Publications for 2015

2015

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