Publications for 2015

2015

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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
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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
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An Empirical Bayes Mixture Model for Effect Size Distributions in Genome-Wide Association Studies.
Thompson WK, Wang Y, Schork AJ, Witoelar A, Zuber V, Xu S, Werge T, Holland D, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Andreassen OA, Dale AM. PLoS genetics Volume 11 (2015) p.e1005717 DOI: 10.1371/journal.pgen.1005717
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
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Unravelling druggable signalling networks that control F508del-CFTR proteostasis.
Hegde RN, Parashuraman S, Iorio F, Ciciriello F, Capuani F, Carissimo A, Carrella D, Belcastro V, Subramanian A, Bounti L, Persico M, Carlile G, Galietta L, Thomas DY, Di Bernardo D, Luini A. eLife Volume 4 (2015) DOI: 10.7554/elife.10365
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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
The BioStudies database.
McEntyre J, Sarkans U, Brazma A. Molecular systems biology Volume 11 (2015) p.847 DOI: 10.15252/msb.20156658
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Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough.
Holmes RK, Tuck AC, Zhu C, Dunn-Davies HR, Kudla G, Clauder-Munster S, Granneman S, Steinmetz LM, Guthrie C, Tollervey D. PLoS genetics Volume 11 (2015) p.e1005735 DOI: 10.1371/journal.pgen.1005735
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Genetic Sharing with Cardiovascular Disease Risk Factors and Diabetes Reveals Novel Bone Mineral Density Loci.
Reppe S, Wang Y, Thompson WK, McEvoy LK, Schork AJ, Zuber V, LeBlanc M, Bettella F, Mills IG, Desikan RS, Djurovic S, Gautvik KM, Dale AM, Andreassen OA, GEFOS Consortium. PloS one Volume 10 (2015) p.e0144531 DOI: 10.1371/journal.pone.0144531
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Identification of epistatic interactions through genome-wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas.
Luzón-Toro B, Bleda M, Navarro E, García-Alonso L, Ruiz-Ferrer M, Medina I, Martín-Sánchez M, Gonzalez CY, Fernández RM, Torroglosa A, Antiñolo G, Dopazo J, Borrego S. BMC medical genomics Volume 8 (2015) p.83 DOI: 10.1186/s12920-015-0160-7
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
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The ELIXIR channel in F1000Research.
Blomberg N, Oliveira A, Mons B, Persson B, Jonassen I. F1000Research Volume 4 (2015) DOI: 10.12688/f1000research.7587.1
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Special issue on bio-ontologies and phenotypes.
Soldatova LN, Collier N, Oellrich A, Groza T, Verspoor K, Rocca-Serra P, Dumontier M, Shah NH. Journal of biomedical semantics Volume 6 (2015) p.40 DOI: 10.1186/s13326-015-0040-2
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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 European Bioinformatics Institute in 2016: Data growth and integration.
Cook CE, Cook CE, Bergman MT, Finn RD, Cochrane G, Birney E, Apweiler R. Nucleic acids research Volume 44 (2016) p.D20-6 DOI: 10.1093/nar/gkv1352
The Pfam protein families database: towards a more sustainable future.
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A. Nucleic acids research Volume 44 (2016) p.D279-85 DOI: 10.1093/nar/gkv1344
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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
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Pipecolic Acid Orchestrates Plant Systemic Acquired Resistance and Defense Priming via Salicylic Acid-Dependent and -Independent Pathways.
Bernsdorff F, Döring AC, Gruner K, Schuck S, Bräutigam A, Zeier J. The Plant cell Volume 28 (2016) p.102-129 DOI: 10.1105/tpc.15.00496
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destiny: diffusion maps for large-scale single-cell data in R.
Angerer P, Haghverdi L, Büttner M, Theis FJ, Marr C, Buettner F. Bioinformatics (Oxford, England) Volume 32 (2016) p.1241-1243 DOI: 10.1093/bioinformatics/btv715
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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
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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
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
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Circular RNA enrichment in platelets is a signature of transcriptome degradation.
Alhasan AA, Izuogu OG, Al-Balool HH, Steyn JS, Evans A, Colzani M, Ghevaert C, Mountford JC, Marenah L, Elliott DJ, Santibanez-Koref M, Jackson MS. Blood Volume 127 (2016) p.e1-e11 DOI: 10.1182/blood-2015-06-649434
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Synthesis of empty african horse sickness virus particles.
Maree S, Maree FF, Putterill JF, de Beer TAP, Huismans H, Theron J. Virus research Volume 213 (2016) p.184-194 DOI: 10.1016/j.virusres.2015.12.006
The Reactome pathway Knowledgebase.
Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, Jassal B, Jupe S, Korninger F, McKay S, Matthews L, May B, Milacic M, Rothfels K, Shamovsky V, Webber M, Weiser J, Williams M, Wu G, Stein L, Hermjakob H, D'Eustachio P. Nucleic acids research Volume 44 (2016) p.D481-7 DOI: 10.1093/nar/gkv1351
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Proton pump inhibitors affect the gut microbiome.
Imhann F, Bonder MJ, Vich Vila A, Fu J, Mujagic Z, Vork L, Tigchelaar EF, Jankipersadsing SA, Cenit MC, Harmsen HJ, Dijkstra G, Franke L, Xavier RJ, Jonkers D, Wijmenga C, Weersma RK, Zhernakova A. Gut Volume 65 (2016) p.740-748 DOI: 10.1136/gutjnl-2015-310376
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Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia.
De Fanti S, Barbieri C, Sarno S, Sevini F, Vianello D, Tamm E, Metspalu E, van Oven M, Hübner A, Sazzini M, Franceschi C, Pettener D, Luiselli D. PloS one Volume 10 (2015) p.e0144391 DOI: 10.1371/journal.pone.0144391
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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
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The Saccharomyces Genome Database: A Tool for Discovery.
Cherry JM. Cold Spring Harbor protocols Volume 2015 (2015) p.pdb.top083840 DOI: 10.1101/pdb.top083840
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The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations.
Cherry JM. Cold Spring Harbor protocols Volume 2015 (2015) p.pdb.prot088922 DOI: 10.1101/pdb.prot088922
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The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes.
Cherry JM. Cold Spring Harbor protocols Volume 2015 (2015) p.pdb.prot088898 DOI: 10.1101/pdb.prot088898
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The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining.
Cherry JM. Cold Spring Harbor protocols Volume 2015 (2015) p.pdb.prot088906 DOI: 10.1101/pdb.prot088906
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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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The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component.
Cherry JM. Cold Spring Harbor protocols Volume 2015 (2015) p.pdb.prot088914 DOI: 10.1101/pdb.prot088914
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Dynamic sensitivity and nonlinear interactions influence the system-level evolutionary patterns of phototransduction proteins.
Invergo BM, Montanucci L, Bertranpetit J. Proceedings. Biological sciences Volume 282 (2015) p.20152215 DOI: 10.1098/rspb.2015.2215
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Single-cell technologies are revolutionizing the approach to rare cells.
Proserpio V, Lönnberg T. Immunology and cell biology Volume 94 (2016) p.225-229 DOI: 10.1038/icb.2015.106
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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
The orchestra of lipid-transfer proteins at the crossroads between metabolism and signaling.
Chiapparino A, Maeda K, Turei D, Saez-Rodriguez J, Gavin AC. Progress in lipid research Volume 61 (2016) p.30-39 DOI: 10.1016/j.plipres.2015.10.004
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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
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
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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
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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
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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
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Quality assurance of the gene ontology using abstraction networks.
Ochs C, Perl Y, Halper M, Geller J, Lomax J. Journal of bioinformatics and computational biology Volume 14 (2016) p.1642001 DOI: 10.1142/s0219720016420014
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PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures.
Peabody MA, Laird MR, Vlasschaert C, Lo R, Brinkman FS. Nucleic acids research Volume 44 (2016) p.D663-8 DOI: 10.1093/nar/gkv1271
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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
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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
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FunTree: advances in a resource for exploring and contextualising protein function evolution.
Sillitoe I, Furnham N. Nucleic acids research Volume 44 (2016) p.D317-23 DOI: 10.1093/nar/gkv1274
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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
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
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The Saccharomyces Genome Database Variant Viewer.
Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM. Nucleic acids research Volume 44 (2016) p.D698-702 DOI: 10.1093/nar/gkv1250
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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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
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Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability.
Pancsa R, Varadi M, Tompa P, Vranken WF. Nucleic acids research Volume 44 (2016) p.D429-34 DOI: 10.1093/nar/gkv1185
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Testing and Validation of Computational Methods for Mass Spectrometry.
Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A. Journal of proteome research Volume 15 (2016) p.809-814 DOI: 10.1021/acs.jproteome.5b00852
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
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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 : Official journal of the Metabolomic Society Volume 12 (2016) p.14 DOI: 10.1007/s11306-015-0879-3
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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
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
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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
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Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.
Mesquita RD, Vionette-Amaral RJ, Lowenberger C, Rivera-Pomar R, Monteiro FA, Minx P, Spieth J, Carvalho AB, Panzera F, Lawson D, Torres AQ, Ribeiro JM, Sorgine MH, Waterhouse RM, Montague MJ, Abad-Franch F, Alves-Bezerra M, Amaral LR, Araujo HM, Araujo RN, Aravind L, Atella GC, Azambuja P, Berni M, Bittencourt-Cunha PR, Braz GR, Calderón-Fernández G, Carareto CM, Christensen MB, Costa IR, Costa SG, Dansa M, Daumas-Filho CR, De-Paula IF, Dias FA, Dimopoulos G, Emrich SJ, Esponda-Behrens N, Fampa P, Fernandez-Medina RD, da Fonseca RN, Fontenele M, Fronick C, Fulton LA, Gandara AC, Garcia ES, Genta FA, Giraldo-Calderón GI, Gomes B, Gondim KC, Granzotto A, Guarneri AA, Guigó R, Harry M, Hughes DS, Jablonka W, Jacquin-Joly E, Juárez MP, Koerich LB, Lange AB, Latorre-Estivalis JM, Lavore A, Lawrence GG, Lazoski C, Lazzari CR, Lopes RR, Lorenzo MG, Lugon MD, Majerowicz D, Marcet PL, Mariotti M, Masuda H, Megy K, Melo AC, Melo AC, Missirlis F, Mota T, Noriega FG, Nouzova M, Nunes RD, Oliveira RL, Oliveira-Silveira G, Ons S, Orchard I, Pagola L, Paiva-Silva GO, Pascual A, Pavan MG, Pedrini N, Peixoto AA, Pereira MH, Pike A, Polycarpo C, Prosdocimi F, Ribeiro-Rodrigues R, Robertson HM, Salerno AP, Salmon D, Santesmasses D, Schama R, Seabra-Junior ES, Silva-Cardoso L, Silva-Neto MA, Souza-Gomes M, Sterkel M, Taracena ML, Tojo M, Tu ZJ, Tubio JM, Ursic-Bedoya R, Venancio TM, Walter-Nuno AB, Wilson D, Warren WC, Wilson RK, Huebner E, Dotson EM, Oliveira PL. Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.14936-14941 DOI: 10.1073/pnas.1506226112
Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks.
Wagih O, Sugiyama N, Ishihama Y, Beltrao P. Molecular & cellular proteomics : MCP Volume 15 (2016) p.236-245 DOI: 10.1074/mcp.m115.052357
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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
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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
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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
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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
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Flexible data integration and curation using a graph-based approach.
Croset S, Rupp J, Romacker M. Bioinformatics (Oxford, England) Volume 32 (2016) p.918-925 DOI: 10.1093/bioinformatics/btv644
*
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
*
Crowdsourcing Twitter annotations to identify first-hand experiences of prescription drug use.
Alvaro N, Conway M, Doan S, Lofi C, Overington J, Collier N. Journal of biomedical informatics Volume 58 (2015) p.280-287 DOI: 10.1016/j.jbi.2015.11.004
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
*
Novel interactions of domain III from the envelope glycoprotein of dengue 2 virus with human plasma proteins.
Huerta V, Ramos Y, Yero A, Pupo D, Martín D, Toledo P, Fleitas N, Gallien S, Martín AM, Márquez GJ, Pérez-Riverol Y, Sarría M, Guirola O, González LJ, Domon B, Chinea G. Journal of proteomics Volume 131 (2016) p.205-213 DOI: 10.1016/j.jprot.2015.11.003
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
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
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
*
ENCODE data at the ENCODE portal.
Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe G, Podduturi NR, Tanaka F, Hong EL, Cherry JM. Nucleic acids research Volume 44 (2016) p.D726-32 DOI: 10.1093/nar/gkv1160
*
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
*
Dynamics of Lgr6⁺ Progenitor Cells in the Hair Follicle, Sebaceous Gland, and Interfollicular Epidermis.
Füllgrabe A, Joost S, Are A, Jacob T, Sivan U, Haegebarth A, Linnarsson S, Simons BD, Clevers H, Toftgård R, Kasper M. Stem cell reports Volume 5 (2015) p.843-855 DOI: 10.1016/j.stemcr.2015.09.013
*
BioJS-HGV Viewer: Genetic Variation Visualizer
Choudhary S, Garcia L, Nightingale A, Martin M. DOI: 10.1101/032573
*
Glioblastoma Stem Cells Respond to Differentiation Cues but Fail to Undergo Commitment and Terminal Cell-Cycle Arrest.
Carén H, Stricker SH, Bulstrode H, Gagrica S, Johnstone E, Bartlett TE, Feber A, Wilson G, Teschendorff AE, Bertone P, Beck S, Pollard SM. Stem cell reports Volume 5 (2015) p.829-842 DOI: 10.1016/j.stemcr.2015.09.014
*
Computational proteomics: Integrating mass spectral data into a biological context.
Carvalho PC, Padron G, Calvete JJ, Perez-Riverol Y. Journal of proteomics Volume 129 (2015) p.1-2 DOI: 10.1016/j.jprot.2015.10.013
*
Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis.
Boroviak T, Loos R, Lombard P, Okahara J, Behr R, Sasaki E, Nichols J, Smith A, Bertone P. Developmental cell Volume 35 (2015) p.366-382 DOI: 10.1016/j.devcel.2015.10.011
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
*
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
*
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
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
*
Fetuin B Is a Secreted Hepatocyte Factor Linking Steatosis to Impaired Glucose Metabolism.
Meex RC, Hoy AJ, Morris A, Brown RD, Lo JC, Burke M, Goode RJ, Kingwell BA, Kraakman MJ, Febbraio MA, Greve JW, Rensen SS, Molloy MP, Lancaster GI, Bruce CR, Watt MJ. Cell metabolism Volume 22 (2015) p.1078-1089 DOI: 10.1016/j.cmet.2015.09.023
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
*
Metadata management for high content screening in OMERO.
Li S, Besson S, Blackburn C, Carroll M, Ferguson RK, Flynn H, Gillen K, Leigh R, Lindner D, Linkert M, Moore WJ, Ramalingam B, Rozbicki E, Rustici G, Tarkowska A, Walczysko P, Williams E, Allan C, Burel JM, Moore J, Swedlow JR. Methods (San Diego, Calif.) Volume 96 (2016) p.27-32 DOI: 10.1016/j.ymeth.2015.10.006
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
*
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
*
Identifying Novel Gene Variants in Coronary Artery Disease and Shared Genes With Several Cardiovascular Risk Factors.
LeBlanc M, Zuber V, Andreassen BK, Witoelar A, Zeng L, Bettella F, Wang Y, McEvoy LK, Thompson WK, Schork AJ, Reppe S, Barrett-Connor E, Ligthart S, Dehghan A, Gautvik KM, Nelson CP, Schunkert H, Samani NJ, CARDIoGRAM Consortium, Ridker PM, Chasman DI, Aukrust P, Djurovic S, Frigessi A, Desikan RS, Dale AM, Andreassen OA. Circulation research Volume 118 (2016) p.83-94 DOI: 10.1161/circresaha.115.306629
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
PhytoPath: an integrative resource for plant pathogen genomics.
Pedro H, Maheswari U, Urban M, Urban M, Urban M, Irvine AG, Cuzick A, McDowall MD, Staines DM, Kulesha E, Hammond-Kosack KE, Kersey PJ. Nucleic acids research Volume 44 (2016) p.D688-93 DOI: 10.1093/nar/gkv1052
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.
Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Lagerstedt I, Mir S, Fernandez Montecelo MA, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Sanz-García E, Sen S, Slowley RA, Wainwright ME, Deshpande MS, Iudin A, Sahni G, Salavert Torres J, Hirshberg M, Mak L, Nadzirin N, Armstrong DR, Clark AR, Smart OS, Korir PK, Kleywegt GJ. Nucleic acids research Volume 44 (2016) p.D385-95 DOI: 10.1093/nar/gkv1047
*
MinION Analysis and Reference Consortium: Phase 1 data release and analysis.
Ip CLC, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, Simpson JT, Snutch TP, Birney E, Buck D, Goodwin S, Jansen HJ, O'Grady J, Olsen HE, MinION Analysis and Reference Consortium. F1000Research Volume 4 (2015) p.1075 DOI: 10.12688/f1000research.7201.1
ChEBI in 2016: Improved services and an expanding collection of metabolites.
Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. Nucleic acids research Volume 44 (2016) p.D1214-9 DOI: 10.1093/nar/gkv1031
*
Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae.
Redmond SN, Eiglmeier K, Mitri C, Markianos K, Guelbeogo WM, Gneme A, Isaacs AT, Coulibaly B, Brito-Fravallo E, Maslen G, Mead D, Niare O, Traore SF, Sagnon N, Kwiatkowski D, Riehle MM, Vernick KD. BMC genomics Volume 16 (2015) p.779 DOI: 10.1186/s12864-015-2009-z
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 Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions.
Iorio F, Shrestha RL, Levin N, Boilot V, Garnett MJ, Saez-Rodriguez J, Draviam VM. PloS one Volume 10 (2015) p.e0139446 DOI: 10.1371/journal.pone.0139446
A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging.
Su J, Ekman C, Oskolkov N, Lahti L, Ström K, Brazma A, Groop L, Rung J, Hansson O. Skeletal muscle Volume 5 (2015) p.35 DOI: 10.1186/s13395-015-0059-1
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
*
Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association.
Strachan NJ, Rotariu O, Lopes B, MacRae M, Fairley S, Laing C, Gannon V, Allison LJ, Hanson MF, Dallman T, Ashton P, Franz E, van Hoek AH, French NP, George T, Biggs PJ, Forbes KJ. Scientific reports Volume 5 (2015) p.14145 DOI: 10.1038/srep14145
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
*
Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins.
Varadi M, Zsolyomi F, Guharoy M, Tompa P. PloS one Volume 10 (2015) p.e0139731 DOI: 10.1371/journal.pone.0139731
*
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
*
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
*
Ptpn22 and Cd2 Variations Are Associated with Altered Protein Expression and Susceptibility to Type 1 Diabetes in Nonobese Diabetic Mice.
Fraser HI, Howlett S, Clark J, Rainbow DB, Stanford SM, Wu DJ, Hsieh YW, Maine CJ, Christensen M, Kuchroo V, Sherman LA, Podolin PL, Todd JA, Steward CA, Peterson LB, Bottini N, Wicker LS. Journal of immunology (Baltimore, Md. : 1950) Volume 195 (2015) p.4841-4852 DOI: 10.4049/jimmunol.1402654
*
DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control.
Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, Kolarova J, Lu Q, Otto C, Wagener R, Arnolds J, Burkhardt B, Claviez A, Drexler HG, Eberth S, Eils R, Flicek P, Haas S, Humme M, Karsch D, Kerstens HHD, Klapper W, Kreuz M, Lawerenz C, Lenzek D, Loeffler M, López C, MacLeod RAF, Martens JHA, Kulis M, Martín-Subero JI, Möller P, Nage I, Picelli S, Vater I, Rohde M, Rosenstiel P, Rosolowski M, Russell RB, Russell RB, Schilhabel M, Schlesner M, Stadler PF, Szczepanowski M, Trümper L, Stunnenberg HG, Küppers R, Ammerpohl O, Lichter P, Siebert R, Hoffmann S, Radlwimmer B. Nature genetics Volume 47 (2015) p.1316-1325 DOI: 10.1038/ng.3413
*
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
Human genomics: The end of the start for population sequencing.
Birney E, Soranzo N. Nature Volume 526 (2015) p.52-53 DOI: 10.1038/526052a
*
Mondo-Mlx Mediates Organismal Sugar Sensing through the Gli-Similar Transcription Factor Sugarbabe.
Mattila J, Havula E, Suominen E, Teesalu M, Surakka I, Hynynen R, Kilpinen H, Väänänen J, Hovatta I, Käkelä R, Ripatti S, Sandmann T, Hietakangas V. Cell reports Volume 13 (2015) p.350-364 DOI: 10.1016/j.celrep.2015.08.081
*
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
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
*
CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis.
Ounzain S, Micheletti R, Arnan C, Plaisance I, Cecchi D, Schroen B, Reverter F, Alexanian M, Gonzales C, Ng SY, Bussotti G, Pezzuto I, Notredame C, Heymans S, Guigó R, Johnson R, Pedrazzini T. Journal of molecular and cellular cardiology Volume 89 (2015) p.98-112 DOI: 10.1016/j.yjmcc.2015.09.016
*
AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators.
Sousa FL, Parente DJ, Shis DL, Hessman JA, Chazelle A, Bennett MR, Teichmann SA, Swint-Kruse L. Journal of molecular biology Volume 428 (2016) p.671-678 DOI: 10.1016/j.jmb.2015.09.015
*
Eyeing the Cyr61/CTGF/NOV (CCN) group of genes in development and diseases: highlights of their structural likenesses and functional dissimilarities.
Krupska I, Bruford EA, Chaqour B. Human genomics Volume 9 (2015) p.24 DOI: 10.1186/s40246-015-0046-y
*
The PDK1-Rsk Signaling Pathway Controls Langerhans Cell Proliferation and Patterning.
Zaru R, Matthews SP, Edgar AJ, Prescott AR, Gomez-Nicola D, Hanauer A, Watts C. Journal of immunology (Baltimore, Md. : 1950) Volume 195 (2015) p.4264-4272 DOI: 10.4049/jimmunol.1501520
*
Glucose-6-phosphate dehydrogenase deficiency and the risk of malaria and other diseases in children in Kenya: a case-control and a cohort study.
Uyoga S, Ndila CM, Macharia AW, Nyutu G, Shah S, Peshu N, Clarke GM, Kwiatkowski DP, Rockett KA, Williams TN, MalariaGEN Consortium. The Lancet. Haematology Volume 2 (2015) p.e437-44 DOI: 10.1016/s2352-3026(15)00152-0
*
Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength.
Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR. Genome biology Volume 16 (2015) p.201 DOI: 10.1186/s13059-015-0749-3
*
Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.
Tsang JC, Yu Y, Burke S, Buettner F, Wang C, Kolodziejczyk AA, Teichmann SA, Lu L, Liu P. Genome biology Volume 16 (2015) p.178 DOI: 10.1186/s13059-015-0739-5
*
The genome of the vervet (Chlorocebus aethiops sabaeus).
Warren WC, Jasinska AJ, García-Pérez R, Svardal H, Tomlinson C, Rocchi M, Archidiacono N, Capozzi O, Minx P, Montague MJ, Kyung K, Hillier LW, Kremitzki M, Graves T, Chiang C, Hughes J, Tran N, Huang Y, Ramensky V, Choi OW, Jung YJ, Schmitt CA, Juretic N, Wasserscheid J, Turner TR, Wiseman RW, Tuscher JJ, Karl JA, Schmitz JE, Zahn R, O'Connor DH, Redmond E, Nisbett A, Jacquelin B, Müller-Trutwin MC, Brenchley JM, Dione M, Antonio M, Schroth GP, Kaplan JR, Jorgensen MJ, Thomas GW, Hahn MW, Raney BJ, Aken B, Nag R, Schmitz J, Churakov G, Noll A, Stanyon R, Webb D, Thibaud-Nissen F, Nordborg M, Marques-Bonet T, Dewar K, Weinstock GM, Wilson RK, Freimer NB. Genome research Volume 25 (2015) p.1921-1933 DOI: 10.1101/gr.192922.115
Using human genetics to make new medicines.
Barrett JC, Dunham I, Birney E. Nature reviews. Genetics Volume 16 (2015) p.561-562 DOI: 10.1038/nrg3998
*
Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.
Huang J, Howie B, McCarthy S, Memari Y, Walter K, Min JL, Danecek P, Malerba G, Trabetti E, Zheng HF, UK10K Consortium, Gambaro G, Richards JB, Durbin R, Timpson NJ, Marchini J, Soranzo N. Nature communications Volume 6 (2015) p.8111 DOI: 10.1038/ncomms9111
*
The UK10K project identifies rare variants in health and disease.
UK10K Consortium, Walter K, Min JL, Huang J, Crooks L, Memari Y, McCarthy S, Perry JR, Xu C, Futema M, Lawson D, Iotchkova V, Schiffels S, Hendricks AE, Danecek P, Li R, Floyd J, Wain LV, Barroso I, Humphries SE, Hurles ME, Zeggini E, Barrett JC, Plagnol V, Richards JB, Greenwood CM, Timpson NJ, Durbin R, Soranzo N. Nature Volume 526 (2015) p.82-90 DOI: 10.1038/nature14962
Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data.
Terfve CD, Wilkes EH, Casado P, Cutillas PR, Saez-Rodriguez J. Nature communications Volume 6 (2015) p.8033 DOI: 10.1038/ncomms9033
*
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
*
Seq-ing improved gene expression estimates from microarrays using machine learning.
Korir PK, Geeleher P, Seoighe C. BMC bioinformatics Volume 16 (2015) p.286 DOI: 10.1186/s12859-015-0712-z
*
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
*
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
*
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
*
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
*
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
*
Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.
Galardini M, Brilli M, Spini G, Rossi M, Roncaglia B, Bani A, Chiancianesi M, Moretto M, Engelen K, Bacci G, Pini F, Biondi EG, Bazzicalupo M, Mengoni A. PLoS computational biology Volume 11 (2015) p.e1004478 DOI: 10.1371/journal.pcbi.1004478
*
Data integration in biological research: an overview.
Lapatas V, Stefanidakis M, Jimenez RC, Via A, Schneider MV. Journal of biological research (Thessalonike, Greece) Volume 22 (2015) p.9 DOI: 10.1186/s40709-015-0032-5
*
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.
*
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
*
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules.
Murrell DS, Cortes-Ciriano I, van Westen GJP, Stott IP, Bender A, Malliavin TE, Glen RC. Journal of cheminformatics Volume 7 (2015) p.45 DOI: 10.1186/s13321-015-0086-2
*
Simultaneously inferring T cell fate and clonality from single cell transcriptomes
Stubbington MJ, Lönnberg T, Proserpio V, Clare S, Speak AO, Dougan G, Teichmann SA. Preprint DOI: 10.1101/025676
*
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, 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
*
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
*
Population Variation and Genetic Control of Modular Chromatin Architecture in Humans.
Waszak SM, Delaneau O, Gschwind AR, Kilpinen H, Raghav SK, Witwicki RM, Orioli A, Wiederkehr M, Panousis NI, Yurovsky A, Romano-Palumbo L, Planchon A, Bielser D, Padioleau I, Udin G, Thurnheer S, Hacker D, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. Cell Volume 162 (2015) p.1039-1050 DOI: 10.1016/j.cell.2015.08.001
*
Microscopy image analysis of p63 immunohistochemically stained laryngeal cancer lesions for predicting patient 5-year survival.
Ninos K, Kostopoulos S, Kalatzis I, Sidiropoulos K, Ravazoula P, Sakellaropoulos G, Panayiotakis G, Economou G, Cavouras D. European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery Volume 273 (2016) p.159-168 DOI: 10.1007/s00405-015-3747-x
*
Fine mapping of bone structure and strength QTLs in heterogeneous stock rat.
Alam I, Koller DL, Cañete T, Blázquez G, Mont-Cardona C, López-Aumatell R, Martínez-Membrives E, Díaz-Morán S, Tobeña A, Fernández-Teruel A, Stridh P, Diez M, Olsson T, Johannesson M, Baud A, Econs MJ, Foroud T. Bone Volume 81 (2015) p.417-426 DOI: 10.1016/j.bone.2015.08.013
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
*
Gut microbiota composition associated with stool consistency.
Tigchelaar EF, Bonder MJ, Jankipersadsing SA, Fu J, Wijmenga C, Zhernakova A. Gut Volume 65 (2016) p.540-542 DOI: 10.1136/gutjnl-2015-310328
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
*
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
*
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
*
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
*
Conservation of Regional Variation in Sex-Specific Sex Chromosome Regulation.
Wright AE, Zimmer F, Harrison PW, Mank JE. Genetics Volume 201 (2015) p.587-598 DOI: 10.1534/genetics.115.179234
*
Computational approaches for inferring the functions of intrinsically disordered proteins.
Varadi M, Vranken W, Guharoy M, Tompa P. Frontiers in molecular biosciences Volume 2 (2015) p.45 DOI: 10.3389/fmolb.2015.00045
*
A new small molecule inhibitor of soluble guanylate cyclase.
Mota F, Gane P, Hampden-Smith K, Allerston CK, Garthwaite J, Selwood DL. Bioorganic & medicinal chemistry Volume 23 (2015) p.5303-5310 DOI: 10.1016/j.bmc.2015.07.074
*
The history of the CATH structural classification of protein domains.
Sillitoe I, Dawson N, Thornton J, Orengo C. Biochimie Volume 119 (2015) p.209-217 DOI: 10.1016/j.biochi.2015.08.004
*
Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury.
Melas IN, Sakellaropoulos T, Iorio F, Alexopoulos LG, Loh WY, Lauffenburger DA, Saez-Rodriguez J, Bai JP. Integrative biology : quantitative biosciences from nano to macro Volume 7 (2015) p.904-920 DOI: 10.1039/c4ib00294f
*
Integrative approaches for signalling and metabolic networks.
Hatzimanikatis V, Saez-Rodriguez J. Integrative biology : quantitative biosciences from nano to macro Volume 7 (2015) p.844-845 DOI: 10.1039/c5ib90030a
Europe: Lifelong learning for all in biomedicine.
Brooksbank C, Johnson C. Nature Volume 524 (2015) p.415 DOI: 10.1038/524415c
*
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
*
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
*
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, Roth B, Ross R, 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.536-541 DOI: 10.1038/nchembio.1867
*
Genetic characterization of three qnrS1-harbouring multidrug-resistance plasmids and qnrS1-containing transposons circulating in Ho Chi Minh City, Vietnam.
Le V, Nhu NTK, Cerdeno-Tarraga A, Campbell JI, Tuyen HT, Nhu TDH, Tam PTT, 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
*
Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.
Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z. Journal of molecular biology Volume 427 (2015) p.3031-3041 DOI: 10.1016/j.jmb.2015.07.016
*
Transcriptional profiling of chronic clinical hepatic schistosomiasis japonica indicates reduced metabolism and immune responses.
Gobert GN, Burke ML, McManus DP, Ellis MK, Chuah C, Ramm GA, Wang Y, Li Y. Parasitology Volume 142 (2015) p.1453-1468 DOI: 10.1017/s0031182015000682
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
*
Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics.
de Angelis MH, Nicholson G, Selloum M, White J, Morgan H, Ramirez-Solis R, Sorg T, Wells S, Fuchs H, Fray M, Adams DJ, Adams NC, Adler T, Aguilar-Pimentel A, Ali-Hadji D, Amann G, André P, Atkins S, Auburtin A, Ayadi A, Becker J, Becker L, Bedu E, Bekeredjian R, Birling MC, Blake A, Bottomley J, Bowl M, Brault V, Busch DH, Bussell JN, Calzada-Wack J, Cater H, Champy MF, Charles P, Chevalier C, Chiani F, Codner GF, Combe R, Cox R, Dalloneau E, Dierich A, Di Fenza A, Doe B, Duchon A, Eickelberg O, Esapa CT, El Fertak L, Feigel T, Emelyanova I, Estabel J, Favor J, Flenniken A, Gambadoro A, Garrett L, Gates H, Gerdin AK, Gkoutos G, Greenaway S, Glasl L, Goetz P, Da Cruz IG, Götz A, Graw J, Guimond A, Hans W, Hicks G, Hölter SM, Höfler H, Hancock JM, Hoehndorf R, Hough T, Houghton R, Hurt A, Ivandic B, Jacobs H, Jacquot S, Jones N, Karp NA, Katus HA, Kitchen S, Klein-Rodewald T, Klingenspor M, Klopstock T, Lalanne V, Leblanc S, Lengger C, le Marchand E, Ludwig T, Lux A, McKerlie C, Maier H, Mandel JL, Marschall S, Mark M, Melvin DG, Meziane H, Micklich K, Mittelhauser C, Monassier L, Moulaert D, Muller S, Naton B, Neff F, Nolan PM, Nutter LM, Ollert M, Pavlovic G, Pellegata NS, Peter E, Petit-Demoulière B, Pickard A, Podrini C, Potter P, Pouilly L, Puk O, Richardson D, Rousseau S, Quintanilla-Fend L, Quwailid MM, Racz I, Rathkolb B, Riet F, Rossant J, Roux M, Rozman J, Ryder E, Salisbury J, Santos L, Schäble KH, Schiller E, Schrewe A, Schulz H, Steinkamp R, Simon M, Stewart M, Stöger C, Stöger T, Sun M, Sunter D, Teboul L, Tilly I, Tocchini-Valentini GP, Tost M, Treise I, Vasseur L, Velot E, Vogt-Weisenhorn D, Wagner C, Walling A, Weber B, Wendling O, Westerberg H, Willershäuser M, Wolf E, Wolter A, Wood J, Wurst W, Yildirim AÖ, Zeh R, Zimmer A, Zimprich A, EUMODIC Consortium, Holmes C, Steel KP, Herault Y, Gailus-Durner V, Mallon AM, Brown SD. Nature genetics Volume 47 (2015) p.969-978 DOI: 10.1038/ng.3360
*
Principles and application of LIMS in mouse clinics.
Maier H, Schütt C, Steinkamp R, Hurt A, Schneltzer E, Gormanns P, Lengger C, Griffiths M, Melvin D, Agrawal N, Alcantara R, Evans A, Gannon D, Holroyd S, Kipp C, Raj NP, Richardson D, LeBlanc S, Vasseur L, Masuya H, Kobayashi K, Suzuki T, Tanaka N, Wakana S, Walling A, Clary D, Gallegos J, Fuchs H, de Angelis MH, Gailus-Durner V. Mammalian genome : official journal of the International Mammalian Genome Society Volume 26 (2015) p.467-481 DOI: 10.1007/s00335-015-9586-7
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
*
Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.
Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, He QY, Menon R, Guan Y, Corrales FJ, Segura V, Casal JI, Pascual-Montano A, Albar JP, Fuentes M, Gonzalez-Gonzalez M, Diez P, Ibarrola N, Degano RM, Mohammed Y, Borchers CH, Urbani A, Soggiu A, Yamamoto T, Salekdeh GH, Archakov A, Ponomarenko E, Lisitsa A, Lichti CF, Mostovenko E, Kroes RA, Rezeli M, Végvári Á, Fehniger TE, Bischoff R, Bischoff R, Vizcaíno JA, Deutsch EW, Lane L, Nilsson CL, Marko-Varga G, Omenn GS, Jeong SK, Lim JS, Paik YK, Hancock WS. Journal of proteome research Volume 14 (2015) p.3415-3431 DOI: 10.1021/pr5013009
*
Roary: rapid large-scale prokaryote pan genome analysis.
Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane JA, Parkhill J. Bioinformatics (Oxford, England) Volume 31 (2015) p.3691-3693 DOI: 10.1093/bioinformatics/btv421
*
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
A large-scale crop protection bioassay data set.
Gaulton A, Kale N, van Westen GJ, Bellis LJ, Bento AP, Davies M, Hersey A, Papadatos G, Forster M, Wege P, Overington JP. Scientific data Volume 2 (2015) p.150032 DOI: 10.1038/sdata.2015.32
*
Structure and evolutionary history of a large family of NLR proteins in the zebrafish
Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni J, Soylemez O, Kondrashov F, Leptin M. Preprint DOI: 10.1101/022061
PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data.
Kurbatova N, Mason JC, 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
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
*
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
*
Expression change in Angiopoietin-1 underlies change in relative brain size in fish.
Chen YC, Harrison PW, Kotrschal A, Kolm N, Mank JE, Panula P. Proceedings. Biological sciences Volume 282 (2015) DOI: 10.1098/rspb.2015.0872
*
Computational and Practical Aspects of Drug Repositioning.
Oprea TI, Overington JP. Assay and drug development technologies Volume 13 (2015) p.299-306 DOI: 10.1089/adt.2015.29011.tiodrrr
*
A draft genome sequence of an invasive mosquito: an Italian Aedes albopictus.
Dritsou V, Topalis P, Windbichler N, Simoni A, Hall A, Lawson D, Hinsley M, Hughes D, Napolioni V, Crucianelli F, Deligianni E, Gasperi G, Gomulski LM, Savini G, Manni M, Scolari F, Malacrida AR, Arcà B, Ribeiro JM, Lombardo F, Saccone G, Salvemini M, Moretti R, Aprea G, Calvitti M, Picciolini M, Papathanos PA, Spaccapelo R, Favia G, Crisanti A, Louis C. Pathogens and global health Volume 109 (2015) p.207-220 DOI: 10.1179/2047773215y.0000000031
*
Identifying novel sequence variants of RNA 3D motifs.
Zirbel CL, Roll J, Sweeney BA, Petrov AI, Pirrung M, Leontis NB. Nucleic acids research Volume 43 (2015) p.7504-7520 DOI: 10.1093/nar/gkv651
*
Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders.
van Schouwenburg PA, Davenport EE, Kienzler AK, Marwah I, Wright B, Lucas M, Malinauskas T, Martin HC, WGS500 Consortium, Lockstone HE, Cazier JB, Chapel HM, Knight JC, Patel SY. Clinical immunology (Orlando, Fla.) Volume 160 (2015) p.301-314 DOI: 10.1016/j.clim.2015.05.020
Molecular and neuronal homology between the olfactory systems of zebrafish and mouse.
Saraiva LR, Ahuja G, Ivandic I, Syed AS, Marioni JC, Korsching SI, Logan DW. Scientific reports Volume 5 (2015) p.11487 DOI: 10.1038/srep11487
*
A random forest approach to capture genetic effects in the presence of population structure.
Stephan J, Stegle O, Beyer A. Nature communications Volume 6 (2015) p.7432 DOI: 10.1038/ncomms8432
*
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.
Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN. American journal of human genetics Volume 97 (2015) p.111-124 DOI: 10.1016/j.ajhg.2015.05.020
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
*
Subclonal diversification of primary breast cancer revealed by multiregion sequencing.
Yates LR, Gerstung M, Knappskog S, Desmedt C, Gundem G, Van Loo P, Aas T, Alexandrov LB, Larsimont D, Davies H, Li Y, Ju YS, Ramakrishna M, Haugland HK, Lilleng PK, Nik-Zainal S, McLaren S, Butler A, Martin S, Glodzik D, Menzies A, Raine K, Hinton J, Jones D, Mudie LJ, Jiang B, Vincent D, Greene-Colozzi A, Adnet PY, Fatima A, Maetens M, Ignatiadis M, Stratton MR, Sotiriou C, Richardson AL, Lønning PE, Wedge DC, Campbell PJ. Nature medicine Volume 21 (2015) p.751-759 DOI: 10.1038/nm.3886
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
*
GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.
Laird MR, Langille MG, Brinkman FS. Bioinformatics (Oxford, England) Volume 31 (2015) p.3348-3349 DOI: 10.1093/bioinformatics/btv376
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
*
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
*
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.
Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J. BMC genomics Volume 16 Suppl 8 (2015) p.S2 DOI: 10.1186/1471-2164-16-s8-s2
*
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Structure (London, England : 1993) Volume 23 (2015) p.1156-1167 DOI: 10.1016/j.str.2015.05.013
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
*
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
*
PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.
Uszkoreit J, Maerkens A, Perez-Riverol Y, Meyer HE, Marcus K, Stephan C, Kohlbacher O, Eisenacher M. Journal of proteome research Volume 14 (2015) p.2988-2997 DOI: 10.1021/acs.jproteome.5b00121
*
Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds.
Dean R, Harrison PW, Wright AE, Zimmer F, Mank JE. Molecular biology and evolution Volume 32 (2015) p.2646-2656 DOI: 10.1093/molbev/msv138
*
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
*
Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism.
Patel S, Roncaglia P, Lovering RC. BMC bioinformatics Volume 16 (2015) p.186 DOI: 10.1186/s12859-015-0622-0
*
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
*
BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services.
Velloso H, Vialle RA, Ortega JM. BMC research notes Volume 8 (2015) p.206 DOI: 10.1186/s13104-015-1190-0
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
*
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
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
*
Diffusion maps for high-dimensional single-cell analysis of differentiation data.
Haghverdi L, Buettner F, Theis FJ. Bioinformatics (Oxford, England) Volume 31 (2015) p.2989-2998 DOI: 10.1093/bioinformatics/btv325
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
*
Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations.
Wilson NK, Kent DG, Buettner F, Shehata M, Macaulay IC, Calero-Nieto FJ, Sánchez Castillo M, Oedekoven CA, Diamanti E, Schulte R, Ponting CP, Voet T, Caldas C, Stingl J, Green AR, Theis FJ, Göttgens B. Cell stem cell Volume 16 (2015) p.712-724 DOI: 10.1016/j.stem.2015.04.004
*
Applying the ARRIVE Guidelines to an In Vivo Database.
Karp NA, Meehan TF, Morgan H, Mason JC, 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
*
Factors influencing success of clinical genome sequencing across a broad spectrum of disorders.
Taylor JC, Martin HC, Lise S, Broxholme J, Cazier JB, Rimmer A, Kanapin A, Lunter G, Fiddy S, Allan C, Aricescu AR, Attar M, Babbs C, Becq J, Beeson D, Bento C, Bignell P, Blair E, Buckle VJ, Bull K, Cais O, Cario H, Chapel H, Copley RR, Cornall R, Craft J, Dahan K, Davenport EE, Dendrou C, Devuyst O, Fenwick AL, Flint J, Fugger L, Gilbert RD, Goriely A, Green A, Greger IH, Grocock R, Gruszczyk AV, Hastings R, Hatton E, Higgs D, Hill A, Holmes C, Howard M, Hughes L, Humburg P, Johnson D, Karpe F, Kingsbury Z, Kini U, Knight JC, Krohn J, Lamble S, Langman C, Lonie L, Luck J, McCarthy D, McGowan SJ, McMullin MF, Miller KA, Murray L, Németh AH, Nesbit MA, Nutt D, Ormondroyd E, Oturai AB, Pagnamenta A, Patel SY, Percy M, Petousi N, Piazza P, Piret SE, Polanco-Echeverry G, Popitsch N, Powrie F, Pugh C, Quek L, Robbins PA, Robson K, Russo A, Sahgal N, van Schouwenburg PA, Schuh A, Silverman E, Simmons A, Sørensen PS, Sweeney E, Taylor J, Thakker RV, Tomlinson I, Trebes A, Twigg SR, Uhlig HH, Vyas P, Vyse T, Wall SA, Watkins H, Whyte MP, Witty L, Wright B, Yau C, Buck D, Humphray S, Ratcliffe PJ, Bell JI, Wilkie AO, Bentley D, Donnelly P, McVean G. Nature genetics Volume 47 (2015) p.717-726 DOI: 10.1038/ng.3304
*
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
*
PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis.
Benavente ED, Coll F, Furnham N, McNerney R, Glynn JR, Campino S, Pain A, Mohareb FR, Clark TG. BMC bioinformatics Volume 16 (2015) p.155 DOI: 10.1186/s12859-015-0603-3
*
Assessing the performance of four different categories of histological criteria in brain tumours grading by means of a computer-aided diagnosis image analysis system.
Kostopoulos S, Konstandinou C, Sidiropoulos K, Ravazoula P, Kalatzis I, Asvestas P, Cavouras D, Glotsos D. Journal of microscopy Volume 260 (2015) p.37-46 DOI: 10.1111/jmi.12264
*
DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder.
Varadi M, Guharoy M, Zsolyomi F, Tompa P. BMC bioinformatics Volume 16 (2015) p.153 DOI: 10.1186/s12859-015-0592-2
*
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
*
Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells.
Ju YS, Tubio JM, Mifsud W, Fu B, Davies HR, Ramakrishna M, Li Y, Yates L, Gundem G, Tarpey PS, Behjati S, Papaemmanuil E, Martin S, Fullam A, Gerstung M, ICGC Prostate Cancer Working Group, ICGC Bone Cancer Working Group, ICGC Breast Cancer Working Group, Nangalia J, Green AR, Caldas C, Borg Å, Tutt A, Lee MT, van't Veer LJ, Tan BK, Aparicio S, Span PN, Martens JW, Knappskog S, Vincent-Salomon A, Børresen-Dale AL, Eyfjörd JE, Myklebost O, Flanagan AM, Foster C, Neal DE, Cooper C, Eeles R, Bova SG, Lakhani SR, Desmedt C, Thomas G, Richardson AL, Purdie CA, Thompson AM, McDermott U, Yang F, Nik-Zainal S, Campbell PJ, Stratton MR. Genome research Volume 25 (2015) p.814-824 DOI: 10.1101/gr.190470.115
*
Targets of drugs are generally, and targets of drugs having side effects are specifically good spreaders of human interactome perturbations.
Perez-Lopez ÁR, Szalay KZ, Türei D, Módos D, Lenti K, Korcsmáros T, Csermely P. Scientific reports Volume 5 (2015) p.10182 DOI: 10.1038/srep10182
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
*
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
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
*
MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.
Wagih O, Reimand J, Bader GD. Nature methods Volume 12 (2015) p.531-533 DOI: 10.1038/nmeth.3396
*
Identification of artesunate as a specific activator of ferroptosis in pancreatic cancer cells.
Eling N, Reuter L, Hazin J, Hamacher-Brady A, Brady NR. Oncoscience Volume 2 (2015) p.517-532 DOI: 10.18632/oncoscience.160
*
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, 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
*
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
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
*
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
*
Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin.
Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, Wedge DC, Fullam A, Alexandrov LB, Tubio JM, Stebbings L, Menzies A, Widaa S, Stratton MR, Jones PH, Campbell PJ. Science (New York, N.Y.) Volume 348 (2015) p.880-886 DOI: 10.1126/science.aaa6806
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
*
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
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
*
IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis.
Dhillon BK, Laird MR, Shay JA, Winsor GL, Lo R, Nizam F, Pereira SK, Waglechner N, McArthur AG, Langille MG, Brinkman FS. Nucleic acids research Volume 43 (2015) p.W104-8 DOI: 10.1093/nar/gkv401
*
A Hybrid of Metabolic Flux Analysis and Bayesian Factor Modeling for Multiomic Temporal Pathway Activation.
Angione C, Pratanwanich N, Lió P. ACS synthetic biology Volume 4 (2015) p.880-889 DOI: 10.1021/sb5003407
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
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
*
Key challenges for the creation and maintenance of specialist protein resources.
Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A. Proteins Volume 83 (2015) p.1005-1013 DOI: 10.1002/prot.24803
*
MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies.
Vuckovic D, Gasparini P, Soranzo N, Iotchkova V. Bioinformatics (Oxford, England) Volume 31 (2015) p.2754-2756 DOI: 10.1093/bioinformatics/btv222
*
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
*
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
*
The BioMart community portal: an innovative alternative to large, centralized data repositories.
Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A. Nucleic acids research Volume 43 (2015) p.W589-98 DOI: 10.1093/nar/gkv350
*
Differential genetic interactions of yeast stress response MAPK pathways.
Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ. Molecular systems biology Volume 11 (2015) p.800 DOI: 10.15252/msb.20145606
*
MicroRNAs enrichment in GWAS of complex human phenotypes.
Goulart LF, Bettella F, Sønderby IE, Schork AJ, Thompson WK, Mattingsdal M, Steen VM, Zuber V, Wang Y, Dale AM, PRACTICAL/ELLIPSE consortium, Andreassen OA, Djurovic S. BMC genomics Volume 16 (2015) p.304 DOI: 10.1186/s12864-015-1513-5
ChEMBL web services: streamlining access to drug discovery data and utilities.
Davies M, Nowotka M, Papadatos G, Dedman N, Gaulton A, Atkinson F, Bellis L, Overington JP. Nucleic acids research Volume 43 (2015) p.W612-20 DOI: 10.1093/nar/gkv352
*
GWAS for executive function and processing speed suggests involvement of the CADM2 gene.
Ibrahim-Verbaas CA, Bressler J, Debette S, Schuur M, Smith AV, Bis JC, Davies G, Trompet S, Smith JA, Wolf C, Chibnik LB, Liu Y, Vitart V, Kirin M, Petrovic K, Polasek O, Zgaga L, Fawns-Ritchie C, Hoffmann P, Karjalainen J, Lahti J, Llewellyn DJ, Schmidt CO, Mather KA, Chouraki V, Sun Q, Resnick SM, Rose LM, Oldmeadow C, Stewart M, Smith BH, Gudnason V, Yang Q, Mirza SS, Jukema JW, deJager PL, Harris TB, Liewald DC, Amin N, Coker LH, Stegle O, Lopez OL, Schmidt R, Teumer A, Ford I, Karbalai N, Becker JT, Jonsdottir MK, Au R, Fehrmann R, Herms S, Nalls M, Zhao W, Turner ST, Yaffe K, Lohman K, van Swieten JC, Kardia S, Knopman DS, Meeks WM, Heiss G, Holliday EG, Schofield PW, Tanaka T, Stott DJ, Wang J, Ridker P, Gow AJ, Pattie A, Starr JM, Hocking LJ, Armstrong NJ, McLachlan S, Shulman JM, Pilling LC, Eiriksdottir G, Scott RJ, Kochan NA, Palotie A, Hsieh YC, Eriksson JG, Penman A, Gottesman RF, Oostra BA, Yu L, DeStefano AL, Beiser A, Garcia M, Rotter JI, Nöthen MM, Hofman A, Slagboom PE, Westendorp R, Buckley BM, Wolf PA, Uitterlinden AG, Psaty BM, Grabe HJ, Bandinelli S, Chasman DI, Grodstein F, Räikkönen K, Lambert JC, Porteous DJ, Generation Scotland, Price JF, Sachdev PS, Ferrucci L, Attia JR, Rudan I, Hayward C, Wright AF, Wilson JF, Cichon S, Franke L, Schmidt H, Ding J, de Craen A, Fornage M, Bennett DA, Deary IJ, Ikram MA, Launer LJ, Fitzpatrick AL, Seshadri S, van Duijn CM, Mosley TH. Molecular psychiatry Volume 21 (2016) p.189-197 DOI: 10.1038/mp.2015.37
*
MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo.
Sheikh BN, Downer NL, Phipson B, Vanyai HK, Kueh AJ, McCarthy DJ, Smyth GK, Thomas T, Voss AK. Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.5437-5442 DOI: 10.1073/pnas.1422872112
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
*
Linking gene expression to phenotypes via pathway information.
Papatheodorou I, Oellrich A, Smedley D. Journal of biomedical semantics Volume 6 (2015) p.17 DOI: 10.1186/s13326-015-0013-5
Cellular phenotype database: a repository for systems microscopy data.
Kirsanova C, Brazma A, Rustici G, Sarkans U. Bioinformatics (Oxford, England) Volume 31 (2015) p.2736-2740 DOI: 10.1093/bioinformatics/btv199
*
GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.
Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CW, GOBLET Consortium. PLoS computational biology Volume 11 (2015) p.e1004143 DOI: 10.1371/journal.pcbi.1004143
*
Inflammaging and cancer: a challenge for the Mediterranean diet.
Ostan R, Lanzarini C, Pini E, Scurti M, Vianello D, Bertarelli C, Fabbri C, Izzi M, Palmas G, Biondi F, Martucci M, Bellavista E, Salvioli S, Capri M, Franceschi C, Santoro A. Nutrients Volume 7 (2015) p.2589-2621 DOI: 10.3390/nu7042589
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
*
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
*
Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.
Benjelloun B, Alberto FJ, Streeter I, Boyer F, Coissac E, Stucki S, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Leempoel K, Alberti A, Engelen S, Chikhi A, Clarke L, Flicek P, Joost S, Taberlet P, Pompanon F, NextGen Consortium. Frontiers in genetics Volume 6 (2015) p.107 DOI: 10.3389/fgene.2015.00107
The EMBL-EBI bioinformatics web and programmatic tools framework.
Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, Park YM, Buso N, Lopez R. Nucleic acids research Volume 43 (2015) p.W580-4 DOI: 10.1093/nar/gkv279
An atlas of mouse CD4(+) T cell transcriptomes.
Stubbington MJ, Mahata B, Svensson V, Deonarine A, Nissen JK, Betz AG, Teichmann SA. Biology direct Volume 10 (2015) p.14 DOI: 10.1186/s13062-015-0045-x
*
Effects of high-dose oral insulin on immune responses in children at high risk for type 1 diabetes: the Pre-POINT randomized clinical trial.
Bonifacio E, Ziegler AG, Klingensmith G, Schober E, Bingley PJ, Rottenkolber M, Theil A, Eugster A, Puff R, Peplow C, Buettner F, Lange K, Hasford J, Achenbach P, Pre-POINT Study Group. JAMA Volume 313 (2015) p.1541-1549 DOI: 10.1001/jama.2015.2928
*
Proteomics data visualisation.
Vizcaíno JA, Barsnes H, Hermjakob H. Proteomics Volume 15 (2015) p.1339-1340 DOI: 10.1002/pmic.201570063
*
Palmitoylation and palmitoyl-transferases in Plasmodium parasites.
Hodson N, Invergo B, Rayner JC, Choudhary JS. Biochemical Society transactions Volume 43 (2015) p.240-245 DOI: 10.1042/bst20140289
*
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
*
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
*
αIIbβ3 variants defined by next-generation sequencing: predicting variants likely to cause Glanzmann thrombasthenia.
Buitrago L, Rendon A, Liang Y, Simeoni I, Negri A, ThromboGenomics Consortium, Filizola M, Ouwehand WH, Coller BS. Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.E1898-907 DOI: 10.1073/pnas.1422238112
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
*
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.
Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, McCarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H, FAANG Consortium. Genome biology Volume 16 (2015) p.57 DOI: 10.1186/s13059-015-0622-4
*
MeDuSa: a multi-draft based scaffolder.
Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lió P, Crescenzi P, Fani R, Fondi M. Bioinformatics (Oxford, England) Volume 31 (2015) p.2443-2451 DOI: 10.1093/bioinformatics/btv171
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
*
Sexual selection drives evolution and rapid turnover of male gene expression.
Harrison PW, Wright AE, Zimmer F, Dean R, Montgomery SH, Pointer MA, Mank JE. Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.4393-4398 DOI: 10.1073/pnas.1501339112
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
*
Spatiotemporal isolation of attosecond soft X-ray pulses in the water window.
Silva F, Teichmann SM, Cousin SL, Hemmer M, Biegert J. Nature communications Volume 6 (2015) p.6611 DOI: 10.1038/ncomms7611
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
*
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
*
TNNI3K in cardiovascular disease and prospects for therapy.
Milano A, Lodder EM, Bezzina CR. Journal of molecular and cellular cardiology Volume 82 (2015) p.167-173 DOI: 10.1016/j.yjmcc.2015.03.008
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
*
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
*
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.1.26.1-1.26.21 DOI: 10.1002/0471250953.bi0126s49
Expression data analysis with Reactome.
Jupe S, Fabregat A, Hermjakob H. Current protocols in bioinformatics Volume 49 (2015) p.8.20.1-8.20.9 DOI: 10.1002/0471250953.bi0820s49
*
Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.
Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Cao KA, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS, Dinger ME. Nature methods Volume 12 (2015) p.339-342 DOI: 10.1038/nmeth.3321
*
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 AASF, Vasconcelos FF, Drechsel D, Marie C, Johnston C, Dolle D, Bithell A, Gillotin S, van den Berg DLC, Ettwiller L, Flicek P, Crawford GE, Parras CM, Berninger B, Buckley NJ, Guillemot F, Castro DS. Cell reports Volume 10 (2015) p.1544-1556 DOI: 10.1016/j.celrep.2015.02.025
*
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
*
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
Harnessing the heart of big data.
Scruggs SB, Watson K, Su AI, Hermjakob H, Yates JR, Lindsey ML, Ping P. Circulation research Volume 116 (2015) p.1115-1119 DOI: 10.1161/circresaha.115.306013
Making proteomics data accessible and reusable: current state of proteomics databases and repositories.
Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA. Proteomics Volume 15 (2015) p.930-949 DOI: 10.1002/pmic.201400302
*
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
*
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
*
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
*
Detection of significant protein coevolution.
Ochoa D, Juan D, Valencia A, Pazos F. Bioinformatics (Oxford, England) Volume 31 (2015) p.2166-2173 DOI: 10.1093/bioinformatics/btv102
*
Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis.
Schwarz RF, Ng CK, Cooke SL, Newman S, Temple J, Piskorz AM, Gale D, Sayal K, Murtaza M, Baldwin PJ, Rosenfeld N, Earl HM, Sala E, Jimenez-Linan M, Parkinson CA, Markowetz F, Brenton JD. PLoS medicine Volume 12 (2015) p.e1001789 DOI: 10.1371/journal.pmed.1001789
BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.
Moreno P, Beisken S, Harsha B, Muthukrishnan V, Tudose I, Dekker A, Dornfeldt S, Taruttis F, Grosse I, Hastings J, Neumann S, Steinbeck C. BMC bioinformatics Volume 16 (2015) p.56 DOI: 10.1186/s12859-015-0486-3
*
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.
Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR. BMC systems biology Volume 9 (2015) p.8 DOI: 10.1186/s12918-015-0144-4
*
Diverse phenotypic consequences of mutations affecting the C-terminus of FLNA.
van Kogelenberg M, Clark AR, Jenkins Z, Morgan T, Anandan A, Sawyer GM, Edwards M, Dudding T, Homfray T, Castle B, Tolmie J, Stewart F, Kivuva E, Pilz DT, Gabbett M, Sutherland-Smith AJ, Robertson SP. Journal of molecular medicine (Berlin, Germany) Volume 93 (2015) p.773-782 DOI: 10.1007/s00109-015-1261-7
*
Optogenetic activation of intracellular adenosine A2A receptor signaling in the hippocampus is sufficient to trigger CREB phosphorylation and impair memory.
Li P, Rial D, Canas PM, Yoo JH, Li W, Zhou X, Wang Y, van Westen GJ, Payen MP, Augusto E, Gonçalves N, Tomé AR, Li Z, Wu Z, Hou X, Zhou Y, IJzerman AP, Boyden ES, Cunha RA, Qu J, Chen JF. Molecular psychiatry Volume 20 (2015) p.1339-1349 DOI: 10.1038/mp.2014.182
*
Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling.
Cortes-Ciriano I, van Westen GJ, Murrell DS, Lenselink EB, Bender A, Malliavin TE. BMC bioinformatics Volume 16 (2015) p.A4-A4 DOI: 10.1186/1471-2105-16-s3-a4
*
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.
Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C, FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y. Science (New York, N.Y.) Volume 347 (2015) p.1010-1014 DOI: 10.1126/science.1259418
*
Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.
Ing-Simmons E, Seitan VC, Faure AJ, Flicek P, Carroll T, Dekker J, Fisher AG, Lenhard B, Merkenschlager M. Genome research Volume 25 (2015) p.504-513 DOI: 10.1101/gr.184986.114
*
Decoding the regulatory network of early blood development from single-cell gene expression measurements.
Moignard V, Woodhouse S, Haghverdi L, Lilly AJ, Tanaka Y, Wilkinson AC, Buettner F, Macaulay IC, Jawaid W, Diamanti E, Nishikawa SI, Piterman N, Kouskoff V, Theis FJ, Fisher J, Göttgens B. Nature biotechnology Volume 33 (2015) p.269-276 DOI: 10.1038/nbt.3154
*
Inferring the microscopic surface energy of protein-protein interfaces from mutation data.
Moal IH, Dapkūnas J, Fernández-Recio J. Proteins Volume 83 (2015) p.640-650 DOI: 10.1002/prot.24761
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
*
Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers.
Shlien A, Campbell BB, de Borja R, Alexandrov LB, Merico D, Wedge D, Van Loo P, Tarpey PS, Coupland P, Behjati S, Pollett A, Lipman T, Heidari A, Deshmukh S, Avitzur N, Meier B, Gerstung M, Hong Y, Merino DM, Ramakrishna M, Remke M, Arnold R, Panigrahi GB, Thakkar NP, Hodel KP, Henninger EE, Göksenin AY, Bakry D, Charames GS, Druker H, Lerner-Ellis J, Mistry M, Dvir R, Grant R, Elhasid R, Farah R, Taylor GP, Nathan PC, Alexander S, Ben-Shachar S, Ling SC, Gallinger S, Constantini S, Dirks P, Huang A, Scherer SW, Grundy RG, Durno C, Aronson M, Gartner A, Meyn MS, Taylor MD, Pursell ZF, Pearson CE, Malkin D, Futreal PA, Stratton MR, Bouffet E, Hawkins C, Campbell PJ, Tabori U, Biallelic Mismatch Repair Deficiency Consortium. Nature genetics Volume 47 (2015) p.257-262 DOI: 10.1038/ng.3202
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
*
Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS.
Bacci G, Bani A, Bazzicalupo M, Ceccherini MT, Galardini M, Nannipieri P, Pietramellara G, Mengoni A. Journal of genomics Volume 3 (2015) p.36-39 DOI: 10.7150/jgen.9204
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
*
Fast inexact mapping using advanced tree exploration on backward search methods.
Salavert J, Tomás A, Tárraga J, Medina I, Dopazo J, Blanquer I. BMC bioinformatics Volume 16 (2015) p.18 DOI: 10.1186/s12859-014-0438-3
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
*
Evolutionary constraint and disease associations of post-translational modification sites in human genomes.
Reimand J, Wagih O, Bader GD. PLoS genetics Volume 11 (2015) p.e1004919 DOI: 10.1371/journal.pgen.1004919
*
FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions
Dunham I, Kulesha E, Iotchkova V, Morganella S, Birney E. Preprint DOI: 10.12688/f1000research.6032.1
*
The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam.
Chiang Z, Vastermark A, Punta M, Coggill PC, Mistry J, Finn RD, Saier MH. Briefings in bioinformatics Volume 16 (2015) p.865-872 DOI: 10.1093/bib/bbu053
*
Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes.
Oellrich A, Collier N, Smedley D, Groza T. PloS one Volume 10 (2015) p.e0116040 DOI: 10.1371/journal.pone.0116040
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O. Nature biotechnology Volume 33 (2015) p.155-160 DOI: 10.1038/nbt.3102
*
Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling.
Cortes-Ciriano I, Murrell DS, van Westen GJ, Bender A, Malliavin TE. Journal of cheminformatics Volume 7 (2015) p.1 DOI: 10.1186/s13321-014-0049-z
*
Mbd3 and deterministic reprogramming
Bertone P, Hendrich B, Silva JC. Preprint DOI: 10.1101/013904
*
The statistical geometry of transcriptome divergence in cell-type evolution and cancer.
Liang C, FANTOM Consortium, Forrest AR, Wagner GP. Nature communications Volume 6 (2015) p.6066 DOI: 10.1038/ncomms7066
*
Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.
Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Nature communications Volume 6 (2015) p.5903 DOI: 10.1038/ncomms6903
*
Strong-field plasmonic photoemission in the mid-IR at <1 GW/cm² intensity.
Teichmann SM, Rácz P, Ciappina MF, Pérez-Hernández JA, Thai A, Fekete J, Elezzabi AY, Veisz L, Biegert J, Dombi P. Scientific reports Volume 5 (2015) p.7584 DOI: 10.1038/srep07584
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
*
Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes.
Gerstung M, Pellagatti A, Malcovati L, Giagounidis A, Porta MG, Jädersten M, Dolatshad H, Verma A, Cross NC, Vyas P, Killick S, Hellström-Lindberg E, Cazzola M, Papaemmanuil E, Campbell PJ, Boultwood J. Nature communications Volume 6 (2015) p.5901 DOI: 10.1038/ncomms6901
*
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
*
Building a pan-genome reference for a population.
Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Journal of computational biology : a journal of computational molecular cell biology Volume 22 (2015) p.387-401 DOI: 10.1089/cmb.2014.0146
*
Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach.
Bacci G, Ceccherini MT, Bani A, Bazzicalupo M, Castaldini M, Galardini M, Giovannetti L, Mocali S, Pastorelli R, Pantani OL, Arfaioli P, Pietramellara G, Viti C, Nannipieri P, Mengoni A. Antonie van Leeuwenhoek Volume 107 (2015) p.785-797 DOI: 10.1007/s10482-014-0372-4
*
Finding our way through phenotypes.
Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P. PLoS biology Volume 13 (2015) p.e1002033 DOI: 10.1371/journal.pbio.1002033
*
Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.
Tan G, Gil M, Löytynoja AP, Goldman N, Dessimoz C. Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.E99-100 DOI: 10.1073/pnas.1417526112
*
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
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
ChEMBL walkthrough: webinar
Bellis LJ. DOI: 10.6019/tol.chemblwalk-w.2015.00001.1
ChEMBL: Exploring bioactive drug-like molecules
Bellis LJ. DOI: 10.6019/tol.chembl-t.2015.00001.1
Genomics resources: webinar
Emery L. DOI: 10.6019/tol.gen-res-w.2015.00001.1
*
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
*
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
SureChEMBL: Accessing chemical patent data: webinar
Papadatos G. DOI: 10.6019/tol.surechembl-w.2015.00001.1
*
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
*
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
UniProt: Programmatic access to UniProtKB: webinar
Pichler K. DOI: 10.6019/tol.unp-program-w.2015.00001.1
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
Complex Portal: Quick tour
Meldal BH. DOI: 10.6019/tol.compor-qt.2015.00001.1
Introduction to IntAct - a Protein-Protein Interactions resource
Meldal B, Porras P. DOI: 10.6019/tol.inta-intr-w.2015.00001.1
*
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
MyChEMBL: webinar
Papadatos G. DOI: 10.6019/tol.mychembl-w.2015.00001.2
*
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
*
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
PRIDE and ProteomeXchange: webinar
Vizcaino JA. DOI: 10.6019/tol.pride-px-w.2015.00001.1
BioSamples RDF: webinar
Brandizi M, Hancocks T. DOI: 10.6019/tol.bsa-rdf-w.2015.00001.1
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Erratum to: Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes.
Winkler C, Krumsiek J, Buettner F, Angermüller C, Giannopoulou EZ, Theis FJ, Ziegler AG, Bonifacio E. Diabetologia Volume 58 (2015) p.206 DOI: 10.1007/s00125-014-3435-1
Reactome: Exploring biological pathways: webinar
Jupe S. DOI: 10.6019/tol.react-w.2015.00001.1
Phylogenetics: An introduction
Emery L. DOI: 10.6019/tol.phyl.2015.00001.1
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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
User experience design
Rowland F, Pundir S, Brooksbank C, Hancocks T. DOI: 10.6019/tol.ux-c.2015.00001.1
Cellular Microscopy Phenotype Ontology (CMPO): Quick tour
Rustici G, Hancocks T. DOI: 10.6019/tol.cmpo-qt.2015.00001.1
Biomedical data: Ethical, legal and social implications
Morgan SL, Hancocks T. DOI: 10.6019/tol.elsi-c.2015.00001.1
Reactome: exploring and analysing biological pathways
Jupe S. DOI: 10.6019/tol.rea-t.2012.00001.2
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Epithelial sodium transport and its control by aldosterone: the story of our internal environment revisited.
Rossier BC, Baker ME, Studer RA. Physiological reviews Volume 95 (2015) p.297-340 DOI: 10.1152/physrev.00011.2014
PDBe: exploring a Protein Data Bank (PDB) entry
Sen S, Mukhopadhyay A. DOI: 10.6019/tol.pdbe-exp-t.2015.00001.1
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Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy.
Türei D, Földvári-Nagy L, Fazekas D, Módos D, Kubisch J, Kadlecsik T, Demeter A, Lenti K, Csermely P, Vellai T, Korcsmáros T. Autophagy Volume 11 (2015) p.155-165 DOI: 10.4161/15548627.2014.994346
PDBe: Searching for biological macromolecular structures
Armstrong DR. DOI: 10.6019/tol.pdbe-intr-w.2015.00001.1
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
UniProt: Exploring protein sequence and functional information - webinar
Pundir S. DOI: 10.6019/tol.unp-expl-w.2015.00001.1
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Preface. Bacterial pangenomics.
Mengoni A, Fondi M, Galardini M. Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.v-vi DOI: 10.1007/978-1-4939-1720-4
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The Protein Ensemble Database.
Varadi M, Tompa P. Advances in experimental medicine and biology Volume 870 (2015) p.335-349 DOI: 10.1007/978-3-319-20164-1_11
EBI Metagenomics resource: Quick tour
Denise H. DOI: 10.6019/tol.mtg-qt.2013.00001.2
PDBe: searching the Protein Data Bank
Sen S, Mukhopadhyay A. DOI: 10.6019/tol.pdbe-sea-t.2015.00001.1
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The cardiovascular gene annotation initiative: Impact on data analysis
Lovering RC, Rodriguez-Lopez M, Campbell NH, Huntley RP, Sawford T, O’Donovan C, Orchard S, Hermjakob H, Martin M, Mayr M, Humphries SE, Talmud PJ. Atherosclerosis Volume 241 (2015) p.e37 DOI: 10.1016/j.atherosclerosis.2015.04.135
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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
Ensembl tools: webinar
Perry E. DOI: 10.6019/tol.ens-too-w.2015.00001.1
ArrayExpress: Quick tour
Burke M. DOI: 10.6019/tol.arrex-qt.2011.00001.2
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Mapping contigs using CONTIGuator.
Galardini M, Mengoni A, Bazzicalupo M. Methods in molecular biology (Clifton, N.J.) Volume 1231 (2015) p.163-176 DOI: 10.1007/978-1-4939-1720-4_11