Publications for 2017

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
Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge.
Sarntivijai S, Diehl AD, He Y. BMC bioinformatics Volume 18 (2017) p.560 DOI: 10.1186/s12859-017-1976-2
Comparison, alignment, and synchronization of cell line information between CLO and EFO.
Ong E, Sarntivijai S, Jupp S, Parkinson H, He Y. BMC bioinformatics Volume 18 (2017) p.557 DOI: 10.1186/s12859-017-1979-z
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.
Tang J, Tanoli ZU, Ravikumar B, Alam Z, Rebane A, Vähä-Koskela M, Peddinti G, van Adrichem AJ, Wakkinen J, Jaiswal A, Karjalainen E, Gautam P, He L, Parri E, Khan S, Gupta A, Ali M, Yetukuri L, Gustavsson AL, Seashore-Ludlow B, Hersey A, Leach AR, Overington JP, Repasky G, Wennerberg K, Aittokallio T. Cell chemical biology Volume 25 (2018) p.224-229.e2 DOI: 10.1016/j.chembiol.2017.11.009
Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses.
Ong E, Xie J, Ni Z, Liu Q, Sarntivijai S, Lin Y, Cooper D, Terryn R, Stathias V, Chung C, Schürer S, He Y. BMC bioinformatics Volume 18 (2017) p.556 DOI: 10.1186/s12859-017-1981-5
Accurate and fast feature selection workflow for high-dimensional omics data.
Perez-Riverol Y, Kuhn M, Vizcaíno JA, Hitz MP, Audain E. PloS one Volume 12 (2017) p.e0189875 DOI: 10.1371/journal.pone.0189875
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A protein standard that emulates homology for the characterization of protein inference algorithms
The M, Edfors F, Perez-Riverol Y, Payne SH, Hoopmann MR, Palmblad M, Forsström B, Käll L. Preprint DOI: 10.1101/236471
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Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.
Flannick J, Fuchsberger C, Mahajan A, Teslovich TM, Agarwala V, Gaulton KJ, Caulkins L, Koesterer R, Ma C, Moutsianas L, McCarthy DJ, Rivas MA, Perry JRB, Sim X, Blackwell TW, Robertson NR, Rayner NW, Cingolani P, Locke AE, Tajes JF, Highland HM, Dupuis J, Chines PS, Lindgren CM, Hartl C, Jackson AU, Chen H, Huyghe JR, van de Bunt M, Pearson RD, Kumar A, Müller-Nurasyid M, Müller-Nurasyid M, Grarup N, Stringham HM, Gamazon ER, Lee J, Chen Y, Scott RA, Below JE, Chen P, Huang J, Go MJ, Stitzel ML, Pasko D, Parker SCJ, Varga TV, Green T, Beer NL, Day-Williams AG, Ferreira T, Fingerlin T, Horikoshi M, Hu C, Huh I, Ikram MK, Kim BJ, Kim Y, Kim YJ, Kwon MS, Lee J, Lee S, Lin KH, Maxwell TJ, Nagai Y, Wang X, Welch RP, Yoon J, Zhang W, Barzilai N, Voight BF, Han BG, Jenkinson CP, Kuulasmaa T, Kuusisto J, Manning A, Ng MCY, Palmer ND, Balkau B, Stančáková A, Abboud HE, Boeing H, Giedraitis V, Prabhakaran D, Gottesman O, Scott J, Carey J, Kwan P, Grant G, Smith JD, Neale BM, Purcell S, Butterworth AS, Howson JMM, Lee HM, Lu Y, Kwak SH, Zhao W, Danesh J, Lam VKL, Park KS, Saleheen D, So WY, Tam CHT, Afzal U, Aguilar D, Arya R, Aung T, Chan E, Navarro C, Cheng CY, Palli D, Correa A, Curran JE, Rybin D, Farook VS, Fowler SP, Freedman BI, Griswold M, Hale DE, Hicks PJ, Khor CC, Kumar S, Lehne B, Thuillier D, Lim WY, Liu J, Loh M, Musani SK, Puppala S, Scott WR, Yengo L, Tan ST, Taylor HA, Thameem F, Wilson G, Wong TY, Njølstad PR, Levy JC, Mangino M, Bonnycastle LL, Schwarzmayr T, Fadista J, Surdulescu GL, Herder C, Groves CJ, Wieland T, Bork-Jensen J, Brandslund I, Christensen C, Koistinen HA, Doney ASF, Kinnunen L, Esko T, Farmer AJ, Hakaste L, Hodgkiss D, Kravic J, Lyssenko V, Hollensted M, Jørgensen ME, Jørgensen T, Ladenvall C, Justesen JM, Käräjämäki A, Kriebel J, Rathmann W, Lannfelt L, Lauritzen T, Narisu N, Linneberg A, Melander O, Milani L, Neville M, Orho-Melander M, Qi L, Qi Q, Roden M, Rolandsson O, Swift A, Rosengren AH, Stirrups K, Wood AR, Mihailov E, Blancher C, Carneiro MO, Maguire J, Poplin R, Shakir K, Fennell T, DePristo M, de Angelis MH, Deloukas P, Gjesing AP, Jun G, Nilsson P, Murphy J, Onofrio R, Thorand B, Hansen T, Meisinger C, Hu FB, Isomaa B, Karpe F, Liang L, Peters A, Huth C, O'Rahilly SP, Palmer CNA, Pedersen O, Rauramaa R, Tuomilehto J, Salomaa V, Watanabe RM, Syvänen AC, Bergman RN, Bharadwaj D, Bottinger EP, Cho YS, Chandak GR, Chan JC, Chia KS, Daly MJ, Ebrahim SB, Langenberg C, Elliott P, Jablonski KA, Lehman DM, Jia W, Ma RCW, Pollin TI, Sandhu M, Tandon N, Froguel P, Barroso I, Teo YY, Zeggini E, Loos RJF, Small KS, Ried JS, DeFronzo RA, Grallert H, Glaser B, Metspalu A, Wareham NJ, Walker M, Banks E, Gieger C, Ingelsson E, Im HK, Illig T, Franks PW, Buck G, Trakalo J, Buck D, Prokopenko I, Mägi R, Lind L, Farjoun Y, Owen KR, Gloyn AL, Strauch K, Tuomi T, Kooner JS, Lee JY, Park T, Donnelly P, Morris AD, Hattersley AT, Bowden DW, Collins FS, Atzmon G, Chambers JC, Spector TD, Laakso M, Strom TM, Bell GI, Blangero J, Duggirala R, Tai ES, McVean G, Hanis CL, Wilson JG, Seielstad M, Frayling TM, Meigs JB, Cox NJ, Sladek R, Lander ES, Gabriel S, Mohlke KL, Meitinger T, Groop L, Abecasis G, Scott LJ, Morris AP, Kang HM, Altshuler D, Burtt NP, Florez JC, Boehnke M, McCarthy MI. Scientific data Volume 4 (2017) p.170179 DOI: 10.1038/sdata.2017.179
Finding the best data for your needs in the PDB archive
Conroy M. DOI: 10.6019/tol.pdbenov17-w.2017.00001.1
GWAS Catalog: Exploring SNP-trait associations
Emery L, MacArthur J. DOI: 10.6019/tol.gwas-t.2017.00001.1
Open Targets: Mining gene and disease associations for improved drug target identification
Carvalho-Silva D. DOI: 10.6019/tol.opentargets-w.2017.00001.1
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Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis
Stojic L, Lun A, Mangei J, Mascalchi P, Quarantotti V, Barr A, Bakal C, Marioni J, Gergely F, Odom D. Preprint DOI: 10.1101/234930
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Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging
Severo MS, Landry JJ, Lindquist RL, Goosmann C, Brinkmann V, Collier P, Hauser AE, Benes V, Henriksson J, Teichmann SA, Levashina EA. Preprint DOI: 10.1101/234492
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The IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation
Pramanik J, Chen X, Kar G, Gomes T, Henriksson J, Miao Z, Natarajan K, McKenzie ANJ, Mahata B, Teichmann SA. Preprint DOI: 10.1101/235010
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Real-time search of all bacterial and viral genomic data
Bradley P, den Bakker H, Rocha E, McVean G, Iqbal Z. Preprint DOI: 10.1101/234955
Condensed tannins affect bacterial and fungal microbiomes and mycotoxin production during ensiling and upon aerobic exposure.
Peng K, Jin L, Niu YD, Huang Q, McAllister TA, Yang HE, Denise H, Xu Z, Acharya S, Wang S, Wang Y. Applied and environmental microbiology (2017) DOI: 10.1128/AEM.02274-17
Sharing and reuse of individual participant data from clinical trials: principles and recommendations.
Ohmann C, Banzi R, Canham S, Battaglia S, Matei M, Ariyo C, Becnel L, Bierer B, Bowers S, Clivio L, Dias M, Druml C, Faure H, Fenner M, Galvez J, Ghersi D, Gluud C, Groves T, Houston P, Karam G, Kalra D, Knowles RL, Krleža-Jerić K, Kubiak C, Kuchinke W, Kush R, Lukkarinen A, Marques PS, Newbigging A, O'Callaghan J, Ravaud P, Schlünder I, Shanahan D, Sitter H, Spalding D, Tudur-Smith C, van Reusel P, van Veen EB, Visser GR, Wilson J, Demotes-Mainard J. BMJ open Volume 7 (2017) p.e018647 DOI: 10.1136/bmjopen-2017-018647
nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.
Schober D, Jacob D, Wilson M, Cruz JA, Marcu A, Grant JR, Moing A, Deborde C, de Figueiredo LF, Haug K, Rocca-Serra P, Easton J, Ebbels TMD, Hao J, Ludwig C, Günther UL, Rosato A, Klein MS, Lewis IA, Luchinat C, Jones AR, Grauslys A, Larralde M, Yokochi M, Kobayashi N, Porzel A, Griffin JL, Viant MR, Wishart DS, Steinbeck C, Salek RM, Neumann S. Analytical chemistry Volume 90 (2018) p.649-656 DOI: 10.1021/acs.analchem.7b02795
In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering.
Wu Q, Ferry QRV, Baeumler TA, Michaels YS, Vitsios DM, Habib O, Arnold R, Jiang X, Maio S, Steinkraus BR, Tapia M, Piazza P, Xu N, Holländer GA, Milne TA, Kim JS, Enright AJ, Bassett AR, Fulga TA. Nature communications Volume 8 (2017) p.2109 DOI: 10.1038/s41467-017-00686-2
Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling.
Tresadern G, Trabanco AA, Pérez-Benito L, Overington JP, van Vlijmen HWT, van Westen GJP. Journal of chemical information and modeling Volume 57 (2017) p.2976-2985 DOI: 10.1021/acs.jcim.7b00338
Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.
Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Peat G, Pignatelli M, Falcone F, Benes CH, Dunham I, Bignell G, McDade SS, Garnett MJ, Saez-Rodriguez J. Cancer research Volume 78 (2018) p.769-780 DOI: 10.1158/0008-5472.can-17-1679
Molecular and functional variation in iPSC-derived sensory neurons.
Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, Patel M, Goncalves A, Ferreira R, Benn CL, Wilbrey A, Bictash M, Impey E, Cao L, Lainez S, Loucif AJ, Whiting PJ, Gutteridge A, Gaffney DJ, HIPSCI Consortium. Nature genetics Volume 50 (2018) p.54-61 DOI: 10.1038/s41588-017-0005-8
The HMMER Web Server for Protein Sequence Similarity Search.
Prakash A, Jeffryes M, Bateman A, Finn RD. Current protocols in bioinformatics Volume 60 (2017) p.3.15.1-3.15.23 DOI: 10.1002/cpbi.40
Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines.
Blattmann P, Henriques D, Zimmermann M, Frommelt F, Sauer U, Saez-Rodriguez J, Aebersold R. Cell systems Volume 5 (2017) p.604-619.e7 DOI: 10.1016/j.cels.2017.11.002
Immuno-oncology from the perspective of somatic evolution.
González S, Volkova N, Beer P, Gerstung M. Seminars in cancer biology Volume 52 (2018) p.75-85 DOI: 10.1016/j.semcancer.2017.12.001
Analysis of the genomic landscape of multiple myeloma highlights novel prognostic markers and disease subgroups.
Bolli N, Biancon G, Moarii M, Gimondi S, Li Y, de Philippis C, Maura F, Sathiaseelan V, Tai YT, Mudie L, O'Meara S, Raine K, Teague JW, Butler AP, Carniti C, Gerstung M, Bagratuni T, Kastritis E, Dimopoulos M, Corradini P, Anderson K, Moreau P, Minvielle S, Campbell PJ, Papaemmanuil E, Avet-Loiseau H, Munshi NC. Leukemia (2017) DOI: 10.1038/leu.2017.344
Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the "Gene-Battery" Model.
Sundaram V, Wang T. BioEssays : news and reviews in molecular, cellular and developmental biology Volume 40 (2018) DOI: 10.1002/bies.201700155
The Human Cell Atlas.
Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N, Human Cell Atlas Meeting Participants. eLife Volume 6 (2017) DOI: 10.7554/elife.27041
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Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting
Iorio F, Behan FM, Goncalves E, Bhosle S, Chen E, Shepherd R, Beaver C, Ansari R, Pooley R, Wilkinson P, Harper S, Butler AP, Stronach E, Saez-Rodriguez J, Yusa K, Garnett MJ. Preprint DOI: 10.1101/228189
Editorial overview: Catalysis and regulation.
Thornton J, Orengo C. Current opinion in structural biology Volume 47 (2017) p.vi-viii DOI: 10.1016/j.sbi.2017.11.005
Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.
Vitsios DM, Kentepozidou E, Quintais L, Benito-Gutiérrez E, van Dongen S, Davis MP, Enright AJ. Nucleic acids research Volume 45 (2017) p.e177 DOI: 10.1093/nar/gkx836
clustComp, a bioconductor package for the comparison of clustering results.
Torrente A, Brazma A. Bioinformatics (Oxford, England) Volume 33 (2017) p.4001-4003 DOI: 10.1093/bioinformatics/btx532
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Variation and Functional Impact of Neanderthal Ancestry in Western Asia.
Taskent RO, Alioglu ND, Fer E, Melike Donertas H, Somel M, Gokcumen O. Genome biology and evolution Volume 9 (2017) p.3516-3524 DOI: 10.1093/gbe/evx216
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DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation.
Richard MA, Huan T, Ligthart S, Gondalia R, Jhun MA, Brody JA, Irvin MR, Marioni R, Shen J, Tsai PC, Montasser ME, Jia Y, Syme C, Salfati EL, Boerwinkle E, Guan W, Mosley TH, Bressler J, Morrison AC, Liu C, Mendelson MM, Uitterlinden AG, van Meurs JB, BIOS Consortium, Franco OH, Zhang G, Li Y, Stewart JD, Bis JC, Psaty BM, Chen YI, Kardia SLR, Zhao W, Turner ST, Absher D, Aslibekyan S, Starr JM, McRae AF, Hou L, Just AC, Schwartz JD, Vokonas PS, Menni C, Spector TD, Shuldiner A, Damcott CM, Rotter JI, Palmas W, Liu Y, Paus T, Horvath S, O'Connell JR, Guo X, Pausova Z, Assimes TL, Sotoodehnia N, Smith JA, Arnett DK, Deary IJ, Baccarelli AA, Bell JT, Whitsel E, Dehghan A, Levy D, Fornage M. American journal of human genetics Volume 101 (2017) p.888-902 DOI: 10.1016/j.ajhg.2017.09.028
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Genetic diversity of the African malaria vector Anopheles gambiae.
Anopheles gambiae 1000 Genomes Consortium, Data analysis group, Partner working group, Sample collections—Angola:, Burkina Faso:, Cameroon:, Gabon:, Guinea:, Guinea-Bissau:, Kenya:, Uganda:, Crosses:, Sequencing and data production, Web application development, Project coordination. Nature Volume 552 (2017) p.96-100 DOI: 10.1038/nature24995
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Assessing the Gene Regulatory Landscape in 1,188 Human Tumors
Calabrese C, Lehmann K, Urban L, Liu F, Erkek S, Fonseca N, Kahles A, Kilpinen-Barrett LH, Markowski J, Waszak S, Korbel J, Zhang Z, Brazma A, Raetsch G, Schwarz R, Stegle O, PCAWG-3. Preprint DOI: 10.1101/225441
Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.
Shahbazi MN, Scialdone A, Skorupska N, Weberling A, Recher G, Zhu M, Jedrusik A, Devito LG, Noli L, Macaulay IC, Buecker C, Khalaf Y, Ilic D, Voet T, Marioni JC, Zernicka-Goetz M. Nature Volume 552 (2017) p.239-243 DOI: 10.1038/nature24675
Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants.
Rifaioglu AS, Doğan T, Saraç ÖS, Ersahin T, Saidi R, Atalay MV, Martin MJ, Cetin-Atalay R. Proteins Volume 86 (2018) p.135-151 DOI: 10.1002/prot.25416
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Community-driven data analysis training for biology
Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg M, Gladman S, Hoogstrate Y, Hotz H, Houwaart T, Jagtap P, Lariviere D, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch F, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D, Backofen R, Taylor J, Nekrutenko A, Grüning B. Preprint DOI: 10.1101/225680
Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells.
Gonçalves E, Sciacovelli M, Costa ASH, Tran MGB, Johnson TI, Machado D, Frezza C, Saez-Rodriguez J. Metabolic engineering Volume 45 (2018) p.149-157 DOI: 10.1016/j.ymben.2017.11.011
Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression.
Berthelot C, Villar D, Horvath JE, Odom DT, Flicek P. Nature ecology & evolution Volume 2 (2018) p.152-163 DOI: 10.1038/s41559-017-0377-2
The challenge of modeling protein assemblies: the CASP12-CAPRI experiment.
Lensink MF, Velankar S, Baek M, Heo L, Seok C, Wodak SJ. Proteins Volume 86 Suppl 1 (2018) p.257-273 DOI: 10.1002/prot.25419
Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.
Griffiths JA, Scialdone A, Marioni JC. BMC genomics Volume 18 (2017) p.904 DOI: 10.1186/s12864-017-4253-x
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5-Formylcytosine controls nucleosome positioning through covalent histone-DNA interaction
Raiber E, Portella G, Martinez Cuesta S, Hardisty R, Murat P, Li Z, Iurlaro M, Dean W, Spindel J, Beraldi D, Dawson M, Reik W, Balasubramanian S. Preprint DOI: 10.1101/224444
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Automated evaluation of quaternary structures from protein crystals
Bliven S, Lafita A, Parker A, Capitani G, Duarte JM. Preprint DOI: 10.1101/224717
Validation of Structures in the Protein Data Bank.
Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ. Structure (London, England : 1993) Volume 25 (2017) p.1916-1927 DOI: 10.1016/j.str.2017.10.009
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NCBI will no longer make taxonomy identifiers for individual influenza strains on January 15, 2018
Hatcher E, Bao Y, Amedeo P, Blinkova O, Cochrane G, Fedorova N, Gruner W, Leipe D, Nakamura Y, Ostapchuk Y, Palanigobu V, Sanders R, Schoch C, Smith C, Wentworth D, Yankie L, Zhdanov S, Karsch-Mizrachi I, Brister JR. Preprint DOI: 10.7287/peerj.preprints.3428
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Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast
Stirparo GG, Boroviak T, Guo G, Nichols J, Smith A, Bertone P. Preprint DOI: 10.1101/222760
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The global distribution and spread of the mobilized colistin resistance gene mcr-1
Wang R, van Dorp L, Shaw L, Bradley P, Wang Q, Wang X, Jin L, Zhang Q, Liu Y, Rieux A, Dorai-Schneiders T, Weinert LA, Iqbal Z, Didelot X, Wang H, Balloux F. Preprint DOI: 10.1101/220921
Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.
Welby E, Lakowski J, Di Foggia V, Budinger D, Gonzalez-Cordero A, Lun ATL, Epstein M, Patel A, Cuevas E, Kruczek K, Naeem A, Minneci F, Hubank M, Jones DT, Marioni JC, Ali RR, Sowden JC. Stem cell reports Volume 9 (2017) p.1898-1915 DOI: 10.1016/j.stemcr.2017.10.018
A high-resolution mRNA expression time course of embryonic development in zebrafish.
White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Billis K, Hourlier T, Füllgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. eLife Volume 6 (2017) DOI: 10.7554/elife.30860
Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus.
Schulz H, Ruppert AK, Herms S, Wolf C, Mirza-Schreiber N, Stegle O, Czamara D, Forstner AJ, Sivalingam S, Schoch S, Moebus S, Pütz B, Hillmer A, Fricker N, Vatter H, Müller-Myhsok B, Nöthen MM, Becker AJ, Hoffmann P, Sander T, Cichon S. Nature communications Volume 8 (2017) p.1511 DOI: 10.1038/s41467-017-01818-4
DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.
Kraiczy J, Nayak KM, Howell KJ, Ross A, Forbester J, Salvestrini C, Mustata R, Perkins S, Andersson-Rolf A, Leenen E, Liebert A, Vallier L, Rosenstiel PC, Stegle O, Dougan G, Heuschkel R, Koo BK, Zilbauer M. Gut (2017) DOI: 10.1136/gutjnl-2017-314817
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Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi
Keilwagen J, Hartung F, Paulini M, Twardziok SO, Grau J. Preprint DOI: 10.1101/219287
To what extent do structural changes in catalytic metal sites affect enzyme function?
Valasatava Y, Rosato A, Furnham N, Thornton JM, Andreini C. Journal of inorganic biochemistry Volume 179 (2018) p.40-53 DOI: 10.1016/j.jinorgbio.2017.11.002
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Corrigendum: High-throughput discovery of novel developmental phenotypes.
Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie Helmut Fuchs SM, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Nutter SNLMJ, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, International Mouse Phenotyping Consortium, Wurst W, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SDM, Adams DJ, Lloyd KCK, McKerlie C, Beaudet AL, Murray MBSA. Nature Volume 551 (2017) p.398 DOI: 10.1038/nature24643
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NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease.
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Genomics in healthcare: GA4GH looks to 2022
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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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Intestinal Fork Head Regulates Nutrient Absorption and Promotes Longevity.
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SourceData: a semantic platform for curating and searching figures.
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The impact of rare variation on gene expression across tissues.
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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.
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A new pan-European Train-the-Trainer programme for bioinformatics: pilot results on feasibility, utility and sustainability of learning.
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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.
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C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis.
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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.
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Uncovering novel repositioning opportunities using the Open Targets platform.
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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
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Best practice data life cycle approaches for the life sciences.
Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. F1000Research Volume 6 (2017) p.1618 DOI: 10.12688/f1000research.12344.2
The RNA m6A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence.
Ivanova I, Much C, Di Giacomo M, Azzi C, Morgan M, Moreira PN, Monahan J, Carrieri C, Enright AJ, O'Carroll D. Molecular cell Volume 67 (2017) p.1059-1067.e4 DOI: 10.1016/j.molcel.2017.08.003
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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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Seaton D, Graf A, Baerenfaller K, Stitt M, Millar A, Gruissem W. Preprint DOI: 10.1101/182071
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
EMBL-EBI, programmatically: take a REST from manual searches
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Marioni JC, Arendt D. Annual review of cell and developmental biology Volume 33 (2017) p.537-553 DOI: 10.1146/annurev-cellbio-100616-060818
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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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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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A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine.
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Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient.
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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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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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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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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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Sequanix: A Dynamic Graphical Interface for Snakemake Workflows
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The evolutionary history of 2,658 cancers
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Building bridges between cellular and molecular structural biology.
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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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Jain M, Tyson JR, Loose M, Ip CL, Eccles DA, O'Grady J, Malla S, Leggett RM, Wallerman O, Jansen HJ, Zalunin V, Birney E, Brown BL, Snutch TP, Olsen HE, MinION Analysis and Reference Consortium. Preprint DOI: 10.12688/f1000research.11354.1
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Joseph AP, Lagerstedt I, Patwardhan A, Topf M, Winn M. Journal of structural biology Volume 199 (2017) p.12-26 DOI: 10.1016/j.jsb.2017.05.007
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Gabryś HS, Buettner F, Sterzing F, Hauswald H, Bangert M. Acta oncologica (Stockholm, Sweden) Volume 56 (2017) p.1197-1203 DOI: 10.1080/0284186x.2017.1324209
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Universal Patterns Of Selection In Cancer And Somatic Tissues
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Literature Evidence in Open Targets - a target validation platform
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Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models.
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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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ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
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Shared Consensus Machine Learning Models for Predicting Blood Stage Malaria Inhibition.
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Adipocyte Accumulation in the Bone Marrow during Obesity and Aging Impairs Stem Cell-Based Hematopoietic and Bone Regeneration.
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Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions.
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Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring.
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HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
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Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.
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Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy.
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ChromoTrace: Reconstruction of 3D Chromosome Configurations by Super-Resolution Microscopy
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Rapid establishment of the European Bank for induced Pluripotent Stem Cells (EBiSC) - the Hot Start experience.
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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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Data management: A global coalition to sustain core data.
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Aging increases cell-to-cell transcriptional variability upon immune stimulation.
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An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge.
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Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.
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A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data.
Ogeh D, Badge R. Bioinformatics (Oxford, England) Volume 33 (2017) p.650-653 DOI: 10.1093/bioinformatics/btw687
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A global perspective on bioinformatics training needs
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TOWARDS COORDINATED INTERNATIONAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES
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Prospective identification of hematopoietic lineage choice by deep learning.
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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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Structure of the Escherichia coli ProQ RNA-binding protein.
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A high-resolution mRNA expression time course of embryonic development in zebrafish
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OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.
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Nuclear RNA Decay Pathways Aid Rapid Remodeling of Gene Expression in Yeast.
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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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Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.
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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
Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Casale FP, Wolford BN, Guan L, Varshney A, Albanus RD, Parker SC, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS. Preprint DOI: 10.1101/105429
A Comparative Analysis of Drug-Induced Hepatotoxicity in Clinically Relevant Situations.
Thiel C, Cordes H, Fabbri L, Aschmann HE, Baier V, Smit I, Atkinson F, Blank LM, Kuepfer L. PLoS computational biology Volume 13 (2017) p.e1005280 DOI: 10.1371/journal.pcbi.1005280
The Genetic Architecture of Major Depressive Disorder in Han Chinese Women.
Peterson RE, Cai N, Bigdeli TB, Li Y, Reimers M, Nikulova A, Webb BT, Bacanu SA, Riley BP, Flint J, Kendler KS. JAMA psychiatry Volume 74 (2017) p.162-168 DOI: 10.1001/jamapsychiatry.2016.3578
Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders.
Evers JM, Laskowski RA, Bertolli M, Clayton-Smith J, Deshpande C, Eason J, Elmslie F, Flinter F, Gardiner C, Hurst JA, Kingston H, Kini U, Lampe AK, Lim D, Male A, Naik S, Parker MJ, Price S, Robert L, Sarkar A, Straub V, Woods G, Thornton JM, DDD Study, Wright CF. Human molecular genetics Volume 26 (2017) p.519-526 DOI: 10.1093/hmg/ddw409
From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB.
Zaru R, Magrane M, O'Donovan C, UniProt Consortium. The Biochemical journal Volume 474 (2017) p.493-515 DOI: 10.1042/BCJ20160991
Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis.
Vitsios DM, Davis MP, van Dongen S, Enright AJ. Nucleic acids research Volume 45 (2017) p.1079-1090 DOI: 10.1093/nar/gkw1031
Synthetic human proteomes for accelerating protein research.
Perez-Riverol Y, Vizcaíno JA. Nature methods Volume 14 (2017) p.240-242 DOI: 10.1038/nmeth.4191
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Cell biology: tracking a cell's cycle.
Marx V. Nature methods Volume 14 (2017) p.233-236 DOI: 10.1038/nmeth.4186
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Postdocs, What Would You Tell Your Younger Self?
Cell Volume 168 (2017) p.745-748 DOI: 10.1016/j.cell.2017.02.016
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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
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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
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
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
Global open data management in metabolomics.
Haug K, Salek RM, Steinbeck C. Current opinion in chemical biology Volume 36 (2017) p.58-63 DOI: 10.1016/j.cbpa.2016.12.024
Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.
Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJ, Cvejic A, Gfeller D. Genome research Volume 27 (2017) p.451-461 DOI: 10.1101/gr.207704.116
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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
System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.
Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M, Vaga S, Vitek O, Saez-Rodriguez J, Aebersold R. Journal of proteome research Volume 16 (2017) p.831-841 DOI: 10.1021/acs.jproteome.6b00815
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.
Gonçalves E, Raguz Nakic Z, Zampieri M, Wagih O, Ochoa D, Sauer U, Beltrao P, Saez-Rodriguez J. PLoS computational biology Volume 13 (2017) p.e1005297 DOI: 10.1371/journal.pcbi.1005297
The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying Neurodegeneration: Evolving Dimensions and Future Directions.
Lloret-Villas A, Varusai TM, Juty N, Laibe C, Le NovÈre N, Hermjakob H, Chelliah V. CPT: pharmacometrics & systems pharmacology Volume 6 (2017) p.73-86 DOI: 10.1002/psp4.12155
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
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
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
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
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 (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
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
Visualising protein structures online
Armstrong A. DOI: 10.6019/tol.pdbe-litemol-w.2017.00001.1
User experience design for more user-friendly applications
Ide-Smith M, Karamanis N. DOI: 10.6019/tol.uxapp-w.2017.00001.1
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
QuickGO - Gene ontology annotation
Georghiou G. DOI: 10.6019/tol.quickgo-w.2017.00001.1
EBI Metagenomics: analysing and exploring metagenomic data
Mitchell A. DOI: 10.6019/tol.ebimetagen-w.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
EMPIAR: Quick tour
Iudin A, Patwardhan A. DOI: 10.6019/tol.empiar-qt.2017.00001.1
Using the MEROPS Database for Investigation of Lysosomal Peptidases, Their Inhibitors, and Substrates.
Rawlings ND. Methods in molecular biology (Clifton, N.J.) Volume 1594 (2017) p.213-226 DOI: 10.1007/978-1-4939-6934-0_14
Exploring protein interactions with UniProt
Pichler K. DOI: 10.6019/tol.unip-interactions-w.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
Ensembl tools: webinar
Perry E. DOI: 10.6019/tol.ens-too-w.2017.00001.2
Reactome: Exploring biological pathways
Jupe S. DOI: 10.6019/tol.reactome_exbp-t.2017.00001.1
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
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
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: Tools for analysis of biological pathways
Jupe S. DOI: 10.6019/tol.reactome_tools-t.2017.00001.1