Publications

Publications

2019

Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.
Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM. Methods in molecular biology (Clifton, N.J.) Volume 1851 (2019) p.263-275 DOI: 10.1007/978-1-4939-8736-8_14

2018

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Metabolic engineering strategies for improvement of ethanol production in cellulolytic Saccharomyces cerevisiae.
Song X, Li Y, Wu Y, Cai M, Liu Q, Gao K, Zhang X, Bai Y, Xu H, Qiao M. FEMS yeast research Volume 18 (2018) DOI: 10.1093/femsyr/foy090
The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019.
Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E, Suveges D, Vrousgou O, Whetzel PL, Amode R, Guillen JA, Riat HS, Trevanion SJ, Hall P, Junkins H, Flicek P, Burdett T, Hindorff LA, Cunningham F, Parkinson H. Nucleic acids research (2018) DOI: 10.1093/nar/gky1120
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.
Dana JM, Gutmanas A, Tyagi N, Qi G, O'Donovan C, Martin M, Velankar S. Nucleic acids research (2018) DOI: 10.1093/nar/gky1114
The European Bioinformatics Institute in 2018: tools, infrastructure and training.
Cook CE, Lopez R, Stroe O, Cochrane G, Brooksbank C, Birney E, Apweiler R. Nucleic acids research (2018) DOI: 10.1093/nar/gky1124
Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars.
Carvalho-Silva D, Garcia L, Morgan SL, Brooksbank C, Dunham I. PLoS computational biology Volume 14 (2018) p.e1006419 DOI: 10.1371/journal.pcbi.1006419
Ensembl 2019.
Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, Bennett R, Bhai J, Billis K, Boddu S, Cummins C, Davidson C, Dodiya KJ, Gall A, Girón CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Laird MR, Lavidas I, Liu Z, Loveland JE, Marugán JC, Maurel T, McMahon AC, Moore B, Morales J, Mudge JM, Nuhn M, Ogeh D, Parker A, Parton A, Patricio M, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sparrow H, Stapleton E, Szuba M, Taylor K, Threadgold G, Thormann A, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Yates AD, Zerbino DR, Flicek P. Nucleic acids research (2018) DOI: 10.1093/nar/gky1113
BioSamples database: an updated sample metadata hub.
Courtot M, Cherubin L, Faulconbridge A, Vaughan D, Green M, Richardson D, Harrison P, Whetzel PL, Parkinson H, Burdett T. Nucleic acids research (2018) DOI: 10.1093/nar/gky1061
ChEMBL: towards direct deposition of bioassay data.
Mendez D, Gaulton A, Bento AP, Chambers J, De Veij M, Félix E, Magariños MP, Mosquera JF, Mutowo P, Nowotka M, Gordillo-Marañón M, Hunter F, Junco L, Mugumbate G, Rodriguez-Lopez M, Atkinson F, Bosc N, Radoux CJ, Segura-Cabrera A, Hersey A, Leach AR. Nucleic acids research (2018) DOI: 10.1093/nar/gky1075
InterPro in 2019: improving coverage, classification and access to protein sequence annotations.
Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD. Nucleic acids research (2018) DOI: 10.1093/nar/gky1100
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UniProt: a worldwide hub of protein knowledge.
UniProt Consortium . Nucleic acids research (2018) DOI: 10.1093/nar/gky1049
The European Nucleotide Archive in 2018.
Harrison PW, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Holt S, Hussein A, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Milano A, Pakseresht N, Rajan J, Reddy K, Richards E, Rosello M, Silvester N, Smirnov D, Toribio AL, Vijayaraja S, Cochrane G. Nucleic acids research (2018) DOI: 10.1093/nar/gky1078
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RNAcentral: a hub of information for non-coding RNA sequences.
The RNAcentral Constortium . Nucleic acids research (2018) DOI: 10.1093/nar/gky1034
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Comparative genomics of the major parasitic worms.
International Helminth Genomes Consortium. Nature genetics (2018) DOI: 10.1038/s41588-018-0262-1
The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Pérez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaíno JA. Nucleic acids research (2018) DOI: 10.1093/nar/gky1106
iProteinDB: An Integrative Database of Drosophila Post-translational Modifications.
Hu Y, Sopko R, Chung V, Foos M, Studer RA, Landry SD, Liu D, Rabinow L, Gnad F, Beltrao P, Perrimon N. G3 (Bethesda, Md.) (2018) DOI: 10.1534/g3.118.200637
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The Gene Ontology Resource: 20 years and still GOing strong.
The Gene Ontology Consortium. Nucleic acids research (2018) DOI: 10.1093/nar/gky1055
Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency.
Pękowska A, Klaus B, Xiang W, Severino J, Daigle N, Klein FA, Oleś M, Casellas R, Ellenberg J, Steinmetz LM, Bertone P, Huber W. Cell systems (2018) DOI: 10.1016/j.cels.2018.09.003
Publisher Correction: 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, Carazo Salas RE, Swedlow JR. Nature methods Volume 15 (2018) p.984 DOI: 10.1038/s41592-018-0169-x
ClinGen advancing genomic data-sharing standards as a GA4GH driver project.
Dolman L, Page A, Babb L, Freimuth RR, Arachchi H, Bizon C, Brush M, Fiume M, Haendel M, Hansen DP, Milosavljevic A, Patel RY, Pawliczek P, Yates AD, Rehm HL. Human mutation Volume 39 (2018) p.1686-1689 DOI: 10.1002/humu.23625
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Signatures of cell death and proliferation in perturbation transcriptomics data - from confounding factor to effective prediction
Szalai B, Subramanian V, Saez-Rodriguez J. Preprint DOI: 10.1101/454348
Parents in science.
Perry E, Tessmar-Raible K, Raible F. Genome biology Volume 19 (2018) p.180 DOI: 10.1186/s13059-018-1549-3
Neutral tumor evolution?
Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz F, PCAWG Evolution and Heterogeneity Working Group, Spellman PT, Morris QD, Lingjærde OC, Wedge DC, Van Loo P. Nature genetics (2018) DOI: 10.1038/s41588-018-0258-x
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes.
Richardson LJ, Rawlings ND, Salazar GA, Almeida A, Haft DR, Ducq G, Sutton GG, Finn RD. Nucleic acids research (2018) DOI: 10.1093/nar/gky1013
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Bacterial contribution to genesis of the novel germ line determinant oskar
Blondel L, Jones TEM, Extavour CG. Preprint DOI: 10.1101/453514
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes.
Meldal BHM, Bye-A-Jee H, Gajdoš L, Hammerová Z, Horácková A, Melicher F, Perfetto L, Pokorný D, Lopez MR, Türková A, Wong ED, Xie Z, Casanova EB, Del-Toro N, Koch M, Porras P, Hermjakob H, Orchard S. Nucleic acids research (2018) DOI: 10.1093/nar/gky1001
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Protein Data Bank: the single global archive for 3D macromolecular structure data.
wwPDB consortium . Nucleic acids research (2018) DOI: 10.1093/nar/gky949
ArrayExpress update - from bulk to single-cell expression data.
Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I, Sarkans U, Brazma A. Nucleic acids research (2018) DOI: 10.1093/nar/gky964
The Pfam protein families database in 2019.
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer ELL, Hirsh L, Paladin L, Piovesan D, Tosatto SCE, Finn RD. Nucleic acids research (2018) DOI: 10.1093/nar/gky995
GENCODE reference annotation for the human and mouse genomes.
Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P. Nucleic acids research (2018) DOI: 10.1093/nar/gky955
A large-scale dataset of in vivo pharmacology assay results.
Hunter FMI, L Atkinson F, Bento AP, Bosc N, Gaulton A, Hersey A, Leach AR. Scientific data Volume 5 (2018) p.180230 DOI: 10.1038/sdata.2018.230
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Publishing peer review materials
Beck J, Funk K, Harrison M, McEntyre J, Breen J, Collings A, Donohoe P, Evans M, Flintoft L, Hamelers A, Hurst P, Lemberger T, Lin J, O'Connor N, Parkin M, Parker S, Rodgers P, Skipper M, Stoner M. Preprint DOI: 10.12688/f1000research.16460.1
Publishing peer review materials.
Beck J, Funk K, Harrison M, McEntyre J, Breen J, Collings A, Donohoe P, Evans M, Flintoft L, Hamelers A, Hurst P, Lemberger T, Lin J, O'Connor N, Parkin M, Parker S, Rodgers P, Skipper M, Stoner M. F1000Research Volume 7 (2018) p.1655 DOI: 10.12688/f1000research.16460.1
FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community.
Harrison PW, Fan J, Richardson D, Clarke L, Zerbino D, Cochrane G, Archibald AL, Schmidt CJ, Flicek P. Animal genetics Volume 49 (2018) p.520-526 DOI: 10.1111/age.12736
Genenames.org: the HGNC and VGNC resources in 2019.
Braschi B, Denny P, Gray K, Jones T, Seal R, Tweedie S, Yates B, Bruford E. Nucleic acids research (2018) DOI: 10.1093/nar/gky930
Haplosaurus computes protein haplotypes for use in precision drug design.
Spooner W, McLaren W, Slidel T, Finch DK, Butler R, Campbell J, Eghobamien L, Rider D, Kiefer CM, Robinson MJ, Hardman C, Cunningham F, Vaughan T, Flicek P, Huntington CC. Nature communications Volume 9 (2018) p.4128 DOI: 10.1038/s41467-018-06542-1
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Using the drug-protein interactome to identify anti-ageing compounds for humans
Fuentealba Valenzuela M, Donertas HM, Williams R, Labbadia J, Thornton J, Partridge L. Preprint DOI: 10.1101/438234
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Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions
C. Silva AS, Martens L, Degroeve S. Preprint DOI: 10.1101/428805
Correction: 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/s41436-018-0327-7
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Expanding the use of spectral libraries in proteomics.
Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H. Journal of proteome research (2018) DOI: 10.1021/acs.jproteome.8b00485
Sixteen diverse 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, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, 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, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham 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, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM. Nature genetics Volume 50 (2018) p.1574-1583 DOI: 10.1038/s41588-018-0223-8
Transform-MinER: transforming molecules in enzyme reactions.
Tyzack JD, Ribeiro AJM, Borkakoti N, Thornton JM. Bioinformatics (Oxford, England) Volume 34 (2018) p.3597-3599 DOI: 10.1093/bioinformatics/bty394
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Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.
CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B. The New England journal of medicine Volume 379 (2018) p.1403-1415 DOI: 10.1056/nejmoa1800474
Human genes: Time to follow the roads less traveled?
Dunham I. PLoS biology Volume 16 (2018) p.e3000034 DOI: 10.1371/journal.pbio.3000034
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Process-specific somatic mutation distributions vary with three-dimensional genome structure
Akdemir KC, Le VT, Killcoyne S, King DA, Lin Y, Tian Y, Inoue A, Amin S, Robinson FS, Herrera RE, Lynn EJ, Chan K, Seth S, Klimczak LJ, Gerstung M, Gordenin DA, O'Brien J, Li L, Verhaak RG, Campbell P, Fitzgerald R, Morrison AJ, Dixon JR, Futreal A. Preprint DOI: 10.1101/426080
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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
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Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies
Eduati F, Jaaks P, Merten CA, Garnett MJ, Saez-Rodriguez J. Preprint DOI: 10.1101/422998
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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
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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
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PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud
Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels T, Foguet C, Glen R, Gonzalez-Beltran A, Guenther U, Handakas E, Hankemeier T, Herman S, Haug K, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khoonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JT, Peluso A, Pireddu L, Piras ME, Reed MA, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek R, Sansone S, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant M, Weber R, Zanetti G, Steinbeck C. Preprint DOI: 10.1101/409151
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RAFTS³G – An efficient and versatile clustering software to analyses in large protein datasets
NICHIO BTD, de Oliveira AMR, de Pierri CR, Santos LGC, Vialle RA, Marchaukoski JN, Pedrosa FdO, Raittz RT. Preprint DOI: 10.1101/407437
PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships.
Meyer HV, Birney E. Bioinformatics (Oxford, England) Volume 34 (2018) p.2951-2956 DOI: 10.1093/bioinformatics/bty197
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
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
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 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
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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
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Selecting causal risk factors from high-throughput experiments using multivariable Mendelian randomization
Zuber V, Colijn JM, Klaver C, Burgess S. Preprint DOI: 10.1101/396333
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
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Conserved phosphorylation hotspots in eukaryotic protein domain families
Strumillo MJ, Oplova M, Vieitez C, Ochoa D, Shahraz M, Busby BP, Sopko R, Studer RA, Perrimon N, Panse VG, Beltrao P. Preprint DOI: 10.1101/391185
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
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
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Genomic landscape and chronological reconstruction of driver events in multiple myeloma
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Dönertaş HM, Fuentealba Valenzuela M, Partridge L, Thornton JM. Aging cell Volume 17 (2018) p.e12819 DOI: 10.1111/acel.12819
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Boroviak T, Stirparo GGG, Dietmann S, Hernando-Herraez I, Mohammed H, Reik W, Smith A, Sasaki E, Nichols J, Bertone P. Preprint DOI: 10.1101/385815
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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
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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
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Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body.
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Genomic, Proteomic and Phenotypic Heterogeneity in HeLa Cells across Laboratories: Implications for Reproducibility of Research Results
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A Measure of Open Data: A Metric and Analysis of Reusable Data Practices in Biomedical Data Resources
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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
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
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
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
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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
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
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
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
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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
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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
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Gene Expression-Based Drug Repurposing to Target Ageing
Donertas HM, Fuentealba Valenzuela M, Partridge L, Thornton J. Preprint DOI: 10.1101/253344
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
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FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies
Sansone S, McQuilton P, Rocca-Serra P, Gonzalez-Beltran A, Izzo M, Lister A, Thurston M, Batista D, Granell R, Adekale M, Dauga D, Ganley E, Hodson S, Lawrence R, Khodiyar V, Tenenbaum J, Axton JM, Ball M, Besson S, Bloom T, Bonazzi V, Jimenez R, Carr D, Chan WM, Chung C, Clement-Stoneham G, Cousijn H, Dayalan S, Dumontier M, Dzale Yeumo E, Edmunds S, Everitt N, Fripp D, Goble C, Golebiewski M, Hall N, Hanisch R, Hucka M, Huerta M, Kenall A, Kiley R, Klenk J, Koureas D, Larkin J, Lemberger T, Lynch N, Schriml L, Ma'ayan A, MacCallum C, Mons B, Moore J, Muller W, Murray H, Nobusada T, Noesgaard D, Paxton-Boyd J, Orchard S, Rustici G, Schurer S, Sharples K, Soares e Silva M, Stanford NJ, Subirats-Coll I, Swedlow J, Tong W, Wilkinson M, Wise J, Yilmaz P. Preprint DOI: 10.1101/245183
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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
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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
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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
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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
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
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
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
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
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
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
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
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
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
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
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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
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
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
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
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
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
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
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
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
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
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
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
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
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
Evaluation of Protein-Ligand Docking by Cyscore.
Cao Y, Dai W, Miao Z. Methods in molecular biology (Clifton, N.J.) Volume 1762 (2018) p.233-243 DOI: 10.1007/978-1-4939-7756-7_12
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
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
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
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
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

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
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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
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
Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions.
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The IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation
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Assessing the Gene Regulatory Landscape in 1,188 Human Tumors
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5-Formylcytosine controls nucleosome positioning through covalent histone-DNA interaction
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NCBI will no longer make taxonomy identifiers for individual influenza strains on January 15, 2018
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The global distribution and spread of the mobilized colistin resistance gene mcr-1
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Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.
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f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.
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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
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Genomic Research Data Generation, Analysis and Sharing - Challenges in the African Setting
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cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.
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Comprehensive Pharmacogenomic Profiling of Malignant Pleural Mesothelioma Identifies a Subgroup Sensitive to FGFR Inhibition.
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Genomics in healthcare: GA4GH looks to 2022
Birney E, Vamathevan J, Goodhand P. Preprint DOI: 10.1101/203554
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Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
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A cancer pharmacogenomic screen powering crowd-sourced advancement of drug combination prediction
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A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.
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The impact of rare variation on gene expression across tissues.
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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
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Corrigendum: A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.
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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
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A screen for combination therapies in BRAF/NRAS wild type melanoma identifies nilotinib plus MEK inhibitor as a synergistic combination
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Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.
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Two independent modes of chromatin organization revealed by cohesin removal.
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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
Compliance with minimum information guidelines in public metabolomics repositories.
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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
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Multi-platform discovery of haplotype-resolved structural variation in human genomes
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UniProt Genomic Mapping for Deciphering Functional Effects of Missense Variants
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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
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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
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A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy.
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Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.
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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
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BraCeR: Reconstruction of B-cell receptor sequences and clonality inference from single-cell RNA-sequencing
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The future of metabolomics in ELIXIR.
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Societal challenges of precision medicine: Bringing order to chaos.
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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
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
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Reports from CAGI: The Critical Assessment of Genome Interpretation.
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PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models.
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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
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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
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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
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Ferrero E, Dunham I, Sanseau P. Journal of translational medicine Volume 15 (2017) p.182 DOI: 10.1186/s12967-017-1285-6
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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
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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
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Emery LR, Morgan SL. PLoS computational biology Volume 13 (2017) p.e1005620 DOI: 10.1371/journal.pcbi.1005620
How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.
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EMBL-EBI, programmatically: take a REST from manual searches
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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
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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
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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
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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
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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
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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
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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
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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
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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
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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
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
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Computational approaches for discovery of mutational signatures in cancer.
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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
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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
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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
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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
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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
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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
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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
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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
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Correction: Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.
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Platelet function is modified by common sequence variation in megakaryocyte super enhancers.
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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
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General guidelines for biomedical software development
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Sequanix: A Dynamic Graphical Interface for Snakemake Workflows
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Model Description Language (MDL): A Standard for Modeling and Simulation.
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The evolutionary history of 2,658 cancers
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Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.
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Building bridges between cellular and molecular structural biology.
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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
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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
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
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
The EBI search engine: EBI search as a service-making biological data accessible for all.
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Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks.
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Watkins X, Garcia LJ, Pundir S, Martin MJ, UniProt Consortium. Bioinformatics (Oxford, England) Volume 33 (2017) p.2040-2041 DOI: 10.1093/bioinformatics/btx120
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
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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
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Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
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HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
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ChromoTrace: Reconstruction of 3D Chromosome Configurations by Super-Resolution Microscopy
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Identifying ELIXIR Core Data Resources
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Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method.
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Direct Keap1-Nrf2 disruption as a potential therapeutic target for Alzheimer's disease.
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A global perspective on bioinformatics training needs
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The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection.
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New drug candidates for liposomal delivery identified by computer modeling of liposomes' remote loading and leakage.
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A high-resolution mRNA expression time course of embryonic development in zebrafish
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Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.
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Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations.
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Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.
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Interactions between genetic variation and cellular environment in skeletal muscle gene expression
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Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis.
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Cell biology: tracking a cell's cycle.
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Postdocs, What Would You Tell Your Younger Self?
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Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders.
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Synthetic human proteomes for accelerating protein research.
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From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB.
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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
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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
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
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 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
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Uniform Resolution of Compact Identifiers for Biomedical Data
Wimalaratne S, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe J, Hermjakob H, Clark T. Preprint DOI: 10.1101/101279
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
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
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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
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
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
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
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
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
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
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
EBI Metagenomics: analysing and exploring metagenomic data
Mitchell A. DOI: 10.6019/tol.ebimetagen-w.2017.00001.1
Ensembl tools: webinar
Perry E. DOI: 10.6019/tol.ens-too-w.2017.00001.2
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
QuickGO - Gene ontology annotation
Georghiou G. DOI: 10.6019/tol.quickgo-w.2017.00001.1
EMPIAR: Quick tour
Iudin A, Patwardhan A. DOI: 10.6019/tol.empiar-qt.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
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
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
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
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
Reactome: Tools for analysis of biological pathways
Jupe S. DOI: 10.6019/tol.reactome_tools-t.2017.00001.1
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
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
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
Reactome: Exploring biological pathways
Jupe S. DOI: 10.6019/tol.reactome_exbp-t.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
Visualising protein structures online
Armstrong A. DOI: 10.6019/tol.pdbe-litemol-w.2017.00001.1
Exploring protein interactions with UniProt
Pichler K. DOI: 10.6019/tol.unip-interactions-w.2017.00001.1
Europe PMC: Quick tour
Parkin M. DOI: 10.6019/tol.epmc-qt.2017.00001.2
Europe PMC: get the most from literature searches
Parkin M. DOI: 10.6019/tol.epmcsearch-w.2017.00001.1

2016

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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
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A Data Citation Roadmap for Scholarly Data Repositories
Fenner M, Crosas M, Grethe J, Kennedy D, Hermjakob H, Rocca-Serra P, Durand G, Berjon R, Karcher S, Martone M, Clark T. Preprint DOI: 10.1101/097196
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
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GeneSeqToFamily: the Ensembl Compara GeneTrees pipeline as a Galaxy workflow
Thanki AS, Soranzo N, Haerty W, Muffato M, Davey RP. Preprint DOI: 10.1101/096529
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Drug repurposing for ageing research using model organisms
Ziehm M, Kaur S, Ivanov DK, Ballester PJ, Marcus D, Partridge L, Thornton JM. Preprint DOI: 10.1101/095380
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
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
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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
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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
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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
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
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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
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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
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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
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Validation of protein crystal structures
Kleywegt GJ. International Tables for Crystallography, Volume F, Crystallography of biological macromolecules, 2nd edition Wiley DOI: 10.1107/97809553602060000111
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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
BioModels quick tour
Chelliah V. DOI: 10.6019/tol.bm-qt.2012.00001.1
PDBe: Searching for biological macromolecular structures
Armstrong DR. DOI: 10.6019/tol.pdbe-intr-w.2015.00001.1
Introduction to training with EMBL-EBI
Brooksbank C. DOI: 10.6019/tol.train-w.2016.00001.1
Ensembl: Genomic features that regulate genes
Perry E. DOI: 10.6019/tol.ensreg-w.2016.00001.1
European Nucleotide Archive (ENA) quick tour
Amid C, Cochrane G. DOI: 10.6019/tol.ena-qt.2011.00001.1
Reactome: exploring and analysing biological pathways
Jupe S. DOI: 10.6019/tol.rea-t.2012.00001.2
PDBe: searching the Protein Data Bank
Sen S, Mukhopadhyay A. DOI: 10.6019/tol.pdbe-sea-t.2015.00001.1
Reactome quick tour
Jupe S. DOI: 10.6019/tol.rea-qt.2014.00001.1
Reactome: Exploring biological pathways: webinar
Jupe S. DOI: 10.6019/tol.react-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
Ensembl Variant Effect Predictor (VEP): webinar
Moore B. DOI: 10.6019/tol.ensvep-w.2016.00001.1
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
Ensembl tools: webinar
Perry E. DOI: 10.6019/tol.ens-too-w.2015.00001.1
EBI: Next Generation Sequencing Practical Course
Perry E. DOI: 10.6019/tol.ngs-v.2012.00001.1
PRIDE: Quick tour
Vizcaino JA. DOI: 10.6019/tol.pride-qt.2014.00001.1
Ensembl: Filmed browser workshop
Perry E, Spudich GM, Carvalho-Silva D. DOI: 10.6019/tol.ensfbw-v.2013.00001.1
EMBO highthrouhput sequencing
Rustici G. DOI: 10.6019/tol.htsembo-v.2011.00001.1
Introduction to 1000 Genomes Project and IGSR data resources
Fairley S. DOI: 10.6019/tol.isgr_w.2016.00001.1
UniProt: Programmatic access to UniProtKB: webinar
Pichler K. DOI: 10.6019/tol.unp-program-w.2015.00001.1
Network analysis of protein interaction data: an introduction
Porras P. DOI: 10.6019/tol.networks_t.2016.00001.1
Genomics resources: webinar
Emery L. DOI: 10.6019/tol.gen-res-w.2015.00001.1
EBI Metagenomics resource: Quick tour
Denise H. DOI: 10.6019/tol.mtg-qt.2013.00001.2
Cellular Microscopy Phenotype Ontology (CMPO): Quick tour
Rustici G, Hancocks T. DOI: 10.6019/tol.cmpo-qt.2015.00001.1
Proteomics: An introduction to EMBL-EBI resources
Orchard S, Charles PD. DOI: 10.6019/tol.pms.2011.00001.1
Pfam: Quick tour
El-Gebali S, Richardson L, Finn R. DOI: 10.6019/tol.pfam-qt.2016.00001.1
Phylogenetics: An introduction
Emery L. DOI: 10.6019/tol.phyl.2015.00001.1
MyChEMBL: webinar
Papadatos G. DOI: 10.6019/tol.mychembl-w.2015.00001.2
SureChEMBL: Accessing chemical patent data: webinar
Papadatos G. DOI: 10.6019/tol.surechembl-w.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
Protein interactions and their importance
Porras P, Sehra M. DOI: 10.6019/tol.pro-int.2012.00001.1
IntAct: Molecular Interactions at the EBI
Orchard S. DOI: 10.6019/tol.inta-t.2012.00001.1
Ensembl browser webinar series (2016)
Perry E, Carvalho-Silva D, Moore B, Sparrow H. DOI: 10.6019/tol.ensbrows-w.2016.00001.1
PRIDE and ProteomeXchange: webinar
Vizcaino JA. DOI: 10.6019/tol.pride-px-w.2015.00001.1
Complex Portal: webinar
Meldal BH. DOI: 10.6019/tol.comport-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
User experience design
Rowland F, Pundir S, Brooksbank C, Hancocks T. DOI: 10.6019/tol.ux-c.2015.00001.1
Biomacromolecular structures
Argasinska J, Symmons MF, Gutmanas A, Kleywegt GJ, . DOI: 10.6019/tol.bms.2011.00001.1
IntAct quick tour
Porras P. DOI: 10.6019/tol.inta-qt.2011.00001.1
UniProt: Exploring protein sequence and functional information - webinar
Pundir S. DOI: 10.6019/tol.unp-expl-w.2015.00001.1
ProteomeXchange submissions via PRIDE
Vizcaino JA, Ternent T, Sehra M, Csordas A. DOI: 10.6019/tol.pxd-t.2014.00001.1
UniProt peptide search and website updates: webinar
Pichler K. DOI: 10.6019/tol.unp-peptide-pub-w.2016.00001.1
InterPro: quick tour
Mitchell A. DOI: 10.6019/tol.intp-qt.2011.00001.1
Complex Portal: Quick tour
Meldal BH. DOI: 10.6019/tol.compor-qt.2015.00001.1
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 IntAct - a Protein-Protein Interactions resource
Meldal B, Porras P. DOI: 10.6019/tol.inta-intr-w.2015.00001.1
ChEMBL: Exploring bioactive drug-like molecules
Bellis LJ. DOI: 10.6019/tol.chembl-t.2015.00001.1
UniProt: Exploring protein sequence and fucntional information
Magrane M, Pundir S. DOI: 10.6019/tol.unp-t.2014.00001.1
ArrayExpress: why and how to submit your data
Burke M. DOI: 10.6019/tol.aesub-w.2016.00001.1
ArrayExpress: Quick tour
Burke M. DOI: 10.6019/tol.arrex-qt.2011.00001.2
ChEMBL qt
Bellis LJ. DOI: 10.6019/tol.chembl-qt.2011.00001.1
EMBL-EBI resources: An introduction
Gopalasingam P. DOI: 10.6019/tol.intr-ebi-res-w.2015.00001.1
UniProt-GOA: Quick tour
Huntley R. DOI: 10.6019/tol.goa-qt.2011.00001.1
ChEMBL walkthrough: webinar
Bellis LJ. DOI: 10.6019/tol.chemblwalk-w.2015.00001.1
BioSamples RDF: webinar
Brandizi M, Hancocks T. DOI: 10.6019/tol.bsa-rdf-w.2015.00001.1
Array Express: Exploring functional genomics data quickly and easily
Füllgrabe A. DOI: 10.6019/tol.aex-t.2016.00001.2
UniProt quick tour
Magrane M. DOI: 10.6019/tol.unp-qt.2014.00001.1
Functional genomics: An introduction to the EMBL-EBI resources
Tang YA, Rustici G. DOI: 10.6019/tol.fng.2014.00001.2
Europe PMC: Quick tour
Rossiter P. DOI: 10.6019/tol.epmc-qt.2013.00001.2
Expression Atlas: Quick tour
Keays M. DOI: 10.6019/tol.gea-qt.2013.00001.2
Biomedical data: Ethical, legal and social implications
Morgan SL, Hancocks T. DOI: 10.6019/tol.elsi-c.2015.00001.1
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
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
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
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
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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
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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
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
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
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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
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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
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
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UniProt: the universal protein knowledgebase.
The UniProt Consortium. Nucleic acids research Volume 45 (2017) p.D158-D169 DOI: 10.1093/nar/gkw1099
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
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
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
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
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
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
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
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
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
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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
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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
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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
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
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
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
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
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
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
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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
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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
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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
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
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
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
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
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
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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
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Benchmarking substrate-based kinase activity inference using phosphoproteomic data
Hernandez-Armenta C, Ochoa D, Goncalves E, Saez-Rodriguez J, Beltrao P. Preprint DOI: 10.1101/080978
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
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
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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
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
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
Identifying ELIXIR Core Data Resources.
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Identifying ELIXIR Core Data Resources
Durinx C, McEntyre J, Appel R, Apweiler R, Barlow M, Blomberg N, Cook C, Gasteiger E, Kim J, Lopez R, Redaschi N, Stockinger H, Teixeira D, Valencia A. Preprint DOI: 10.12688/f1000research.9656.1
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Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich
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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
The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.
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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
Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles.
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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
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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
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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
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Overview of the interactive task in BioCreative V.
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Warped Matrix Factorisation for Multi-view Data Integration
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Pleiotropic Analysis of Lung Cancer and Blood Triglycerides.
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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.
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An Atlas of Human Kinase Regulation
Ochoa D, Jonikas M, Lawrence RT, El Debs B, Selkrig J, Typas A, Villen J, Santos S, Beltrao P. Preprint DOI: 10.1101/067900
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
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
Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond.
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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
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The genetic architecture of type 2 diabetes.
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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
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
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 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
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A high density map for navigating the human Polycomb complexome
Hauri S, Comoglio F, Seimiya M, Gerstung M, Glatter T, Hansen K, Aebersold R, Paro R, Gstaiger M, Beisel C. Preprint DOI: 10.1101/059964
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
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
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
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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
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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
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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.
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Personally tailored cancer management based on knowledge banks of genomic and clinical data
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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.
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Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
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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
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Baldi P, Przytycka T. Bioinformatics (Oxford, England) Volume 32 (2016) p.i1-i2 DOI: 10.1093/bioinformatics/btw326
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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
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
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
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Genomic Classification and Prognosis in Acute Myeloid Leukemia.
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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
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Common genetic variation drives molecular heterogeneity in human iPSCs
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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
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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
Landscape of somatic mutations in 560 breast cancer whole-genome sequences.
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The topography of mutational processes in breast cancer genomes.
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Improved definition of the mouse transcriptome via targeted RNA sequencing.
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Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci
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Structure and evolutionary history of a large family of NLR proteins in the zebrafish.
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From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.
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Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.
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Omics Discovery Index - Discovering and Linking Public Omics Datasets
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Ten Simple Rules for Taking Advantage of git and GitHub
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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
Extending gene ontology in the context of extracellular RNA and vesicle communication.
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A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.
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Lithium Promotes Longevity through GSK3/NRF2-Dependent Hormesis.
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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
Mutational History of a Human Cell Lineage from Somatic to Induced Pluripotent Stem Cells.
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Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB. PLoS computational biology Volume 12 (2016) p.e1004862 DOI: 10.1371/journal.pcbi.1004862
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Standardized benchmarking in the quest for orthologs.
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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
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Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.
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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
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation.
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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.
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Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design.
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UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB.
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T cell fate and clonality inference from single-cell transcriptomes.
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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
Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.
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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
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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
Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells.
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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
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Computational clustering for viral reference proteomes.
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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
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Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes.
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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
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
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
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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
The UniProtKB guide to the human proteome.
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Activation of the TGFβ pathway impairs endothelial to haematopoietic transition.
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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.
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Clustering Genes of Common Evolutionary History.
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The Time Is Right to Focus on Model Organism Metabolomes.
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Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources.
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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
Web-based volume slicer for 3D electron-microscopy data from EMDB.
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Genomic insights into the Ixodes scapularis tick vector of Lyme disease.
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MOCCASIN: converting MATLAB ODE models to SBML.
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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
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.
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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
Characterising Complex Enzyme Reaction Data.
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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
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
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
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
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
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Short template switch events explain mutation clusters in the human genome
Löytynoja A, Goldman N. Preprint DOI: 10.1101/038380
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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
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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)
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
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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
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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
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BioJS-HGV Viewer: Genetic Variation Visualizer
Choudhary S, Garcia L, Nightingale A, Martin M. DOI: 10.1101/032573
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
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
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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
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
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

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
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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 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
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
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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
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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
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 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
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
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
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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
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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
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
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
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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
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
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
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
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
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
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
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
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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
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
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
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
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
Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.
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Modeling Signaling Networks to Advance New Cancer Therapies.
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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.
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PubChemRDF: towards the semantic annotation of PubChem compound and substance databases.
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Structure and evolutionary history of a large family of NLR proteins in the zebrafish
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A draft genome sequence of an invasive mosquito: an Italian Aedes albopictus.
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Identifying novel sequence variants of RNA 3D motifs.
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Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders.
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A random forest approach to capture genetic effects in the presence of population structure.
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The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.
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Molecular and neuronal homology between the olfactory systems of zebrafish and mouse.
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The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding.
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BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.
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Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling.
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Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.
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Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.
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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
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
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ISMB/ECCB 2015.
Moreau Y, Beerenwinkel N. Bioinformatics (Oxford, England) Volume 31 (2015) p.i1-2 DOI: 10.1093/bioinformatics/btv303
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 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
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
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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
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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
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
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
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
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
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
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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
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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
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
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
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
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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
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
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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
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
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
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
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
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
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
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
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
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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
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
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
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
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
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
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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
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Proteomics data visualisation.
Vizcaíno JA, Barsnes H, Hermjakob H. Proteomics Volume 15 (2015) p.1339-1340 DOI: 10.1002/pmic.201570063
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
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
Kinase-two-hybrid: towards the conditional interactome.
Ochoa D, Beltrao P. Molecular systems biology Volume 11 (2015) p.798 DOI: 10.15252/msb.20156107
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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
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
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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
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
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
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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
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
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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
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
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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
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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
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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
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
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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
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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
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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
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
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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
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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
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
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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
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
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
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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
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
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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
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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
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
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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
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
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Mbd3 and deterministic reprogramming
Bertone P, Hendrich B, Silva JC. Preprint DOI: 10.1101/013904
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
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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
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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
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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
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
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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
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
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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
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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
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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
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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
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
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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
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
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
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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
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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
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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
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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

2014

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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
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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
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
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
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
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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
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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
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
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
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
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
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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
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
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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
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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.
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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
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
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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
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
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
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Cell-Line Annotation on Europe PubMed Central
Kim J. Preprint DOI: 10.1101/011700
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
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
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
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
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
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
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
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.
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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
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
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
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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
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.
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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
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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
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
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
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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.
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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
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RNAcentral: an international database of ncRNA sequences.
RNAcentral Consortium. Nucleic acids research Volume 43 (2015) p.D123-9 DOI: 10.1093/nar/gku991
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
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
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
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
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
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
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UniProt: a hub for protein information.
UniProt Consortium. Nucleic acids research Volume 43 (2015) p.D204-12 DOI: 10.1093/nar/gku989
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
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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.
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Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation.
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Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.
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Activities at the Universal Protein Resource (UniProt).
Nucleic acids research Volume 42 (2014) p.7486-7486 DOI: 10.1093/nar/gku469
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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
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LIMIX: genetic analysis of multiple traits
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A rapidly reversible chemical dimerizer system to study lipid signaling in living cells.
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Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis.
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MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
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jmzTab: a java interface to the mzTab data standard.
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qcML: an exchange format for quality control metrics from mass spectrometry experiments.
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MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.
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Defining functional DNA elements in the human genome.
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Phylogenetic quantification of intra-tumour heterogeneity.
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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
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Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells.
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Exploring the biological and chemical complexity of the ligases.
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The reference genome sequence of Saccharomyces cerevisiae: then and now.
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Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish.
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Leucine modulates dynamic phosphorylation events in insulin signaling pathway and enhances insulin-dependent glycogen synthesis in human skeletal muscle cells.
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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.
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Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt.
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Revisiting the training of logic models of protein signaling networks with ASP
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A promoter-level mammalian expression atlas.
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ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
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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
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
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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
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
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
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
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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
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
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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
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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
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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
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
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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
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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
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
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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
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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
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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
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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
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
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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
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Delivering ICT Infrastructure for Biomedical Research
Rahman SA, Furnham N, Holliday GL and Thornton JM. Nature methods Volume 11 (2014) p.171-174
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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
diXa data warehouse: Exploring data from toxicogenomics studies
Matser V. DOI: 10.6019/tol.dixa-t.2014.00001.1
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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
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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
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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
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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
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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
Metabolomics: an introduction
Salek R, Emery L, Beisken S. DOI: 10.6019/tol.mbs.2014.00001.1

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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
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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
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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
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
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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
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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
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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
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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
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
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
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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 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
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
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
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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
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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
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
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
Evolution of the thermopsin peptidase family (A5).
Rawlings ND. PloS one Volume 8 (2013) p.e78998 DOI: 10.1371/journal.pone.0078998
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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
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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
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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
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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
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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
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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
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
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
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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
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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
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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
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
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Activities at the Universal Protein Resource (UniProt).
UniProt Consortium. Nucleic acids research Volume 42 (2014) p.D191-8 DOI: 10.1093/nar/gkt1140
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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
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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
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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
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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
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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
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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
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
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
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
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
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
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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
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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
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Immunology meets genomics.
Teichmann SA. Briefings in functional genomics Volume 12 (2013) p.469-470 DOI: 10.1093/bfgp/elt037
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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
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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
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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
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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
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
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
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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
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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
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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
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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
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
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
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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
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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
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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
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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
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Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
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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
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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
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
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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
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Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype.
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