, wet and dry.
Teichmann S, Pain E. Science (New York, N.Y.) Volume 349 (2015) p.662 DOI: 10.1126/science.349.6248.662
Europe: Lifelong learning for all in biomedicine.
Brooksbank C, Johnson C. Nature Volume 524 (2015) p.415 DOI: 10.1038/524415c
Genetic characterization of three qnrS1-harbouring multidrug-resistance plasmids and qnrS1-containing transposons circulating in Ho Chi Minh City, Vietnam.
Le V, Nhu NT, Cerdeno-Tarraga A, Campbell JI, Tuyen HT, Nhu Tdo H, Tam PT, Schultsz C, Thwaites G, Thomson NR, Baker S. Journal of medical microbiology Volume 64 (2015) p.869-878 DOI: 10.1099/jmm.0.000100
*
Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury.
Melas IN, Sakellaropoulos T, Iorio F, Alexopoulos LG, Loh WY, Lauffenburger DA, Saez-Rodriguez J, Bai JP. Integrative biology : quantitative biosciences from nano to macro Volume 7 (2015) p.904-920 DOI: 10.1039/c4ib00294f
*
Integrative approaches for signalling and metabolic networks.
Hatzimanikatis V, Saez-Rodriguez J. Integrative biology : quantitative biosciences from nano to macro Volume 7 (2015) p.844-845 DOI: 10.1039/c5ib90030a
Improving the Sequence Ontology terminology for genomic variant annotation.
Cunningham F, Moore B, Ruiz-Schultz N, Ritchie GR, Eilbeck K. Journal of biomedical semantics Volume 6 (2015) p.32 DOI: 10.1186/s13326-015-0030-4
Where Next for Genetics and Genomics?
Tyler-Smith C, Yang H, Landweber LF, Dunham I, Knoppers BM, Donnelly P, Mardis ER, Snyder M, McVean G. PLoS biology Volume 13 (2015) p.e1002216 DOI: 10.1371/journal.pbio.1002216
Representing virus-host interactions and other multi-organism processes in the Gene Ontology.
Foulger RE, Osumi-Sutherland D, McIntosh BK, Hulo C, Masson P, Poux S, Le Mercier P, Lomax J. BMC microbiology Volume 15 (2015) p.146 DOI: 10.1186/s12866-015-0481-x
The eNanoMapper database for nanomaterial safety information.
Jeliazkova N, Chomenidis C, Doganis P, Fadeel B, Grafström R, Hardy B, Hastings J, Hegi M, Jeliazkov V, Kochev N, Kohonen P, Munteanu CR, Sarimveis H, Smeets B, Sopasakis P, Tsiliki G, Vorgrimmler D, Willighagen E. Beilstein journal of nanotechnology Volume 6 (2015) p.1609-1634 DOI: 10.3762/bjnano.6.165
Activity, assay and target data curation and quality in the ChEMBL database.
Papadatos G, Gaulton A, Hersey A, Overington JP. Journal of computer-aided molecular design Volume 29 (2015) p.885-896 DOI: 10.1007/s10822-015-9860-5
Precision medicine: Look to the mice.
Lloyd KC, Meehan T, Beaudet A, Murray S, Svenson K, McKerlie C, West D, Morse I, Parkinson H, Brown S, Mallon AM, Moore M. Science (New York, N.Y.) Volume 349 (2015) p.390 DOI: 10.1126/science.349.6246.390-a
Delicate Metabolic Control and Coordinated Stress Response Critically Determine Antifungal Tolerance of Candida albicans Biofilm Persisters.
Li P, Seneviratne CJ, Alpi E, Vizcaino JA, Jin L. Antimicrobial agents and chemotherapy Volume 59 (2015) p.6101-6112 DOI: 10.1128/AAC.00543-15
Epigenome data release: a participant-centered approach to privacy protection.
Dyke SO, Cheung WA, Joly Y, Ammerpohl O, Lutsik P, Rothstein MA, Caron M, Busche S, Bourque G, Rönnblom L, Flicek P, Beck S, Hirst M, Stunnenberg H, Siebert R, Walter J, Pastinen T. Genome biology Volume 16 (2015) p.142 DOI: 10.1186/s13059-015-0723-0
Sharing and Reuse of Sensitive Data and Samples: Supporting Researchers in Identifying Ethical and Legal Requirements.
Sariyar M, Schluender I, Smee C, Suhr S. Biopreservation and biobanking Volume 13 (2015) p.263-270 DOI: 10.1089/bio.2015.0014
Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites.
Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M, Michálek J, Saxena A, Shanmugam D, Tayyrov A, Veluchamy A, Ali S, Bernal A, del Campo J, Cihlář J, Flegontov P, Gornik SG, Hajdušková E, Horák A, Janouškovec J, Katris NJ, Mast FD, Miranda-Saavedra D, Mourier T, Naeem R, Nair M, Panigrahi AK, Rawlings ND, Padron-Regalado E, Ramaprasad A, Samad N, Tomčala A, Wilkes J, Neafsey DE, Doerig C, Bowler C, Keeling PJ, Roos DS, Dacks JB, Templeton TJ, Waller RF, Lukeš J, Oborník M, Pain A. eLife Volume 4 (2015) p.e06974 DOI: 10.7554/eLife.06974
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases.
Fu G, Batchelor C, Dumontier M, Hastings J, Willighagen E, Bolton E. Journal of cheminformatics Volume 7 (2015) p.34 DOI: 10.1186/s13321-015-0084-4
*
Third Report on Chicken Genes and Chromosomes 2015.
Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RP, Damas J, Davis RV, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MA, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JM, Wragg D, Zhou H. Cytogenetic and genome research Volume 145 (2015) p.78-179 DOI: 10.1159/000430927
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.
Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G. Database : the journal of biological databases and curation Volume 2015 (2015) p.bav063 DOI: 10.1093/database/bav063
*
European Adder bites in dogs in southern Germany. A retrospective study over a 6.5-year period.
Turković V, Teichmann S, Dörfelt R. Tierarztliche Praxis. Ausgabe K, Kleintiere/Heimtiere Volume 43 (2015) p.221-230 DOI: 10.15654/tpk-140364
Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells.
Núñez de Villavicencio-Díaz T, Ramos Gómez Y, Oliva Argüelles B, Fernández Masso JR, Rodríguez-Ulloa A, Cruz García Y, Guirola-Cruz O, Perez-Riverol Y, Javier González L, Tiscornia I, Victoria S, Bollati-Fogolín M, Besada Pérez V, Guerra Vallespi M. Data in Brief Volume 4 (2015) p.468-473 DOI: 10.1016/j.dib.2015.06.024
A large-scale crop protection bioassay data set.
Gaulton A, Kale N, van Westen GJ, Bellis LJ, Bento AP, Davies M, Hersey A, Papadatos G, Forster M, Wege P, Overington JP. Scientific data Volume 2 (2015) p.150032 DOI: 10.1038/sdata.2015.32
*
Structure and evolutionary history of a large family of NLR proteins in the zebrafish
Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni J, Soylemez O, Kondrashov F, Leptin M. Preprint DOI: 10.1101/022061
PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data.
Kurbatova N, Mason JC, Morgan H, Meehan TF, Karp NA. PloS one Volume 10 (2015) p.e0131274 DOI: 10.1371/journal.pone.0131274
Computational assignment of cell-cycle stage from single-cell transcriptome data.
Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, Marioni JC, Buettner F. Methods (San Diego, Calif.) Volume 85 (2015) p.54-61 DOI: 10.1016/j.ymeth.2015.06.021
Computational and Practical Aspects of Drug Repositioning.
Oprea TI, Overington JP. Assay and drug development technologies Volume 13 (2015) p.299-306 DOI: 10.1089/adt.2015.29011.tiodrrr
*
A draft genome sequence of an invasive mosquito: an Italian Aedes albopictus.
Dritsou V, Topalis P, Windbichler N, Simoni A, Hall A, Lawson D, Hinsley M, Hughes D, Napolioni V, Crucianelli F, Deligianni E, Gasperi G, Gomulski LM, Savini G, Manni M, Scolari F, Malacrida AR, Arcà B, Ribeiro JM, Lombardo F, Saccone G, Salvemini M, Moretti R, Aprea G, Calvitti M, Picciolini M, Papathanos PA, Spaccapelo R, Favia G, Crisanti A, Louis C. Pathogens and global health Volume 109 (2015) p.207-220 DOI: 10.1179/2047773215Y.0000000031
Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.
Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T, Quest for Orthologs Species Tree Working Group. Genome biology and evolution Volume 7 (2015) p.1988-1999 DOI: 10.1093/gbe/evv121
The European Genome-phenome Archive of human data consented for biomedical research.
Lappalainen I, Almeida-King J, Kumanduri V, Senf A, Spalding JD, Ur-Rehman S, Saunders G, Kandasamy J, Caccamo M, Leinonen R, Vaughan B, Laurent T, Rowland F, Marin-Garcia P, Barker J, Jokinen P, Torres AC, de Argila JR, Llobet OM, Medina I, Puy MS, Alberich M, de la Torre S, Navarro A, Paschall J, Flicek P. Nature genetics Volume 47 (2015) p.692-695 DOI: 10.1038/ng.3312
Identifying novel sequence variants of RNA 3D motifs.
Zirbel CL, Roll J, Sweeney BA, Petrov AI, Pirrung M, Leontis NB. Nucleic acids research Volume 43 (2015) p.7504-7520 DOI: 10.1093/nar/gkv651
*
Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders.
van Schouwenburg PA, Davenport EE, Kienzler AK, Marwah I, Wright B, Lucas M, Malinauskas T, Martin HC, WGS500 Consortium, Lockstone HE, Cazier JB, Chapel HM, Knight JC, Patel SY. Clinical immunology (Orlando, Fla.) Volume 160 (2015) p.301-314 DOI: 10.1016/j.clim.2015.05.020
Molecular and neuronal homology between the olfactory systems of zebrafish and mouse.
Saraiva LR, Ahuja G, Ivandic I, Syed AS, Marioni JC, Korsching SI, Logan DW. Scientific reports Volume 5 (2015) p.11487 DOI: 10.1038/srep11487
A random forest approach to capture genetic effects in the presence of population structure.
Stephan J, Stegle O, Beyer A. Nature communications Volume 6 (2015) p.7432 DOI: 10.1038/ncomms8432
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.
Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN. American journal of human genetics Volume 97 (2015) p.111-124 DOI: 10.1016/j.ajhg.2015.05.020
The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding.
Xie X, Stubbington MJ, Nissen JK, Andersen KG, Hebenstreit D, Teichmann SA, Betz AG. PLoS genetics Volume 11 (2015) p.e1005251 DOI: 10.1371/journal.pgen.1005251
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.
Vallejos CA, Marioni JC, Richardson S. PLoS computational biology Volume 11 (2015) p.e1004333 DOI: 10.1371/journal.pcbi.1004333
Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling.
Mak L, Marcus D, Howlett A, Yarova G, Duchateau G, Klaffke W, Bender A, Glen RC. Journal of cheminformatics Volume 7 (2015) p.31 DOI: 10.1186/s13321-015-0083-5
Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.
Duarte AM, Psomopoulos FE, Blanchet C, Bonvin AM, Corpas M, Franc A, Jimenez RC, de Lucas JM, Nyrönen T, Sipos G, Suhr SB. Frontiers in genetics Volume 6 (2015) p.197 DOI: 10.3389/fgene.2015.00197
Chimira: analysis of small RNA sequencing data and microRNA modifications.
Vitsios DM, Enright AJ. Bioinformatics (Oxford, England) Volume 31 (2015) p.3365-3367 DOI: 10.1093/bioinformatics/btv380
The Importance of Biological Databases in Biological Discovery.
Baxevanis AD, Bateman A. Current protocols in bioinformatics Volume 50 (2015) p.1.1.1-8 DOI: 10.1002/0471250953.bi0101s50
Searching and Navigating UniProt Databases.
Pundir S, Magrane M, Martin MJ, O'Donovan C, UniProt Consortium. Current protocols in bioinformatics Volume 50 (2015) p.1.27.1-10 DOI: 10.1002/0471250953.bi0127s50
The ocean sampling day consortium.
Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, Fernandez-Guerra A, Jeanthon C, Rahav E, Ullrich M, Wichels A, Gerdts G, Polymenakou P, Kotoulas G, Siam R, Abdallah RZ, Sonnenschein EC, Cariou T, O'Gara F, Jackson S, Orlic S, Steinke M, Busch J, Duarte B, Caçador I, Canning-Clode J, Bobrova O, Marteinsson V, Reynisson E, Loureiro CM, Luna GM, Quero GM, Löscher CR, Kremp A, DeLorenzo ME, Øvreås L, Tolman J, LaRoche J, Penna A, Frischer M, Davis T, Katherine B, Meyer CP, Ramos S, Magalhães C, Jude-Lemeilleur F, Aguirre-Macedo ML, Wang S, Poulton N, Jones S, Collin R, Fuhrman JA, Conan P, Alonso C, Stambler N, Goodwin K, Yakimov MM, Baltar F, Bodrossy L, Van De Kamp J, Frampton DM, Ostrowski M, Van Ruth P, Malthouse P, Claus S, Deneudt K, Mortelmans J, Pitois S, Wallom D, Salter I, Costa R, Schroeder DC, Kandil MM, Amaral V, Biancalana F, Santana R, Pedrotti ML, Yoshida T, Ogata H, Ingleton T, Munnik K, Rodriguez-Ezpeleta N, Berteaux-Lecellier V, Wecker P, Cancio I, Vaulot D, Bienhold C, Ghazal H, Chaouni B, Essayeh S, Ettamimi S, Zaid el H, Boukhatem N, Bouali A, Chahboune R, Barrijal S, Timinouni M, El Otmani F, Bennani M, Mea M, Todorova N, Karamfilov V, Ten Hoopen P, Cochrane G, L'Haridon S, Bizsel KC, Vezzi A, Lauro FM, Martin P, Jensen RM, Hinks J, Gebbels S, Rosselli R, De Pascale F, Schiavon R, Dos Santos A, Villar E, Pesant S, Cataletto B, Malfatti F, Edirisinghe R, Silveira JA, Barbier M, Turk V, Tinta T, Fuller WJ, Salihoglu I, Serakinci N, Ergoren MC, Bresnan E, Iriberri J, Nyhus PA, Bente E, Karlsen HE, Golyshin PN, Gasol JM, Moncheva S, Dzhembekova N, Johnson Z, Sinigalliano CD, Gidley ML, Zingone A, Danovaro R, Tsiamis G, Clark MS, Costa AC, El Bour M, Martins AM, Collins RE, Ducluzeau AL, Martinez J, Costello MJ, Amaral-Zettler LA, Gilbert JA, Davies N, Field D, Glöckner FO. GigaScience Volume 4 (2015) p.27 DOI: 10.1186/s13742-015-0066-5
*
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.
Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J. BMC genomics Volume 16 Suppl 8 (2015) p.S2 DOI: 10.1186/1471-2164-16-S8-S2
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Structure (London, England : 1993) Volume 23 (2015) p.1156-1167 DOI: 10.1016/j.str.2015.05.013
Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life.
Faddeeva A, Studer RA, Kraaijeveld K, Sie D, Ylstra B, Mariën J, op den Camp HJ, Datema E, den Dunnen JT, van Straalen NM, Roelofs D. PloS one Volume 10 (2015) p.e0130600 DOI: 10.1371/journal.pone.0130600
Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.
Swat MJ, Moodie S, Wimalaratne SM, Kristensen NR, Lavielle M, Mari A, Magni P, Smith MK, Bizzotto R, Pasotti L, Mezzalana E, Comets E, Sarr C, Terranova N, Blaudez E, Chan P, Chard J, Chatel K, Chenel M, Edwards D, Franklin C, Giorgino T, Glont M, Girard P, Grenon P, Harling K, Hooker AC, Kaye R, Keizer R, Kloft C, Kok JN, Kokash N, Laibe C, Laveille C, Lestini G, Mentré F, Munafo A, Nordgren R, Nyberg HB, Parra-Guillen ZP, Plan E, Ribba B, Smith G, Trocóniz IF, Yvon F, Milligan PA, Harnisch L, Karlsson M, Hermjakob H, Le Novère N. CPT: pharmacometrics & systems pharmacology Volume 4 (2015) p.316-319 DOI: 10.1002/psp4.57
Efficient set tests for the genetic analysis of correlated traits.
Casale FP, Rakitsch B, Lippert C, Stegle O. Nature methods Volume 12 (2015) p.755-758 DOI: 10.1038/nmeth.3439
*
ISMB/ECCB 2015 Proceedings Papers Committee.
Bioinformatics (Oxford, England) Volume 31 (2015) p.i3-i8 DOI: 10.1093/bioinformatics/btv310
Empirical inference of circuitry and plasticity in a kinase signaling network.
Wilkes EH, Terfve C, Gribben JG, Saez-Rodriguez J, Cutillas PR. Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.7719-7724 DOI: 10.1073/pnas.1423344112
Whole-genome fingerprint of the DNA methylome during human B cell differentiation.
Kulis M, Merkel A, Heath S, Queirós AC, Schuyler RP, Castellano G, Beekman R, Raineri E, Esteve A, Clot G, Verdaguer-Dot N, Duran-Ferrer M, Russiñol N, Vilarrasa-Blasi R, Ecker S, Pancaldi V, Rico D, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, Pascual M, Agirre X, Prosper F, Alignani D, Paiva B, Caron G, Fest T, Muench MO, Fomin ME, Lee ST, Wiemels JL, Valencia A, Gut M, Flicek P, Stunnenberg HG, Siebert R, Küppers R, Gut IG, Campo E, Martín-Subero JI. Nature genetics Volume 47 (2015) p.746-756 DOI: 10.1038/ng.3291
R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.
Cannone JJ, Sweeney BA, Petrov AI, Gutell RR, Zirbel CL, Leontis N. Nucleic acids research Volume 43 (2015) p.W15-23 DOI: 10.1093/nar/gkv543
Towards recommendations for metadata and data handling in plant phenotyping.
Krajewski P, Chen D, Ćwiek H, van Dijk AD, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap JP, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S. Journal of experimental botany Volume 66 (2015) p.5417-5427 DOI: 10.1093/jxb/erv271
Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.
Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C. Systematic biology Volume 64 (2015) p.778-791 DOI: 10.1093/sysbio/syv033
Concept selection for phenotypes and diseases using learn to rank.
Collier N, Oellrich A, Groza T. Journal of biomedical semantics Volume 6 (2015) p.24 DOI: 10.1186/s13326-015-0019-z
*
ISMB/ECCB 2015.
Moreau Y, Beerenwinkel N. Bioinformatics (Oxford, England) Volume 31 (2015) p.i1-2 DOI: 10.1093/bioinformatics/btv303
NMR Exchange Format: a unified and open standard for representation of NMR restraint data.
Gutmanas A, Adams PD, Bardiaux B, Berman HM, Case DA, Fogh RH, Güntert P, Hendrickx PM, Herrmann T, Kleywegt GJ, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, Ragan TJ, Schwieters CD, Tejero R, Ulrich EL, Velankar S, Vranken WF, Wedell JR, Westbrook J, Wishart DS, Vuister GW. Nature structural & molecular biology Volume 22 (2015) p.433-434 DOI: 10.1038/nsmb.3041
COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.
Salek RM, Neumann S, Schober D, Hummel J, Billiau K, Kopka J, Correa E, Reijmers T, Rosato A, Tenori L, Turano P, Marin S, Deborde C, Jacob D, Rolin D, Dartigues B, Conesa P, Haug K, Rocca-Serra P, O'Hagan S, Hao J, van Vliet M, Sysi-Aho M, Ludwig C, Bouwman J, Cascante M, Ebbels T, Griffin JL, Moing A, Nikolski M, Oresic M, Sansone SA, Viant MR, Goodacre R, Günther UL, Hankemeier T, Luchinat C, Walther D, Steinbeck C. Metabolomics : Official journal of the Metabolomic Society Volume 11 (2015) p.1587-1597 DOI: 10.1007/s11306-015-0810-y
Comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells.
Núñez de Villavicencio-Díaz T, Ramos Gómez Y, Oliva Argüelles B, Fernández Masso JR, Rodríguez-Ulloa A, Cruz García Y, Guirola-Cruz O, Perez-Riverol Y, Javier González L, Tiscornia I, Victoria S, Bollati-Fogolín M, Besada Pérez V, Guerra Vallespi M. Journal of proteomics Volume 126 (2015) p.163-171 DOI: 10.1016/j.jprot.2015.05.024
Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.
Henriques D, Rocha M, Saez-Rodriguez J, Banga JR. Bioinformatics (Oxford, England) Volume 31 (2015) p.2999-3007 DOI: 10.1093/bioinformatics/btv314
Applying the ARRIVE Guidelines to an In Vivo Database.
Karp NA, Meehan TF, Morgan H, Mason JC, Blake A, Kurbatova N, Smedley D, Jacobsen J, Mott RF, Iyer V, Matthews P, Melvin DG, Wells S, Flenniken AM, Masuya H, Wakana S, White JK, Lloyd KC, Reynolds CL, Paylor R, West DB, Svenson KL, Chesler EJ, de Angelis MH, Tocchini-Valentini GP, Sorg T, Herault Y, Parkinson H, Mallon AM, Brown SD. PLoS biology Volume 13 (2015) p.e1002151 DOI: 10.1371/journal.pbio.1002151
Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus.
Aguiar B, Vieira J, Cunha AE, Fonseca NA, Iezzoni A, van Nocker S, Vieira CP. PloS one Volume 10 (2015) p.e0126138 DOI: 10.1371/journal.pone.0126138
*
Correction: Abundant Genetic Overlap between Blood Lipids and Immune-Mediated Diseases Indicates Shared Molecular Genetic Mechanisms.
Andreassen OA, Desikan RS, Wang Y, Thompson WK, Schork AJ, Zuber V, Doncheva NT, Ellinghaus E, Albrecht M, Mattingsdal M, Franke A, Lie BA, Mills IG, Aukrust P, McEvoy LK, Djurovic S, Karlsen TH, Dale AM. PloS one Volume 10 (2015) p.e0128048 DOI: 10.1371/journal.pone.0128048
The Classification and Evolution of Enzyme Function.
Martínez Cuesta S, Rahman SA, Furnham N, Thornton JM. Biophysical journal Volume 109 (2015) p.1082-1086 DOI: 10.1016/j.bpj.2015.04.020
*
Erratum: A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans.
Timpson NJ, Walter K, Min JL, Tachmazidou I, Malerba G, Shin SY, Chen L, Futema M, Southam L, Iotchkova V, Cocca M, Huang J, Memari Y, McCarthy S, Danecek P, Muddyman D, Mangino M, Menni C, Perry JR, Ring SM, Gaye A, Dedoussis G, Farmaki AE, Burton P, Talmud PJ, Gambaro G, Spector TD, Smith GD, Durbin R, Richards JB, Humphries SE, Zeggini E, Soranzo N, UK10K Consortium. Nature communications Volume 6 (2015) p.7171 DOI: 10.1038/ncomms8171
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.
Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M. Database : the journal of biological databases and curation Volume 2015 (2015) p.bav043 DOI: 10.1093/database/bav043
SpeckTackle: JavaScript charts for spectroscopy.
Beisken S, Conesa P, Haug K, Salek RM, Steinbeck C. Journal of cheminformatics Volume 7 (2015) p.17 DOI: 10.1186/s13321-015-0065-7
Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards.
Ten Hoopen P, Pesant S, Kottmann R, Kopf A, Bicak M, Claus S, Deneudt K, Borremans C, Thijsse P, Dekeyzer S, Schaap DM, Bowler C, Glöckner FO, Cochrane G. Standards in genomic sciences Volume 10 (2015) p.20 DOI: 10.1186/s40793-015-0001-5
A single-cell model of PIP3 dynamics using chemical dimerization.
MacNamara A, Stein F, Feng S, Schultz C, Saez-Rodriguez J. Bioorganic & medicinal chemistry Volume 23 (2015) p.2868-2876 DOI: 10.1016/j.bmc.2015.04.074
HMMER web server: 2015 update.
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR. Nucleic acids research Volume 43 (2015) p.W30-8 DOI: 10.1093/nar/gkv397
DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M. eLife Volume 4 (2015) p.e05255 DOI: 10.7554/eLife.05255
*
Bacteria and the evolution of honest signals. The case of ornamental throat feathers in spotless starlings
Ruiz‐Rodríguez M, Tomás G, Martín‐Gálvez D, Ruiz‐Castellano C, Soler JJ, McGraw K. Functional ecology. Volume 29 (2015) p.701-709 DOI: 10.1111/1365-2435.12376
The technology and biology of single-cell RNA sequencing.
Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA. Molecular cell Volume 58 (2015) p.610-620 DOI: 10.1016/j.molcel.2015.04.005
*
Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.
Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J, GTEx Consortium, Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG. Science (New York, N.Y.) Volume 348 (2015) p.666-669 DOI: 10.1126/science.1261877
Prospective derivation of a living organoid biobank of colorectal cancer patients.
van de Wetering M, Francies HE, Francis JM, Bounova G, Iorio F, Pronk A, van Houdt W, van Gorp J, Taylor-Weiner A, Kester L, McLaren-Douglas A, Blokker J, Jaksani S, Bartfeld S, Volckman R, van Sluis P, Li VS, Seepo S, Sekhar Pedamallu C, Cibulskis K, Carter SL, McKenna A, Lawrence MS, Lichtenstein L, Stewart C, Koster J, Versteeg R, van Oudenaarden A, Saez-Rodriguez J, Vries RG, Getz G, Wessels L, Stratton MR, McDermott U, Meyerson M, Garnett MJ, Clevers H. Cell Volume 161 (2015) p.933-945 DOI: 10.1016/j.cell.2015.03.053
Nomenclature of Toso, Fas apoptosis inhibitory molecule 3, and IgM FcR.
Kubagawa H, Carroll MC, Jacob CO, Lang KS, Lee KH, Mak T, McAndrews M, Morse HC, Nolan GP, Ohno H, Richter GH, Seal R, Wang JY, Wiestner A, Coligan JE. Journal of immunology (Baltimore, Md. : 1950) Volume 194 (2015) p.4055-4057 DOI: 10.4049/jimmunol.1500222
Domain atrophy creates rare cases of functional partial protein domains.
Prakash A, Bateman A. Genome biology Volume 16 (2015) p.88 DOI: 10.1186/s13059-015-0655-8
The relationship between target-class and the physicochemical properties of antibacterial drugs.
Mugumbate G, Overington JP. Bioorganic & medicinal chemistry Volume 23 (2015) p.5218-5224 DOI: 10.1016/j.bmc.2015.04.063
Longevity GWAS Using the Drosophila Genetic Reference Panel.
Ivanov DK, Escott-Price V, Ziehm M, Magwire MM, Mackay TF, Partridge L, Thornton JM. The journals of gerontology. Series A, Biological sciences and medical sciences Volume 70 (2015) p.1470-1478 DOI: 10.1093/gerona/glv047
*
Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.
Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E. PLoS genetics Volume 11 (2015) p.e1005177 DOI: 10.1371/journal.pgen.1005177
*
Operon and non-operon gene clusters in the C. elegans genome.
Blumenthal T, Davis P, Garrido-Lecca A. WormBook : the online review of C. elegans biology (2015) p.1-20 DOI: 10.1895/wormbook.1.175.1
Towards the computational design of protein post-translational regulation.
Strumillo M, Beltrao P. Bioorganic & medicinal chemistry Volume 23 (2015) p.2877-2882 DOI: 10.1016/j.bmc.2015.04.056
ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.
Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R. Bioinformatics (Oxford, England) Volume 31 (2015) p.2903-2905 DOI: 10.1093/bioinformatics/btv250
BetaCavityWeb: a webserver for molecular voids and channels.
Kim JK, Cho Y, Lee M, Laskowski RA, Ryu SE, Sugihara K, Kim DS. Nucleic acids research Volume 43 (2015) p.W413-8 DOI: 10.1093/nar/gkv360
RSAT 2015: Regulatory Sequence Analysis Tools.
Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon JA, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier-Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M, van Helden J. Nucleic acids research Volume 43 (2015) p.W50-6 DOI: 10.1093/nar/gkv362
Key challenges for the creation and maintenance of specialist protein resources.
Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A. Proteins Volume 83 (2015) p.1005-1013 DOI: 10.1002/prot.24803
MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies.
Vuckovic D, Gasparini P, Soranzo N, Iotchkova V. Bioinformatics (Oxford, England) Volume 31 (2015) p.2754-2756 DOI: 10.1093/bioinformatics/btv222
Introducing the PRIDE Archive RESTful web services.
Reisinger F, del-Toro N, Ternent T, Hermjakob H, Vizcaíno JA. Nucleic acids research Volume 43 (2015) p.W599-604 DOI: 10.1093/nar/gkv382
The BioMart community portal: an innovative alternative to large, centralized data repositories.
Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A. Nucleic acids research Volume 43 (2015) p.W589-98 DOI: 10.1093/nar/gkv350
Differential genetic interactions of yeast stress response MAPK pathways.
Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ. Molecular systems biology Volume 11 (2015) p.800 DOI: 10.15252/msb.20145606
ChEMBL web services: streamlining access to drug discovery data and utilities.
Davies M, Nowotka M, Papadatos G, Dedman N, Gaulton A, Atkinson F, Bellis L, Overington JP. Nucleic Acids Research Volume 43 (2015) p.W612-20 DOI: 10.1093/nar/gkv352
MicroRNAs enrichment in GWAS of complex human phenotypes.
Goulart LF, Bettella F, Sønderby IE, Schork AJ, Thompson WK, Mattingsdal M, Steen VM, Zuber V, Wang Y, Dale AM, PRACTICAL/ELLIPSE consortium, Andreassen OA, Djurovic S. BMC genomics Volume 16 (2015) p.304 DOI: 10.1186/s12864-015-1513-5
High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.
Achim K, Pettit JB, Saraiva LR, Gavriouchkina D, Larsson T, Arendt D, Marioni JC. Nature biotechnology Volume 33 (2015) p.503-509 DOI: 10.1038/nbt.3209
Cellular phenotype database: a repository for systems microscopy data.
Kirsanova C, Brazma A, Rustici G, Sarkans U. Bioinformatics (Oxford, England) Volume 31 (2015) p.2736-2740 DOI: 10.1093/bioinformatics/btv199
*
GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.
Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CW, GOBLET Consortium. PLoS computational biology Volume 11 (2015) p.e1004143 DOI: 10.1371/journal.pcbi.1004143
Abundant genetic overlap between blood lipids and immune-mediated diseases indicates shared molecular genetic mechanisms.
Andreassen OA, Desikan RS, Wang Y, Thompson WK, Schork AJ, Zuber V, Doncheva NT, Ellinghaus E, Albrecht M, Mattingsdal M, Franke A, Lie BA, Mills IG, Aukrust P, McEvoy LK, Djurovic S, Karlsen TH, Dale AM. PloS one Volume 10 (2015) p.e0123057 DOI: 10.1371/journal.pone.0123057
The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI.
Squizzato S, Park YM, Buso N, Gur T, Cowley A, Li W, Uludag M, Pundir S, Cham JA, McWilliam H, Lopez R. Nucleic acids research Volume 43 (2015) p.W585-8 DOI: 10.1093/nar/gkv316
Reply to '"Mycobacterium indicus pranii" is a strain of Mycobacterium intracellulare': "M. indicus pranii" is a distinct strain, not derived from M. intracellulare, and is an organism at an evolutionary transition point between a fast grower and slow grower.
Rahman SA, Singh Y, Kohli S, Ahmad J, Ehtesham NZ, Tyagi AK, Hasnain SE. mBio Volume 6 (2015) DOI: 10.1128/mBio.00352-15
Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.
Benjelloun B, Alberto FJ, Streeter I, Boyer F, Coissac E, Stucki S, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Leempoel K, Alberti A, Engelen S, Chikhi A, Clarke L, Flicek P, Joost S, Taberlet P, Pompanon F, NextGen Consortium. Frontiers in Genetics Volume 6 (2015) p.107 DOI: 10.3389/fgene.2015.00107
The EMBL-EBI bioinformatics web and programmatic tools framework.
Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, Park YM, Buso N, Lopez R. Nucleic acids research Volume 43 (2015) p.W580-4 DOI: 10.1093/nar/gkv279
An atlas of mouse CD4(+) T cell transcriptomes.
Stubbington MJ, Mahata B, Svensson V, Deonarine A, Nissen JK, Betz AG, Teichmann SA. Biology direct Volume 10 (2015) p.14 DOI: 10.1186/s13062-015-0045-x
*
Proteomics data visualisation.
Vizcaíno JA, Barsnes H, Hermjakob H. Proteomics Volume 15 (2015) p.1339-1340 DOI: 10.1002/pmic.201570063
*
Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes.
Jakubec D, Hostas J, Laskowski RA, Hobza P, Vondrásek J. Journal of chemical theory and computation Volume 11 (2015) p.1939-1948 DOI: 10.1021/ct501168n
How plants manage food reserves at night: quantitative models and open questions.
Scialdone A, Howard M. Frontiers in plant science Volume 6 (2015) p.204 DOI: 10.3389/fpls.2015.00204
Insight into neutral and disease-associated human genetic variants through interpretable predictors.
van den Berg BA, Reinders MJ, de Ridder D, de Beer TA. PloS one Volume 10 (2015) p.e0120729 DOI: 10.1371/journal.pone.0120729
Kinase-two-hybrid: towards the conditional interactome.
Ochoa D, Beltrao P. Molecular systems biology Volume 11 (2015) p.798 DOI: 10.15252/msb.20156107
MeDuSa: a multi-draft based scaffolder.
Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lió P, Crescenzi P, Fani R, Fondi M. Bioinformatics (Oxford, England) Volume 31 (2015) p.2443-2451 DOI: 10.1093/bioinformatics/btv171
*
Discovery of molecular markers to discriminate corneal endothelial cells in the human body.
Yoshihara M, Ohmiya H, Hara S, Kawasaki S, FANTOM consortium, Hayashizaki Y, Itoh M, Kawaji H, Tsujikawa M, Nishida K. PloS one Volume 10 (2015) p.e0117581 DOI: 10.1371/journal.pone.0117581
*
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.
Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, McCarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H, FAANG Consortium. Genome biology Volume 16 (2015) p.57 DOI: 10.1186/s13059-015-0622-4
The ensembl regulatory build.
Zerbino DR, Wilder SP, Johnson N, Juettemann T, Flicek PR. Genome biology Volume 16 (2015) p.56 DOI: 10.1186/s13059-015-0621-5
Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation.
Mugumbate G, Abrahams KA, Cox JA, Papadatos G, van Westen G, Lelièvre J, Calus ST, Loman NJ, Ballell L, Barros D, Overington JP, Besra GS. PloS one Volume 10 (2015) p.e0121492 DOI: 10.1371/journal.pone.0121492
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.
Hastings J, Jeliazkova N, Owen G, Tsiliki G, Munteanu CR, Steinbeck C, Willighagen E. Journal of biomedical semantics Volume 6 (2015) p.10 DOI: 10.1186/s13326-015-0005-5
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology.
Porras P, Duesbury M, Fabregat A, Ueffing M, Orchard S, Gloeckner CJ, Hermjakob H. Proteomics Volume 15 (2015) p.1390-1404 DOI: 10.1002/pmic.201400390
Draft Genome Sequence of a Highly Virulent Strain of the Plant Pathogen Dickeya solani, IFB0099.
Golanowska M, Galardini M, Bazzicalupo M, Hugouvieux-Cotte-Pattat N, Mengoni A, Potrykus M, Slawiak M, Lojkowska E. Genome announcements Volume 3 (2015) DOI: 10.1128/genomeA.00109-15
*
Tumor cell migration screen identifies SRPK1 as breast cancer metastasis determinant.
van Roosmalen W, Le Dévédec SE, Golani O, Smid M, Pulyakhina I, Timmermans AM, Look MP, Zi D, Pont C, de Graauw M, Naffar-Abu-Amara S, Kirsanova C, Rustici G, Hoen PA, Martens JW, Foekens JA, Geiger B, van de Water B. The Journal of clinical investigation Volume 125 (2015) p.1648-1664 DOI: 10.1172/JCI74440
Structural and evolutionary versatility in protein complexes with uneven stoichiometry.
Marsh JA, Rees HA, Ahnert SE, Teichmann SA. Nature communications Volume 6 (2015) p.6394 DOI: 10.1038/ncomms7394
Shared resources, shared costs--leveraging biocuration resources.
Orchard S, Hermjakob H. Database : the journal of biological databases and curation Volume 2015 (2015) DOI: 10.1093/database/bav009
Determination of common genetic variants within the non-structural proteins of foot-and-mouth disease viruses isolated in sub-Saharan Africa.
Nsamba P, de Beer TA, Chitray M, Scott K, Vosloo W, Maree FF. Veterinary microbiology Volume 177 (2015) p.106-122 DOI: 10.1016/j.vetmic.2015.03.007
Chemical databases: curation or integration by user-defined equivalence?
Hersey A, Chambers J, Bellis L, Patrícia Bento A, Gaulton A, Overington JP. Drug discovery today. Technologies Volume 14 (2015) p.17-24 DOI: 10.1016/j.ddtec.2015.01.005
Section level search functionality in Europe PMC.
Kafkas Ş, Pi X, Marinos N, Talo' F, Morrison A, McEntyre JR. Journal of biomedical semantics Volume 6 (2015) p.7 DOI: 10.1186/s13326-015-0003-7
*
Investigating Protein Structure and Evolution with SCOP2.
Andreeva A, Howorth D, Chothia C, Kulesha E, Murzin AG. Current protocols in bioinformatics Volume 49 (2015) p.1.26.1-21 DOI: 10.1002/0471250953.bi0126s49
Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.
Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Cao KA, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS, Dinger ME. Nature methods Volume 12 (2015) p.339-342 DOI: 10.1038/nmeth.3321
*
Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers.
Onengut-Gumuscu S, Chen WM, Burren O, Cooper NJ, Quinlan AR, Mychaleckyj JC, Farber E, Bonnie JK, Szpak M, Schofield E, Achuthan P, Guo H, Fortune MD, Stevens H, Walker NM, Ward LD, Kundaje A, Kellis M, Daly MJ, Barrett JC, Cooper JD, Deloukas P, Type 1 Diabetes Genetics Consortium, Todd JA, Wallace C, Concannon P, Rich SS. Nature genetics Volume 47 (2015) p.381-386 DOI: 10.1038/ng.3245
Expression data analysis with Reactome.
Jupe S, Fabregat A, Hermjakob H. Current protocols in bioinformatics Volume 49 (2015) p.8.20.1-9 DOI: 10.1002/0471250953.bi0820s49
*
Whole-genome sequence-based analysis of thyroid function.
Taylor PN, Porcu E, Chew S, Campbell PJ, Traglia M, Brown SJ, Mullin BH, Shihab HA, Min J, Walter K, Memari Y, Huang J, Barnes MR, Beilby JP, Charoen P, Danecek P, Dudbridge F, Forgetta V, Greenwood C, Grundberg E, Johnson AD, Hui J, Lim EM, McCarthy S, Muddyman D, Panicker V, Perry JR, Bell JT, Yuan W, Relton C, Gaunt T, Schlessinger D, Abecasis G, Cucca F, Surdulescu GL, Woltersdorf W, Zeggini E, Zheng HF, Toniolo D, Dayan CM, Naitza S, Walsh JP, Spector T, Davey Smith G, Durbin R, Richards JB, Sanna S, Soranzo N, Timpson NJ, Wilson SG, UK0K Consortium. Nature communications Volume 6 (2015) p.5681 DOI: 10.1038/ncomms6681
Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis.
Raposo AA, Vasconcelos FF, Drechsel D, Marie C, Johnston C, Dolle D, Bithell A, Gillotin S, van den Berg DL, Ettwiller L, Flicek P, Crawford GE, Parras CM, Berninger B, Buckley NJ, Guillemot F, Castro DS. Cell reports (2015) DOI: 10.1016/j.celrep.2015.02.025
*
A public repository for mass spectrometry imaging data.
Römpp A, Wang R, Albar JP, Urbani A, Hermjakob H, Spengler B, Vizcaíno JA. Analytical and bioanalytical chemistry Volume 407 (2015) p.2027-2033 DOI: 10.1007/s00216-014-8357-8
Making proteomics data accessible and reusable: current state of proteomics databases and repositories.
Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA. Proteomics Volume 15 (2015) p.930-949 DOI: 10.1002/pmic.201400302
*
A contribution to the rational design of Ru(CO)3Cl2L complexes for in vivo delivery of CO.
Seixas JD, Santos MF, Mukhopadhyay A, Coelho AC, Reis PM, Veiros LF, Marques AR, Penacho N, Gonçalves AM, Romão MJ, Bernardes GJ, Santos-Silva T, Romão CC. Dalton transactions (Cambridge, England : 2003) Volume 44 (2015) p.5058-5075 DOI: 10.1039/c4dt02966f
Harnessing the heart of big data.
Scruggs SB, Watson K, Su AI, Hermjakob H, Yates JR, Lindsey ML, Ping P. Circulation research Volume 116 (2015) p.1115-1119 DOI: 10.1161/CIRCRESAHA.115.306013
*
The 3D organization of chromatin explains evolutionary fragile genomic regions.
Berthelot C, Muffato M, Abecassis J, Roest Crollius H. Cell reports Volume 10 (2015) p.1913-1924 DOI: 10.1016/j.celrep.2015.02.046
*
Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution.
Wright AE, Harrison PW, Zimmer F, Montgomery SH, Pointer MA, Mank JE. Molecular ecology Volume 24 (2015) p.1218-1235 DOI: 10.1111/mec.13113
Development of data representation standards by the human proteome organization proteomics standards initiative.
Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H. Journal of the American Medical Informatics Association : JAMIA Volume 22 (2015) p.495-506 DOI: 10.1093/jamia/ocv001
Automatic concept recognition using the human phenotype ontology reference and test suite corpora.
Groza T, Köhler S, Doelken S, Collier N, Oellrich A, Smedley D, Couto FM, Baynam G, Zankl A, Robinson PN. Database : the journal of biological databases and curation Volume 2015 (2015) DOI: 10.1093/database/bav005
BioModels: Content, Features, Functionality, and Use.
Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V. CPT: pharmacometrics & systems pharmacology Volume 4 (2015) p.e3 DOI: 10.1002/psp4.3
BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.
Moreno P, Beisken S, Harsha B, Muthukrishnan V, Tudose I, Dekker A, Dornfeldt S, Taruttis F, Grosse I, Hastings J, Neumann S, Steinbeck C. BMC bioinformatics Volume 16 (2015) p.56 DOI: 10.1186/s12859-015-0486-3
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.
Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR. BMC systems biology Volume 9 (2015) p.8 DOI: 10.1186/s12918-015-0144-4
*
Diverse phenotypic consequences of mutations affecting the C-terminus of FLNA.
van Kogelenberg M, Clark AR, Jenkins Z, Morgan T, Anandan A, Sawyer GM, Edwards M, Dudding T, Homfray T, Castle B, Tolmie J, Stewart F, Kivuva E, Pilz DT, Gabbett M, Sutherland-Smith AJ, Robertson SP. Journal of molecular medicine (Berlin, Germany) Volume 93 (2015) p.773-782 DOI: 10.1007/s00109-015-1261-7
*
Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling.
Cortes-Ciriano I, van Westen GJ, Murrell DS, Lenselink EB, Bender A, Malliavin TE. BMC bioinformatics Volume 16 (2015) p.A4-A4 DOI: 10.1186/1471-2105-16-S3-A4
*
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.
Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C, FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y. Science (New York, N.Y.) Volume 347 (2015) p.1010-1014 DOI: 10.1126/science.1259418
Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.
Ing-Simmons E, Seitan VC, Faure AJ, Flicek P, Carroll T, Dekker J, Fisher AG, Lenhard B, Merkenschlager M. Genome research Volume 25 (2015) p.504-513 DOI: 10.1101/gr.184986.114
A quick guide for building a successful bioinformatics community.
Budd A, Corpas M, Brazas MD, Fuller JC, Goecks J, Mulder NJ, Michaut M, Ouellette BF, Pawlik A, Blomberg N. PLoS computational biology Volume 11 (2015) p.e1003972 DOI: 10.1371/journal.pcbi.1003972
Open source libraries and frameworks for biological data visualisation: a guide for developers.
Wang R, Perez-Riverol Y, Hermjakob H, Vizcaíno JA. Proteomics Volume 15 (2015) p.1356-1374 DOI: 10.1002/pmic.201400377
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.
Villaveces JM, Jiménez RC, Porras P, Del-Toro N, Duesbury M, Dumousseau M, Orchard S, Choi H, Ping P, Zong NC, Askenazi M, Habermann BH, Hermjakob H. Database : the journal of biological databases and curation Volume 2015 (2015) DOI: 10.1093/database/bau131
Known Allergen Structures Predict Schistosoma mansoni IgE-Binding Antigens in Human Infection.
Farnell EJ, Tyagi N, Ryan S, Chalmers IW, Pinot de Moira A, Jones FM, Wawrzyniak J, Fitzsimmons CM, Tukahebwa EM, Furnham N, Maizels RM, Dunne DW. Frontiers in immunology Volume 6 (2015) p.26 DOI: 10.3389/fimmu.2015.00026
Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.
Agirre X, Castellano G, Pascual M, Heath S, Kulis M, Segura V, Bergmann A, Esteve A, Merkel A, Raineri E, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, Russiñol N, Queirós AC, Beekman R, Rodríguez-Madoz JR, San José-Enériz E, Fang F, Gutiérrez NC, García-Verdugo JM, Robson MI, Schirmer EC, Guruceaga E, Martens JH, Gut M, Calasanz MJ, Flicek P, Siebert R, Campo E, Miguel JF, Melnick A, Stunnenberg HG, Gut IG, Prosper F, Martín-Subero JI. Genome research Volume 25 (2015) p.478-487 DOI: 10.1101/gr.180240.114
What you need to know to make the most of big data in biology.
Thornton J. Lancet (London, England) Volume 385 Suppl 1 (2015) p.S5-6 DOI: 10.1016/s0140-6736(15)60321-x
SPARQL-enabled identifier conversion with Identifiers.org.
Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C. Bioinformatics (Oxford, England) Volume 31 (2015) p.1875-1877 DOI: 10.1093/bioinformatics/btv064
*
Avianbase: a community resource for bird genomics.
Eöry L, Gilbert MT, Li C, Li B, Archibald A, Aken BL, Zhang G, Jarvis E, Flicek P, Burt DW. Genome biology Volume 16 (2015) p.21 DOI: 10.1186/s13059-015-0588-2
Ten simple rules for organizing an unconference.
Budd A, Dinkel H, Corpas M, Fuller JC, Rubinat L, Devos DP, Khoueiry PH, Förstner KU, Georgatos F, Rowland F, Sharan M, Binder JX, Grace T, Traphagen K, Gristwood A, Wood NT. PLoS computational biology Volume 11 (2015) p.e1003905 DOI: 10.1371/journal.pcbi.1003905
Computational and analytical challenges in single-cell transcriptomics.
Stegle O, Teichmann SA, Marioni JC. Nature reviews. Genetics Volume 16 (2015) p.133-145 DOI: 10.1038/nrg3833
BRAF inhibitor resistance mediated by the AKT pathway in an oncogenic BRAF mouse melanoma model.
Perna D, Karreth FA, Rust AG, Perez-Mancera PA, Rashid M, Iorio F, Alifrangis C, Arends MJ, Bosenberg MW, Bollag G, Tuveson DA, Adams DJ. Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.E536-45 DOI: 10.1073/pnas.1418163112
Cooperative development of logical modelling standards and tools with CoLoMoTo.
Naldi A, Monteiro PT, Müssel C, Consortium for Logical Models and Tools, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C. Bioinformatics (Oxford, England) Volume 31 (2015) p.1154-1159 DOI: 10.1093/bioinformatics/btv013
*
Extending reference assembly models.
Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P. Genome biology Volume 16 (2015) p.13 DOI: 10.1186/s13059-015-0587-3
Testing the mean matrix in high-dimensional transposable data.
Touloumis A, Tavaré S, Marioni JC. Biometrics Volume 71 (2015) p.157-166 DOI: 10.1111/biom.12257
*
FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions
Dunham I, Kulesha E, Iotchkova V, Morganella S, Birney E. Preprint DOI: 10.12688/f1000research.6032.1
*
The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam.
Chiang Z, Vastermark A, Punta M, Coggill PC, Mistry J, Finn RD, Saier MH. Briefings in bioinformatics Volume 16 (2015) p.865-872 DOI: 10.1093/bib/bbu053
Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes.
Oellrich A, Collier N, Smedley D, Groza T. PloS one Volume 10 (2015) p.e0116040 DOI: 10.1371/journal.pone.0116040
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O. Nature biotechnology Volume 33 (2015) p.155-160 DOI: 10.1038/nbt.3102
Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling.
Cortes-Ciriano I, Murrell DS, van Westen GJ, Bender A, Malliavin TE. Journal of cheminformatics Volume 7 (2015) p.1 DOI: 10.1186/s13321-014-0049-z
*
Mbd3 and deterministic reprogramming
Bertone P, Hendrich B, Silva JC. Preprint DOI: 10.1101/013904
*
The statistical geometry of transcriptome divergence in cell-type evolution and cancer.
Liang C, FANTOM Consortium, Forrest AR, Wagner GP. Nature communications Volume 6 (2015) p.6066 DOI: 10.1038/ncomms7066
Identifying novel biomarkers through data mining-a realistic scenario?
Griss J, Perez-Riverol Y, Hermjakob H, Vizcaíno JA. Proteomics. Clinical applications Volume 9 (2015) p.437-443 DOI: 10.1002/prca.201400107
Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage.
Hagmann J, Becker C, Müller J, Stegle O, Meyer RC, Wang G, Schneeberger K, Fitz J, Altmann T, Bergelson J, Borgwardt K, Weigel D. PLoS genetics Volume 11 (2015) p.e1004920 DOI: 10.1371/journal.pgen.1004920
ADME SARfari: comparative genomics of drug metabolizing systems.
Davies M, Dedman N, Hersey A, Papadatos G, Hall MD, Cucurull-Sanchez L, Jeffrey P, Hasan S, Eddershaw PJ, Overington JP. Bioinformatics (Oxford, England) Volume 31 (2015) p.1695-1697 DOI: 10.1093/bioinformatics/btv010
*
Building a pan-genome reference for a population.
Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Journal of computational biology : a journal of computational molecular cell biology Volume 22 (2015) p.387-401 DOI: 10.1089/cmb.2014.0146
*
Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach.
Bacci G, Ceccherini MT, Bani A, Bazzicalupo M, Castaldini M, Galardini M, Giovannetti L, Mocali S, Pastorelli R, Pantani OL, Arfaioli P, Pietramellara G, Viti C, Nannipieri P, Mengoni A. Antonie van Leeuwenhoek Volume 107 (2015) p.785-797 DOI: 10.1007/s10482-014-0372-4
RNA-Rocket: an RNA-Seq analysis resource for infectious disease research.
Warren AS, Aurrecoechea C, Brunk B, Desai P, Emrich S, Giraldo-Calderón GI, Harb O, Hix D, Lawson D, Machi D, Mao C, McClelland M, Nordberg E, Shukla M, Vosshall LB, Wattam AR, Will R, Yoo HS, Sobral B. Bioinformatics (Oxford, England) Volume 31 (2015) p.1496-1498 DOI: 10.1093/bioinformatics/btv002
Finding our way through phenotypes.
Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P. PLoS biology Volume 13 (2015) p.e1002033 DOI: 10.1371/journal.pbio.1002033
Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.
Tan G, Gil M, Löytynoja AP, Goldman N, Dessimoz C. Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.E99-100 DOI: 10.1073/pnas.1417526112
Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.
Kafkas Ş, Kim JH, Pi X, McEntyre JR. Journal of biomedical semantics Volume 6 (2015) p.1 DOI: 10.1186/2041-1480-6-1
*
Gateways to the FANTOM5 promoter level mammalian expression atlas.
Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, Bertin N, Bono H, de Hoon M, Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T, Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, 't Hoen PA, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P, Hayashizaki Y, Forrest AR, Kawaji H, FANTOM consortium. Genome biology Volume 16 (2015) p.22 DOI: 10.1186/s13059-014-0560-6
From pangenome to panphenome and back.
Galardini M, Mengoni A, Mocali S. Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.257-270 DOI: 10.1007/978-1-4939-1720-4_16
Integrated allelic, transcriptional, and phenomic dissection of the cardiac effects of titin truncations in health and disease.
Roberts AM, Ware JS, Herman DS, Schafer S, Baksi J, Bick AG, Buchan RJ, Walsh R, John S, Wilkinson S, Mazzarotto F, Felkin LE, Gong S, MacArthur JA, Cunningham F, Flannick J, Gabriel SB, Altshuler DM, Macdonald PS, Heinig M, Keogh AM, Hayward CS, Banner NR, Pennell DJ, O'Regan DP, San TR, de Marvao A, Dawes TJ, Gulati A, Birks EJ, Yacoub MH, Radke M, Gotthardt M, Wilson JG, O'Donnell CJ, Prasad SK, Barton PJ, Fatkin D, Hubner N, Seidman JG, Seidman CE, Cook SA. Science translational medicine Volume 7 (2015) p.270ra6 DOI: 10.1126/scitranslmed.3010134
Collaborative computational project for electron cryo-microscopy.
Wood C, Burnley T, Patwardhan A, Scheres S, Topf M, Roseman A, Winn M. Acta crystallographica. Section D, Biological crystallography Volume 71 (2015) p.123-126 DOI: 10.1107/S1399004714018070
*
Predicting malignancy from mammography findings and image-guided core biopsies.
Ferreira P, Fonseca NA, Dutra I, Woods R, Burnside E. International journal of data mining and bioinformatics Volume 11 (2015) p.257-276 DOI: 10.1504/ijdmb.2015.067319
*
Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.
Lehmann KV, Kahles A, Kandoth C, Lee W, Schultz N, Stegle O, Rätsch G. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2015) p.44-55
*
Erratum to: Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes.
Winkler C, Krumsiek J, Buettner F, Angermüller C, Giannopoulou EZ, Theis FJ, Ziegler AG, Bonifacio E. Diabetologia Volume 58 (2015) p.206 DOI: 10.1007/s00125-014-3435-1
*
High-throughput phenomics.
Viti C, Decorosi F, Marchi E, Galardini M, Giovannetti L. Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.99-123 DOI: 10.1007/978-1-4939-1720-4_7
Enhancer evolution across 20 mammalian species.
Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ, Turner JM, Bertelsen MF, Murchison EP, Flicek P, Odom DT. Cell Volume 160 (2015) p.554-566 DOI: 10.1016/j.cell.2015.01.006
*
Preface. Bacterial pangenomics.
Mengoni A, Fondi M, Galardini M. Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.v-vi DOI: 10.1007/978-1-4939-1720-4
Genetic Interaction Scoring Procedure for Bacterial Species.
Wagih O, Parts L. Advances in experimental medicine and biology Volume 883 (2015) p.169-185 DOI: 10.1007/978-3-319-23603-2_10
*
Emerging Drug Target In Pancreatic Cancer: Placing Sirtuin 1 on the Canvas.
Giry-Laterriere M, Pinho AV, Eling N, Chantrill L, Rooman I. Current cancer drug targets Volume 15 (2015) p.463-468 DOI: 10.2174/1568009615666150512102957
*
The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues.
Lowe R, Slodkowicz G, Goldman N, Rakyan VK. Epigenetics Volume 10 (2015) p.274-281 DOI: 10.1080/15592294.2014.1003744
*
Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.
Dudley JT, Listgarten J, Stegle O, Brenner SE, Parts L. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2015) p.342-346
*
The cardiovascular gene annotation initiative: Impact on data analysis
Lovering RC, Rodriguez-Lopez M, Campbell NH, Huntley RP, Sawford T, O’Donovan C, Orchard S, Hermjakob H, Martin M, Mayr M, Humphries SE, Talmud PJ. Atherosclerosis Volume 241 (2015) p.e37 DOI: 10.1016/j.atherosclerosis.2015.04.135

2014

*
FORGE : A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions.
Dunham I, Kulesha E, Iotchkova V, Morganella S, Birney E. Preprint DOI: 10.1101/013045
*
VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.
Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S, VectorBase Consortium, Madey G, Collins FH, Lawson D. Nucleic acids research Volume 43 (2015) p.D707-13 DOI: 10.1093/nar/gku1117
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N. BMC bioinformatics Volume 15 (2014) p.369 DOI: 10.1186/s12859-014-0369-z
Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.
Peat JR, Dean W, Clark SJ, Krueger F, Smallwood SA, Ficz G, Kim JK, Marioni JC, Hore TA, Reik W. Cell reports Volume 9 (2014) p.1990-2000 DOI: 10.1016/j.celrep.2014.11.034
Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.
Lopez R, Cowley A, Li W, McWilliam H. Current protocols in bioinformatics Volume 48 (2014) p.3.12.1-50 DOI: 10.1002/0471250953.bi0312s48
Using the MEROPS Database for Proteolytic Enzymes and Their Inhibitors and Substrates.
Rawlings ND, Barrett AJ, Bateman A. Current protocols in bioinformatics Volume 48 (2014) p.1.25.1-33 DOI: 10.1002/0471250953.bi0125s48
diXa: a data infrastructure for chemical safety assessment.
Hendrickx DM, Aerts HJ, Caiment F, Clark D, Ebbels TM, Evelo CT, Gmuender H, Hebels DG, Herwig R, Hescheler J, Jennen DG, Jetten MJ, Kanterakis S, Keun HC, Matser V, Overington JP, Pilicheva E, Sarkans U, Segura-Lepe MP, Sotiriadou I, Wittenberger T, Wittwehr C, Zanzi A, Kleinjans JC. Bioinformatics (Oxford, England) Volume 31 (2015) p.1505-1507 DOI: 10.1093/bioinformatics/btu827
TermGenie - a web-application for pattern-based ontology class generation.
Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall CJ. Journal of biomedical semantics Volume 5 (2014) p.48 DOI: 10.1186/2041-1480-5-48
Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.
Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R. Molecular systems biology Volume 10 (2014) p.767 DOI: 10.15252/msb.20145112
*
Meeting report: advancing practical applications of biodiversity ontologies.
Walls RL, Guralnick R, Deck J, Buntzman A, Buttigieg PL, Davies N, Denslow MW, Gallery RE, Parnell JJ, Osumi-Sutherland D, Robbins RJ, Rocca-Serra P, Wieczorek J, Zheng J. Standards in Genomic Sciences Volume 9 (2014) p.17-17 DOI: 10.1186/1944-3277-9-17
*
Structure, dynamics, assembly, and evolution of protein complexes.
Marsh JA, Teichmann SA. Annual review of biochemistry Volume 84 (2015) p.551-575 DOI: 10.1146/annurev-biochem-060614-034142
Ten recommendations for software engineering in research.
Hastings J, Haug K, Steinbeck C. GigaScience Volume 3 (2014) p.31 DOI: 10.1186/2047-217X-3-31
Analysis of the tryptic search space in UniProt databases.
Alpi E, Griss J, da Silva AW, Bely B, Antunes R, Zellner H, Ríos D, O'Donovan C, Vizcaíno JA, Martin MJ. Proteomics Volume 15 (2015) p.48-57 DOI: 10.1002/pmic.201400227
Genetic resources for methane production from biomass described with the Gene Ontology.
Purwantini E, Torto-Alalibo T, Lomax J, Setubal JC, Tyler BM, Mukhopadhyay B. Frontiers in Microbiology Volume 5 (2014) p.634 DOI: 10.3389/fmicb.2014.00634
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank.
Westbrook JD, Shao C, Feng Z, Zhuravleva M, Velankar S, Young J. Bioinformatics (Oxford, England) Volume 31 (2015) p.1274-1278 DOI: 10.1093/bioinformatics/btu789
Exploiting combinatorial patterns in cancer genomic data for personalized therapy and new target discovery.
Schubert M, Iorio F. Pharmacogenomics Volume 15 (2014) p.1943-1946 DOI: 10.2217/pgs.14.157
Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
Perica T, Kondo Y, Tiwari SP, McLaughlin SH, Kemplen KR, Zhang X, Steward A, Reuter N, Clarke J, Teichmann SA. Science (New York, N.Y.) Volume 346 (2014) p.1254346 DOI: 10.1126/science.1254346
*
Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy.
Weiss MS, Peñalver Bernabé B, Shin S, Asztalos S, Dubbury SJ, Mui MD, Bellis AD, Bluver D, Tonetti DA, Saez-Rodriguez J, Broadbelt LJ, Jeruss JS, Shea LD. Integrative biology : quantitative biosciences from nano to macro Volume 6 (2014) p.1170-1182 DOI: 10.1039/c4ib00086b
*
Non-coding RNA gene families in the genomes of anopheline mosquitoes.
Dritsou V, Deligianni E, Dialynas E, Allen J, Poulakakis N, Louis C, Lawson D, Topalis P. BMC genomics Volume 15 (2014) p.1038 DOI: 10.1186/1471-2164-15-1038
Triticeae resources in Ensembl Plants.
Bolser DM, Kerhornou A, Walts B, Kersey P. Plant & cell physiology Volume 56 (2015) p.e3 DOI: 10.1093/pcp/pcu183
Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.
Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VL, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DS, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MK, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GW, Tojo M, Topalis P, Tubio JM, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MA, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJ. Science (New York, N.Y.) Volume 347 (2015) p.1258522 DOI: 10.1126/science.1258522
*
Gene Ontology Consortium: going forward.
Gene Ontology Consortium. Nucleic acids research Volume 43 (2015) p.D1049-56 DOI: 10.1093/nar/gku1179
The InterPro protein families database: the classification resource after 15 years.
Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD. Nucleic acids research Volume 43 (2015) p.D213-21 DOI: 10.1093/nar/gku1243
Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis.
Cubillos FA, Stegle O, Grondin C, Canut M, Tisné S, Gy I, Loudet O. The Plant cell Volume 26 (2014) p.4298-4310 DOI: 10.1105/tpc.114.130310
Small molecule annotation for the Protein Data Bank.
Sen S, Young J, Berrisford JM, Chen M, Conroy MJ, Dutta S, Di Costanzo L, Gao G, Ghosh S, Hudson BP, Igarashi R, Kengaku Y, Liang Y, Peisach E, Persikova I, Mukhopadhyay A, Narayanan BC, Sahni G, Sato J, Sekharan M, Shao C, Tan L, Zhuravleva MA. Database : the journal of biological databases and curation Volume 2014 (2014) p.bau116 DOI: 10.1093/database/bau116
The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.
Chipman AD, Ferrier DE, Brena C, Qu J, Hughes DS, Schröder R, Torres-Oliva M, Znassi N, Jiang H, Almeida FC, Alonso CR, Apostolou Z, Aqrawi P, Arthur W, Barna JC, Blankenburg KP, Brites D, Capella-Gutiérrez S, Coyle M, Dearden PK, Du Pasquier L, Duncan EJ, Ebert D, Eibner C, Erikson G, Evans PD, Extavour CG, Francisco L, Gabaldón T, Gillis WJ, Goodwin-Horn EA, Green JE, Griffiths-Jones S, Grimmelikhuijzen CJ, Gubbala S, Guigó R, Han Y, Hauser F, Havlak P, Hayden L, Helbing S, Holder M, Hui JH, Hunn JP, Hunnekuhl VS, Jackson L, Javaid M, Jhangiani SN, Jiggins FM, Jones TE, Kaiser TS, Kalra D, Kenny NJ, Korchina V, Kovar CL, Kraus FB, Lapraz F, Lee SL, Lv J, Mandapat C, Manning G, Mariotti M, Mata R, Mathew T, Neumann T, Newsham I, Ngo DN, Ninova M, Okwuonu G, Ongeri F, Palmer WJ, Patil S, Patraquim P, Pham C, Pu LL, Putman NH, Rabouille C, Ramos OM, Rhodes AC, Robertson HE, Robertson HM, Ronshaugen M, Rozas J, Saada N, Sánchez-Gracia A, Scherer SE, Schurko AM, Siggens KW, Simmons D, Stief A, Stolle E, Telford MJ, Tessmar-Raible K, Thornton R, van der Zee M, von Haeseler A, Williams JM, Willis JH, Wu Y, Zou X, Lawson D, Muzny DM, Worley KC, Gibbs RA, Akam M, Richards S. PLoS biology Volume 12 (2014) p.e1002005 DOI: 10.1371/journal.pbio.1002005
*
The structural basis for enhancer-dependent assembly and activation of the AAA transcriptional activator NorR.
Bush M, Ghosh T, Sawicka M, Moal IH, Bates PA, Dixon R, Zhang X. Molecular microbiology Volume 95 (2015) p.17-30 DOI: 10.1111/mmi.12844
Solid tumors of childhood display specific serum microRNA profiles.
Murray MJ, Raby KL, Saini HK, Bailey S, Wool SV, Tunnacliffe JM, Enright AJ, Nicholson JC, Coleman N. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology Volume 24 (2015) p.350-360 DOI: 10.1158/1055-9965.EPI-14-0669
The IPD and IMGT/HLA database: allele variant databases.
Robinson J, Halliwell JA, Hayhurst JD, Flicek P, Parham P, Marsh SG. Nucleic Acids Research Volume 43 (2015) p.D423-31 DOI: 10.1093/nar/gku1161
*
INFRAFRONTIER--providing mutant mouse resources as research tools for the international scientific community.
INFRAFRONTIER Consortium. Nucleic acids research Volume 43 (2015) p.D1171-5 DOI: 10.1093/nar/gku1193
BioModels: ten-year anniversary.
Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C. Nucleic Acids Research Volume 43 (2015) p.D542-8 DOI: 10.1093/nar/gku1181
Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.
Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E. PLoS genetics Volume 10 (2014) p.e1004798 DOI: 10.1371/journal.pgen.1004798
Anatomy of enzyme channels.
Pravda L, Berka K, Svobodová Vařeková R, Sehnal D, Banáš P, Laskowski RA, Koča J, Otyepka M. BMC bioinformatics Volume 15 (2014) p.379 DOI: 10.1186/s12859-014-0379-x
Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone.
Piccirillo SG, Spiteri I, Sottoriva A, Touloumis A, Ber S, Price SJ, Heywood R, Francis NJ, Howarth KD, Collins VP, Venkitaraman AR, Curtis C, Marioni JC, Tavaré S, Watts C. Cancer research Volume 75 (2015) p.194-202 DOI: 10.1158/0008-5472.CAN-13-3131
Content discovery and retrieval services at the European Nucleotide Archive.
Silvester N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Ten Hoopen P, Kay S, Leinonen R, Li W, Liu X, Lopez R, Pakseresht N, Pallreddy S, Plaister S, Radhakrishnan R, Rossello M, Senf A, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Nucleic acids research Volume 43 (2015) p.D23-9 DOI: 10.1093/nar/gku1129
The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.
Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M, Gasper DJ, Kelly SM, Chang J, Thomas MJ, Johnson J, Berlin AM, Lara M, Russell P, Swofford R, Turner-Maier J, Young S, Hourlier T, Aken B, Searle S, Sun X, Yi Y, Suresh M, Tumpey TM, Siepel A, Wisely SM, Dessimoz C, Kawaoka Y, Birren BW, Lindblad-Toh K, Di Palma F, Engelhardt JF, Palermo RE, Katze MG. Nature biotechnology Volume 32 (2014) p.1250-1255 DOI: 10.1038/nbt.3079
A community computational challenge to predict the activity of pairs of compounds.
Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y, NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A, NCI-DREAM Community. Nature biotechnology Volume 32 (2014) p.1213-1222 DOI: 10.1038/nbt.3052
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.
Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C. Nucleic Acids Research Volume 43 (2015) p.D240-9 DOI: 10.1093/nar/gku1158
Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array.
Wong YC, Kwong QB, Lee HL, Ong CK, Mayes S, Chew FT, Appleton DR, Kulaveerasingam H. Microarrays (Basel, Switzerland) Volume 3 (2014) p.263-281 DOI: 10.3390/microarrays3040263
Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals.
Wong ES, Thybert D, Schmitt BM, Stefflova K, Odom DT, Flicek P. Genome research Volume 25 (2015) p.167-178 DOI: 10.1101/gr.177840.114
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.
Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH, UniProt Consortium. Bioinformatics (Oxford, England) Volume 31 (2015) p.926-932 DOI: 10.1093/bioinformatics/btu739
Rfam 12.0: updates to the RNA families database.
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD. Nucleic acids research Volume 43 (2015) p.D130-7 DOI: 10.1093/nar/gku1063
Characterization of gene mutations and copy number changes in acute myeloid leukemia using a rapid target enrichment protocol.
Bolli N, Manes N, McKerrell T, Chi J, Park N, Gundem G, Quail MA, Sathiaseelan V, Herman B, Crawley C, Craig JI, Conte N, Grove C, Papaemmanuil E, Campbell PJ, Varela I, Costeas P, Vassiliou GS. Haematologica Volume 100 (2015) p.214-222 DOI: 10.3324/haematol.2014.113381
*
Europe PMC: a full-text literature database for the life sciences and platform for innovation.
Europe PMC Consortium. Nucleic acids research Volume 43 (2015) p.D1042-8 DOI: 10.1093/nar/gku1061
The GOA database: gene Ontology annotation updates for 2015.
Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ, O'Donovan C. Nucleic acids research Volume 43 (2015) p.D1057-63 DOI: 10.1093/nar/gku1113
Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics.
Louis A, Nguyen NT, Muffato M, Roest Crollius H. Nucleic Acids Research Volume 43 (2015) p.D682-9 DOI: 10.1093/nar/gku1112
Origin of the response to adrenal and sex steroids: Roles of promiscuity and co-evolution of enzymes and steroid receptors.
Baker ME, Nelson DR, Studer RA. The Journal of steroid biochemistry and molecular biology Volume 151 (2015) p.12-24 DOI: 10.1016/j.jsbmb.2014.10.020
The potential utility of predicted one bond carbon-proton coupling constants in the structure elucidation of small organic molecules by NMR spectroscopy.
Venkata C, Forster MJ, Howe PW, Steinbeck C. PloS one Volume 9 (2014) p.e111576 DOI: 10.1371/journal.pone.0111576
A comparative encyclopedia of DNA elements in the mouse genome.
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, Mouse ENCODE Consortium. Nature Volume 515 (2014) p.355-364 DOI: 10.1038/nature13992
*
Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features.
Ain QU, Méndez-Lucio O, Ciriano IC, Malliavin T, van Westen GJ, Bender A. Integrative biology : quantitative biosciences from nano to macro Volume 6 (2014) p.1023-1033 DOI: 10.1039/c4ib00175c
*
Principles of regulatory information conservation between mouse and human.
Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B, mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. Nature Volume 515 (2014) p.371-375 DOI: 10.1038/nature13985
PomBase 2015: updates to the fission yeast database.
McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V. Nucleic Acids Research Volume 43 (2015) p.D656-61 DOI: 10.1093/nar/gku1040
Genenames.org: the HGNC resources in 2015.
Gray KA, Yates B, Seal RL, Wright MW, Bruford EA. Nucleic acids research Volume 43 (2015) p.D1079-85 DOI: 10.1093/nar/gku1071
ArrayExpress update--simplifying data submissions.
Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A. Nucleic acids research Volume 43 (2015) p.D1113-6 DOI: 10.1093/nar/gku1057
*
Overview of gene structure in C. elegans.
Spieth J, Lawson D, Davis P, Williams G, Howe K. WormBook : the online review of C. elegans biology (2014) p.1-18 DOI: 10.1895/wormbook.1.65.2
Variation in genomic landscape of clear cell renal cell carcinoma across Europe.
Scelo G, Riazalhosseini Y, Greger L, Letourneau L, Gonzàlez-Porta M, Wozniak MB, Bourgey M, Harnden P, Egevad L, Jackson SM, Karimzadeh M, Arseneault M, Lepage P, How-Kit A, Daunay A, Renault V, Blanché H, Tubacher E, Sehmoun J, Viksna J, Celms E, Opmanis M, Zarins A, Vasudev NS, Seywright M, Abedi-Ardekani B, Carreira C, Selby PJ, Cartledge JJ, Byrnes G, Zavadil J, Su J, Holcatova I, Brisuda A, Zaridze D, Moukeria A, Foretova L, Navratilova M, Mates D, Jinga V, Artemov A, Nedoluzhko A, Mazur A, Rastorguev S, Boulygina E, Heath S, Gut M, Bihoreau MT, Lechner D, Foglio M, Gut IG, Skryabin K, Prokhortchouk E, Cambon-Thomsen A, Rung J, Bourque G, Brennan P, Tost J, Banks RE, Brazma A, Lathrop GM. Nature communications Volume 5 (2014) p.5135 DOI: 10.1038/ncomms6135
*
Synaptic, transcriptional and chromatin genes disrupted in autism.
De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S, Singh T, Klei L, Kosmicki J, Shih-Chen F, Aleksic B, Biscaldi M, Bolton PF, Brownfeld JM, Cai J, Campbell NG, Carracedo A, Chahrour MH, Chiocchetti AG, Coon H, Crawford EL, Curran SR, Dawson G, Duketis E, Fernandez BA, Gallagher L, Geller E, Guter SJ, Hill RS, Ionita-Laza J, Jimenz Gonzalez P, Kilpinen H, Klauck SM, Kolevzon A, Lee I, Lei I, Lei J, Lehtimäki T, Lin CF, Ma'ayan A, Marshall CR, McInnes AL, Neale B, Owen MJ, Ozaki N, Parellada M, Parr JR, Purcell S, Puura K, Rajagopalan D, Rehnström K, Reichenberg A, Sabo A, Sachse M, Sanders SJ, Schafer C, Schulte-Rüther M, Skuse D, Stevens C, Szatmari P, Tammimies K, Valladares O, Voran A, Li-San W, Weiss LA, Willsey AJ, Yu TW, Yuen RK, DDD Study, Homozygosity Mapping Collaborative for Autism, UK10K Consortium, Cook EH, Freitag CM, Gill M, Hultman CM, Lehner T, Palotie A, Schellenberg GD, Sklar P, State MW, Sutcliffe JS, Walsh CA, Scherer SW, Zwick ME, Barett JC, Cutler DJ, Roeder K, Devlin B, Daly MJ, Buxbaum JD. Nature Volume 515 (2014) p.209-215 DOI: 10.1038/nature13772
Ensembl 2015.
Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SM, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P. Nucleic acids research Volume 43 (2015) p.D662-9 DOI: 10.1093/nar/gku1010
*
RNAcentral: an international database of ncRNA sequences.
RNAcentral Consortium. Nucleic acids research Volume 43 (2015) p.D123-9 DOI: 10.1093/nar/gku991
CATH: comprehensive structural and functional annotations for genome sequences.
Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, Lehtinen S, Studer RA, Thornton J, Orengo CA. Nucleic acids research Volume 43 (2015) p.D376-81 DOI: 10.1093/nar/gku947
Evidence of convergent evolution in humans and macaques supports an adaptive role for copy number variation of the β-defensin-2 gene.
Ottolini B, Hornsby MJ, Abujaber R, MacArthur JA, Badge RM, Schwarzacher T, Albertson DG, Bevins CL, Solnick JV, Hollox EJ. Genome biology and evolution Volume 6 (2014) p.3025-3038 DOI: 10.1093/gbe/evu236
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.
Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall CJ, Binder JX, Malone J, Vasant D, Parkinson H, Schriml LM. Nucleic acids research Volume 43 (2015) p.D1071-8 DOI: 10.1093/nar/gku1011
PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains.
Kruger FA, Gaulton A, Nowotka M, Overington JP. Bioinformatics (Oxford, England) Volume 31 (2015) p.776-778 DOI: 10.1093/bioinformatics/btu711
*
UniProt: a hub for protein information.
UniProt Consortium. Nucleic acids research Volume 43 (2015) p.D204-12 DOI: 10.1093/nar/gku989
Genome3D: exploiting structure to help users understand their sequences.
Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cozzetto D, Dana JM, Filippis I, Gough J, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mistry J, Murzin AG, Ochoa-Montaño B, Oates ME, Punta M, Rackham OJ, Stahlhacke J, Sternberg MJ, Velankar S, Orengo C. Nucleic acids research Volume 43 (2015) p.D382-6 DOI: 10.1093/nar/gku973
Comparative transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 provide insights into mechanisms of stress acclimation.
Billis K, Billini M, Tripp HJ, Kyrpides NC, Mavromatis K. PloS one Volume 9 (2014) p.e109738 DOI: 10.1371/journal.pone.0109738
Computational approaches to interpreting genomic sequence variation.
Ritchie GR, Flicek P. Genome medicine Volume 6 (2014) p.87 DOI: 10.1186/s13073-014-0087-1
Visualisation of BioPAX Networks using BioLayout Express (3D).
Wright DW, Angus T, Enright AJ, Freeman TC. F1000Research Volume 3 (2014) p.246 DOI: 10.12688/f1000research.5499.1
The cavefish genome reveals candidate genes for eye loss.
McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A, Ma L, Minx P, Murphy D, O'Quin KE, Rétaux S, Rohner N, Searle SM, Stahl BA, Tabin C, Volff JN, Yoshizawa M, Warren WC. Nature communications Volume 5 (2014) p.5307 DOI: 10.1038/ncomms6307
*
Single Cell Genomics meeting in Stockholm: from single cells to cell types.
Scialdone A, Achim K, Marioni JC. Genome biology Volume 15 (2014) p.496 DOI: 10.1186/s13059-014-0496-x
The complex portal--an encyclopaedia of macromolecular complexes.
Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S. Nucleic Acids Research Volume 43 (2015) p.D479-84 DOI: 10.1093/nar/gku975
Genetic resources for advanced biofuel production described with the Gene Ontology.
Torto-Alalibo T, Purwantini E, Lomax J, Setubal JC, Mukhopadhyay B, Tyler BM. Frontiers in Microbiology Volume 5 (2014) p.528 DOI: 10.3389/fmicb.2014.00528
Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.
Orchard S, Albar JP, Binz PA, Kettner C, Jones AR, Salek RM, Vizcaino JA, Deutsch EW, Hermjakob H. Proteomics Volume 14 (2014) p.2363-2368 DOI: 10.1002/pmic.201470164
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei.
Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F, Boshart M, Berriman M, Breitling R, Bringaud F, Bütikofer P, Cattanach AM, Bannerman-Chukualim B, Creek DJ, Crouch K, de Koning HP, Denise H, Ebikeme C, Fairlamb AH, Ferguson MA, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Mäser P, Michels PA, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AG, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F. Nucleic acids research Volume 43 (2015) p.D637-44 DOI: 10.1093/nar/gku944
Cancer evolution: mathematical models and computational inference.
Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F. Systematic biology Volume 64 (2015) p.e1-25 DOI: 10.1093/sysbio/syu081
A molecular fragment cheminformatics roadmap for mesoscopic simulation.
Truszkowski A, Daniel M, Kuhn H, Neumann S, Steinbeck C, Zielesny A, Epple M. Journal of cheminformatics Volume 6 (2014) p.45 DOI: 10.1186/s13321-014-0045-3
Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.
Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P, Wilson MD. eLife Volume 3 (2014) p.e02626 DOI: 10.7554/eLife.02626
*
Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression.
Nelson AC, Cutty SJ, Niini M, Stemple DL, Flicek P, Houart C, Bruce AE, Wardle FC. BMC biology Volume 12 (2014) p.81 DOI: 10.1186/s12915-014-0081-5
A 3D cellular context for the macromolecular world.
Patwardhan A, Ashton A, Brandt R, Butcher S, Carzaniga R, Chiu W, Collinson L, Doux P, Duke E, Ellisman MH, Franken E, Grünewald K, Heriche JK, Koster A, Kühlbrandt W, Lagerstedt I, Larabell C, Lawson CL, Saibil HR, Sanz-García E, Subramaniam S, Verkade P, Swedlow JR, Kleywegt GJ. Nature structural & molecular biology Volume 21 (2014) p.841-845 DOI: 10.1038/nsmb.2897
Understanding the functional difference between growth arrest-specific protein 6 and protein S: an evolutionary approach.
Studer RA, Opperdoes FR, Nicolaes GA, Mulder AB, Mulder R. Open biology Volume 4 (2014) DOI: 10.1098/rsob.140121
RNA-Seq gene profiling--a systematic empirical comparison.
Fonseca NA, Marioni J, Brazma A. PloS one Volume 9 (2014) p.e107026 DOI: 10.1371/journal.pone.0107026
Response to On prompt update of literature references in the Protein Data Bank.
Berman HM, Burley SK, Kleywegt GJ, Nakamura H, Markley JL. Acta crystallographica. Section D, Biological crystallography Volume 70 (2014) p.2780 DOI: 10.1107/S1399004714020513
Identifying cell types from spatially referenced single-cell expression datasets.
Pettit JB, Tomer R, Achim K, Richardson S, Azizi L, Marioni J. PLoS computational biology Volume 10 (2014) p.e1003824 DOI: 10.1371/journal.pcbi.1003824
*
A standardized framing for reporting protein identifications in mzIdentML 1.2.
Seymour SL, Farrah T, Binz PA, Chalkley RJ, Cottrell JS, Searle BC, Tabb DL, Vizcaíno JA, Prieto G, Uszkoreit J, Eisenacher M, Martínez-Bartolomé S, Ghali F, Jones AR. Proteomics Volume 14 (2014) p.2389-2399 DOI: 10.1002/pmic.201400080
*
Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.
Jiang X, Peery A, Hall AB, Sharma A, Chen XG, Waterhouse RM, Komissarov A, Riehle MM, Shouche Y, Sharakhova MV, Lawson D, Pakpour N, Arensburger P, Davidson VL, Eiglmeier K, Emrich S, George P, Kennedy RC, Mane SP, Maslen G, Oringanje C, Qi Y, Settlage R, Tojo M, Tubio JM, Unger MF, Wang B, Vernick KD, Ribeiro JM, James AA, Michel K, Riehle MA, Luckhart S, Sharakhov IV, Tu Z. Genome biology Volume 15 (2014) p.459 DOI: 10.1186/s13059-014-0459-2
*
Rule-based integration of RNA-Seq analyses tools for identification of novel transcripts.
Inamdar H, Datta A, Manjari KS, Joshi R. Journal of bioinformatics and computational biology Volume 12 (2014) p.1450026 DOI: 10.1142/s0219720014500267
Warped linear mixed models for the genetic analysis of transformed phenotypes.
Fusi N, Lippert C, Lawrence ND, Stegle O. Nature communications Volume 5 (2014) p.4890 DOI: 10.1038/ncomms5890
An integrated ontology resource to explore and study host-virus relationships.
Masson P, Hulo C, de Castro E, Foulger R, Poux S, Bridge A, Lomax J, Bougueleret L, Xenarios I, Le Mercier P. PloS one Volume 9 (2014) p.e108075 DOI: 10.1371/journal.pone.0108075
A formal re-description of the cockroach Hebardina concinna anchored on DNA Barcodes confirms wing polymorphism and identifies morphological characters for field identification.
Yue Q, Wu K, Qiu D, Hu J, Liu D, Wei X, Chen J, Cook CE. PloS one Volume 9 (2014) p.e106789 DOI: 10.1371/journal.pone.0106789
Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells.
Cossetti C, Iraci N, Mercer TR, Leonardi T, Alpi E, Drago D, Alfaro-Cervello C, Saini HK, Davis MP, Schaeffer J, Vega B, Stefanini M, Zhao C, Muller W, Garcia-Verdugo JM, Mathivanan S, Bachi A, Enright AJ, Mattick JS, Pluchino S. Molecular cell Volume 56 (2014) p.193-204 DOI: 10.1016/j.molcel.2014.08.020
*
App for the calculation of blood lactate markers.
Newell J, Korir P, Moore B, Pedlar C. Journal of sports sciences Volume 33 (2015) p.568-569 DOI: 10.1080/02640414.2014.953982
The Ensembl REST API: Ensembl Data for Any Language.
Yates A, Beal K, Keenan S, McLaren W, Pignatelli M, Ritchie GR, Ruffier M, Taylor K, Vullo A, Flicek P. Bioinformatics (Oxford, England) Volume 31 (2015) p.143-145 DOI: 10.1093/bioinformatics/btu613
*
A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans.
Timpson NJ, Walter K, Min JL, Tachmazidou I, Malerba G, Shin SY, Chen L, Futema M, Southam L, Iotchkova V, Cocca M, Huang J, Memari Y, McCarthy S, Danecek P, Muddyman D, Mangino M, Menni C, Perry JR, Ring SM, Gaye A, Dedoussis G, Farmaki AE, Burton P, Talmud PJ, Gambaro G, Spector TD, Smith GD, Durbin R, Richards JB, Humphries SE, Zeggini E, Soranzo N, UK1OK Consortium Members, UK1OK Consortium Members. Nature communications Volume 5 (2014) p.4871 DOI: 10.1038/ncomms5871
Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants.
Beisken S, Earll M, Baxter C, Portwood D, Ament Z, Kende A, Hodgman C, Seymour G, Smith R, Fraser P, Seymour M, Salek RM, Steinbeck C. Scientific data Volume 1 (2014) p.140029 DOI: 10.1038/sdata.2014.29
The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.
Ahola V, Lehtonen R, Somervuo P, Salmela L, Koskinen P, Rastas P, Välimäki N, Paulin L, Kvist J, Wahlberg N, Tanskanen J, Hornett EA, Ferguson LC, Luo S, Cao Z, de Jong MA, Duplouy A, Smolander OP, Vogel H, McCoy RC, Qian K, Chong WS, Zhang Q, Ahmad F, Haukka JK, Joshi A, Salojärvi J, Wheat CW, Grosse-Wilde E, Hughes D, Katainen R, Pitkänen E, Ylinen J, Waterhouse RM, Turunen M, Vähärautio A, Ojanen SP, Schulman AH, Taipale M, Lawson D, Ukkonen E, Mäkinen V, Goldsmith MR, Holm L, Auvinen P, Frilander MJ, Hanski I. Nature communications Volume 5 (2014) p.4737 DOI: 10.1038/ncomms5737
UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers.
Chambers J, Davies M, Gaulton A, Papadatos G, Hersey A, Overington JP. Journal of cheminformatics Volume 6 (2014) p.43 DOI: 10.1186/s13321-014-0043-5
The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.
Corpas M, Jimenez RC, Bongcam-Rudloff E, Budd A, Brazas MD, Fernandes PL, Gaeta B, van Gelder C, Korpelainen E, Lewitter F, McGrath A, MacLean D, Palagi PM, Rother K, Taylor J, Via A, Watson M, Schneider MV, Attwood TK. Bioinformatics (Oxford, England) Volume 31 (2015) p.140-142 DOI: 10.1093/bioinformatics/btu601
Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference.
Hastings J, Brass A, Caine C, Jay C, Stevens R. Journal of biomedical semantics Volume 5 (2014) p.38 DOI: 10.1186/2041-1480-5-38
Fast randomization of large genomic datasets while preserving alteration counts.
Gobbi A, Iorio F, Dawson KJ, Wedge DC, Tamborero D, Alexandrov LB, Lopez-Bigas N, Garnett MJ, Jurman G, Saez-Rodriguez J. Bioinformatics (Oxford, England) Volume 30 (2014) p.i617-23 DOI: 10.1093/bioinformatics/btu474
*
ECCB 2014: The 13th European Conference on Computational Biology.
Devignes MD, Moreau Y. Bioinformatics (Oxford, England) Volume 30 (2014) p.i345-8 DOI: 10.1093/bioinformatics/btu512
*
High-flux table-top soft x-ray source driven by sub-2-cycle, CEP stable, 1.85-μm 1-kHz pulses for carbon K-edge spectroscopy.
Cousin SL, Silva F, Teichmann S, Hemmer M, Buades B, Biegert J. Optics letters Volume 39 (2014) p.5383-5386 DOI: 10.1364/ol.39.005383
Transcriptional diversity during lineage commitment of human blood progenitors.
Chen L, Kostadima M, Martens JHA, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SBG, Astle WJ, Attwood A, Bariana T, de Bono B, Breschi A, Chambers JC, Consortium B, Choudry FA, Clarke L, Coupland P, van der Ent M, Erber WN, Jansen JH, Favier R, Fenech ME, Foad N, Freson K, van Geet C, Gomez K, Guigo R, Hampshire D, Kelly AM, Kerstens HHD, Kooner JS, Laffan M, Lentaigne C, Labalette C, Martin T, Meacham S, Mumford A, Nürnberg S, Palumbo E, van der Reijden BA, Richardson D, Sammut SJ, Slodkowicz G, Tamuri AU, Vasquez L, Voss K, Watt S, Westbury S, Flicek P, Loos R, Goldman N, Bertone P, Read RJ, Richardson S, Cvejic A, Soranzo N, Ouwehand WH, Stunnenberg HG, Frontini M, Rendon A. Science (New York, N.Y.) Volume 345 (2014) p.1251033 DOI: 10.1126/science.1251033
*
Proceedings of the 13th European Conference on Computational Biology (ECCB’14), September 7-10, 2014, Strasbourg, France.
Bioinformatics (Oxford, England) Volume 30 (2014) p.i341-645 DOI: 10.1093/bioinformatics/btu511
Gibbon genome and the fast karyotype evolution of small apes.
Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA. Nature Volume 513 (2014) p.195-201 DOI: 10.1038/nature13679
Resetting transcription factor control circuitry toward ground-state pluripotency in human.
Takashima Y, Guo G, Loos R, Nichols J, Ficz G, Krueger F, Oxley D, Santos F, Clarke J, Mansfield W, Reik W, Bertone P, Smith A. Cell Volume 158 (2014) p.1254-1269 DOI: 10.1016/j.cell.2014.08.029
*
Databases and data sources: EBI and ELIXIR
Crosswell LC, Thornton JM. Comprehensive Biomedical Physics Vol. 6: Bioinformatics Elsevier
*
Virtual screening on an α-helix to β-strand switchable region of the FGFR2 extracellular domain revealed positive and negative modulators.
Diaz C, Corentin H, Thierry V, Chantal A, Tanguy B, David S, Jean-Marc H, Pascual F, Françoise B, Edgardo F. Proteins Volume 82 (2014) p.2982-2997 DOI: 10.1002/prot.24657
Random Forest ensembles for detection and prediction of Alzheimer's disease with a good between-cohort robustness.
Lebedev AV, Westman E, Van Westen GJ, Kramberger MG, Lundervold A, Aarsland D, Soininen H, Kłoszewska I, Mecocci P, Tsolaki M, Vellas B, Lovestone S, Simmons A, Alzheimer's Disease Neuroimaging Initiative and the AddNeuroMed consortium. NeuroImage. Clinical Volume 6 (2014) p.115-125 DOI: 10.1016/j.nicl.2014.08.023
Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs.
Kultys M, Nicholas L, Schwarz R, Goldman N, King J. BMC proceedings Volume 8 (2014) p.S8 DOI: 10.1186/1753-6561-8-S2-S8
*
Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules.
Grison A, Zucchelli S, Urzì A, Zamparo I, Lazarevic D, Pascarella G, Roncaglia P, Giorgetti A, Garcia-Esparcia P, Vlachouli C, Simone R, Persichetti F, Forrest AR, Hayashizaki Y, Carloni P, Ferrer I, Lodovichi C, Plessy C, FANTOM Consortium, Carninci P, Gustincich S. BMC genomics Volume 15 (2014) p.729 DOI: 10.1186/1471-2164-15-729
*
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
SEQC/MAQC-III Consortium. Nature biotechnology Volume 32 (2014) p.903-914 DOI: 10.1038/nbt.2957
How to submit MS proteomics data to ProteomeXchange via the PRIDE database.
Ternent T, Csordas A, Qi D, Gómez-Baena G, Beynon RJ, Jones AR, Hermjakob H, Vizcaíno JA. Proteomics Volume 14 (2014) p.2233-2241 DOI: 10.1002/pmic.201400120
Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.
Greger L, Su J, Rung J, Ferreira PG, Geuvadis consortium, Lappalainen T, Dermitzakis ET, Brazma A. PloS one Volume 9 (2014) p.e104567 DOI: 10.1371/journal.pone.0104567
BioModels linked dataset.
Wimalaratne SM, Grenon P, Hermjakob H, Le Novère N, Laibe C. BMC systems biology Volume 8 (2014) p.91 DOI: 10.1186/s12918-014-0091-5
*
Binding of the transcription factor Atf1 to promoters serves as a barrier to phase nucleosome arrays and avoid cryptic transcription.
García P, Paulo E, Gao J, Wahls WP, Ayté J, Lowy E, Hidalgo E. Nucleic acids research Volume 42 (2014) p.10351-10359 DOI: 10.1093/nar/gku704
High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.
Schmitt BM, Rudolph KL, Karagianni P, Fonseca NA, White RJ, Talianidis I, Odom DT, Marioni JC, Kutter C. Genome research Volume 24 (2014) p.1797-1807 DOI: 10.1101/gr.176784.114
CLO: The cell line ontology.
Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. Journal of biomedical semantics Volume 5 (2014) p.37 DOI: 10.1186/2041-1480-5-37
A document classifier for medicinal chemistry publications trained on the ChEMBL corpus.
Papadatos G, van Westen GJ, Croset S, Santos R, Trubian S, Overington JP. Journal of cheminformatics Volume 6 (2014) p.40 DOI: 10.1186/s13321-014-0040-8
Signaling networks in MS: a systems-based approach to developing new pharmacological therapies.
Kotelnikova E, Bernardo-Faura M, Silberberg G, Kiani NA, Messinis D, Melas IN, Artigas L, Schwartz E, Mazo I, Masso M, Alexopoulos LG, Mas JM, Olsson T, Tegner J, Martin R, Zamora A, Paul F, Saez-Rodriguez J, Villoslada P. Multiple sclerosis (Houndmills, Basingstoke, England) Volume 21 (2015) p.138-146 DOI: 10.1177/1352458514543339
*
PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees.
Lucas JM, Muffato M, Roest Crollius H. BMC bioinformatics Volume 15 (2014) p.268 DOI: 10.1186/1471-2105-15-268
*
Endothelial C-type natriuretic peptide maintains vascular homeostasis.
Moyes AJ, Khambata RS, Villar I, Bubb KJ, Baliga RS, Lumsden NG, Xiao F, Gane PJ, Rebstock AS, Worthington RJ, Simone MI, Mota F, Rivilla F, Vallejo S, Peiró C, Sánchez Ferrer CF, Djordjevic S, Caulfield MJ, MacAllister RJ, Selwood DL, Ahluwalia A, Hobbs AJ. The Journal of clinical investigation Volume 124 (2014) p.4039-4051 DOI: 10.1172/JCI74281
*
A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer.
Vollan HK, Rueda OM, Chin SF, Curtis C, Turashvili G, Shah S, Lingjærde OC, Yuan Y, Ng CK, Dunning MJ, Dicks E, Provenzano E, Sammut S, McKinney S, Ellis IO, Pinder S, Purushotham A, Murphy LC, Kristensen VN, METABRIC Group, Brenton JD, Pharoah PD, Børresen-Dale AL, Aparicio S, Caldas C. Molecular oncology Volume 9 (2015) p.115-127 DOI: 10.1016/j.molonc.2014.07.019
Antibody informatics for drug discovery.
Shirai H, Prades C, Vita R, Marcatili P, Popovic B, Xu J, Overington JP, Hirayama K, Soga S, Tsunoyama K, Clark D, Lefranc MP, Ikeda K. Biochimica et biophysica acta Volume 1844 (2014) p.2002-2015 DOI: 10.1016/j.bbapap.2014.07.006
Comparative analysis of the transcriptome across distant species.
Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Nature Volume 512 (2014) p.445-448 DOI: 10.1038/nature13424
*
Cuckoo hosts shift from accepting to rejecting parasitic eggs across their lifetime.
Molina-Morales M, Martínez JG, Martín-Gálvez D, Dawson DA, Burke T, Avilés JM. Evolution; international journal of organic evolution Volume 68 (2014) p.3020-3029 DOI: 10.1111/evo.12471
*
Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC. Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.E3366 DOI: 10.1073/pnas.1410434111
Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing.
Papatheodorou I, Petrovs R, Thornton JM. Bioinformatics (Oxford, England) Volume 30 (2014) p.2999-3003 DOI: 10.1093/bioinformatics/btu493
*
The Protein Data Bank archive as an open data resource.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL. Journal of computer-aided molecular design Volume 28 (2014) p.1009-1014 DOI: 10.1007/s10822-014-9770-y
Big data and other challenges in the quest for orthologs.
Sonnhammer EL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C, Quest for Orthologs consortium. Bioinformatics (Oxford, England) Volume 30 (2014) p.2993-2998 DOI: 10.1093/bioinformatics/btu492
*
Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges.
Kufareva I, Katritch V, Participants of GPCR Dock 2013, Stevens RC, Abagyan R. Structure (London, England : 1993) Volume 22 (2014) p.1120-1139 DOI: 10.1016/j.str.2014.06.012
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.
Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S. Bio Systems Volume 124 (2014) p.26-38 DOI: 10.1016/j.biosystems.2014.07.002
Standardized description of scientific evidence using the Evidence Ontology (ECO).
Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M. Database : the journal of biological databases and curation Volume 2014 (2014) DOI: 10.1093/database/bau075
Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, Andrews SR, Stegle O, Reik W, Kelsey G. Nature methods Volume 11 (2014) p.817-820 DOI: 10.1038/nmeth.3035
*
The common marmoset genome provides insight into primate biology and evolution.
Marmoset Genome Sequencing and Analysis Consortium. Nature genetics Volume 46 (2014) p.850-857 DOI: 10.1038/ng.3042
Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets.
Barrera A, Alastruey-Izquierdo A, Martín MJ, Cuesta I, Vizcaíno JA. PLoS computational biology Volume 10 (2014) p.e1003733 DOI: 10.1371/journal.pcbi.1003733
Genomic analysis of the causative agents of coccidiosis in domestic chickens.
Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, Dunn M, Hung SS, Kawahara F, Miranda-Saavedra D, Malas TB, Mourier T, Naghra H, Nair M, Otto TD, Rawlings ND, Rivailler P, Sanchez-Flores A, Sanders M, Subramaniam C, Tay YL, Woo Y, Wu X, Barrell B, Dear PH, Doerig C, Gruber A, Ivens AC, Parkinson J, Rajandream MA, Shirley MW, Wan KL, Berriman M, Tomley FM, Pain A. Genome research Volume 24 (2014) p.1676-1685 DOI: 10.1101/gr.168955.113
Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress.
Marguerat S, Lawler K, Brazma A, Bähler J. RNA biology Volume 11 (2014) p.702-714 DOI: 10.4161/rna.29196
*
The correlation between reading and mathematics ability at age twelve has a substantial genetic component.
Davis OS, Band G, Pirinen M, Haworth CM, Meaburn EL, Kovas Y, Harlaar N, Docherty SJ, Hanscombe KB, Trzaskowski M, Curtis CJ, Strange A, Freeman C, Bellenguez C, Su Z, Pearson R, Vukcevic D, Langford C, Deloukas P, Hunt S, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Edkins S, Bumpstead SJ, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski JA, Markus HS, Mathew CG, Palmer CN, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Barroso I, Peltonen L, Dale PS, Petrill SA, Schalkwyk LS, Craig IW, Lewis CM, Price TS, Wellcome Trust Case Control Consortium 2, Donnelly P, Plomin R, Spencer CC. Nature communications Volume 5 (2014) p.4204 DOI: 10.1038/ncomms5204
Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking.
Jayaseelan KV, Steinbeck C. BMC bioinformatics Volume 15 (2014) p.234 DOI: 10.1186/1471-2105-15-234
Maximum likelihood inference of small trees in the presence of long branches.
Parks SL, Goldman N. Systematic biology Volume 63 (2014) p.798-811 DOI: 10.1093/sysbio/syu044
On best practices in the development of bioinformatics software.
Leprevost Fda V, Barbosa VC, Francisco EL, Perez-Riverol Y, Carvalho PC. Frontiers in genetics Volume 5 (2014) p.199 DOI: 10.3389/fgene.2014.00199
*
High-resolution genome screen for bone mineral density in heterogeneous stock rat.
Alam I, Koller DL, Cañete T, Blázquez G, López-Aumatell R, Martínez-Membrives E, Díaz-Morán S, Tobeña A, Fernández-Teruel A, Stridh P, Diez M, Olsson T, Johannesson M, Baud A, Econs MJ, Foroud T. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research Volume 29 (2014) p.1619-1626 DOI: 10.1002/jbmr.2195
*
Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange.
Beer R, Herbst K, Ignatiadis N, Kats I, Adlung L, Meyer H, Niopek D, Christiansen T, Georgi F, Kurzawa N, Meichsner J, Rabe S, Riedel A, Sachs J, Schessner J, Schmidt F, Walch P, Niopek K, Heinemann T, Eils R, Di Ventura B. Molecular bioSystems Volume 10 (2014) p.1709-1718 DOI: 10.1039/c3mb70594c
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.
Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H. Molecular & cellular proteomics : MCP Volume 13 (2014) p.2765-2775 DOI: 10.1074/mcp.O113.036681
*
Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.
Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. Genome biology Volume 15 (2014) p.R88 DOI: 10.1186/gb-2014-15-6-r88
Genome sequencing of normal cells reveals developmental lineages and mutational processes.
Behjati S, Huch M, van Boxtel R, Karthaus W, Wedge DC, Tamuri AU, Martincorena I, Petljak M, Alexandrov LB, Gundem G, Tarpey PS, Roerink S, Blokker J, Maddison M, Mudie L, Robinson B, Nik-Zainal S, Campbell P, Goldman N, van de Wetering M, Cuppen E, Clevers H, Stratton MR. Nature Volume 513 (2014) p.422-425 DOI: 10.1038/nature13448
*
Extracellular vesicles and their synthetic analogues in aging and age-associated brain diseases.
Smith JA, Leonardi T, Huang B, Iraci N, Vega B, Pluchino S. Biogerontology Volume 16 (2015) p.147-185 DOI: 10.1007/s10522-014-9510-7
Proteochemometric modeling in a Bayesian framework.
Cortes-Ciriano I, van Westen GJ, Lenselink EB, Murrell DS, Bender A, Malliavin T. Journal of cheminformatics Volume 6 (2014) p.35 DOI: 10.1186/1758-2946-6-35
SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments.
Di Tommaso P, Bussotti G, Kemena C, Capriotti E, Chatzou M, Prieto P, Notredame C. Nucleic acids research Volume 42 (2014) p.W356-60 DOI: 10.1093/nar/gku459
*
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Guziolowski C, Videla S, Eduati F, Thiele S, Cokelaer T, Siegel A, Saez-Rodriguez J. Bioinformatics (Oxford, England) Volume 30 (2014) p.1942-1942 DOI: 10.1093/bioinformatics/btu357
*
Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation.
Famiglietti ML, Estreicher A, Gos A, Bolleman J, Géhant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I, UniProt Consortium. Human mutation Volume 35 (2014) p.927-935 DOI: 10.1002/humu.22594
*
CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes.
Hasegawa Y, Tang D, Takahashi N, Hayashizaki Y, Forrest AR, FANTOM Consortium, Suzuki H. Scientific reports Volume 4 (2014) p.5228 DOI: 10.1038/srep05228
A controlled vocabulary for pathway entities and events.
Jupe S, Jassal B, Williams M, Wu G. Database : the journal of biological databases and curation Volume 2014 (2014) DOI: 10.1093/database/bau060
Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies.
Hastings J, Frishkoff GA, Smith B, Jensen M, Poldrack RA, Lomax J, Bandrowski A, Imam F, Turner JA, Martone ME. Frontiers in neuroinformatics Volume 8 (2014) p.62 DOI: 10.3389/fninf.2014.00062
*
A unifying model of genome evolution under parsimony.
Paten B, Zerbino DR, Hickey G, Haussler D. BMC bioinformatics Volume 15 (2014) p.206 DOI: 10.1186/1471-2105-15-206
*
Distinct developmental profile of lower-body adipose tissue defines resistance against obesity-associated metabolic complications.
Pinnick KE, Nicholson G, Manolopoulos KN, McQuaid SE, Valet P, Frayn KN, Denton N, Min JL, Zondervan KT, Fleckner J, MolPAGE Consortium, McCarthy MI, Holmes CC, Karpe F. Diabetes Volume 63 (2014) p.3785-3797 DOI: 10.2337/db14-0385
*
Relationship between genome and epigenome--challenges and requirements for future research.
Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, Bressac-de Paillerets B, Bussemakers M, Clarke L, Conesa A, Estivill X, Fazeli A, Grgurević N, Gut I, Heijmans BT, Hermouet S, Houwing-Duistermaat J, Iacobucci I, Ilaš J, Kandimalla R, Krauss-Etschmann S, Lasko P, Lehmann S, Lindroth A, Majdič G, Marcotte E, Martinelli G, Martinet N, Meyer E, Miceli C, Mills K, Moreno-Villanueva M, Morvan G, Nickel D, Niesler B, Nowacki M, Nowak J, Ossowski S, Pelizzola M, Pochet R, Potočnik U, Radwanska M, Raes J, Rattray M, Robinson MD, Roelen B, Sauer S, Schinzer D, Slagboom E, Spector T, Stunnenberg HG, Tiligada E, Torres-Padilla ME, Tsonaka R, Van Soom A, Vidaković M, Widschwendter M. BMC genomics Volume 15 (2014) p.487 DOI: 10.1186/1471-2164-15-487
Representing kidney development using the gene ontology.
Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP. PloS one Volume 9 (2014) p.e99864 DOI: 10.1371/journal.pone.0099864
*
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.
Delaneau O, Marchini J, 1000 Genomes Project Consortium, 1000 Genomes Project Consortium. Nature communications Volume 5 (2014) p.3934 DOI: 10.1038/ncomms4934
*
ISMB 2014 Proceedings Papers Committee.
Bioinformatics (Oxford, England) Volume 30 (2014) p.i3-i8 DOI: 10.1093/bioinformatics/btu322
Improving functional annotation for industrial microbes: a case study with Pichia pastoris.
Dikicioglu D, Wood V, Rutherford KM, McDowall MD, Oliver SG. Trends in biotechnology Volume 32 (2014) p.396-399 DOI: 10.1016/j.tibtech.2014.05.003
Genomes and phenomes of a population of outbred rats and its progenitors.
Baud A, Guryev V, Hummel O, Johannesson M, Rat Genome Sequencing and Mapping Consortium, Flint J. Scientific data Volume 1 (2014) p.140011 DOI: 10.1038/sdata.2014.11
*
iRAP - an integrated RNA-seq Analysis Pipeline
Fonseca NA, Petryszak R, Marioni J, Brazma A. Preprint DOI: 10.1101/005991
*
Large-scale identification of phosphorylation sites for profiling protein kinase selectivity.
Imamura H, Sugiyama N, Wakabayashi M, Ishihama Y. Journal of proteome research Volume 13 (2014) p.3410-3419 DOI: 10.1021/pr500319y
*
Activities at the Universal Protein Resource (UniProt).
Nucleic acids research Volume 42 (2014) p.7486-7486 DOI: 10.1093/nar/gku469
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.
Malone J, Brown A, Lister AL, Ison J, Hull D, Parkinson H, Stevens R. Journal of biomedical semantics Volume 5 (2014) p.25 DOI: 10.1186/2041-1480-5-25
A community effort to assess and improve drug sensitivity prediction algorithms.
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G. Nature biotechnology Volume 32 (2014) p.1202-1212 DOI: 10.1038/nbt.2877
Transporter assays and assay ontologies: useful tools for drug discovery.
Zdrazil B, Chichester C, Zander Balderud L, Engkvist O, Gaulton A, Overington JP. Drug discovery today. Technologies Volume 12 (2014) p.e47-54 DOI: 10.1016/j.ddtec.2014.03.005
The evolution of enzyme function in the isomerases.
Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM. Current opinion in structural biology Volume 26 (2014) p.121-130 DOI: 10.1016/j.sbi.2014.06.002
*
Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank.
Dutta S, Dimitropoulos D, Feng Z, Persikova I, Sen S, Shao C, Westbrook J, Young J, Zhuravleva MA, Kleywegt GJ, Berman HM. Biopolymers Volume 101 (2014) p.659-668 DOI: 10.1002/bip.22434
Transporter taxonomy - a comparison of different transport protein classification schemes.
Viereck M, Gaulton A, Digles D, Ecker GF. Drug discovery today. Technologies Volume 12 (2014) p.e37-46 DOI: 10.1016/j.ddtec.2014.03.004
Protein flexibility facilitates quaternary structure assembly and evolution.
Marsh JA, Teichmann SA. PLoS biology Volume 12 (2014) p.e1001870 DOI: 10.1371/journal.pbio.1001870
*
Transparent thin shield for radio frequency transmit coils.
Rivera DS, Schulz J, Siegert T, Zuber V, Turner R. Magma (New York, N.Y.) Volume 28 (2015) p.49-56 DOI: 10.1007/s10334-014-0448-1
*
Screening and hit evaluation of a chemical library against blood-stage Plasmodium falciparum.
Avery VM, Bashyam S, Burrows JN, Duffy S, Papadatos G, Puthukkuti S, Sambandan Y, Singh S, Spangenberg T, Waterson D, Willis P. Malaria journal Volume 13 (2014) p.190 DOI: 10.1186/1475-2875-13-190
Long-range enhancers regulating Myc expression are required for normal facial morphogenesis.
Uslu VV, Petretich M, Ruf S, Langenfeld K, Fonseca NA, Marioni JC, Spitz F. Nature genetics Volume 46 (2014) p.753-758 DOI: 10.1038/ng.2971
The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification.
Boroviak T, Loos R, Bertone P, Smith A, Nichols J. Nature cell biology Volume 16 (2014) p.516-528 DOI: 10.1038/ncb2965
*
LIMIX: genetic analysis of multiple traits
Lippert C, Casale FP, Rakitsch B, Stegle O. Preprint DOI: 10.1101/003905
*
A method for increasing expressivity of Gene Ontology annotations using a compositional approach.
Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ. BMC bioinformatics Volume 15 (2014) p.155 DOI: 10.1186/1471-2105-15-155
Ribosomic DNA intergenic spacer 1 region is useful when identifying Candida parapsilosis spp. complex based on high-resolution melting analysis.
Gago S, Alastruey-Izquierdo A, Marconi M, Buitrago MJ, Kerhornou A, Kersey PJ, Mellado E, Cuenca-Estrella M, Rodríguez-Tudela JL, Cuesta I. Medical mycology Volume 52 (2014) p.472-481 DOI: 10.1093/mmy/myu009
A rapidly reversible chemical dimerizer system to study lipid signaling in living cells.
Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C. Angewandte Chemie (International ed. in English) Volume 53 (2014) p.6720-6723 DOI: 10.1002/anie.201402294
Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling.
van Westen GJ, Bender A, Overington JP. Journal of chemical biology Volume 7 (2014) p.119-123 DOI: 10.1007/s12154-014-0112-2
De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.
Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P. PloS one Volume 9 (2014) p.e96855 DOI: 10.1371/journal.pone.0096855
Mining Molecular Pharmacological Effects from Biomedical Text: a Case Study for Eliciting Anti-Obesity/Diabetes Effects of Chemical Compounds.
Dura E, Muresan S, Engkvist O, Blomberg N, Chen H. Molecular informatics Volume 33 (2014) p.332-342 DOI: 10.1002/minf.201300144
An atlas of genetic influences on human blood metabolites.
Shin SY, Fauman EB, Petersen AK, Krumsiek J, Santos R, Huang J, Arnold M, Erte I, Forgetta V, Yang TP, Walter K, Menni C, Chen L, Vasquez L, Valdes AM, Hyde CL, Wang V, Ziemek D, Roberts P, Xi L, Grundberg E, Multiple Tissue Human Expression Resource (MuTHER) Consortium, Waldenberger M, Richards JB, Mohney RP, Milburn MV, John SL, Trimmer J, Theis FJ, Overington JP, Suhre K, Brosnan MJ, Gieger C, Kastenmüller G, Spector TD, Soranzo N. Nature genetics Volume 46 (2014) p.543-550 DOI: 10.1038/ng.2982
Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis.
Mahata B, Zhang X, Kolodziejczyk AA, Proserpio V, Haim-Vilmovsky L, Taylor AE, Hebenstreit D, Dingler FA, Moignard V, Göttgens B, Arlt W, McKenzie AN, Teichmann SA. Cell reports Volume 7 (2014) p.1130-1142 DOI: 10.1016/j.celrep.2014.04.011
*
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR, Saez-Rodriguez J. BMC Bioinformatics Volume 15 (2014) p.136 DOI: 10.1186/1471-2105-15-136
Posterior localization of ApVas1 positions the preformed germ plasm in the sexual oviparous pea aphid Acyrthosiphon pisum.
Lin GW, Cook CE, Miura T, Chang CC. EvoDevo Volume 5 (2014) p.18 DOI: 10.1186/2041-9139-5-18
*
'Big data' in pharmaceutical science: challenges and opportunities.
Dossetter AG, Ecker G, Laverty H, Overington J. Future medicinal chemistry Volume 6 (2014) p.857-864 DOI: 10.4155/fmc.14.45
*
Gene conversion violates the stepwise mutation model for microsatellites in y-chromosomal palindromic repeats.
Balaresque P, King TE, Parkin EJ, Heyer E, Carvalho-Silva D, Kraaijenbrink T, de Knijff P, Tyler-Smith C, Jobling MA. Human mutation Volume 35 (2014) p.609-617 DOI: 10.1002/humu.22542
jmzTab: a java interface to the mzTab data standard.
Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, Vizcaíno JA. Proteomics Volume 14 (2014) p.1328-1332 DOI: 10.1002/pmic.201300560
qcML: an exchange format for quality control metrics from mass spectrometry experiments.
Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L. Molecular & cellular proteomics : MCP Volume 13 (2014) p.1905-1913 DOI: 10.1074/mcp.M113.035907
MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.
Beisken S, Earll M, Portwood D, Seymour M, Steinbeck C. Molecular informatics Volume 33 (2014) p.307-310 DOI: 10.1002/minf.201400016
Practical aspects of protein co-evolution.
Ochoa D, Pazos F. Frontiers in Cell and Developmental Biology Volume 2 (2014) p.14 DOI: 10.3389/fcell.2014.00014
*
Defining functional DNA elements in the human genome.
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC. Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.6131-6138 DOI: 10.1073/pnas.1318948111
Phylogenetic quantification of intra-tumour heterogeneity.
Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F. PLoS computational biology Volume 10 (2014) p.e1003535 DOI: 10.1371/journal.pcbi.1003535
*
Neural lineage induction reveals multi-scale dynamics of 3D chromatin organization
Pekowska A, Klaus B, Klein FA, Anders S, Oles M, Steinmetz LM, Bertone P, Huber W. Preprint DOI: 10.1101/004168
A short guide to long non-coding RNA gene nomenclature.
Wright MW. Human genomics Volume 8 (2014) p.7 DOI: 10.1186/1479-7364-8-7
*
tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.
Cejuela JM, McQuilton P, Ponting L, Marygold SJ, Stefancsik R, Millburn GH, Rost B, FlyBase Consortium. Database : the journal of biological databases and curation Volume 2014 (2014) p.bau033 DOI: 10.1093/database/bau033
Chemical, target, and bioactive properties of allosteric modulation.
van Westen GJ, Gaulton A, Overington JP. PLoS computational biology Volume 10 (2014) p.e1003559 DOI: 10.1371/journal.pcbi.1003559
*
Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.
International Glossina Genome Initiative. Science (New York, N.Y.) Volume 344 (2014) p.380-386 DOI: 10.1126/science.1249656
Integrative knowledge management to enhance pharmaceutical R&D.
Marti-Solano M, Birney E, Bril A, Della Pasqua O, Kitano H, Mons B, Xenarios I, Sanz F. Nature reviews. Drug discovery Volume 13 (2014) p.239-240 DOI: 10.1038/nrd4290
*
Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells.
Arner E, Forrest AR, Ehrlund A, Mejhert N, Itoh M, Kawaji H, Lassmann T, Laurencikiene J, Rydén M, Arner P, FANTOM Consortium. PloS one Volume 9 (2014) p.e80274 DOI: 10.1371/journal.pone.0080274
*
Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.
Morikawa H, Ohkura N, Vandenbon A, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Standley DM, Date H, Sakaguchi S, FANTOM Consortium. Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.5289-5294 DOI: 10.1073/pnas.1312717110
*
Peroxidase gene discovery from the horseradish transcriptome.
Näätsaari L, Krainer FW, Schubert M, Glieder A, Thallinger GG. BMC genomics Volume 15 (2014) p.227 DOI: 10.1186/1471-2164-15-227
Exploring the biological and chemical complexity of the ligases.
Holliday GL, Rahman SA, Furnham N, Thornton JM. Journal of molecular biology Volume 426 (2014) p.2098-2111 DOI: 10.1016/j.jmb.2014.03.008
*
The reference genome sequence of Saccharomyces cerevisiae: then and now.
Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM. G3 (Bethesda, Md.) Volume 4 (2014) p.389-398 DOI: 10.1534/g3.113.008995
*
BetaVoid: molecular voids via beta-complexes and Voronoi diagrams.
Kim JK, Cho Y, Laskowski RA, Ryu SE, Sugihara K, Kim DS. Proteins Volume 82 (2014) p.1829-1849 DOI: 10.1002/prot.24537
gitter: a robust and accurate method for quantification of colony sizes from plate images.
Wagih O, Parts L. G3 (Bethesda, Md.) Volume 4 (2014) p.547-552 DOI: 10.1534/g3.113.009431
*
Leucine modulates dynamic phosphorylation events in insulin signaling pathway and enhances insulin-dependent glycogen synthesis in human skeletal muscle cells.
Di Camillo B, Eduati F, Nair SK, Avogaro A, Toffolo GM. BMC cell biology Volume 15 (2014) p.9 DOI: 10.1186/1471-2121-15-9
Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish.
Spivakov M, Auer TO, Peravali R, Dunham I, Dolle D, Fujiyama A, Toyoda A, Aizu T, Minakuchi Y, Loosli F, Naruse K, Birney E, Wittbrodt J. G3 (Bethesda, Md.) Volume 4 (2014) p.433-445 DOI: 10.1534/g3.113.008722
*
Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis.
Das D, Murzin AG, Rawlings ND, Finn RD, Coggill P, Bateman A, Godzik A, Aravind L. BMC bioinformatics Volume 15 (2014) p.75 DOI: 10.1186/1471-2105-15-75
Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt.
Huntley RP, Sawford T, Martin MJ, O'Donovan C. GigaScience Volume 3 (2014) p.4 DOI: 10.1186/2047-217X-3-4
*
Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).
Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Smith L, Zhang F, Bonnet E. Standards in Genomic Sciences Volume 9 (2014) p.1285-1301 DOI: 10.4056/sigs.5279417
*
Characterizing genetic variants for clinical action.
Ramos EM, Din-Lovinescu C, Berg JS, Brooks LD, Duncanson A, Dunn M, Good P, Hubbard TJ, Jarvik GP, O'Donnell C, Sherry ST, Aronson N, Biesecker LG, Blumberg B, Calonge N, Colhoun HM, Epstein RS, Flicek P, Gordon ES, Green ED, Green RC, Hurles M, Kawamoto K, Knaus W, Ledbetter DH, Levy HP, Lyon E, Maglott D, McLeod HL, Rahman N, Randhawa G, Wicklund C, Manolio TA, Chisholm RL, Williams MS. American journal of medical genetics. Part C, Seminars in medical genetics Volume 166C (2014) p.93-104 DOI: 10.1002/ajmg.c.31386
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data.
Poux S, Magrane M, Arighi CN, Bridge A, O'Donovan C, Laiho K, UniProt Consortium. Database : the journal of biological databases and curation Volume 2014 (2014) p.bau016 DOI: 10.1093/database/bau016
Bioinformatics curriculum guidelines: toward a definition of core competencies.
Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B, Schneider MV. PLoS computational biology Volume 10 (2014) p.e1003496 DOI: 10.1371/journal.pcbi.1003496
Evolution of transcription factor binding in metazoans - mechanisms and functional implications.
Villar D, Flicek P, Odom DT. Nature reviews. Genetics Volume 15 (2014) p.221-233 DOI: 10.1038/nrg3481
*
Revisiting the training of logic models of protein signaling networks with ASP
Videla S, Guziolowski C, Eduati F, Thiele S, Grabe N, Saez-Rodriguez J, Siegel A. Computational Methods in Systems Biology Springer Berlin Heidelberg DOI: 10.1007/978-3-642-33636-2_20
*
A promoter-level mammalian expression atlas.
FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y. Nature Volume 507 (2014) p.462-470 DOI: 10.1038/nature13182
*
Ontologies in biological data visualization.
Carpendale S, Chen M, Evanko D, Gehlenborg N, Gorg C, Hunter L, Rowland F, Storey MA, Strobelt H. IEEE computer graphics and applications Volume 34 (2014) p.8-15 DOI: 10.1109/mcg.2014.33
ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H. Nature biotechnology Volume 32 (2014) p.223-226 DOI: 10.1038/nbt.2839
An atlas of active enhancers across human cell types and tissues.
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A. Nature Volume 507 (2014) p.455-461 DOI: 10.1038/nature12787
The ChEMBL database: a taster for medicinal chemists.
Papadatos G, Overington JP. Future medicinal chemistry Volume 6 (2014) p.361-364 DOI: 10.4155/fmc.14.8
Ten simple rules for running interactive workshops.
Pavelin K, Pundir S, Cham JA. PLoS computational biology Volume 10 (2014) p.e1003485 DOI: 10.1371/journal.pcbi.1003485
Information visualisation for science and policy: engaging users and avoiding bias.
McInerny GJ, Chen M, Freeman R, Gavaghan D, Meyer M, Rowland F, Spiegelhalter DJ, Stefaner M, Tessarolo G, Hortal J. Trends in ecology & evolution Volume 29 (2014) p.148-157 DOI: 10.1016/j.tree.2014.01.003
*
Eavesdropping cuckoos: further insights on great spotted cuckoo preference by magpie nests and egg colour.
Soler JJ, Avilés JM, Martín-Gálvez D, de Neve L, Soler M. Oecologia Volume 175 (2014) p.105-115 DOI: 10.1007/s00442-014-2901-2
Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.
Rueedi R, Ledda M, Nicholls AW, Salek RM, Marques-Vidal P, Morya E, Sameshima K, Montoliu I, Da Silva L, Collino S, Martin FP, Rezzi S, Steinbeck C, Waterworth DM, Waeber G, Vollenweider P, Beckmann JS, Le Coutre J, Mooser V, Bergmann S, Genick UK, Kutalik Z. PLoS genetics Volume 10 (2014) p.e1004132 DOI: 10.1371/journal.pgen.1004132
Genomic standards consortium projects.
Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G. Standards in genomic sciences Volume 9 (2014) p.599-601 DOI: 10.4056/sigs.5559680
A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.
Tamuri AU, Goldman N, dos Reis M. Genetics Volume 197 (2014) p.257-271 DOI: 10.1534/genetics.114.162263
FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences.
Garcia L, Yachdav G, Martin MJ. F1000Research Volume 3 (2014) p.47 DOI: 10.12688/f1000research.3-47.v2
BioJS: an open source standard for biological visualisation - its status in 2014.
Corpas M, Jimenez R, Carbon SJ, García A, Garcia L, Goldberg T, Gomez J, Kalderimis A, Lewis SE, Mulvany I, Pawlik A, Rowland F, Salazar G, Schreiber F, Sillitoe I, Spooner WH, Thanki AS, Villaveces JM, Yachdav G, Hermjakob H. F1000Research Volume 3 (2014) p.55 DOI: 10.12688/f1000research.3-55.v1
KEGGViewer, a BioJS component to visualize KEGG Pathways.
Villaveces JM, Jimenez RC, Habermann BH. F1000Research Volume 3 (2014) p.43 DOI: 10.12688/f1000research.3-43.v1
Sequence, a BioJS component for visualising sequences.
Gomez J, Jimenez R. F1000Research Volume 3 (2014) p.52 DOI: 10.12688/f1000research.3-52.v1
PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers.
Villaveces JM, Jimenez RC, Habermann BH. F1000Research Volume 3 (2014) p.44 DOI: 10.12688/f1000research.3-44.v1
*
FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences
Garcia L, Yachdav G, Martin M. Preprint DOI: 10.12688/f1000research.3-47.v1
*
Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia.
Camps C, Saini HK, Mole DR, Choudhry H, Reczko M, Guerra-Assunção JA, Tian YM, Buffa FM, Harris AL, Hatzigeorgiou AG, Enright AJ, Ragoussis J. Molecular cancer Volume 13 (2014) p.28 DOI: 10.1186/1476-4598-13-28
Serum levels of mature microRNAs in DICER1-mutated pleuropulmonary blastoma.
Murray MJ, Bailey S, Raby KL, Saini HK, de Kock L, Burke GA, Foulkes WD, Enright AJ, Coleman N, Tischkowitz M. Oncogenesis Volume 3 (2014) p.e87 DOI: 10.1038/oncsis.2014.1
Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier.
Rinschen MM, Wu X, König T, Pisitkun T, Hagmann H, Pahmeyer C, Lamkemeyer T, Kohli P, Schnell N, Schermer B, Dryer S, Brooks BR, Beltrao P, Krueger M, Brinkkoetter PT, Benzing T. Journal of the American Society of Nephrology : JASN Volume 25 (2014) p.1509-1522 DOI: 10.1681/ASN.2013070760
*
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
Meyer P, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Sauro HM, Stolovitzky G, Saez-Rodriguez J. BMC systems biology Volume 8 (2014) p.13 DOI: 10.1186/1752-0509-8-13
DAF-16/FoxO directly regulates an atypical AMP-activated protein kinase gamma isoform to mediate the effects of insulin/IGF-1 signaling on aging in Caenorhabditis elegans.
Tullet JM, Araiz C, Sanders MJ, Au C, Benedetto A, Papatheodorou I, Clark E, Schmeisser K, Jones D, Schuster EF, Thornton JM, Gems D. PLoS genetics Volume 10 (2014) p.e1004109 DOI: 10.1371/journal.pgen.1004109
*
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. Journal of biomedical semantics Volume 5 (2014) p.5 DOI: 10.1186/2041-1480-5-5
Deep Sequencing Insights in Therapeutic shRNA Processing and siRNA Target Cleavage Precision.
Denise H, Moschos SA, Sidders B, Burden F, Perkins H, Carter N, Stroud T, Kennedy M, Fancy SA, Lapthorn C, Lavender H, Kinloch R, Suhy D, Corbau R. Molecular therapy. Nucleic acids Volume 3 (2014) p.e145 DOI: 10.1038/mtna.2013.73
Functional annotation of noncoding sequence variants.
Ritchie GR, Dunham I, Zeggini E, Flicek P. Nature methods Volume 11 (2014) p.294-296 DOI: 10.1038/nmeth.2832
*
Do climatic conditions affect host and parasite phenotypes differentially? A case study of magpies and great spotted cuckoos.
Soler JJ, De Neve L, Martín-Gálvez D, Molina-Morales M, Pérez-Contreras T, Ruiz-Rodríguez M. Oecologia Volume 174 (2014) p.327-338 DOI: 10.1007/s00442-013-2772-y
Random monoallelic gene expression increases upon embryonic stem cell differentiation.
Eckersley-Maslin MA, Thybert D, Bergmann JH, Marioni JC, Flicek P, Spector DL. Developmental cell Volume 28 (2014) p.351-365 DOI: 10.1016/j.devcel.2014.01.017
*
MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans.
Riesen M, Feyst I, Rattanavirotkul N, Ezcurra M, Tullet JM, Papatheodorou I, Ziehm M, Au C, Gilliat AF, Hellberg J, Thornton JM, Gems D. Aging Volume 6 (2014) p.98-117 DOI: 10.18632/aging.100638
Efficient ring perception for the Chemistry Development Kit.
May JW, Steinbeck C. Journal of cheminformatics Volume 6 (2014) p.3 DOI: 10.1186/1758-2946-6-3
Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records.
Federhen S, Clark K, Barrett T, Parkinson H, Ostell J, Kodama Y, Mashima J, Nakamura Y, Cochrane G, Karsch-Mizrachi I. Standards in genomic sciences Volume 9 (2014) p.1275-1277 DOI: 10.4056/sigs.4851102
Genetic pleiotropy between multiple sclerosis and schizophrenia but not bipolar disorder: differential involvement of immune-related gene loci.
Andreassen OA, Harbo HF, Wang Y, Thompson WK, Schork AJ, Mattingsdal M, Zuber V, Bettella F, Ripke S, Kelsoe JR, Kendler KS, O'Donovan MC, Sklar P, Psychiatric Genomics Consortium (PGC) Bipolar Disorder and Schizophrenia Work Groups, International Multiple Sclerosis Genetics Consortium (IMSGC), McEvoy LK, Desikan RS, Lie BA, Djurovic S, Dale AM. Molecular psychiatry Volume 20 (2015) p.207-214 DOI: 10.1038/mp.2013.195
*
Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy.
Cerase A, Smeets D, Tang YA, Gdula M, Kraus F, Spivakov M, Moindrot B, Leleu M, Tattermusch A, Demmerle J, Nesterova TB, Green C, Otte AP, Schermelleh L, Brockdorff N. Proceedings of the National Academy of Sciences of the United States of America Volume 111 (2014) p.2235-2240 DOI: 10.1073/pnas.1312951111
Citrullination regulates pluripotency and histone H1 binding to chromatin.
Christophorou MA, Castelo-Branco G, Halley-Stott RP, Oliveira CS, Loos R, Radzisheuskaya A, Mowen KA, Bertone P, Silva JC, Zernicka-Goetz M, Nielsen ML, Gurdon JB, Kouzarides T. Nature Volume 507 (2014) p.104-108 DOI: 10.1038/nature12942
InterProScan 5: genome-scale protein function classification.
Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S. Bioinformatics (Oxford, England) Volume 30 (2014) p.1236-1240 DOI: 10.1093/bioinformatics/btu031
*
Reliable protocols for whole-mount fluorescent in situ hybridization (FISH) in the pea aphid Acyrthosiphon pisum: a comprehensive survey and analysis.
Chung CY, Cook CE, Lin GW, Huang TY, Chang CC. Insect science Volume 21 (2014) p.265-277 DOI: 10.1111/1744-7917.12086
PIP₃ induces the recycling of receptor tyrosine kinases.
Laketa V, Zarbakhsh S, Traynor-Kaplan A, Macnamara A, Subramanian D, Putyrski M, Mueller R, Nadler A, Mentel M, Saez-Rodriguez J, Pepperkok R, Schultz C. Science signaling Volume 7 (2014) p.ra5 DOI: 10.1126/scisignal.2004532
*
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.
Wheeler TJ, Clements J, Finn RD. BMC bioinformatics Volume 15 (2014) p.7 DOI: 10.1186/1471-2105-15-7
EC-BLAST: a tool to automatically search and compare enzyme reactions.
Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM. Nature methods Volume 11 (2014) p.171-174 DOI: 10.1038/nmeth.2803
The EBI RDF platform: linked open data for the life sciences.
Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM. Bioinformatics (Oxford, England) Volume 30 (2014) p.1338-1339 DOI: 10.1093/bioinformatics/btt765
*
Frequency and function of KIR+ CD8+ T cells in HTLV-1 infection.
Twigger K, Rowan A, Seich al Basatena N, MacNamara A, Retiere C, Gould K, Taylor GP, Asquith B, Bangham CR. Retrovirology Volume 11 (2014) p.P79-P79 DOI: 10.1186/1742-4690-11-S1-P79
*
T-Coffee: Tree-based consistency objective function for alignment evaluation.
Magis C, Taly JF, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Notredame C. Methods in molecular biology (Clifton, N.J.) Volume 1079 (2014) p.117-129 DOI: 10.1007/978-1-62703-646-7_7
*
A survey of molecular descriptors used in mass spectrometry based proteomics.
Audain E, Sanchez A, Vizcaíno JA, Perez-Riverol Y. Current topics in medicinal chemistry Volume 14 (2014) p.388-397 DOI: 10.2174/1568026613666131204113537
*
Editorial: Genomics and proteomics behind drug design.
Perez-Riverol Y, Carvalho PC. Current topics in medicinal chemistry Volume 14 (2014) p.343 DOI: 10.2174/1568026613666131204101110
diXa data warehouse: Exploring data from toxicogenomics studies
Matser V. DOI: 10.6019/tol.dixa-t.2014.00001.1
*
A novel RCE1 isoform is required for H-Ras plasma membrane localization and is regulated by USP17.
Jaworski J, Govender U, McFarlane C, de la Vega M, Greene MK, Rawlings ND, Johnston JA, Scott CJ, Burrows JF. The Biochemical journal Volume 457 (2014) p.289-300 DOI: 10.1042/bj20131213
*
Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.
Iantorno S, Gori K, Goldman N, Gil M, Dessimoz C. Methods in molecular biology (Clifton, N.J.) Volume 1079 (2014) p.59-73 DOI: 10.1007/978-1-62703-646-7_4
*
Delivering ICT Infrastructure for Biomedical Research
Rahman SA, Furnham N, Holliday GL and Thornton JM. Nature methods Volume 11 (2014) p.171-174
Metabolomics: an introduction
Salek R, Emery L, Beisken S. DOI: 10.6019/tol.mbs.2014.00001.1
Heterogeneity of genomic evolution and mutational profiles in multiple myeloma.
Bolli N, Avet-Loiseau H, Wedge DC, Van Loo P, Alexandrov LB, Martincorena I, Dawson KJ, Iorio F, Nik-Zainal S, Bignell GR, Hinton JW, Li Y, Tubio JM, McLaren S, O' Meara S, Butler AP, Teague JW, Mudie L, Anderson E, Rashid N, Tai YT, Shammas MA, Sperling AS, Fulciniti M, Richardson PG, Parmigiani G, Magrangeas F, Minvielle S, Moreau P, Attal M, Facon T, Futreal PA, Anderson KC, Campbell PJ, Munshi NC. Nature communications Volume 5 (2014) p.2997 DOI: 10.1038/ncomms3997
*
The NAD Binding Domain and the Short Chain Dehydrogenase/Reductase (SDR) Superfamily
Furnham N, Holliday GL, Thornton JM. Protein Families: Relating Protein Sequence, Structure and Function Wiley, UK
*
A predictive model for assistive technology adoption for people with dementia.
Zhang S, McClean SI, Nugent CD, Donnelly MP, Galway L, Scotney BW, Cleland I. IEEE journal of biomedical and health informatics Volume 18 (2014) p.375-383 DOI: 10.1109/jbhi.2013.2267549

2013

*
Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes.
Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT, Flicek P. Genome biology Volume 14 (2013) p.R148 DOI: 10.1186/gb-2013-14-12-r148
*
Reconstructing Native American migrations from whole-genome and whole-exome data.
Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, 1000 Genomes Project, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, Bustamante CD. PLoS genetics Volume 9 (2013) p.e1004023 DOI: 10.1371/journal.pgen.1004023
ISEV position paper: extracellular vesicle RNA analysis and bioinformatics.
Hill AF, Pegtel DM, Lambertz U, Leonardi T, O'Driscoll L, Pluchino S, Ter-Ovanesyan D, Nolte-'t Hoen EN. Journal of extracellular vesicles Volume 2 (2013) DOI: 10.3402/jev.v2i0.22859
Evolution and functional cross-talk of protein post-translational modifications.
Beltrao P, Bork P, Krogan NJ, van Noort V. Molecular systems biology Volume 9 (2013) p.714 DOI: 10.1002/msb.201304521
WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis.
Zerbino DR, Johnson N, Juettemann T, Wilder SP, Flicek P. Bioinformatics (Oxford, England) Volume 30 (2014) p.1008-1009 DOI: 10.1093/bioinformatics/btt737
Archaic humans: Four makes a party.
Birney E, Pritchard JK. Nature Volume 505 (2014) p.32-34 DOI: 10.1038/nature12847
Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions.
Nayduch D, Cohnstaedt LW, Saski C, Lawson D, Kersey P, Fife M, Carpenter S. Virus research Volume 182 (2014) p.43-49 DOI: 10.1016/j.virusres.2013.12.009
*
Network based elucidation of drug response: from modulators to targets.
Iorio F, Saez-Rodriguez J, di Bernardo D. BMC systems biology Volume 7 (2013) p.139 DOI: 10.1186/1752-0509-7-139
*
Characterization, design, and function of the mitochondrial proteome: from organs to organisms.
Lotz C, Lin AJ, Black CM, Zhang J, Lau E, Deng N, Wang Y, Zong NC, Choi JH, Xu T, Liem DA, Korge P, Weiss JN, Hermjakob H, Yates JR, Apweiler R, Ping P. Journal of proteome research Volume 13 (2014) p.433-446 DOI: 10.1021/pr400539j
Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.
de Beer TA, Laskowski RA, Parks SL, Sipos B, Goldman N, Thornton JM. PLoS computational biology Volume 9 (2013) p.e1003382 DOI: 10.1371/journal.pcbi.1003382
*
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T. BMC systems biology Volume 7 (2013) p.135 DOI: 10.1186/1752-0509-7-135
*
Epimutation profiling in Beckwith-Wiedemann syndrome: relationship with assisted reproductive technology.
Tee L, Lim DH, Dias RP, Baudement MO, Slater AA, Kirby G, Hancocks T, Stewart H, Hardy C, Macdonald F, Maher ER. Clinical epigenetics Volume 5 (2013) p.23 DOI: 10.1186/1868-7083-5-23
*
Suppression of type 1 pilus assembly in uropathogenic Escherichia coli by chemical inhibition of subunit polymerization.
Lo AW, Van de Water K, Gane PJ, Chan AW, Steadman D, Stevens K, Selwood DL, Waksman G, Remaut H. The Journal of antimicrobial chemotherapy Volume 69 (2014) p.1017-1026 DOI: 10.1093/jac/dkt467
*
Nutrigenomics of high fat diet induced obesity in mice suggests relationships between susceptibility to fatty liver disease and the proteasome.
Waller-Evans H, Hue C, Fearnside J, Rothwell AR, Lockstone HE, Caldérari S, Wilder SP, Cazier JB, Scott J, Gauguier D. PloS one Volume 8 (2013) p.e82825 DOI: 10.1371/journal.pone.0082825
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations.
Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H. Nucleic acids research Volume 42 (2014) p.D1001-6 DOI: 10.1093/nar/gkt1229
Ensembl 2014.
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kähäri AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ruffier M, Sheppard D, Taylor K, Thormann A, Trevanion SJ, Vullo A, Wilder SP, Wilson M, Zadissa A, Aken BL, Birney E, Cunningham F, Harrow J, Herrero J, Hubbard TJ, Kinsella R, Muffato M, Parker A, Spudich G, Yates A, Yates A, Zerbino DR, Searle SM. Nucleic acids research Volume 42 (2014) p.D749-55 DOI: 10.1093/nar/gkt1196
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.
Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM. Nucleic acids research Volume 42 (2014) p.D485-9 DOI: 10.1093/nar/gkt1243
DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.
Gaudet P, Munoz-Torres M, Robinson-Rechavi M, Attwood T, Bateman A, Cherry JM, Kania R, O'Donovan C, Yamasaki C. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat077 DOI: 10.1093/database/bat077
Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.
Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A. Nucleic acids research Volume 42 (2014) p.D926-32 DOI: 10.1093/nar/gkt1270
iPfam: a database of protein family and domain interactions found in the Protein Data Bank.
Finn RD, Miller BL, Clements J, Bateman A. Nucleic acids research Volume 42 (2014) p.D364-73 DOI: 10.1093/nar/gkt1210
*
The Amborella genome and the evolution of flowering plants.
Amborella Genome Project. Science (New York, N.Y.) Volume 342 (2013) p.1241089 DOI: 10.1126/science.1241089
*
Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.
Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB. Science (New York, N.Y.) Volume 342 (2013) p.1516-1517 DOI: 10.1126/science.1241130
SCOP2 prototype: a new approach to protein structure mining.
Andreeva A, Howorth D, Chothia C, Kulesha E, Murzin AG. Nucleic acids research Volume 42 (2014) p.D310-4 DOI: 10.1093/nar/gkt1242
Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria.
Pande S, Merker H, Bohl K, Reichelt M, Schuster S, de Figueiredo LF, Kaleta C, Kost C. The ISME journal Volume 8 (2014) p.953-962 DOI: 10.1038/ismej.2013.211
Evolution of the thermopsin peptidase family (A5).
Rawlings ND. PloS one Volume 8 (2013) p.e78998 DOI: 10.1371/journal.pone.0078998
PDBe: Protein Data Bank in Europe.
Gutmanas A, Alhroub Y, Battle GM, Berrisford JM, Bochet E, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Gore SP, Haslam P, Haslam P, Hatherley R, Hendrickx PM, Hirshberg M, Lagerstedt I, Mir S, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sanz-García E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ. Nucleic acids research Volume 42 (2014) p.D285-91 DOI: 10.1093/nar/gkt1180
Pfam: the protein families database.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M. Nucleic acids research Volume 42 (2014) p.D222-30 DOI: 10.1093/nar/gkt1223
*
LUD, a new protein domain associated with lactate utilization.
Hwang WC, Bakolitsa C, Punta M, Coggill PC, Bateman A, Axelrod HL, Rawlings ND, Sedova M, Peterson SN, Eberhardt RY, Aravind L, Pascual J, Godzik A. BMC bioinformatics Volume 14 (2013) p.341 DOI: 10.1186/1471-2105-14-341
Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants.
MacArthur JA, Morales J, Tully RE, Astashyn A, Gil L, Bruford EA, Larsson P, Flicek P, Dalgleish R, Maglott DR, Cunningham F. Nucleic acids research Volume 42 (2014) p.D873-8 DOI: 10.1093/nar/gkt1198
*
Targeting CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti-PD-L1 immunotherapy in pancreatic cancer.
Feig C, Jones JO, Kraman M, Wells RJ, Deonarine A, Chan DS, Connell CM, Roberts EW, Zhao Q, Caballero OL, Teichmann SA, Janowitz T, Jodrell DI, Tuveson DA, Fearon DT. Proceedings of the National Academy of Sciences of the United States of America Volume 110 (2013) p.20212-20217 DOI: 10.1073/pnas.1320318110
Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure.
Marsh JA, Teichmann SA. BioEssays : news and reviews in molecular, cellular and developmental biology Volume 36 (2014) p.209-218 DOI: 10.1002/bies.201300134
*
Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya.
Borrmann S, Straimer J, Mwai L, Abdi A, Rippert A, Okombo J, Muriithi S, Sasi P, Kortok MM, Lowe B, Campino S, Assefa S, Auburn S, Manske M, Maslen G, Peshu N, Kwiatkowski DP, Marsh K, Nzila A, Clark TG. Scientific reports Volume 3 (2013) p.3318 DOI: 10.1038/srep03318
The European Bioinformatics Institute's data resources 2014.
Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J. Nucleic acids research Volume 42 (2014) p.D18-25 DOI: 10.1093/nar/gkt1206
*
Policy challenges of clinical genome sequencing.
Wright CF, Middleton A, Burton H, Cunningham F, Humphries SE, Hurst J, Birney E, Firth HV. BMJ (Clinical research ed.) Volume 347 (2013) p.f6845 DOI: 10.1136/bmj.f6845
*
Saccharomyces genome database provides new regulation data.
Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM. Nucleic acids research Volume 42 (2014) p.D717-25 DOI: 10.1093/nar/gkt1158
Updates to BioSamples database at European Bioinformatics Institute.
Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, Sarkans U, Brazma A, Parkinson H. Nucleic acids research Volume 42 (2014) p.D50-2 DOI: 10.1093/nar/gkt1081
*
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.
Lees JG, Lee D, Studer RA, Dawson NL, Sillitoe I, Das S, Yeats C, Dessailly BH, Rentzsch R, Orengo CA. Nucleic acids research Volume 42 (2014) p.D240-5 DOI: 10.1093/nar/gkt1205
myChEMBL: a virtual machine implementation of open data and cheminformatics tools.
Ochoa R, Davies M, Papadatos G, Atkinson F, Overington JP. Bioinformatics (Oxford, England) Volume 30 (2014) p.298-300 DOI: 10.1093/bioinformatics/btt666
LigSearch: a knowledge-based web server to identify likely ligands for a protein target.
de Beer TA, Laskowski RA, Duban ME, Chan AW, Anderson WF, Thornton JM. Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2395-2402 DOI: 10.1107/S0907444913022294
*
Filling out the structural map of the NTF2-like superfamily.
Eberhardt RY, Chang Y, Bateman A, Murzin AG, Axelrod HL, Hwang WC, Aravind L. BMC bioinformatics Volume 14 (2013) p.327 DOI: 10.1186/1471-2105-14-327
*
Comment on on the propagation of errors by Jaskolski (2013).
Berman H, Kleywegt GJ, Nakamura H, Markley JL. Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2297 DOI: 10.1107/S090744491302917X
*
Comment on timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013).
Berman H, Kleywegt GJ, Nakamura H, Markley JL. Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2296 DOI: 10.1107/S0907444913029168
*
Activities at the Universal Protein Resource (UniProt).
UniProt Consortium. Nucleic acids research Volume 42 (2014) p.D191-8 DOI: 10.1093/nar/gkt1140
*
Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.
Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK, Witwicki RM, Migliavacca E, Yurovsky A, Lappalainen T, Hernandez N, Reymond A, Dermitzakis ET, Deplancke B. Bioinformatics (Oxford, England) Volume 30 (2014) p.165-171 DOI: 10.1093/bioinformatics/btt667
The Reactome pathway knowledgebase.
Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P. Nucleic acids research Volume 42 (2014) p.D472-7 DOI: 10.1093/nar/gkt1102
*
Improving the performance of Transposable Elements detection tools.
Loureiro T, Camacho R, Vieira J, Fonseca NA. Journal of integrative bioinformatics Volume 10 (2013) p.231 DOI: 10.2390/biecoll-jib-2013-231
*
Genetic heterogeneity in the leader and P1-coding regions of foot-and-mouth disease virus serotypes A and O in Africa.
Chitray M, de Beer TA, Vosloo W, Maree FF. Archives of virology Volume 159 (2014) p.947-961 DOI: 10.1007/s00705-013-1838-9
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H. Nucleic acids research Volume 42 (2014) p.D358-63 DOI: 10.1093/nar/gkt1115
*
Selectome update: quality control and computational improvements to a database of positive selection.
Moretti S, Laurenczy B, Gharib WH, Castella B, Kuzniar A, Schabauer H, Studer RA, Valle M, Salamin N, Stockinger H, Robinson-Rechavi M. Nucleic acids research Volume 42 (2014) p.D917-21 DOI: 10.1093/nar/gkt1065
Gramene 2013: comparative plant genomics resources.
Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D'Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D. Nucleic acids research Volume 42 (2014) p.D1193-9 DOI: 10.1093/nar/gkt1110
*
Current status and new features of the Consensus Coding Sequence database.
Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JG, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD. Nucleic acids research Volume 42 (2014) p.D865-72 DOI: 10.1093/nar/gkt1059
Assembly information services in the European Nucleotide Archive.
Pakseresht N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Gur T, Jang M, Kay S, Leinonen R, Li W, Liu X, Lopez R, McWilliam H, Oisel A, Pallreddy S, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Squizzato S, ten Hoopen P, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Nucleic acids research Volume 42 (2014) p.D38-43 DOI: 10.1093/nar/gkt1082
The ChEMBL bioactivity database: an update.
Bento AP, Gaulton A, Hersey A, Bellis LJ, Chambers J, Davies M, Krüger FA, Light Y, Mak L, McGlinchey S, Nowotka M, Papadatos G, Santos R, Overington JP. Nucleic acids research Volume 42 (2014) p.D1083-90 DOI: 10.1093/nar/gkt1031
*
Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.
Sharma SK, Bolser D, de Boer J, Sønderkær M, Amoros W, Carboni MF, D'Ambrosio JM, de la Cruz G, Di Genova A, Douches DS, Eguiluz M, Guo X, Guzman F, Hackett CA, Hamilton JP, Li G, Li Y, Lozano R, Maass A, Marshall D, Martinez D, McLean K, Mejía N, Milne L, Munive S, Nagy I, Ponce O, Ramirez M, Simon R, Thomson SJ, Torres Y, Waugh R, Zhang Z, Huang S, Visser RG, Bachem CW, Sagredo B, Feingold SE, Orjeda G, Veilleux RE, Bonierbale M, Jacobs JM, Milbourne D, Martin DM, Bryan GJ. G3 (Bethesda, Md.) Volume 3 (2013) p.2031-2047 DOI: 10.1534/g3.113.007153
TreeFam v9: a new website, more species and orthology-on-the-fly.
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A. Nucleic acids research Volume 42 (2014) p.D922-5 DOI: 10.1093/nar/gkt1055
The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.
Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, Mason JC, Matthews P, Oakley DJ, Qazi A, Regnart J, Retha A, Santos LA, Sneddon DJ, Warren J, Westerberg H, Wilson RJ, Melvin DG, Smedley D, Brown SD, Flicek P, Skarnes WC, Mallon AM, Parkinson H. Nucleic acids research Volume 42 (2014) p.D802-9 DOI: 10.1093/nar/gkt977
A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources.
Rebholz-Schuhmann D, Grabmüller C, Kavaliauskas S, Croset S, Woollard P, Backofen R, Filsell W, Clark D. Drug discovery today Volume 19 (2014) p.882-889 DOI: 10.1016/j.drudis.2013.10.024
WormBase 2014: new views of curated biology.
Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Ozersky P, Paulini M, Raciti D, Schindelman G, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wong JD, Yook K, Schedl T, Hodgkin J, Berriman M, Kersey P, Spieth J, Stein L, Sternberg PW. Nucleic acids research Volume 42 (2014) p.D789-93 DOI: 10.1093/nar/gkt1063
Systematic evaluation of spliced alignment programs for RNA-seq data.
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P, RGASP Consortium. Nature methods Volume 10 (2013) p.1185-1191 DOI: 10.1038/nmeth.2722
Assessment of transcript reconstruction methods for RNA-seq.
Steijger T, Abril JF, Engström PG, Kokocinski F, RGASP Consortium, Hubbard TJ, Guigó R, Harrow J, Bertone P. Nature methods Volume 10 (2013) p.1177-1184 DOI: 10.1038/nmeth.2714
*
Immunology meets genomics.
Teichmann SA. Briefings in functional genomics Volume 12 (2013) p.469-470 DOI: 10.1093/bfgp/elt037
*
Path2Models: large-scale generation of computational models from biochemical pathway maps.
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N. BMC systems biology Volume 7 (2013) p.116 DOI: 10.1186/1752-0509-7-116
*
Depletion of HPV16 early genes induces autophagy and senescence in a cervical carcinogenesis model, regardless of viral physical state.
Hanning JE, Saini HK, Murray MJ, Caffarel MM, van Dongen S, Ward D, Barker EM, Scarpini CG, Groves IJ, Stanley MA, Enright AJ, Pett MR, Coleman N. The Journal of pathology Volume 231 (2013) p.354-366 DOI: 10.1002/path.4244
*
The Nucleic Acid Database: new features and capabilities.
Coimbatore Narayanan B, Westbrook J, Ghosh S, Petrov AI, Sweeney B, Zirbel CL, Leontis NB, Berman HM. Nucleic acids research Volume 42 (2014) p.D114-22 DOI: 10.1093/nar/gkt980
The functional therapeutic chemical classification system.
Croset S, Overington JP, Rebholz-Schuhmann D. Bioinformatics (Oxford, England) Volume 30 (2014) p.876-883 DOI: 10.1093/bioinformatics/btt628
*
Update of the human and mouse SERPIN gene superfamily.
Heit C, Jackson BC, McAndrews M, Wright MW, Thompson DC, Silverman GA, Nebert DW, Vasiliou V. Human genomics Volume 7 (2013) p.22 DOI: 10.1186/1479-7364-7-22
*
A high-content small molecule screen identifies sensitivity of glioblastoma stem cells to inhibition of polo-like kinase 1.
Danovi D, Folarin A, Gogolok S, Ender C, Elbatsh AM, Engström PG, Stricker SH, Gagrica S, Georgian A, Yu D, U KP, Harvey KJ, Ferretti P, Paddison PJ, Preston JE, Abbott NJ, Bertone P, Smith A, Pollard SM. PloS one Volume 8 (2013) p.e77053 DOI: 10.1371/journal.pone.0077053
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.
Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R, McAnulla C, Maguire E, Maslen J, Mitchell A, Nuka G, Oisel A, Pesseat S, Radhakrishnan R, Rocca-Serra P, Scheremetjew M, Sterk P, Vaughan D, Cochrane G, Field D, Sansone SA. Nucleic acids research Volume 42 (2014) p.D600-6 DOI: 10.1093/nar/gkt961
*
IMG 4 version of the integrated microbial genomes comparative analysis system.
Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M, Anderson I, Billis K, Varghese N, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC. Nucleic acids research Volume 42 (2014) p.D560-7 DOI: 10.1093/nar/gkt963
Ensembl Genomes 2013: scaling up access to genome-wide data.
Kersey PJ, Allen JE, Christensen M, Davis P, Falin LJ, Grabmueller C, Hughes DS, Humphrey J, Kerhornou A, Khobova J, Langridge N, McDowall MD, Maheswari U, Maslen G, Nuhn M, Ong CK, Paulini M, Paulini M, Pedro H, Toneva I, Tuli MA, Walts B, Williams G, Wilson D, Youens-Clark K, Monaco MK, Stein J, Wei X, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Staines DM. Nucleic acids research Volume 42 (2014) p.D546-52 DOI: 10.1093/nar/gkt979
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Waller M, Barrett AJ, Bateman A. Nucleic acids research Volume 42 (2014) p.D503-9 DOI: 10.1093/nar/gkt953
PDBsum additions.
de Beer TA, Berka K, Thornton JM, Laskowski RA. Nucleic acids research Volume 42 (2014) p.D292-6 DOI: 10.1093/nar/gkt940
*
The role of reporting standards for metabolite annotation and identification in metabolomic studies.
Salek RM, Steinbeck C, Viant MR, Goodacre R, Dunn WB. GigaScience Volume 2 (2013) p.13 DOI: 10.1186/2047-217X-2-13
*
IMG/M 4 version of the integrated metagenome comparative analysis system.
Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Pillay M, Ratner A, Huang J, Pagani I, Tringe S, Huntemann M, Billis K, Varghese N, Tennessen K, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC. Nucleic acids research Volume 42 (2014) p.D568-73 DOI: 10.1093/nar/gkt919
*
Smoothing 3D protein structure motifs through graph mining and amino acid similarities.
Dhifli W, Saidi R, Nguifo EM. Journal of computational biology : a journal of computational molecular cell biology Volume 21 (2014) p.162-172 DOI: 10.1089/cmb.2013.0092
An estimated 5% of new protein structures solved today represent a new Pfam family.
Mistry J, Kloppmann E, Rost B, Punta M. Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2186-2193 DOI: 10.1107/S0907444913027157
*
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources.
Rebholz-Schuhmann D, Kafkas S, Kim JH, Li C, Jimeno Yepes A, Hoehndorf R, Backofen R, Lewin I. Journal of biomedical semantics Volume 4 (2013) p.28 DOI: 10.1186/2041-1480-4-28
Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.
Lagerstedt I, Moore WJ, Patwardhan A, Sanz-García E, Best C, Swedlow JR, Kleywegt GJ. Journal of structural biology Volume 184 (2013) p.173-181 DOI: 10.1016/j.jsb.2013.09.021
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.
Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall CJ, Lomax J. Journal of biomedical semantics Volume 4 (2013) p.20 DOI: 10.1186/2041-1480-4-20
From a gene-centric to whole-proteome view of differentiation of T helper cell subsets.
Lönnberg T, Chen Z, Lahesmaa R. Briefings in functional genomics Volume 12 (2013) p.471-482 DOI: 10.1093/bfgp/elt033
*
Biomarkers in autism spectrum disorder: the old and the new.
Ruggeri B, Sarkans U, Schumann G, Persico AM. Psychopharmacology Volume 231 (2014) p.1201-1216 DOI: 10.1007/s00213-013-3290-7
Evaluation and cross-comparison of lexical entities of biological interest (LexEBI).
Rebholz-Schuhmann D, Kim JH, Yan Y, Dixit A, Friteyre C, Hoehndorf R, Backofen R, Lewin I. PloS one Volume 8 (2013) p.e75185 DOI: 10.1371/journal.pone.0075185
CAST-ChIP maps cell-type-specific chromatin states in the Drosophila central nervous system.
Schauer T, Schwalie PC, Handley A, Margulies CE, Flicek P, Ladurner AG. Cell reports Volume 5 (2013) p.271-282 DOI: 10.1016/j.celrep.2013.09.001
*
Target prediction for an open access set of compounds active against Mycobacterium tuberculosis.
Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA. PLoS computational biology Volume 9 (2013) p.e1003253 DOI: 10.1371/journal.pcbi.1003253
*
Estimating error rates in bioactivity databases.
Tiikkainen P, Bellis L, Light Y, Franke L. Journal of chemical information and modeling Volume 53 (2013) p.2499-2505 DOI: 10.1021/ci400099q
Integrative annotation of variants from 1092 humans: application to cancer genomics.
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Science (New York, N.Y.) Volume 342 (2013) p.1235587 DOI: 10.1126/science.1235587
Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.
Orchard S, Binz PA, Jones AR, Vizcaino JA, Deutsch EW, Hermjakob H. Proteomics Volume 13 (2013) p.2931-2937 DOI: 10.1002/pmic.201370166
*
A long road towards the structure of respiratory complex I, a giant molecular proton pump.
Sazanov LA, Baradaran R, Efremov RG, Berrisford JM, Minhas G. Biochemical Society transactions Volume 41 (2013) p.1265-1271 DOI: 10.1042/bst20130193
*
Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
International Multiple Sclerosis Genetics Consortium (IMSGC), Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, Oturai A, Saarela J, Fontaine B, Hemmer B, Martin C, Zipp F, D'Alfonso S, Martinelli-Boneschi F, Taylor B, Harbo HF, Kockum I, Hillert J, Olsson T, Ban M, Oksenberg JR, Hintzen R, Barcellos LF, Wellcome Trust Case Control Consortium 2 (WTCCC2), International IBD Genetics Consortium (IIBDGC), Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard HB, Baker A, Band G, Baranzini SE, Barizzone N, Barrett J, Bellenguez C, Bergamaschi L, Bernardinelli L, Berthele A, Biberacher V, Binder TM, Blackburn H, Bomfim IL, Brambilla P, Broadley S, Brochet B, Brundin L, Buck D, Butzkueven H, Caillier SJ, Camu W, Carpentier W, Cavalla P, Celius EG, Coman I, Comi G, Corrado L, Cosemans L, Cournu-Rebeix I, Cree BA, Cusi D, Damotte V, Defer G, Delgado SR, Deloukas P, di Sapio A, Dilthey AT, Donnelly P, Dubois B, Duddy M, Edkins S, Elovaara I, Esposito F, Evangelou N, Fiddes B, Field J, Franke A, Freeman C, Frohlich IY, Galimberti D, Gieger C, Gourraud PA, Graetz C, Graham A, Grummel V, Guaschino C, Hadjixenofontos A, Hakonarson H, Halfpenny C, Hall G, Hall P, Hamsten A, Harley J, Harrower T, Hawkins C, Hellenthal G, Hillier C, Hobart J, Hoshi M, Hunt SE, Jagodic M, Jelčić I, Jochim A, Kendall B, Kermode A, Kilpatrick T, Koivisto K, Konidari I, Korn T, Kronsbein H, Langford C, Larsson M, Lathrop M, Lebrun-Frenay C, Lechner-Scott J, Lee MH, Leone MA, Leppä V, Liberatore G, Lie BA, Lill CM, Lindén M, Link J, Luessi F, Lycke J, Macciardi F, Männistö S, Manrique CP, Martin R, Martinelli V, Mason D, Mazibrada G, McCabe C, Mero IL, Mescheriakova J, Moutsianas L, Myhr KM, Nagels G, Nicholas R, Nilsson P, Piehl F, Pirinen M, Price SE, Quach H, Reunanen M, Robberecht W, Robertson NP, Rodegher M, Rog D, Salvetti M, Schnetz-Boutaud NC, Sellebjerg F, Selter RC, Schaefer C, Shaunak S, Shen L, Shields S, Siffrin V, Slee M, Sorensen PS, Sorosina M, Sospedra M, Spurkland A, Strange A, Sundqvist E, Thijs V, Thorpe J, Ticca A, Tienari P, van Duijn C, Visser EM, Vucic S, Westerlind H, Wiley JS, Wilkins A, Wilson JF, Winkelmann J, Zajicek J, Zindler E, Haines JL, Pericak-Vance MA, Ivinson AJ, Stewart G, Hafler D, Hauser SL, Compston A, McVean G, De Jager P, Sawcer SJ, McCauley JL. Nature genetics Volume 45 (2013) p.1353-1360 DOI: 10.1038/ng.2770
Capturing cooperative interactions with the PSI-MI format.
Van Roey K, Orchard S, Kerrien S, Dumousseau M, Ricard-Blum S, Hermjakob H, Gibson TJ. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat066 DOI: 10.1093/database/bat066
*
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets.
van Westen GJ, Swier RF, Cortes-Ciriano I, Wegner JK, Overington JP, Ijzerman AP, van Vlijmen HW, Bender A. Journal of cheminformatics Volume 5 (2013) p.42 DOI: 10.1186/1758-2946-5-42
BioServices: a common Python package to access biological Web Services programmatically.
Cokelaer T, Pultz D, Harder LM, Serra-Musach J, Saez-Rodriguez J. Bioinformatics (Oxford, England) Volume 29 (2013) p.3241-3242 DOI: 10.1093/bioinformatics/btt547
Accounting for technical noise in single-cell RNA-seq experiments.
Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG. Nature methods Volume 10 (2013) p.1093-1095 DOI: 10.1038/nmeth.2645
*
HIV-1 uncoating in human CD4+ T cells: kinetic and functional analyses.
Chen N, Zhou L, Gane PG, Price A, Zufferey M, Luban J, James L, Selwood D, Fassati A. Retrovirology Volume 10 (2013) p.P13-P13 DOI: 10.1186/1742-4690-10-S1-P13
*
Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype.
Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, Schuon AK, Pe'er D, Steinmetz LM. PLoS genetics Volume 9 (2013) p.e1003803 DOI: 10.1371/journal.pgen.1003803
ISCB computational biology Wikipedia competition.
Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P, Rost B. PLoS computational biology Volume 9 (2013) p.e1003242 DOI: 10.1371/journal.pcbi.1003242
*
Metabolic flux is a determinant of the evolutionary rates of enzyme-encoding genes.
Colombo M, Laayouni H, Invergo BM, Bertranpetit J, Montanucci L. Evolution; international journal of organic evolution Volume 68 (2014) p.605-613 DOI: 10.1111/evo.12262
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.
Gonçalves E, Mirlach F, Saez-Rodriguez J. F1000Research Volume 2 (2013) p.192 DOI: 10.12688/f1000research.2-192.v2
*
A variant in LDLR is associated with abdominal aortic aneurysm.
Bradley DT, Hughes AE, Badger SA, Jones GT, Harrison SC, Wright BJ, Bumpstead S, Baas AF, Grétarsdóttir S, Burnand K, Child AH, Clough RE, Cockerill G, Hafez H, Scott DJ, Ariëns RA, Johnson A, Sohrabi S, Smith A, Thompson MM, van Bockxmeer FM, Waltham M, Matthíasson SE, Thorleifsson G, Thorsteinsdottir U, Blankensteijn JD, Teijink JA, Wijmenga C, de Graaf J, Kiemeney LA, Wild JB, Edkins S, Gwilliam R, Hunt SE, Potter S, Lindholt JS, Golledge J, Norman PE, van Rij A, Powell JT, Eriksson P, Stefánsson K, Thompson JR, Humphries SE, Sayers RD, Deloukas P, Samani NJ, Bown MJ. Circulation. Cardiovascular genetics Volume 6 (2013) p.498-504 DOI: 10.1161/circgenetics.113.000165
*
Organizing a PhD symposium--an inside view. Setting up a scientific meeting is challenging--a PhD symposium offers its own unique opportunities and pitfalls.
Schröder MS, Harnett D, Minke BA, Nair PS, Committee Member Consortium. EMBO reports Volume 14 (2013) p.856-860 DOI: 10.1038/embor.2013.147
*
Transcriptome and genome sequencing uncovers functional variation in humans.
Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM, Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET. Nature Volume 501 (2013) p.506-511 DOI: 10.1038/nature12531
*
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
't Hoen PA, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, Karlberg O, Brännvall M, GEUVADIS Consortium, den Dunnen JT, van Ommen GJ, Gut IG, Guigó R, Estivill X, Syvänen AC, Dermitzakis ET, Lappalainen T. Nature biotechnology Volume 31 (2013) p.1015-1022 DOI: 10.1038/nbt.2702
*
Monitoring named entity recognition: the League Table.
Rebholz-Schuhmann D, Kafkas S, Kim JH, Jimeno Yepes A, Lewin I. Journal of biomedical semantics Volume 4 (2013) p.19 DOI: 10.1186/2041-1480-4-19
OntoQuery: easy-to-use web-based OWL querying.
Tudose I, Hastings J, Muthukrishnan V, Owen G, Turner S, Dekker A, Kale N, Ennis M, Steinbeck C. Bioinformatics (Oxford, England) Volume 29 (2013) p.2955-2957 DOI: 10.1093/bioinformatics/btt514
*
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments.
Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, Lenhard B, Giorgetti L, Heard E, Fisher AG, Flicek P, Dekker J, Merkenschlager M. Genome research Volume 23 (2013) p.2066-2077 DOI: 10.1101/gr.161620.113
*
Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.
Coggill P, Eberhardt RY, Finn RD, Chang Y, Jaroszewski L, Godzik A, Das D, Xu Q, Axelrod HL, Aravind L, Murzin AG, Bateman A. BMC bioinformatics Volume 14 (2013) p.265 DOI: 10.1186/1471-2105-14-265
Exploiting disjointness axioms to improve semantic similarity measures.
Ferreira JD, Hastings J, Couto FM. Bioinformatics (Oxford, England) Volume 29 (2013) p.2781-2787 DOI: 10.1093/bioinformatics/btt491
*
Recommendations of the wwPDB NMR Validation Task Force.
Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL. Structure (London, England : 1993) Volume 21 (2013) p.1563-1570 DOI: 10.1016/j.str.2013.07.021
*
The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment.
i5K Consortium. The Journal of heredity Volume 104 (2013) p.595-600 DOI: 10.1093/jhered/est050
*
How community has shaped the Protein Data Bank.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL. Structure (London, England : 1993) Volume 21 (2013) p.1485-1491 DOI: 10.1016/j.str.2013.07.010
*
Characterization of Vibrio cholerae bacteriophages isolated from the environmental waters of the Lake Victoria region of Kenya.
Maina AN, Mwaura FB, Oyugi J, Goulding D, Toribio AL, Kariuki S. Current microbiology Volume 68 (2014) p.64-70 DOI: 10.1007/s00284-013-0447-x
*
The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery.
Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN, Redman E, Holroyd N, Bartley DJ, Beasley H, Britton C, Curran D, Devaney E, Gilabert A, Hunt M, Jackson F, Johnston SL, Kryukov I, Li K, Morrison AA, Reid AJ, Sargison N, Saunders GI, Wasmuth JD, Wolstenholme A, Berriman M, Gilleard JS, Cotton JA. Genome biology Volume 14 (2013) p.R88 DOI: 10.1186/gb-2013-14-8-r88
*
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort.
Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Lægreid A. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat062 DOI: 10.1093/database/bat062
*
The COMBREX project: design, methodology, and initial results.
Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S. PLoS biology Volume 11 (2013) p.e1001638 DOI: 10.1371/journal.pbio.1001638
*
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
Ripke S, O'Dushlaine C, Chambert K, Moran JL, Kähler AK, Akterin S, Bergen SE, Collins AL, Crowley JJ, Fromer M, Kim Y, Lee SH, Lee SH, Magnusson PK, Sanchez N, Stahl EA, Williams S, Wray NR, Xia K, Bettella F, Borglum AD, Bulik-Sullivan BK, Cormican P, Craddock N, de Leeuw C, Durmishi N, Gill M, Golimbet V, Golimbet V, Hamshere ML, Holmans P, Hougaard DM, Kendler KS, Lin K, Morris DW, Mors O, Mortensen PB, Neale BM, O'Neill FA, Owen MJ, Milovancevic MP, Posthuma D, Powell J, Richards AL, Riley BP, Ruderfer D, Rujescu D, Sigurdsson E, Silagadze T, Smit AB, Stefansson H, Steinberg S, Suvisaari J, Tosato S, Verhage M, Walters JT, Multicenter Genetic Studies of Schizophrenia Consortium, Levinson DF, Gejman PV, Kendler KS, Laurent C, Mowry BJ, O'Donovan MC, Owen MJ, Pulver AE, Riley BP, Schwab SG, Wildenauer DB, Dudbridge F, Holmans P, Shi J, Albus M, Alexander M, Campion D, Cohen D, Dikeos D, Duan J, Eichhammer P, Godard S, Hansen M, Lerer FB, Liang KY, Maier W, Mallet J, Nertney DA, Nestadt G, Norton N, O'Neill FA, Papadimitriou GN, Ribble R, Sanders AR, Silverman JM, Walsh D, Williams NM, Wormley B, Psychosis Endophenotypes International Consortium, Arranz MJ, Bakker S, Bender S, Bramon E, Collier D, Crespo-Facorro B, Hall J, Iyegbe C, Jablensky A, Kahn RS, Kalaydjieva L, Lawrie S, Lewis CM, Lin K, Linszen DH, Mata I, McIntosh A, Murray RM, Ophoff RA, Powell J, Rujescu D, Van Os J, Walshe M, Weisbrod M, Wiersma D, Wellcome Trust Case Control Consortium 2, Donnelly P, Barroso I, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin AP, Deloukas P, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Spencer CC, Band G, Bellenguez C, Freeman C, Hellenthal G, Giannoulatou E, Pirinen M, Pearson RD, Strange A, Su Z, Vukcevic D, Donnelly P, Langford C, Hunt SE, Edkins S, Gwilliam R, Blackburn H, Bumpstead SJ, Dronov S, Gillman M, Gray E, Hammond N, Jayakumar A, McCann OT, Liddle J, Potter SC, Ravindrarajah R, Ricketts M, Tashakkori-Ghanbaria A, Waller MJ, Weston P, Widaa S, Whittaker P, Barroso I, Deloukas P, Mathew CG, Blackwell JM, Brown MA, Corvin AP, McCarthy MI, Spencer CC, Bramon E, Corvin AP, O'Donovan MC, Stefansson K, Scolnick E, Purcell S, McCarroll SA, Sklar P, Hultman CM, Sullivan PF. Nature genetics Volume 45 (2013) p.1150-1159 DOI: 10.1038/ng.2742
*
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D. Proteins Volume 81 (2013) p.1980-1987 DOI: 10.1002/prot.24356
KNIME-CDK: Workflow-driven cheminformatics.
Beisken S, Meinl T, Wiswedel B, de Figueiredo LF, Berthold M, Steinbeck C. BMC bioinformatics Volume 14 (2013) p.257 DOI: 10.1186/1471-2105-14-257
*
Association of gut microbiota with post-operative clinical course in Crohn's disease.
Dey N, Soergel DA, Repo S, Brenner SE. BMC gastroenterology Volume 13 (2013) p.131 DOI: 10.1186/1471-230X-13-131
*
Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas.
Petrov AI, Zirbel CL, Leontis NB. RNA Volume 19 (2013) p.1327-1340 DOI: 10.1261/rna.039438.113
*
Integration of cardiac proteome biology and medicine by a specialized knowledgebase.
Zong NC, Li H, Li H, Lam MP, Jimenez RC, Kim CS, Deng N, Kim AK, Choi JH, Zelaya I, Liem D, Meyer D, Odeberg J, Fang C, Lu HJ, Xu T, Weiss J, Duan H, Uhlen M, Yates JR, Apweiler R, Ge J, Hermjakob H, Ping P. Circulation research Volume 113 (2013) p.1043-1053 DOI: 10.1161/CIRCRESAHA.113.301151
A fast Peptide Match service for UniProt Knowledgebase.
Chen C, Li Z, Huang H, Suzek BE, Wu CH, UniProt Consortium. Bioinformatics (Oxford, England) Volume 29 (2013) p.2808-2809 DOI: 10.1093/bioinformatics/btt484
*
Vitellogenin underwent subfunctionalization to acquire caste and behavioral specific expression in the harvester ant Pogonomyrmex barbatus.
Corona M, Libbrecht R, Wurm Y, Riba-Grognuz O, Studer RA, Keller L. PLoS genetics Volume 9 (2013) p.e1003730 DOI: 10.1371/journal.pgen.1003730
*
Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor.
Martello G, Bertone P, Smith A. The EMBO journal Volume 32 (2013) p.2561-2574 DOI: 10.1038/emboj.2013.177
*
Adhesion to carbon nanotube conductive scaffolds forces action-potential appearance in immature rat spinal neurons.
Fabbro A, Sucapane A, Toma FM, Calura E, Rizzetto L, Carrieri C, Roncaglia P, Martinelli V, Scaini D, Masten L, Turco A, Gustincich S, Prato M, Ballerini L. PloS one Volume 8 (2013) p.e73621 DOI: 10.1371/journal.pone.0073621
*
Fine mapping of type 1 diabetes regions Idd9.1 and Idd9.2 reveals genetic complexity.
Hamilton-Williams EE, Rainbow DB, Cheung J, Christensen M, Lyons PA, Peterson LB, Steward CA, Sherman LA, Wicker LS. Mammalian genome : official journal of the International Mammalian Genome Society Volume 24 (2013) p.358-375 DOI: 10.1007/s00335-013-9466-y
Cellular resolution models for even skipped regulation in the entire Drosophila embryo.
Ilsley GR, Fisher J, Apweiler R, De Pace AH, Luscombe NM. eLife Volume 2 (2013) p.e00522 DOI: 10.7554/eLife.00522
*
Evolutionary biology: The handiwork of tinkering.
Flicek P. Nature Volume 500 (2013) p.158-159 DOI: 10.1038/500158a
*
Computational approaches to identify functional genetic variants in cancer genomes.
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N, International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group. Nature methods Volume 10 (2013) p.723-729 DOI: 10.1038/nmeth.2562
*
Holistic systems biology approaches to molecular mechanisms of human helper T cell differentiation to functionally distinct subsets.
Chen Z, Lönnberg T, Lahesmaa R. Scandinavian journal of immunology Volume 78 (2013) p.172-180 DOI: 10.1111/sji.12071
*
Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.
Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT. Cell Volume 154 (2013) p.530-540 DOI: 10.1016/j.cell.2013.07.007
*
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.
Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall CJ, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J. BMC genomics Volume 14 (2013) p.513 DOI: 10.1186/1471-2164-14-513
*
Meta-analysis of gene-level associations for rare variants based on single-variant statistics.
Hu YJ, Berndt SI, Gustafsson S, Ganna A, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Hirschhorn J, North KE, Ingelsson E, Lin DY. American journal of human genetics Volume 93 (2013) p.236-248 DOI: 10.1016/j.ajhg.2013.06.011
*
DNA damage in mammalian neural stem cells leads to astrocytic differentiation mediated by BMP2 signaling through JAK-STAT.
Schneider L, Pellegatta S, Favaro R, Pisati F, Roncaglia P, Testa G, Nicolis SK, Finocchiaro G, d'Adda di Fagagna F. Stem cell reports Volume 1 (2013) p.123-138 DOI: 10.1016/j.stemcr.2013.06.004
*
Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat.
Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L, Tschannen MR, Kaisaki PJ, Otto GW, Ma MC, Keane TM, Hummel O, Saar K, Chen W, Guryev V, Gopalakrishnan K, Garrett MR, Joe B, Citterio L, Bianchi G, McBride M, Dominiczak A, Adams DJ, Serikawa T, Flicek P, Cuppen E, Hubner N, Petretto E, Gauguier D, Kwitek A, Jacob H, Aitman TJ. Cell Volume 154 (2013) p.691-703 DOI: 10.1016/j.cell.2013.06.040
Evolution of protein structures and interactions from the perspective of residue contact networks.
Zhang X, Perica T, Teichmann SA. Current opinion in structural biology Volume 23 (2013) p.954-963 DOI: 10.1016/j.sbi.2013.07.004
Detecting and comparing non-coding RNAs in the high-throughput era.
Bussotti G, Notredame C, Enright AJ. International journal of molecular sciences Volume 14 (2013) p.15423-15458 DOI: 10.3390/ijms140815423
*
The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases.
Moulos P, Klein J, Jupp S, Stevens R, Bascands JL, Schanstra JP. BMC bioinformatics Volume 14 (2013) p.235 DOI: 10.1186/1471-2105-14-235
*
Peroxiredoxin-3 is overexpressed in prostate cancer and promotes cancer cell survival by protecting cells from oxidative stress.
Whitaker HC, Patel D, Howat WJ, Warren AY, Kay JD, Sangan T, Marioni JC, Mitchell J, Aldridge S, Luxton HJ, Massie C, Lynch AG, Neal DE. British journal of cancer Volume 109 (2013) p.983-993 DOI: 10.1038/bjc.2013.396
*
An overview of tools for the validation of protein NMR structures.
Vuister GW, Fogh RH, Hendrickx PM, Doreleijers JF, Gutmanas A. Journal of biomolecular NMR Volume 58 (2014) p.259-285 DOI: 10.1007/s10858-013-9750-x
Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data.
Ziehm M, Piper MD, Thornton JM. Aging cell Volume 12 (2013) p.917-922 DOI: 10.1111/acel.12123
Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv.
Ziehm M, Thornton JM. Aging cell Volume 12 (2013) p.910-916 DOI: 10.1111/acel.12121
*
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. GigaScience Volume 2 (2013) p.10 DOI: 10.1186/2047-217X-2-10
*
A genome-wide association analysis of a broad psychosis phenotype identifies three loci for further investigation.
Psychosis Endophenotypes International Consortium, Wellcome Trust Case-Control Consortium 2, Bramon E, Pirinen M, Strange A, Lin K, Freeman C, Bellenguez C, Su Z, Band G, Pearson R, Vukcevic D, Langford C, Deloukas P, Hunt S, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Edkins S, Bumpstead SJ, Arranz MJ, Bakker S, Bender S, Bruggeman R, Cahn W, Chandler D, Collier DA, Crespo-Facorro B, Dazzan P, de Haan L, Di Forti M, Dragović M, Giegling I, Hall J, Iyegbe C, Jablensky A, Kahn RS, Kalaydjieva L, Kravariti E, Lawrie S, Linszen DH, Mata I, McDonald C, McIntosh A, Myin-Germeys I, Ophoff RA, Pariante CM, Paunio T, Picchioni M, Psychiatric Genomics Consortium, Ripke S, Rujescu D, Sauer H, Shaikh M, Sussmann J, Suvisaari J, Tosato S, Toulopoulou T, Van Os J, Walshe M, Weisbrod M, Whalley H, Wiersma D, Blackwell JM, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski JA, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Wood NW, Barroso I, Peltonen L, Lewis CM, Murray RM, Donnelly P, Powell J, Spencer CC. Biological psychiatry Volume 75 (2014) p.386-397 DOI: 10.1016/j.biopsych.2013.03.033
*
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Guziolowski C, Videla S, Eduati F, Thiele S, Cokelaer T, Siegel A, Saez-Rodriguez J. Bioinformatics (Oxford, England) Volume 29 (2013) p.2320-2326 DOI: 10.1093/bioinformatics/btt393
*
The role of salt bridges, charge density, and subunit flexibility in determining disassembly routes of protein complexes.
Hall Z, Hernández H, Marsh JA, Teichmann SA, Robinson CV. Structure (London, England : 1993) Volume 21 (2013) p.1325-1337 DOI: 10.1016/j.str.2013.06.004
*
Tetrazole-based deoxyamodiaquines: synthesis, ADME/PK profiling and pharmacological evaluation as potential antimalarial agents.
Tukulula M, Njoroge M, Mugumbate GC, Gut J, Rosenthal PJ, Barteau S, Streckfuss J, Heudi O, Kameni-Tcheudji J, Chibale K. Bioorganic & medicinal chemistry Volume 21 (2013) p.4904-4913 DOI: 10.1016/j.bmc.2013.06.067
*
SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping.
Betancourt LH, De Bock PJ, Staes A, Timmerman E, Perez-Riverol Y, Sanchez A, Besada V, Gonzalez LJ, Vandekerckhove J, Gevaert K. Journal of proteomics Volume 91 (2013) p.164-171 DOI: 10.1016/j.jprot.2013.06.033
*
JBioWH: an open-source Java framework for bioinformatics data integration.
Vera R, Perez-Riverol Y, Perez S, Ligeti B, Kertész-Farkas A, Pongor S. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat051 DOI: 10.1093/database/bat051
The impact of mathematical modeling on the understanding of diabetes and related complications.
Ajmera I, Swat M, Laibe C, Le Novère N, Chelliah V. CPT: pharmacometrics & systems pharmacology Volume 2 (2013) p.e54 DOI: 10.1038/psp.2013.30
The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold.
Rigden DJ, Xu Q, Chang Y, Eberhardt RY, Finn RD, Rawlings ND. F1000Research Volume 2 (2013) p.154 DOI: 10.12688/f1000research.2-154.v2
*
A guide to best practices for Gene Ontology (GO) manual annotation.
Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat054 DOI: 10.1093/database/bat054
*
The evolution of the Anopheles 16 genomes project.
Neafsey DE, Christophides GK, Collins FH, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Howell PI, Kafatos FC, Lawson D, Muskavitch MA, Waterhouse RM, Williams LJ, Besansky NJ. G3 (Bethesda, Md.) Volume 3 (2013) p.1191-1194 DOI: 10.1534/g3.113.006247
*
Genome-wide association study of intraocular pressure identifies the GLCCI1/ICA1 region as a glaucoma susceptibility locus.
Blue Mountains Eye Study (BMES), Wellcome Trust Case Control Consortium 2 (WTCCC2). Human molecular genetics Volume 22 (2013) p.4653-4660 DOI: 10.1093/hmg/ddt293
*
Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes.
White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, Salisbury J, Clare S, Ingham NJ, Podrini C, Houghton R, Estabel J, Bottomley JR, Melvin DG, Sunter D, Adams NC, Sanger Institute Mouse Genetics Project, Tannahill D, Logan DW, Macarthur DG, Flint J, Mahajan VB, Tsang SH, Smyth I, Watt FM, Skarnes WC, Dougan G, Adams DJ, Ramirez-Solis R, Bradley A, Steel KP. Cell Volume 154 (2013) p.452-464 DOI: 10.1016/j.cell.2013.06.022
*
Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.
Gonzàlez-Porta M, Frankish A, Rung J, Harrow J, Brazma A. Genome biology Volume 14 (2013) p.R70 DOI: 10.1186/gb-2013-14-7-r70
*
Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing.
Majewski IJ, Mittempergher L, Davidson NM, Bosma A, Willems SM, Horlings HM, de Rink I, Greger L, Hooijer GK, Peters D, Nederlof PM, Hofland I, de Jong J, Wesseling J, Kluin RJ, Brugman W, Kerkhoven R, Nieboer F, Roepman P, Broeks A, Muley TR, Jassem J, Niklinski J, van Zandwijk N, Brazma A, Oshlack A, van den Heuvel M, Bernards R. The Journal of pathology Volume 230 (2013) p.270-276 DOI: 10.1002/path.4209
*
Correction.
Journal of the American Chemical Society Volume 135 (2013) p.10178 DOI: 10.1021/ja403136h
Kraken: a set of tools for quality control and analysis of high-throughput sequence data.
Davis MP, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright AJ. Methods (San Diego, Calif.) Volume 63 (2013) p.41-49 DOI: 10.1016/j.ymeth.2013.06.027
*
Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML.
Ghali F, Krishna R, Lukasse P, Martínez-Bartolomé S, Reisinger F, Hermjakob H, Vizcaíno JA, Jones AR. Molecular & cellular proteomics : MCP Volume 12 (2013) p.3026-3035 DOI: 10.1074/mcp.O113.029777
Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum.
Lawler K, Hammond-Kosack K, Brazma A, Coulson RM. BMC systems biology Volume 7 (2013) p.52 DOI: 10.1186/1752-0509-7-52
*
Best practices in bioinformatics training for life scientists.
Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J, Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK. Briefings in bioinformatics Volume 14 (2013) p.528-537 DOI: 10.1093/bib/bbt043
Genome-wide meta-analysis identifies new susceptibility loci for migraine.
Anttila V, Winsvold BS, Gormley P, Kurth T, Bettella F, McMahon G, Kallela M, Malik R, de Vries B, Terwindt G, Medland SE, Todt U, McArdle WL, Quaye L, Koiranen M, Ikram MA, Lehtimäki T, Stam AH, Ligthart L, Wedenoja J, Dunham I, Neale BM, Palta P, Hamalainen E, Schürks M, Rose LM, Buring JE, Ridker PM, Steinberg S, Stefansson H, Jakobsson F, Lawlor DA, Evans DM, Ring SM, Färkkilä M, Artto V, Kaunisto MA, Freilinger T, Schoenen J, Frants RR, Pelzer N, Weller CM, Zielman R, Heath AC, Madden PAF, Montgomery GW, Martin NG, Borck G, Göbel H, Heinze A, Heinze-Kuhn K, Williams FMK, Hartikainen AL, Pouta A, van den Ende J, Uitterlinden AG, Hofman A, Amin N, Hottenga JJ, Vink JM, Heikkilä K, Alexander M, Muller-Myhsok B, Schreiber S, Meitinger T, Wichmann HE, Aromaa A, Eriksson JG, Traynor B, Trabzuni D, North American Brain Expression Consortium, UK Brain Expression Consortium, Rossin E, Lage K, Jacobs SBR, Gibbs JR, Birney E, Kaprio J, Penninx BW, Boomsma DI, van Duijn C, Raitakari O, Jarvelin MR, Zwart JA, Cherkas L, Strachan DP, Kubisch C, Ferrari MD, van den Maagdenberg AMJM, Dichgans M, Wessman M, Smith GD, Stefansson K, Daly MJ, Nyholt DR, Chasman D, Palotie A. Nature genetics Volume 45 (2013) p.912-917 DOI: 10.1038/ng.2676
*
Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics.
Leprevost FV, Lima DB, Crestani J, Perez-Riverol Y, Zanchin N, Barbosa VC, Carvalho PC. Journal of proteomics Volume 89 (2013) p.179-182 DOI: 10.1016/j.jprot.2013.06.013
*
The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.
Li JW, Bolser D, Manske M, Giorgi FM, Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D, Schneider MV. Briefings in bioinformatics Volume 14 (2013) p.548-555 DOI: 10.1093/bib/bbt045
*
Polymer models of chromatin organization.
Barbieri M, Scialdone A, Piccolo A, Chiariello AM, di Lanno C, Prisco A, Pombo A, Nicodemi M. Frontiers in Genetics Volume 4 (2013) p.113 DOI: 10.3389/fgene.2013.00113
*
Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization.
Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H, Lahesmaa R. Immunity Volume 38 (2013) p.1271-1284 DOI: 10.1016/j.immuni.2013.05.011
*
ISMB/ECCB 2013 Proceedings Papers Committee.
Bioinformatics (Oxford, England) Volume 29 (2013) p.i3-i8 DOI: 10.1093/bioinformatics/btt281
*
Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways.
Mancini C, Roncaglia P, Brussino A, Stevanin G, Lo Buono N, Krmac H, Maltecca F, Gazzano E, Bartoletti Stella A, Calvaruso MA, Iommarini L, Cagnoli C, Forlani S, Le Ber I, Durr A, Brice A, Ghigo D, Casari G, Porcelli AM, Funaro A, Gasparre G, Gustincich S, Brusco A. BMC medical genomics Volume 6 (2013) p.22 DOI: 10.1186/1755-8794-6-22
*
LIN28 Expression in malignant germ cell tumors downregulates let-7 and increases oncogene levels.
Murray MJ, Saini HK, Siegler CA, Hanning JE, Barker EM, van Dongen S, Ward DM, Raby KL, Groves IJ, Scarpini CG, Pett MR, Thornton CM, Enright AJ, Nicholson JC, Coleman N, CCLG. Cancer research Volume 73 (2013) p.4872-4884 DOI: 10.1158/0008-5472.CAN-12-2085
Metingear: a development environment for annotating genome-scale metabolic models.
May JW, James AG, Steinbeck C. Bioinformatics (Oxford, England) Volume 29 (2013) p.2213-2215 DOI: 10.1093/bioinformatics/btt342
*
Mutations in GDP-mannose pyrophosphorylase B cause congenital and limb-girdle muscular dystrophies associated with hypoglycosylation of α-dystroglycan.
Carss KJ, Stevens E, Foley AR, Cirak S, Riemersma M, Torelli S, Hoischen A, Willer T, van Scherpenzeel M, Moore SA, Messina S, Bertini E, Bönnemann CG, Abdenur JE, Grosmann CM, Kesari A, Punetha J, Quinlivan R, Waddell LB, Young HK, Wraige E, Yau S, Brodd L, Feng L, Sewry C, MacArthur DG, North KN, Hoffman E, Stemple DL, Hurles ME, van Bokhoven H, Campbell KP, Lefeber DJ, UK10K Consortium, Lin YY, Muntoni F. American journal of human genetics Volume 93 (2013) p.29-41 DOI: 10.1016/j.ajhg.2013.05.009
*
Epigenetic functions of smchd1 repress gene clusters on the inactive X chromosome and on autosomes.
Gendrel AV, Tang YA, Suzuki M, Godwin J, Nesterova TB, Greally JM, Heard E, Brockdorff N. Molecular and cellular biology Volume 33 (2013) p.3150-3165 DOI: 10.1128/MCB.00145-13
*
Genetic and archaeological perspectives on the initial modern human colonization of southern Asia.