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 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
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
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
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
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
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
*
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, 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
Open Targets: Mining gene and disease associations for improved drug target identification
Carvalho-Silva D. DOI: 10.6019/tol.opentargets-w.2017.00001.1
GWAS Catalog: Exploring SNP-trait associations
Emery L, MacArthur J. DOI: 10.6019/tol.gwas-t.2017.00001.1
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
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
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
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
Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing.
Bach K, Pensa S, Grzelak M, Hadfield J, Adams DJ, Marioni JC, Khaled WT. Nature communications Volume 8 (2017) p.2128 DOI: 10.1038/s41467-017-02001-5
Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.
Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Peat G, Pignatelli M, Falcone F, Benes CH, Dunham I, Bignell G, McDade SS, Garnett MJ, Saez-Rodriguez J. Cancer research Volume 78 (2018) p.769-780 DOI: 10.1158/0008-5472.can-17-1679
The HMMER Web Server for Protein Sequence Similarity Search.
Prakash A, Jeffryes M, Bateman A, Finn RD. Current protocols in bioinformatics Volume 60 (2017) p.3.15.1-3.15.23 DOI: 10.1002/cpbi.40
Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines.
Blattmann P, Henriques D, Zimmermann M, Frommelt F, Sauer U, Saez-Rodriguez J, Aebersold R. Cell systems Volume 5 (2017) p.604-619.e7 DOI: 10.1016/j.cels.2017.11.002
Immuno-oncology from the perspective of somatic evolution.
González S, Volkova N, Beer P, Gerstung M. Seminars in cancer biology (2017) DOI: 10.1016/j.semcancer.2017.12.001
Analysis of the genomic landscape of multiple myeloma highlights novel prognostic markers and disease subgroups.
Bolli N, Biancon G, Moarii M, Gimondi S, Li Y, de Philippis C, Maura F, Sathiaseelan V, Tai YT, Mudie L, O'Meara S, Raine K, Teague JW, Butler AP, Carniti C, Gerstung M, Bagratuni T, Kastritis E, Dimopoulos M, Corradini P, Anderson K, Moreau P, Minvielle S, Campbell PJ, Papaemmanuil E, Avet-Loiseau H, Munshi NC. Leukemia (2017) DOI: 10.1038/leu.2017.344
The Human Cell Atlas.
Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N, Human Cell Atlas Meeting Participants. eLife Volume 6 (2017) DOI: 10.7554/elife.27041
*
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
*
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
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
*
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
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
Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.
Shahbazi MN, Scialdone A, Skorupska N, Weberling A, Recher G, Zhu M, Jedrusik A, Devito LG, Noli L, Macaulay IC, Buecker C, Khalaf Y, Ilic D, Voet T, Marioni JC, Zernicka-Goetz M. Nature Volume 552 (2017) p.239-243 DOI: 10.1038/nature24675
*
Genetic diversity of the African malaria vector Anopheles gambiae.
Anopheles gambiae 1000 Genomes Consortium, Data analysis group, Partner working group, Sample collections—Angola:, Burkina Faso:, Cameroon:, Gabon:, Guinea:, Guinea-Bissau:, Kenya:, Uganda:, Crosses:, Sequencing and data production, Web application development, Project coordination. Nature Volume 552 (2017) p.96-100 DOI: 10.1038/nature24995
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
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
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
A high-resolution mRNA expression time course of embryonic development in zebrafish.
White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Billis K, Hourlier T, Füllgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. eLife Volume 6 (2017) DOI: 10.7554/elife.30860
Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.
Welby E, Lakowski J, Di Foggia V, Budinger D, Gonzalez-Cordero A, Lun ATL, Epstein M, Patel A, Cuevas E, Kruczek K, Naeem A, Minneci F, Hubank M, Jones DT, Marioni JC, Ali RR, Sowden JC. Stem cell reports Volume 9 (2017) p.1898-1915 DOI: 10.1016/j.stemcr.2017.10.018
DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.
Kraiczy J, Nayak KM, Howell KJ, Ross A, Forbester J, Salvestrini C, Mustata R, Perkins S, Andersson-Rolf A, Leenen E, Liebert A, Vallier L, Rosenstiel PC, Stegle O, Dougan G, Heuschkel R, Koo BK, Zilbauer M. Gut (2017) DOI: 10.1136/gutjnl-2017-314817
Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus.
Schulz H, Ruppert AK, Herms S, Wolf C, Mirza-Schreiber N, Stegle O, Czamara D, Forstner AJ, Sivalingam S, Schoch S, Moebus S, Pütz B, Hillmer A, Fricker N, Vatter H, Müller-Myhsok B, Nöthen MM, Becker AJ, Hoffmann P, Sander T, Cichon S. Nature communications Volume 8 (2017) p.1511 DOI: 10.1038/s41467-017-01818-4
*
Corrigendum: High-throughput discovery of novel developmental phenotypes.
Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie Helmut Fuchs SM, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Nutter SNLMJ, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, International Mouse Phenotyping Consortium, Wurst W, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SDM, Adams DJ, Lloyd KCK, McKerlie C, Beaudet AL, Murray MBSA. Nature Volume 551 (2017) p.398 DOI: 10.1038/nature24643
To what extent do structural changes in catalytic metal sites affect enzyme function?
Valasatava Y, Rosato A, Furnham N, Thornton JM, Andreini C. Journal of inorganic biochemistry Volume 179 (2018) p.40-53 DOI: 10.1016/j.jinorgbio.2017.11.002
f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.
Buettner F, Pratanwanich N, McCarthy DJ, Marioni JC, Stegle O. Genome biology Volume 18 (2017) p.212 DOI: 10.1186/s13059-017-1334-8
ComplexViewer: visualization of curated macromolecular complexes.
Combe CW, Sivade MD, Hermjakob H, Heimbach J, Meldal BHM, Micklem G, Orchard S, Rappsilber J. Bioinformatics (Oxford, England) Volume 33 (2017) p.3673-3675 DOI: 10.1093/bioinformatics/btx497
On expert curation and scalability: UniProtKB/Swiss-Prot as a case study.
Poux S, Arighi CN, Magrane M, Bateman A, Wei CH, Lu Z, Boutet E, Bye-A-Jee H, Famiglietti ML, Roechert B, UniProt Consortium T. Bioinformatics (Oxford, England) Volume 33 (2017) p.3454-3460 DOI: 10.1093/bioinformatics/btx439
Sub-minute Phosphoregulation of Cell Cycle Systems during Plasmodium Gamete Formation.
Invergo BM, Brochet M, Yu L, Choudhary J, Beltrao P, Billker O. Cell reports Volume 21 (2017) p.2017-2029 DOI: 10.1016/j.celrep.2017.10.071
*
NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease.
Schwerd T, Bryant RV, Pandey S, Capitani M, Meran L, Cazier JB, Jung J, Mondal K, Parkes M, Mathew CG, Fiedler K, McCarthy DJ, WGS500 Consortium, Oxford IBD cohort study investigators, COLORS in IBD group investigators, UK IBD Genetics Consortium, Sullivan PB, Rodrigues A, Travis SPL, Moore C, Sambrook J, Ouwehand WH, Roberts DJ, Danesh J, INTERVAL Study, Russell RK, Wilson DC, Kelsen JR, Cornall R, Denson LA, Kugathasan S, Knaus UG, Serra EG, Anderson CA, Duerr RH, McGovern DP, Cho J, Powrie F, Li VS, Muise AM, Uhlig HH. Mucosal immunology Volume 11 (2018) p.562-574 DOI: 10.1038/mi.2017.74
*
Genomic Research Data Generation, Analysis and Sharing - Challenges in the African Setting
Mulder N, Adebamowo CA, Adebamowo SN, Adebayo O, Adeleye O, Alibi M, Baichoo S, Benkahla A, Fadlelmola FM, Ghazal H, Ghedira K, Matimba A, Moussa A, Mungloo-Dilmohamud Z, Owolabi MO, Radouani F, Rotimi CN, Stein DJ, Souiai O. Data Science Journal Volume 16 (2017) p.49 DOI: 10.5334/dsj-2017-049
Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean.
Kılınç GM, Koptekin D, Atakuman Ç, Sümer AP, Dönertaş HM, Yaka R, Bilgin CC, Büyükkarakaya AM, Baird D, Altınışık E, Flegontov P, Götherström A, Togan İ, Somel M. Proceedings. Biological sciences Volume 284 (2017) DOI: 10.1098/rspb.2017.2064
Reactome enhanced pathway visualization.
Sidiropoulos K, Viteri G, Sevilla C, Jupe S, Webber M, Orlic-Milacic M, Jassal B, May B, Shamovsky V, Duenas C, Rothfels K, Matthews L, Song H, Stein L, Haw R, D'Eustachio P, Ping P, Hermjakob H, Fabregat A. Bioinformatics (Oxford, England) Volume 33 (2017) p.3461-3467 DOI: 10.1093/bioinformatics/btx441
cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.
Martin-Herranz DE, Ribeiro AJM, Krueger F, Thornton JM, Reik W, Stubbs TM. Nucleic acids research Volume 45 (2017) p.11559-11569 DOI: 10.1093/nar/gkx814
PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.
Meehan TF, Conte N, Goldstein T, Inghirami G, Murakami MA, Brabetz S, Gu Z, Wiser JA, Dunn P, Begley DA, Krupke DM, Bertotti A, Bruna A, Brush MH, Byrne AT, Caldas C, Christie AL, Clark DA, Dowst H, Dry JR, Doroshow JH, Duchamp O, Evrard YA, Ferretti S, Frese KK, Goodwin NC, Greenawalt D, Haendel MA, Hermans E, Houghton PJ, Jonkers J, Kemper K, Khor TO, Lewis MT, Lloyd KCK, Mason J, Medico E, Neuhauser SB, Olson JM, Peeper DS, Rueda OM, Seong JK, Trusolino L, Vinolo E, Wechsler-Reya RJ, Weinstock DM, Welm A, Weroha SJ, Amant F, Pfister SM, Kool M, Parkinson H, Butte AJ, Bult CJ. Cancer research Volume 77 (2017) p.e62-e66 DOI: 10.1158/0008-5472.can-17-0582
LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data.
Sehnal D, Deshpande M, Vařeková RS, Mir S, Berka K, Midlik A, Pravda L, Velankar S, Koča J. Nature methods Volume 14 (2017) p.1121-1122 DOI: 10.1038/nmeth.4499
Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.
Jasinska AJ, Zelaya I, Service SK, Peterson CB, Cantor RM, Choi OW, DeYoung J, Eskin E, Fairbanks LA, Fears S, Furterer AE, Huang YS, Ramensky V, Schmitt CA, Svardal H, Jorgensen MJ, Kaplan JR, Villar D, Aken BL, Flicek P, Nag R, Wong ES, Blangero J, Dyer TD, Bogomolov M, Benjamini Y, Weinstock GM, Dewar K, Sabatti C, Wilson RK, Jentsch JD, Warren W, Coppola G, Woods RP, Freimer NB. Nature genetics Volume 49 (2017) p.1714-1721 DOI: 10.1038/ng.3959
PDBsum: Structural summaries of PDB entries.
Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM. Protein science : a publication of the Protein Society Volume 27 (2018) p.129-134 DOI: 10.1002/pro.3289
*
Proteomics and phosphoproteomics in precision medicine: applications and challenges.
Giudice G, Petsalaki E. Briefings in bioinformatics (2017) DOI: 10.1093/bib/bbx141
Report of the International Stem Cell Banking Initiative Workshop Activity: Current Hurdles and Progress in Seed-Stock Banking of Human Pluripotent Stem Cells.
Kim JH, Kurtz A, Yuan BZ, Zeng F, Lomax G, Loring JF, Crook J, Ju JH, Clarke L, Inamdar MS, Pera M, Firpo MT, Sheldon M, Rahman N, O'Shea O, Pranke P, Zhou Q, Isasi R, Rungsiwiwut R, Kawamata S, Oh S, Ludwig T, Masui T, Novak TJ, Takahashi T, Fujibuchi W, Koo SK, Stacey GN. Stem cells translational medicine Volume 6 (2017) p.1956-1962 DOI: 10.1002/sctm.17-0144
Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.
Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC, Odom DT, Flicek P. Nature communications Volume 8 (2017) p.1092 DOI: 10.1038/s41467-017-01037-x
Universal Patterns of Selection in Cancer and Somatic Tissues.
Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K, Van Loo P, Davies H, Stratton MR, Campbell PJ. Cell Volume 171 (2017) p.1029-1041.e21 DOI: 10.1016/j.cell.2017.09.042
*
Genomics in healthcare: GA4GH looks to 2022
Birney E, Vamathevan J, Goodhand P. Preprint DOI: 10.1101/203554
A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction.
Bowl MR, Simon MM, Ingham NJ, Greenaway S, Santos L, Cater H, Taylor S, Mason J, Kurbatova N, Pearson S, Bower LR, Clary DA, Meziane H, Reilly P, Minowa O, Kelsey L, International Mouse Phenotyping Consortium, Tocchini-Valentini GP, Gao X, Bradley A, Skarnes WC, Moore M, Beaudet AL, Justice MJ, Seavitt J, Dickinson ME, Wurst W, de Angelis MH, Herault Y, Wakana S, Nutter LMJ, Flenniken AM, McKerlie C, Murray SA, Svenson KL, Braun RE, West DB, Lloyd KCK, Adams DJ, White J, Karp N, Flicek P, Smedley D, Meehan TF, Parkinson HE, Teboul LM, Wells S, Steel KP, Mallon AM, Brown SDM. Nature communications Volume 8 (2017) p.886 DOI: 10.1038/s41467-017-00595-4
DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.
Howell KJ, Kraiczy J, Nayak KM, Gasparetto M, Ross A, Lee C, Mak TN, Koo BK, Kumar N, Lawley T, Sinha A, Rosenstiel P, Heuschkel R, Stegle O, Zilbauer M. Gastroenterology Volume 154 (2018) p.585-598 DOI: 10.1053/j.gastro.2017.10.007
*
Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis.
Yang F, Wang J, GTEx Consortium, Pierce BL, Chen LS. Genome research Volume 27 (2017) p.1859-1871 DOI: 10.1101/gr.216754.116
Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach.
Guruceaga E, Garin-Muga A, Prieto G, Bejarano B, Marcilla M, Marín-Vicente C, Perez-Riverol Y, Casal JI, Vizcaíno JA, Corrales FJ, Segura V. Journal of proteome research Volume 16 (2017) p.4374-4390 DOI: 10.1021/acs.jproteome.7b00388
*
Co-expression networks reveal the tissue-specific regulation of transcription and splicing.
Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, GTEx Consortium, Engelhardt BE, Battle A. Genome research Volume 27 (2017) p.1843-1858 DOI: 10.1101/gr.216721.116
Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer.
Gonçalves E, Fragoulis A, Garcia-Alonso L, Cramer T, Saez-Rodriguez J, Beltrao P. Cell systems Volume 5 (2017) p.386-398.e4 DOI: 10.1016/j.cels.2017.08.013
*
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.
Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F, Broad-DREAM Community, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA. Cell systems Volume 5 (2017) p.485-497.e3 DOI: 10.1016/j.cels.2017.09.004
*
A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog
Morales J, Bowler EH, Buniello A, Cerezo M, Hall P, Harris LW, Hastings E, Junkins HA, Malangone C, McMahon AC, Milano A, Welter D, Burdett T, Cunningham F, Flicek P, Parkinson H, Hindorff L, MacArthur JAL. Preprint DOI: 10.1101/129395
*
Genetic effects on gene expression across human tissues.
GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lead analysts:, Laboratory, Data Analysis &Coordinating Center (LDACC):, NIH program management:, Biospecimen collection:, Pathology:, eQTL manuscript working group:, Battle A, Brown CD, Engelhardt BE, Montgomery SB. Nature Volume 550 (2017) p.204-213 DOI: 10.1038/nature24277
OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.
Perez-Riverol Y, Ternent T, Koch M, Barsnes H, Vrousgou O, Jupp S, Vizcaíno JA. Proteomics Volume 17 (2017) DOI: 10.1002/pmic.201700244
*
Corrigendum: A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.
Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, Nik-Zainal S. Nature genetics Volume 49 (2017) p.1661 DOI: 10.1038/ng1117-1661a
Single-cell epigenomics: Recording the past and predicting the future.
Kelsey G, Stegle O, Reik W. Science (New York, N.Y.) Volume 358 (2017) p.69-75 DOI: 10.1126/science.aan6826
*
Dynamic landscape and regulation of RNA editing in mammals.
Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Chawla A, Del Sal G, Peltz G, Brunet A, Conrad DF, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB. Nature Volume 550 (2017) p.249-254 DOI: 10.1038/nature24041
*
Landscape of X chromosome inactivation across human tissues.
Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG. Nature Volume 550 (2017) p.244-248 DOI: 10.1038/nature24265
*
The impact of rare variation on gene expression across tissues.
Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Bassik MC, Merker JD, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Hall IM, Battle A, Montgomery SB. Nature Volume 550 (2017) p.239-243 DOI: 10.1038/nature24267
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
*
Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.
Hadinnapola C, Bleda M, Haimel M, Screaton N, Swift A, Dorfmüller P, Preston SD, Southwood M, Hernandez-Sanchez J, Martin J, Treacy C, Yates K, Bogaard H, Church C, Coghlan G, Condliffe R, Corris PA, Gibbs S, Girerd B, Holden S, Humbert M, Kiely DG, Lawrie A, Machado R, MacKenzie Ross R, Moledina S, Montani D, Newnham M, Peacock A, Pepke-Zaba J, Rayner-Matthews P, Shamardina O, Soubrier F, Southgate L, Suntharalingam J, Toshner M, Trembath R, Vonk Noordegraaf A, Wilkins MR, Wort SJ, Wharton J, NIHR BioResource–Rare Diseases Consortium; UK National Cohort Study of Idiopathic and Heritable PAH, Gräf S, Morrell NW. Circulation Volume 136 (2017) p.2022-2033 DOI: 10.1161/circulationaha.117.028351
*
A screen for combination therapies in BRAF/NRAS wild type melanoma identifies nilotinib plus MEK inhibitor as a synergistic combination
Ranzani M, Kemper K, Michaut M, Krijgsman O, Aben N, Iyer V, Wong K, Roumeliotis TI, Del Castillo Velasco-Herrera M, Nsengimana J, Turner G, Thompson N, Shahrabi A, Sjoberg M, Rashid M, Speak AO, Grinkevich V, Behan F, Tamborero D, Iorio F, van Dongen S, Bignell GR, Alsinet C, Chen S, Supper E, Dutton-Regester K, Pritchard A, Wong C, Enright A, Newton-Bishop J, McDermott U, Hayward NK, Choudhary JS, Yusa K, Wessels L, Garnett MJ, Peeper D, Adams DJ. Preprint DOI: 10.1101/195354
Two independent modes of chromatin organization revealed by cohesin removal.
Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, H Haering C, Mirny L, Spitz F. Nature Volume 551 (2017) p.51-56 DOI: 10.1038/nature24281
Compliance with minimum information guidelines in public metabolomics repositories.
Spicer RA, Salek R, Steinbeck C. Scientific data Volume 4 (2017) p.170137 DOI: 10.1038/sdata.2017.137
*
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
*
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
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.
Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR. Journal of proteome research Volume 16 (2017) p.4288-4298 DOI: 10.1021/acs.jproteome.7b00370
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
The future of metabolomics in ELIXIR.
van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Le Corguillé G, Moreno P, Moschonas NK, Neumann S, O'Donovan C, Reczko M, Rocca-Serra P, Rosato A, Salek RM, Sansone SA, Satagopam V, Schober D, Shimmo R, Spicer RA, Spjuth O, Thévenot EA, Viant MR, Weber RJM, Willighagen EL, Zanetti G, Steinbeck C. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.12342.2
Societal challenges of precision medicine: Bringing order to chaos.
Salgado R, Moore H, Martens JWM, Lively T, Malik S, McDermott U, Michiels S, Moscow JA, Tejpar S, McKee T, Lacombe D, IBCD-Faculty. European journal of cancer (Oxford, England : 1990) Volume 84 (2017) p.325-334 DOI: 10.1016/j.ejca.2017.07.028
*
Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Fonseca NA, He Y, Kahles A, Lehmann K, Liu F, Shiraishi Y, Soulette CM, Urban L, Demircioğlu D, Greger L, Li S, Liu D, Perry MD, Xiang L, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Sekhar Pedamallu C, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Francis Ouellette B, 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
PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models.
Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J. Structure (London, England : 1993) Volume 25 (2017) p.1317-1318 DOI: 10.1016/j.str.2017.08.001
More on the Best Evolutionary Rate for Phylogenetic Analysis.
Klopfstein S, Massingham T, Goldman N. Systematic biology Volume 66 (2017) p.769-785 DOI: 10.1093/sysbio/syx051
*
Reports from CAGI: The Critical Assessment of Genome Interpretation.
Hoskins RA, Repo S, Barsky D, Andreoletti G, Moult J, Brenner SE. Human mutation Volume 38 (2017) p.1039-1041 DOI: 10.1002/humu.23290
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
Gearing up to handle the mosaic nature of life in the quest for orthologs.
Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT, Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S. Bioinformatics (Oxford, England) (2017) DOI: 10.1093/bioinformatics/btx542
*
Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
Seaton D, Graf A, Baerenfaller K, Stitt M, Millar A, Gruissem W. Preprint DOI: 10.1101/182071
A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity.
Kuepfer L, Clayton O, Thiel C, Cordes H, Nudischer R, Blank LM, Baier V, Heymans S, Caiment F, Roth A, Fluri DA, Kelm JM, Castell J, Selevsek N, Schlapbach R, Keun H, Hynes J, Sarkans U, Gmuender H, Herwig R, Niederer S, Schuchhardt J, Segall M, Kleinjans J. Archives of toxicology Volume 92 (2018) p.553-555 DOI: 10.1007/s00204-017-2041-7
In silico prediction of novel therapeutic targets using gene-disease association data.
Ferrero E, Dunham I, Sanseau P. Journal of translational medicine Volume 15 (2017) p.182 DOI: 10.1186/s12967-017-1285-6
The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training.
Morgan SL, Palagi PM, Fernandes PL, Koperlainen E, Dimec J, Marek D, Larcombe L, Rustici G, Attwood TK, Via A. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.12332.1
The application of project-based learning in bioinformatics training.
Emery LR, Morgan SL. PLoS computational biology Volume 13 (2017) p.e1005620 DOI: 10.1371/journal.pcbi.1005620
EMBL-EBI, programmatically: take a REST from manual searches
Burke M, Armstrong D, Carvalho-Silva D, Castro L, Cowley A, Finn R, Foix A, Katuri J, Laird M, Lee J, Levchenko M, Lopez R, Nightingale A, Nowotka M, Perry E, Pichler K, Pundir S, Morgan S, Saunders G, Garcia P, Squizzato S. DOI: 10.6019/tol.ebiprogrammatically-w.2017.00001.1
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data.
Zhang C, Bijlard J, Staiger C, Scollen S, van Enckevort D, Hoogstrate Y, Senf A, Hiltemann S, Repo S, Pipping W, Bierkens M, Payralbe S, Stringer B, Heringa J, Stubbs A, Bonino Da Silva Santos LO, Belien J, Weistra W, Azevedo R, van Bochove K, Meijer G, Boiten JW, Rambla J, Fijneman R, Spalding JD, Abeln S. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.12168.1
A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology.
Penas DR, Henriques D, González P, Doallo R, Saez-Rodriguez J, Banga JR. PloS one Volume 12 (2017) p.e0182186 DOI: 10.1371/journal.pone.0182186
*
A pan cancer analysis of promoter activity highlights the regulatory role of alternative transcription start sites and their association with noncoding mutations
Demircioglu D, Kindermans M, Nandi T, Cukuroglu E, Calabrese C, Fonseca NA, Kahles A, Lehmann K, Stegle O, PCAWG-3, PCAWG-Network, Brazma A, Brooks A, Raetsch G, Tan P, Goeke J. Preprint DOI: 10.1101/176487
mRNA 3' uridylation and poly(A) tail length sculpt the mammalian maternal transcriptome.
Morgan M, Much C, DiGiacomo M, Azzi C, Ivanova I, Vitsios DM, Pistolic J, Collier P, Moreira PN, Benes V, Enright AJ, O'Carroll D. Nature Volume 548 (2017) p.347-351 DOI: 10.1038/nature23318
Navigating freely-available software tools for metabolomics analysis.
Spicer R, Salek RM, Moreno P, Cañueto D, Steinbeck C. Metabolomics Volume 13 (2017) p.106 DOI: 10.1007/s11306-017-1242-7
*
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Nature biotechnology Volume 35 (2017) p.725-731 DOI: 10.1038/nbt.3893
The metagenomic data life-cycle: standards and best practices.
Ten Hoopen P, Finn RD, Bongo LA, Corre E, Fosso B, Meyer F, Mitchell A, Pelletier E, Pesole G, Santamaria M, Willassen NP, Cochrane G. GigaScience Volume 6 (2017) p.1-11 DOI: 10.1093/gigascience/gix047
Automated assembly of species metabolomes through data submission into a public repository.
Salek RM, Conesa P, Cochrane K, Haug K, Williams M, Kale N, Moreno P, Jayaseelan KV, Macias JR, Nainala VC, Hall RD, Reed LK, Viant MR, O'Donovan C, Steinbeck C. GigaScience Volume 6 (2017) p.1-4 DOI: 10.1093/gigascience/gix062
BioContainers: an open-source and community-driven framework for software standardization.
da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y. Bioinformatics (Oxford, England) Volume 33 (2017) p.2580-2582 DOI: 10.1093/bioinformatics/btx192
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
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
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Genoscope Technical Team, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Tara Oceans Consortium Coordinators, Pesant S, Karsenti E, Wincker P. Scientific data Volume 4 (2017) p.170093 DOI: 10.1038/sdata.2017.93
mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.
Larralde M, Lawson TN, Weber RJM, Moreno P, Haug K, Rocca-Serra P, Viant MR, Steinbeck C, Salek RM. Bioinformatics (Oxford, England) Volume 33 (2017) p.2598-2600 DOI: 10.1093/bioinformatics/btx169
Impact of Alternative Splicing on the Human Proteome.
Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. Cell reports Volume 20 (2017) p.1229-1241 DOI: 10.1016/j.celrep.2017.07.025
*
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
Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS. Cell reports Volume 20 (2017) p.2201-2214 DOI: 10.1016/j.celrep.2017.08.010
*
Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution
Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC, Odom DT, Flicek P. Preprint DOI: 10.1101/059873
*
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
*
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 CJ, PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/099861
*
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, Yanina Bertucci P, Brunet T, Collier P, Benes V, Marioni JC, Arendt D. Preprint DOI: 10.1101/167742
*
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-Gagnere G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider M. Preprint DOI: 10.1101/167619
Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity.
Dönertaş HM, İzgi H, Kamacıoğlu A, He Z, Khaitovich P, Somel M. Scientific reports Volume 7 (2017) p.5894 DOI: 10.1038/s41598-017-05927-4
*
Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours
Haghverdi L, Lun ATL, Morgan MD, Marioni JC. Preprint DOI: 10.1101/165118
*
Online resources for PCAWG data exploration, visualization, and discovery
Goldman M, Zhang J, Fonseca NA, Xiang Q, Craft B, Pineiro E, O'Connor BD, Bazant W, Barrera E, Munoz A, Petryszak R, Fuellgrabe A, Al-Shahrour F, Keays M, Haussler D, Weinstein J, Huber W, Valencia A, Papatheodorou I, Zhu J, Ferreti V, Vazquez M, PCAWG-12 working group, PCAWG network. Preprint DOI: 10.1101/163907
*
Correction: Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.
Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C, BEEHIVE collaboration. PLoS biology Volume 15 (2017) p.e1002608 DOI: 10.1371/journal.pbio.1002608
Platelet function is modified by common sequence variation in megakaryocyte super enhancers.
Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts AS, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide ME, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M, Ouwehand WH, Astle WJ, Downes K, Kostadima M, Frontini M. Nature communications Volume 8 (2017) p.16058 DOI: 10.1038/ncomms16058
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
*
The evolutionary history of 2,658 cancers
Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Mitchell TJ, Rubanova Y, Anur P, Rosebrock D, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vazquez-Garcia I, Haase K, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp S, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, PCAWG Evolution and Heterogeneity Working Group, PCAWG network. Preprint DOI: 10.1101/161562
*
Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.
Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat RR, Li X, Pal LR, Kundu K, Yin Y, Moult J, Jiang Y, Pejaver V, Pagel KA, Li B, Mooney SD, Radivojac P, Shah S, Carraro M, Gasparini A, Leonardi E, Giollo M, Ferrari C, Tosatto SCE, Bachar E, Azaria JR, Ofran Y, Unger R, Niroula A, Vihinen M, Chang B, Wang MH, Franke A, Petersen BS, Pirooznia M, Zandi P, McCombie R, Potash JB, Altman RB, Klein TE, Hoskins RA, Repo S, Brenner SE, Morgan AA. Human mutation Volume 38 (2017) p.1182-1192 DOI: 10.1002/humu.23280
Building bridges between cellular and molecular structural biology.
Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M, Kleywegt GJ. eLife Volume 6 (2017) DOI: 10.7554/elife.25835
Linking functions: an additional role for an intrinsically disordered linker domain in the transcriptional coactivator CBP.
Contreras-Martos S, Piai A, Kosol S, Varadi M, Bekesi A, Lebrun P, Volkov AN, Gevaert K, Pierattelli R, Felli IC, Tompa P. Scientific reports Volume 7 (2017) p.4676 DOI: 10.1038/s41598-017-04611-x
Extracellular vesicles are independent metabolic units with asparaginase activity.
Iraci N, Gaude E, Leonardi T, Costa ASH, Cossetti C, Peruzzotti-Jametti L, Bernstock JD, Saini HK, Gelati M, Vescovi AL, Bastos C, Faria N, Occhipinti LG, Enright AJ, Frezza C, Pluchino S. Nature chemical biology Volume 13 (2017) p.951-955 DOI: 10.1038/nchembio.2422
The EBI search engine: EBI search as a service-making biological data accessible for all.
Park YM, Squizzato S, Buso N, Gur T, Lopez R. Nucleic acids research Volume 45 (2017) p.W545-W549 DOI: 10.1093/nar/gkx359
Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks.
Raisaro JL, Tramèr F, Ji Z, Bu D, Zhao Y, Carey K, Lloyd D, Sofia H, Baker D, Flicek P, Shringarpure S, Bustamante C, Wang S, Jiang X, Ohno-Machado L, Tang H, Wang X, Hubaux JP. Journal of the American Medical Informatics Association : JAMIA Volume 24 (2017) p.799-805 DOI: 10.1093/jamia/ocw167
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
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
Alignment of 1000 Genomes Project reads to reference assembly GRCh38.
Zheng-Bradley X, Streeter I, Fairley S, Richardson D, Clarke L, Flicek P, 1000 Genomes Project Consortium. GigaScience Volume 6 (2017) p.1-8 DOI: 10.1093/gigascience/gix038
ProtVista: visualization of protein sequence annotations.
Watkins X, Garcia LJ, Pundir S, Martin MJ, UniProt Consortium. Bioinformatics (Oxford, England) Volume 33 (2017) p.2040-2041 DOI: 10.1093/bioinformatics/btx120
Programmatic access to bioinformatics tools from EMBL-EBI update: 2017.
Chojnacki S, Cowley A, Lee J, Foix A, Lopez R. Nucleic acids research Volume 45 (2017) p.W550-W553 DOI: 10.1093/nar/gkx273
*
Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity.
Hendricks AE, Bochukova EG, Marenne G, Keogh JM, Atanassova N, Bounds R, Wheeler E, Mistry V, Henning E, Körner A, Muddyman D, McCarthy S, Hinney A, Hebebrand J, Scott RA, Langenberg C, Wareham NJ, Surendran P, Howson JM, Butterworth AS, Danesh J, Nordestgaard BG, Nielsen SF, Afzal S, Papadia S, Ashford S, Garg S, Millhauser GL, Palomino RI, Kwasniewska A, Tachmazidou I, O'Rahilly S, Zeggini E, Barroso I, Farooqi IS, Understanding Society Scientific Group, EPIC-CVD Consortium, UK10K Consortium. Scientific reports Volume 7 (2017) p.4394 DOI: 10.1038/s41598-017-03054-8
*
Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer
Fonseca NA, He Y, Greger L, Brazma A, Zhang Z, PCAWG-3. Preprint DOI: 10.1101/148684
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.
McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H. PLoS biology Volume 15 (2017) p.e2001414 DOI: 10.1371/journal.pbio.2001414
Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.
Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P, Karp N, Santos L, Fiegel T, Ring N, Westerberg H, Greenaway S, Sneddon D, Morgan H, Codner GF, Stewart ME, Brown J, Horner N, International Mouse Phenotyping Consortium, Haendel M, Washington N, Mungall CJ, Reynolds CL, Gallegos J, Gailus-Durner V, Sorg T, Pavlovic G, Bower LR, Moore M, Morse I, Gao X, Tocchini-Valentini GP, Obata Y, Cho SY, Seong JK, Seavitt J, Beaudet AL, Dickinson ME, Herault Y, Wurst W, de Angelis MH, Lloyd KCK, Flenniken AM, Nutter LMJ, Newbigging S, McKerlie C, Justice MJ, Murray SA, Svenson KL, Braun RE, White JK, Bradley A, Flicek P, Wells S, Skarnes WC, Adams DJ, Parkinson H, Mallon AM, Brown SDM, Smedley D. Nature genetics Volume 49 (2017) p.1231-1238 DOI: 10.1038/ng.3901
Prevalence of sexual dimorphism in mammalian phenotypic traits.
Karp NA, Mason J, Beaudet AL, Benjamini Y, Bower L, Braun RE, Brown SDM, Chesler EJ, Dickinson ME, Flenniken AM, Fuchs H, Angelis MH, Gao X, Guo S, Greenaway S, Heller R, Herault Y, Justice MJ, Kurbatova N, Lelliott CJ, Lloyd KCK, Mallon AM, Mank JE, Masuya H, McKerlie C, Meehan TF, Mott RF, Murray SA, Parkinson H, Ramirez-Solis R, Santos L, Seavitt JR, Smedley D, Sorg T, Speak AO, Steel KP, Svenson KL, International Mouse Phenotyping Consortium, Wakana S, West D, Wells S, Westerberg H, Yaacoby S, White JK. Nature communications Volume 8 (2017) p.15475 DOI: 10.1038/ncomms15475
Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1.
Suri M, Evers JMG, Laskowski RA, O'Brien S, Baker K, Clayton-Smith J, Dabir T, Josifova D, Joss S, Kerr B, Kraus A, McEntagart M, Morton J, Smith A, Splitt M, Thornton JM, DDD Study, Wright CF. Molecular genetics & genomic medicine Volume 5 (2017) p.495-507 DOI: 10.1002/mgg3.304
*
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
Menschaert G, Wang X, Jones AR, Ghali F, Fenyo D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaino J. Preprint DOI: 10.1101/152579
*
Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.
Cai B, Li B, Kiga N, Thusberg J, Bergquist T, Chen YC, Niknafs N, Carter H, Tokheim C, Beleva-Guthrie V, Douville C, Bhattacharya R, Yeo HTG, Fan J, Sengupta S, Kim D, Cline M, Turner T, Diekhans M, Zaucha J, Pal LR, Cao C, Yu CH, Yin Y, Carraro M, Giollo M, Ferrari C, Leonardi E, Tosatto SCE, Bobe J, Ball M, Hoskins RA, Repo S, Church G, Brenner SE, Moult J, Gough J, Stanke M, Karchin R, Mooney SD. Human mutation Volume 38 (2017) p.1266-1276 DOI: 10.1002/humu.23265
The Image Data Resource: A Bioimage Data Integration and Publication Platform.
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR. Nature methods Volume 14 (2017) p.775-781 DOI: 10.1038/nmeth.4326
Drug repurposing for aging research using model organisms.
Ziehm M, Kaur S, Ivanov DK, Ballester PJ, Marcus D, Partridge L, Thornton JM. Aging cell Volume 16 (2017) p.1006-1015 DOI: 10.1111/acel.12626
*
Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs.
Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Nature Volume 546 (2017) p.686 DOI: 10.1038/nature23012
*
Inferring synteny between genome assemblies: a systematic evaluation
Liu D, Hunt M, Tsai IJ. Preprint DOI: 10.1101/149989
A community proposal to integrate proteomics activities in ELIXIR.
Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.11751.1
*
Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers
Meier B, Volkova N, Hong Y, Schofield P, Campbell PJ, Gerstung M, Gartner A. Preprint DOI: 10.1101/149153
Four simple recommendations to encourage best practices in research software.
Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.11407.1
Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery.
Nowotka MM, Gaulton A, Mendez D, Bento AP, Hersey A, Leach A. Expert opinion on drug discovery Volume 12 (2017) p.757-767 DOI: 10.1080/17460441.2017.1339032
*
Integrating long-range connectivity information into de Bruijn graphs
Turner I, Garimella KV, Iqbal Z, McVean G. Preprint DOI: 10.1101/147777
Literature evidence in open targets - a target validation platform.
Kafkas Ş, Dunham I, McEntyre J. Journal of biomedical semantics Volume 8 (2017) p.20 DOI: 10.1186/s13326-017-0131-3
Dead simple OWL design patterns.
Osumi-Sutherland D, Courtot M, Balhoff JP, Mungall C. Journal of biomedical semantics Volume 8 (2017) p.18 DOI: 10.1186/s13326-017-0126-0
*
Accurate And Fast Feature Selection Workflow For High-Dimensional Omics Data
Perez-Riverol Y, Kun M, Vizcaino JA, Hitz M, Audain E. Preprint DOI: 10.1101/144162
Structural Variation Shapes the Landscape of Recombination in Mouse.
Morgan AP, Gatti DM, Najarian ML, Keane TM, Galante RJ, Pack AI, Mott R, Churchill GA, de Villena FP. Genetics Volume 206 (2017) p.603-619 DOI: 10.1534/genetics.116.197988
Benchmarking substrate-based kinase activity inference using phosphoproteomic data.
Hernandez-Armenta C, Ochoa D, Gonçalves E, Saez-Rodriguez J, Beltrao P. Bioinformatics (Oxford, England) Volume 33 (2017) p.1845-1851 DOI: 10.1093/bioinformatics/btx082
*
PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance.
Nadon C, Van Walle I, Gerner-Smidt P, Campos J, Chinen I, Concepcion-Acevedo J, Gilpin B, Smith AM, Man Kam K, Perez E, Trees E, Kubota K, Takkinen J, Nielsen EM, Carleton H, FWD-NEXT Expert Panel. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin Volume 22 (2017) DOI: 10.2807/1560-7917.es.2017.22.23.30544
MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry.
Jain M, Tyson JR, Loose M, Ip CLC, Eccles DA, O'Grady J, Malla S, Leggett RM, Wallerman O, Jansen HJ, Zalunin V, Birney E, Brown BL, Snutch TP, Olsen HE, MinION Analysis and Reference Consortium. F1000Research Volume 6 (2017) p.760 DOI: 10.12688/f1000research.11354.1
*
SpatialDE - Identification Of Spatially Variable Genes
Svensson V, Teichmann SA, Stegle O. Preprint DOI: 10.1101/143321
Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.
Tachmazidou I, Süveges D, Min JL, Ritchie GRS, Steinberg J, Walter K, Iotchkova V, Schwartzentruber J, Huang J, Memari Y, McCarthy S, Crawford AA, Bombieri C, Cocca M, Farmaki AE, Gaunt TR, Jousilahti P, Kooijman MN, Lehne B, Malerba G, Männistö S, Matchan A, Medina-Gomez C, Metrustry SJ, Nag A, Ntalla I, Paternoster L, Rayner NW, Sala C, Scott WR, Shihab HA, Southam L, St Pourcain B, Traglia M, Trajanoska K, Zaza G, Zhang W, Artigas MS, Bansal N, Benn M, Chen Z, Danecek P, Lin WY, Locke A, Luan J, Manning AK, Mulas A, Sidore C, Tybjaerg-Hansen A, Varbo A, Zoledziewska M, Finan C, Hatzikotoulas K, Hendricks AE, Kemp JP, Moayyeri A, Panoutsopoulou K, Szpak M, Wilson SG, Boehnke M, Cucca F, Di Angelantonio E, Langenberg C, Lindgren C, McCarthy MI, Morris AP, Nordestgaard BG, Scott RA, Tobin MD, Wareham NJ, SpiroMeta Consortium, GoT2D Consortium, Burton P, Chambers JC, Smith GD, Dedoussis G, Felix JF, Franco OH, Gambaro G, Gasparini P, Hammond CJ, Hofman A, Jaddoe VWV, Kleber M, Kooner JS, Perola M, Relton C, Ring SM, Rivadeneira F, Salomaa V, Spector TD, Stegle O, Toniolo D, Uitterlinden AG, arcOGEN Consortium, Understanding Society Scientific Group, UK10K Consortium, Barroso I, Greenwood CMT, Perry JRB, Walker BR, Butterworth AS, Xue Y, Durbin R, Small KS, Soranzo N, Timpson NJ, Zeggini E. American journal of human genetics Volume 100 (2017) p.865-884 DOI: 10.1016/j.ajhg.2017.04.014
Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.
Joseph AP, Lagerstedt I, Patwardhan A, Topf M, Winn M. Journal of structural biology Volume 199 (2017) p.12-26 DOI: 10.1016/j.jsb.2017.05.007
*
Phenotype prediction in an ​Escherichia coli​ strain panel
Galardini​ M, Koumoutsi​​ A, Herrera-Dominguez​​ L, Cordero Varela​ J, Telzerow​ A, Wagih​ O, Wartel​ M, Clermont​ O, Denamur​ E, Typas​ A, Beltrao​ P. Preprint DOI: 10.1101/141879
MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni.
Protasio AV, van Dongen S, Collins J, Quintais L, Ribeiro DM, Sessler F, Hunt M, Rinaldi G, Collins JJ, Enright AJ, Berriman M. PLoS neglected tropical diseases Volume 11 (2017) p.e0005559 DOI: 10.1371/journal.pntd.0005559
A MILI-independent piRNA biogenesis pathway empowers partial germline reprogramming.
Vasiliauskaitė L, Vitsios D, Berrens RV, Carrieri C, Reik W, Enright AJ, O'Carroll D. Nature structural & molecular biology Volume 24 (2017) p.604-606 DOI: 10.1038/nsmb.3413
*
Joint Profiling Of Chromatin Accessibility, DNA Methylation And Transcription In Single Cells
Clark SJ, Argelaguet R, Kapourani C, Stubbs TM, Lee HJ, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W. Preprint DOI: 10.1101/138685
The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.
Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR. Molecular & cellular proteomics : MCP Volume 16 (2017) p.1275-1285 DOI: 10.1074/mcp.m117.068429
*
Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.
Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, Gough J, Katsonis P, Leonardi E, Lichtarge O, Menin C, Martelli PL, Niroula A, Pal LR, Repo S, Scaini MC, Vihinen M, Wei Q, Xu Q, Yang Y, Yin Y, Zaucha J, Zhao H, Zhou Y, Brenner SE, Moult J, Tosatto SCE. Human mutation Volume 38 (2017) p.1042-1050 DOI: 10.1002/humu.23235
Erratum to: DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.
Angermueller C, Lee HJ, Reik W, Stegle O. Genome biology Volume 18 (2017) p.90 DOI: 10.1186/s13059-017-1233-z
Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution.
Davis MP, Carrieri C, Saini HK, van Dongen S, Leonardi T, Bussotti G, Monahan JM, Auchynnikava T, Bitetti A, Rappsilber J, Allshire RC, Shkumatava A, O'Carroll D, Enright AJ. EMBO reports Volume 18 (2017) p.1231-1247 DOI: 10.15252/embr.201744059
Common genetic variation drives molecular heterogeneity in human iPSCs.
Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Nature Volume 546 (2017) p.370-375 DOI: 10.1038/nature22403
*
The Human Cell Atlas
Regev A, Teichmann S, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Gottgens B, Hacohen N, Haniffa M, Hemberg M, Kim SK, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundeberg J, Majumder P, Marioni J, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Philipakis A, Ponting CP, Quake SR, Reik W, Rozenblatt-Rosen O, Sanes JR, Satija R, Shumacher T, Shalek AK, Shapiro E, Sharma P, Shin J, Stegle O, Stratton M, Stubbington MJT, van Oudenaarden A, Wagner A, Watt FM, Weissman JS, Wold B, Xavier RJ, Yosef N, Human Cell Atlas Meeting Participants. Preprint DOI: 10.1101/121202
Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.
Cabezas-Wallscheid N, Buettner F, Sommerkamp P, Klimmeck D, Ladel L, Thalheimer FB, Pastor-Flores D, Roma LP, Renders S, Zeisberger P, Przybylla A, Schönberger K, Scognamiglio R, Altamura S, Florian CM, Fawaz M, Vonficht D, Tesio M, Collier P, Pavlinic D, Geiger H, Schroeder T, Benes V, Dick TP, Rieger MA, Stegle O, Trumpp A. Cell Volume 169 (2017) p.807-823.e19 DOI: 10.1016/j.cell.2017.04.018
Discovering and linking public omics data sets using the Omics Discovery Index.
Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H. Nature biotechnology Volume 35 (2017) p.406-409 DOI: 10.1038/nbt.3790
Anna Tramontano 1957-2017.
Thornton JM, Valencia A, Schwede T. Nature structural & molecular biology Volume 24 (2017) p.431-432 DOI: 10.1038/nsmb.3410
An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.
Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu FH, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser DM, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Palma FD, Phillips AL, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD. Genome research Volume 27 (2017) p.885-896 DOI: 10.1101/gr.217117.116
*
Applications of the 1000 Genomes Project resources.
Zheng-Bradley X, Flicek P. Briefings in functional genomics Volume 16 (2017) p.163-170 DOI: 10.1093/bfgp/elw027
*
Universal patterns of selection in cancer and somatic tissues
Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K, Van Loo P, Davies H, Stratton MR, Campbell PJ. Preprint DOI: 10.1101/132324
Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
Beier S, Himmelbach A, Colmsee C, Zhang XQ, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Sampath D, Heavens D, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Houben A, Doležel J, Ayling S, Lonardi S, Langridge P, Muehlbauer GJ, Kersey P, Clark MD, Caccamo M, Schulman AH, Platzer M, Close TJ, Hansson M, Zhang G, Braumann I, Li C, Waugh R, Scholz U, Stein N, Mascher M. Scientific data Volume 4 (2017) p.170044 DOI: 10.1038/sdata.2017.44
Mechanism-based biomarker discovery.
Antoranz A, Sakellaropoulos T, Saez-Rodriguez J, Alexopoulos LG. Drug discovery today Volume 22 (2017) p.1209-1215 DOI: 10.1016/j.drudis.2017.04.013
UniEuk: Time to Speak a Common Language in Protistology!
Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C. The Journal of eukaryotic microbiology Volume 64 (2017) p.407-411 DOI: 10.1111/jeu.12414
*
Transcription factor activities enhance markers of drug response in cancer
Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Falcone F, Bignell G, McDade SS, Garnett MJ, Saez-Rodriguez J. Preprint DOI: 10.1101/129478
Trends in the Electron Microscopy Data Bank (EMDB).
Patwardhan A. Acta crystallographica. Section D, Structural biology Volume 73 (2017) p.503-508 DOI: 10.1107/s2059798317004181
Joint genetic analysis using variant sets reveals polygenic gene-context interactions.
Casale FP, Horta D, Rakitsch B, Stegle O. PLoS genetics Volume 13 (2017) p.e1006693 DOI: 10.1371/journal.pgen.1006693
DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.
Angermueller C, Lee HJ, Reik W, Stegle O, Stegle O. Genome biology Volume 18 (2017) p.67 DOI: 10.1186/s13059-017-1189-z
Multi-tissue DNA methylation age predictor in mouse.
Stubbs TM, Bonder MJ, Stark AK, Krueger F, BI Ageing Clock Team, von Meyenn F, Stegle O, Reik W. Genome biology Volume 18 (2017) p.68 DOI: 10.1186/s13059-017-1203-5
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM. Genome research Volume 27 (2017) p.849-864 DOI: 10.1101/gr.213611.116
*
Sub-minute phosphoregulation of cell-cycle systems during Plasmodium gamete formation revealed by a high-resolution time course
Invergo BM, Brochet M, Yu L, Choudhary J, Beltrao P, Billker O. Preprint DOI: 10.1101/126276
*
The Fes tyrosine kinase guides CD19 receptor fate in B-cells by shaping regulatory Src phosphorylation networks
Helbig A, Kofler M, Petsalaki E, Gish G, Lorenzen K, Tucholska M, Zhang C, Roth FP, Colwill K, Pawson T. Preprint DOI: 10.1101/125088
Short template switch events explain mutation clusters in the human genome.
Löytynoja A, Goldman N. Genome research Volume 27 (2017) p.1039-1049 DOI: 10.1101/gr.214973.116
*
Literature Evidence in Open Targets - a target validation platform
Kafkas Ş, Dunham I, McEntyre J. Preprint DOI: 10.1101/124719
Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models.
Eduati F, Doldàn-Martelli V, Klinger B, Cokelaer T, Sieber A, Kogera F, Dorel M, Garnett MJ, Blüthgen N, Saez-Rodriguez J. Cancer research Volume 77 (2017) p.3364-3375 DOI: 10.1158/0008-5472.can-17-0078
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.
McCarthy DJ, Campbell KR, Lun AT, Wills QF. Bioinformatics (Oxford, England) Volume 33 (2017) p.1179-1186 DOI: 10.1093/bioinformatics/btw777
A chromosome conformation capture ordered sequence of the barley genome.
Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang XQ, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N. Nature Volume 544 (2017) p.427-433 DOI: 10.1038/nature22043
Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold.
Pearson WR, Li W, Lopez R. Nucleic acids research Volume 45 (2017) p.e46 DOI: 10.1093/nar/gkw1207
*
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
3' Uridylation controls mature microRNA turnover during CD4 T-cell activation.
Gutiérrez-Vázquez C, Enright AJ, Rodríguez-Galán A, Pérez-García A, Collier P, Jones MR, Benes V, Mizgerd JP, Mittelbrunn M, Ramiro AR, Sánchez-Madrid F. RNA (New York, N.Y.) Volume 23 (2017) p.882-891 DOI: 10.1261/rna.060095.116
Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity.
Thomas DC, Clare S, Sowerby JM, Pardo M, Juss JK, Goulding DA, van der Weyden L, Storisteanu D, Prakash A, Espéli M, Flint S, Lee JC, Hoenderdos K, Kane L, Harcourt K, Mukhopadhyay S, Umrania Y, Antrobus R, Nathan JA, Adams DJ, Bateman A, Choudhary JS, Lyons PA, Condliffe AM, Chilvers ER, Dougan G, Smith KG. The Journal of experimental medicine Volume 214 (2017) p.1111-1128 DOI: 10.1084/jem.20161382
*
Dissecting the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich
Iorio F, Garcia-Alonso L, Brammeld J, Martincorena I, Wille DR, McDermott U, Saez-Rodriguez J. Preprint DOI: 10.1101/077701
Microbiology Managers: Managerial Training in the RItrain Project.
Paterson RRM, Lima N, Brooksbank C, Guarini E, Pasterk M, Lavitrano M, RItrain project consortium. Trends in microbiology Volume 25 (2017) p.425-428 DOI: 10.1016/j.tim.2017.03.002
Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma.
Arseneault M, Monlong J, Vasudev NS, Laskar RS, Safisamghabadi M, Harnden P, Egevad L, Nourbehesht N, Panichnantakul P, Holcatova I, Brisuda A, Janout V, Kollarova H, Foretova L, Navratilova M, Mates D, Jinga V, Zaridze D, Mukeria A, Jandaghi P, Brennan P, Brazma A, Tost J, Scelo G, Banks RE, Lathrop M, Bourque G, Riazalhosseini Y. Scientific reports Volume 7 (2017) p.44876 DOI: 10.1038/srep44876
Orchestrating differential data access for translational research: a pilot implementation.
Brandizi M, Melnichuk O, Bild R, Kohlmayer F, Rodriguez-Castro B, Spengler H, Kuhn KA, Kuchinke W, Ohmann C, Mustonen T, Linden M, Nyrönen T, Lappalainen I, Brazma A, Sarkans U. BMC medical informatics and decision making Volume 17 (2017) p.30 DOI: 10.1186/s12911-017-0424-6
Somatic mutations reveal asymmetric cellular dynamics in the early human embryo.
Ju YS, Martincorena I, Gerstung M, Petljak M, Alexandrov LB, Rahbari R, Wedge DC, Davies HR, Ramakrishna M, Fullam A, Martin S, Alder C, Patel N, Gamble S, O'Meara S, Giri DD, Sauer T, Pinder SE, Purdie CA, Borg Å, Stunnenberg H, van de Vijver M, Tan BK, Caldas C, Tutt A, Ueno NT, van 't Veer LJ, Martens JW, Sotiriou C, Knappskog S, Span PN, Lakhani SR, Eyfjörd JE, Børresen-Dale AL, Richardson A, Thompson AM, Viari A, Hurles ME, Nik-Zainal S, Campbell PJ, Stratton MR. Nature Volume 543 (2017) p.714-718 DOI: 10.1038/nature21703
Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.
Huang Y, Kim JK, Do DV, Lee C, Penfold CA, Zylicz JJ, Marioni JC, Hackett JA, Surani MA. eLife Volume 6 (2017) DOI: 10.7554/elife.22345
*
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
McMurry J, Juty N, Blomberg N, Burdett A, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows D, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hermjakob H, Heriche J, Ison J, Jimenez R, Jupp S, Kunze J, Laibe C, Le Novere N, Malone J, Martin M, McEntyre J, Morris C, Muilu J, Mueller W, Rocca-Serra P, Sansone S, Sariyar M, Snoep J, Stanford NJ, Soiland-Reyes S, Swainston N, Washington N, Williams A, Wimalaratne S, Winfree L, Wolstencroft K, Goble C, Mungall C, Haendel M, Parkinson H. Preprint DOI: 10.1101/117812
*
Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression
Kar G, Kim J, Kolodziejczyk AA, Natarajan K, Torlai Triglia E, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA. Preprint DOI: 10.1101/117267
Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions.
Zaman S, Sarntivijai S, Abernethy DR. Gene regulation and systems biology Volume 11 (2017) p.1177625017696075 DOI: 10.1177/1177625017696075
Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring.
Imamura H, Wagih O, Niinae T, Sugiyama N, Beltrao P, Ishihama Y. Journal of proteome research Volume 16 (2017) p.1825-1830 DOI: 10.1021/acs.jproteome.7b00087
HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
Davies H, Glodzik D, Morganella S, Yates LR, Staaf J, Zou X, Ramakrishna M, Martin S, Boyault S, Sieuwerts AM, Simpson PT, King TA, Raine K, Eyfjord JE, Kong G, Borg Å, Birney E, Stunnenberg HG, van de Vijver MJ, Børresen-Dale AL, Martens JW, Span PN, Lakhani SR, Vincent-Salomon A, Sotiriou C, Tutt A, Thompson AM, Van Laere S, Richardson AL, Viari A, Campbell PJ, Stratton MR, Nik-Zainal S. Nature medicine Volume 23 (2017) p.517-525 DOI: 10.1038/nm.4292
Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.
Cheung WA, Shao X, Morin A, Siroux V, Kwan T, Ge B, Aïssi D, Chen L, Vasquez L, Allum F, Guénard F, Bouzigon E, Simon MM, Boulier E, Redensek A, Watt S, Datta A, Clarke L, Flicek P, Mead D, Paul DS, Beck S, Bourque G, Lathrop M, Tchernof A, Vohl MC, Demenais F, Pin I, Downes K, Stunnenberg HG, Soranzo N, Pastinen T, Grundberg E. Genome biology Volume 18 (2017) p.50 DOI: 10.1186/s13059-017-1173-7
Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy.
Tong P, Monahan J, Prendergast JG. PLoS genetics Volume 13 (2017) p.e1006673 DOI: 10.1371/journal.pgen.1006673
*
ChromoTrace: Reconstruction of 3D Chromosome Configurations by Super-Resolution Microscopy
Morganella S, Oedegaard O, Alexander S, Ries J, Fitzgerald T, Ellenberg J, Birney E. Preprint DOI: 10.1101/115436
Rapid establishment of the European Bank for induced Pluripotent Stem Cells (EBiSC) - the Hot Start experience.
De Sousa PA, Steeg R, Wachter E, Bruce K, King J, Hoeve M, Khadun S, McConnachie G, Holder J, Kurtz A, Seltmann S, Dewender J, Reimann S, Stacey G, O'Shea O, Chapman C, Healy L, Zimmermann H, Bolton B, Rawat T, Atkin I, Veiga A, Kuebler B, Serano BM, Saric T, Hescheler J, Brüstle O, Peitz M, Thiele C, Geijsen N, Holst B, Clausen C, Lako M, Armstrong L, Gupta SK, Kvist AJ, Hicks R, Jonebring A, Brolén G, Ebneth A, Cabrera-Socorro A, Foerch P, Geraerts M, Stummann TC, Harmon S, George C, Streeter I, Clarke L, Parkinson H, Harrison PW, Faulconbridge A, Cherubin L, Burdett T, Trigueros C, Patel MJ, Lucas C, Hardy B, Predan R, Dokler J, Brajnik M, Keminer O, Pless O, Gribbon P, Claussen C, Ringwald A, Kreisel B, Courtney A, Allsopp TE. Stem cell research Volume 20 (2017) p.105-114 DOI: 10.1016/j.scr.2017.03.002
Direct Keap1-Nrf2 disruption as a potential therapeutic target for Alzheimer's disease.
Kerr F, Sofola-Adesakin O, Ivanov DK, Gatliff J, Gomez Perez-Nievas B, Bertrand HC, Martinez P, Callard R, Snoeren I, Cochemé HM, Adcott J, Khericha M, Castillo-Quan JI, Wells G, Noble W, Thornton J, Partridge L. PLoS genetics Volume 13 (2017) p.e1006593 DOI: 10.1371/journal.pgen.1006593
Data management: A global coalition to sustain core data.
Anderson WP, Global Life Science Data Resources Working Group. Nature Volume 543 (2017) p.179 DOI: 10.1038/543179a
The druggable genome and support for target identification and validation in drug development.
Finan C, Gaulton A, Kruger FA, Lumbers RT, Shah T, Engmann J, Galver L, Kelley R, Karlsson A, Santos R, Overington JP, Hingorani AD, Casas JP. Science translational medicine Volume 9 (2017) DOI: 10.1126/scitranslmed.aag1166
*
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
Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.
Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MS, Fogg LG, Nair AS, Liligeto U, Stubbington MJ, Ly LH, Bagger FO, Zwiessele M, Lawrence ND, Souza-Fonseca-Guimaraes F, Bunn PT, Engwerda CR, Heath WR, Billker O, Stegle O, Haque A, Teichmann SA. Science immunology Volume 2 (2017) DOI: 10.1126/sciimmunol.aal2192
An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge.
Pundir S, Onwubiko J, Zaru R, Rosanoff S, Antunes R, Bingley M, Watkins X, O'Donovan C, Martin MJ. Protein engineering, design & selection : PEDS Volume 30 (2017) p.245-251 DOI: 10.1093/protein/gzx008
*
A global perspective on bioinformatics training needs
Brazas MD, Brooksbank C, Jimenez RC, Blackford S, Palagi PM, De Las Rivas J, Ouellette B, Kumuthini J, Korpelainen E, Lewitter F, van Gelder CWG, Mulder N, Corpas M, Schneider M, Tan T, Clements D, Davies A, Attwood TK. Preprint DOI: 10.1101/098996
*
Towards coordinated international support of core data resources for the life sciences
Anderson W, Apweiler R, Bateman A, Bauer GA, Berman H, Blake JA, Blomberg N, Burley SK, Cochrane G, Di Francesco V, Donohue T, Durinx C, Game A, Green E, Gojobori T, Goodhand P, Hamosh A, Hermjakob H, Kanehisa M, Kiley R, McEntyre J, McKibbin R, Miyano S, Pauly B, Perrimon N, Ragan MA, Richards G, Teo Y, Westerfield M, Westhof E, Lasko PF. Preprint DOI: 10.1101/110825
*
A high-resolution mRNA expression time course of embryonic development in zebrafish
White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Hourlier T, Fuellgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. Preprint DOI: 10.1101/107631
New drug candidates for liposomal delivery identified by computer modeling of liposomes' remote loading and leakage.
Cern A, Marcus D, Tropsha A, Barenholz Y, Goldblum A. Journal of controlled release : official journal of the Controlled Release Society Volume 252 (2017) p.18-27 DOI: 10.1016/j.jconrel.2017.02.015
Structure of the Escherichia coli ProQ RNA-binding protein.
Gonzalez GM, Hardwick SW, Maslen SL, Skehel JM, Holmqvist E, Vogel J, Bateman A, Luisi BF, Broadhurst RW. RNA (New York, N.Y.) Volume 23 (2017) p.696-711 DOI: 10.1261/rna.060343.116
Promoter shape varies across populations and affects promoter evolution and expression noise.
Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE. Nature genetics Volume 49 (2017) p.550-558 DOI: 10.1038/ng.3791
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.
Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK. Structure (London, England : 1993) Volume 25 (2017) p.536-545 DOI: 10.1016/j.str.2017.01.004
Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations.
Brammeld JS, Petljak M, Martincorena I, Williams SP, Alonso LG, Dalmases A, Bellosillo B, Robles-Espinoza CD, Price S, Barthorpe S, Tarpey P, Alifrangis C, Bignell G, Vidal J, Young J, Stebbings L, Beal K, Stratton MR, Saez-Rodriguez J, Garnett M, Montagut C, Iorio F, McDermott U. Genome research Volume 27 (2017) p.613-625 DOI: 10.1101/gr.213546.116
Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.
Koo BM, Kritikos G, Farelli JD, Todor H, Tong K, Kimsey H, Wapinski I, Galardini M, Cabal A, Peters JM, Hachmann AB, Rudner DZ, Allen KN, Typas A, Gross CA. Cell systems Volume 4 (2017) p.291-305.e7 DOI: 10.1016/j.cels.2016.12.013
Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.
Imprialou M, Kahles A, Steffen JG, Osborne EJ, Gan X, Lempe J, Bhomra A, Belfield E, Visscher A, Greenhalgh R, Harberd NP, Goram R, Hein J, Robert-Seilaniantz A, Jones J, Stegle O, Kover P, Tsiantis M, Nordborg M, Rätsch G, Clark RM, Mott R. Genetics Volume 205 (2017) p.1425-1441 DOI: 10.1534/genetics.116.192823
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.
Henriques D, Villaverde AF, Rocha M, Saez-Rodriguez J, Banga JR. PLoS computational biology Volume 13 (2017) p.e1005379 DOI: 10.1371/journal.pcbi.1005379
*
Interactions between genetic variation and cellular environment in skeletal muscle gene expression
Taylor D, Knowles DA, Scott LJ, Ramirez AH, Paolo Casale F, Wolford BN, Guan L, Varshney A, D'Oliveira Albanus R, Parker SCJ, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS. Preprint DOI: 10.1101/105429
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
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
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
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
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
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
*
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
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
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
New insights into the GINS complex explain the controversy between existing structural models.
Carroni M, De March M, Medagli B, Krastanova I, Taylor IA, Amenitsch H, Araki H, Pisani FM, Patwardhan A, Onesti S. Scientific reports Volume 7 (2017) p.40188 DOI: 10.1038/srep40188
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
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
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
Visualising protein structures online
Armstrong A. DOI: 10.6019/tol.pdbe-litemol-w.2017.00001.1
Ensembl tools: webinar
Perry E. DOI: 10.6019/tol.ens-too-w.2017.00001.2
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
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
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
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
QuickGO - Gene ontology annotation
Georghiou G. DOI: 10.6019/tol.quickgo-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
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
EBI Metagenomics: analysing and exploring metagenomic data
Mitchell A. DOI: 10.6019/tol.ebimetagen-w.2017.00001.1
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
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