Publications for 2016

2016

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Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease.
Carss KJ, Arno G, Erwood M, Stephens J, Sanchis-Juan A, Hull S, Megy K, Grozeva D, Dewhurst E, Malka S, Plagnol V, Penkett C, Stirrups K, Rizzo R, Wright G, Josifova D, Bitner-Glindzicz M, Scott RH, Clement E, Allen L, Armstrong R, Brady AF, Carmichael J, Chitre M, Henderson RHH, Hurst J, MacLaren RE, Murphy E, Paterson J, Rosser E, Thompson DA, Wakeling E, Ouwehand WH, Michaelides M, Moore AT, NIHR-BioResource Rare Diseases Consortium, Webster AR, Raymond FL. American journal of human genetics Volume 100 (2017) p.75-90 DOI: 10.1016/j.ajhg.2016.12.003
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A Data Citation Roadmap for Scholarly Data Repositories
Fenner M, Crosas M, Grethe J, Kennedy D, Hermjakob H, Rocca-Serra P, Durand G, Berjon R, Karcher S, Martone M, Clark T. Preprint DOI: 10.1101/097196
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Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy.
Weber RJM, Lawson TN, Salek RM, Ebbels TMD, Glen RC, Goodacre R, Griffin JL, Haug K, Koulman A, Moreno P, Ralser M, Steinbeck C, Dunn WB, Viant MR. Metabolomics : Official journal of the Metabolomic Society Volume 13 (2017) p.12 DOI: 10.1007/s11306-016-1147-x
Genetic variants regulating expression levels and isoform diversity during embryogenesis.
Cannavò E, Koelling N, Harnett D, Garfield D, Casale FP, Ciglar L, Gustafson HE, Viales RR, Marco-Ferreres R, Degner JF, Zhao B, Stegle O, Birney E, Furlong EE. Nature Volume 541 (2017) p.402-406 DOI: 10.1038/nature20802
Minimizing proteome redundancy in the UniProt Knowledgebase.
Bursteinas B, Britto R, Bely B, Auchincloss A, Rivoire C, Redaschi N, O'Donovan C, Martin MJ. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw139
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Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.
Singhal A, Leaman R, Catlett N, Lemberger T, McEntyre J, Polson S, Xenarios I, Arighi C, Lu Z. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw161
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GeneSeqToFamily: the Ensembl Compara GeneTrees pipeline as a Galaxy workflow
Thanki AS, Soranzo N, Haerty W, Davey RP. Preprint DOI: 10.1101/096529
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Drug repurposing for ageing research using model organisms
Ziehm M, Kaur S, Ivanov DK, Ballester PJ, Marcus D, Partridge L, Thornton JM. Preprint DOI: 10.1101/095380
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Modelling difficulties in abstract thinking in psychosis: the importance of socio-developmental background.
Berg AO, Melle I, Zuber V, Simonsen C, Nerhus M, Ueland T, Andreassen OA, Sundet K, Vaskinn A. Cognitive neuropsychiatry Volume 22 (2017) p.39-52 DOI: 10.1080/13546805.2016.1259998
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Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity.
Wahl S, Drong A, Lehne B, Loh M, Scott WR, Kunze S, Tsai PC, Ried JS, Zhang W, Yang Y, Tan S, Fiorito G, Franke L, Guarrera S, Kasela S, Kriebel J, Richmond RC, Adamo M, Afzal U, Ala-Korpela M, Albetti B, Ammerpohl O, Apperley JF, Beekman M, Bertazzi PA, Black SL, Blancher C, Bonder MJ, Brosch M, Carstensen-Kirberg M, de Craen AJ, de Lusignan S, Dehghan A, Elkalaawy M, Fischer K, Franco OH, Gaunt TR, Hampe J, Hashemi M, Isaacs A, Jenkinson A, Jha S, Kato N, Krogh V, Laffan M, Meisinger C, Meitinger T, Mok ZY, Motta V, Ng HK, Nikolakopoulou Z, Nteliopoulos G, Panico S, Pervjakova N, Prokisch H, Rathmann W, Roden M, Rota F, Rozario MA, Sandling JK, Schafmayer C, Schramm K, Siebert R, Slagboom PE, Soininen P, Stolk L, Strauch K, Tai ES, Tarantini L, Thorand B, Tigchelaar EF, Tumino R, Uitterlinden AG, van Duijn C, van Meurs JB, Vineis P, Wickremasinghe AR, Wijmenga C, Yang TP, Yuan W, Zhernakova A, Batterham RL, Smith GD, Deloukas P, Heijmans BT, Herder C, Hofman A, Lindgren CM, Milani L, van der Harst P, Peters A, Illig T, Relton CL, Waldenberger M, Järvelin MR, Bollati V, Soong R, Spector TD, Scott J, McCarthy MI, Elliott P, Bell JT, Matullo G, Gieger C, Kooner JS, Grallert H, Chambers JC. Nature Volume 541 (2017) p.81-86 DOI: 10.1038/nature20784
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Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification.
Oyola SO, Ariani CV, Hamilton WL, Kekre M, Amenga-Etego LN, Ghansah A, Rutledge GG, Redmond S, Manske M, Jyothi D, Jacob CG, Otto TD, Rockett K, Newbold CI, Berriman M, Kwiatkowski DP. Malaria journal Volume 15 (2016) p.597 DOI: 10.1186/s12936-016-1641-7
Efficient randomization of biological networks while preserving functional characterization of individual nodes.
Iorio F, Bernardo-Faura M, Gobbi A, Cokelaer T, Jurman G, Saez-Rodriguez J. BMC bioinformatics Volume 17 (2016) p.542 DOI: 10.1186/s12859-016-1402-1
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Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition.
Mateo F, Arenas EJ, Aguilar H, Serra-Musach J, de Garibay GR, Boni J, Maicas M, Du S, Iorio F, Herranz-Ors C, Islam A, Prado X, Llorente A, Petit A, Vidal A, Català I, Soler T, Venturas G, Rojo-Sebastian A, Serra H, Cuadras D, Blanco I, Lozano J, Canals F, Sieuwerts AM, de Weerd V, Look MP, Puertas S, García N, Perkins AS, Bonifaci N, Skowron M, Gómez-Baldó L, Hernández V, Martínez-Aranda A, Martínez-Iniesta M, Serrat X, Cerón J, Brunet J, Barretina MP, Gil M, Falo C, Fernández A, Morilla I, Pernas S, Plà MJ, Andreu X, Seguí MA, Ballester R, Castellà E, Nellist M, Morales S, Valls J, Velasco A, Matias-Guiu X, Figueras A, Sánchez-Mut JV, Sánchez-Céspedes M, Cordero A, Gómez-Miragaya J, Palomero L, Gómez A, Gajewski TF, Cohen EEW, Jesiotr M, Bodnar L, Quintela-Fandino M, López-Bigas N, Valdés-Mas R, Puente XS, Viñals F, Casanovas O, Graupera M, Hernández-Losa J, Ramón Y Cajal S, García-Alonso L, Saez-Rodriguez J, Esteller M, Sierra A, Martín-Martín N, Matheu A, Carracedo A, González-Suárez E, Nanjundan M, Cortés J, Lázaro C, Odero MD, Martens JWM, Moreno-Bueno G, Barcellos-Hoff MH, Villanueva A, Gomis RR, Pujana MA. Oncogene Volume 36 (2017) p.2737-2749 DOI: 10.1038/onc.2016.427
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Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE.
Wu YL, Stubbington MJ, Daly M, Teichmann SA, Rada C. The Journal of experimental medicine Volume 214 (2017) p.183-196 DOI: 10.1084/jem.20161056
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Dissecting cancer resistance to therapies with cell-type-specific dynamic logic models
Eduati F, Doldàn-Martelli V, Klinger B, Cokelaer T, Sieber A, Kogera F, Dorel M, Garnett MJ, Blüthgen N, Saez-Rodriguez J. Preprint DOI: 10.1101/094755
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easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies.
Grimm DG, Roqueiro D, Salomé PA, Kleeberger S, Greshake B, Zhu W, Liu C, Lippert C, Stegle O, Schölkopf B, Weigel D, Borgwardt KM. The Plant cell Volume 29 (2017) p.5-19 DOI: 10.1105/tpc.16.00551
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Omics Discovery Index - Discovering and Linking Public Omics Datasets
Perez-Riverol Y, Bai M, Leprevost F, Squizzato S, Park YM, et al. DOI: 10.1101/049205
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Novel inhibitors of Mycobacterium tuberculosis GuaB2 identified by a target based high-throughput phenotypic screen.
Cox JA, Mugumbate G, Del Peral LV, Jankute M, Abrahams KA, Jervis P, Jackenkroll S, Perez A, Alemparte C, Esquivias J, Lelièvre J, Ramon F, Barros D, Ballell L, Besra GS. Scientific reports Volume 6 (2016) p.38986 DOI: 10.1038/srep38986
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Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.
Dolle DD, Liu Z, Cotten M, Simpson JT, Iqbal Z, Durbin R, McCarthy SA, Keane TM. Genome research Volume 27 (2017) p.300-309 DOI: 10.1101/gr.211748.116
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The Degradation Pathway of the Mitophagy Receptor Atg32 Is Re-Routed by a Posttranslational Modification.
Levchenko M, Lorenzi I, Dudek J. PloS one Volume 11 (2016) p.e0168518 DOI: 10.1371/journal.pone.0168518
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Two independent modes of chromosome organization are revealed by cohesin removal
Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering C, Mirny L, Spitz F. Preprint DOI: 10.1101/094185
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Rapid identification of optimal drug combinations for personalized cancer therapy using microfluidics
Eduati F, Utharala R, Madhavan D, Neumann UP, Cramer T, Saez-Rodriguez J, Merten CA. Preprint DOI: 10.1101/093906
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On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study
Poux S, Arighi CN, Magrane M, Bateman A, Wei C, Lu Z, Boutet E, Bye-A-Jee H, Famiglietti ML, Roechert B, The UniProt Consortium. Preprint DOI: 10.1101/094011
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Chromosomal rearrangements are commonly post-transcriptionally attenuated in cancer
Gonçalves E, Fragoulis A, Garcia-Alonso L, Cramer T, Saez-Rodriguez J, Beltrao P. Preprint DOI: 10.1101/093369
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Integration of EGA secure data access into Galaxy.
Hoogstrate Y, Zhang C, Senf A, Bijlard J, Hiltemann S, van Enckevort D, Repo S, Heringa J, Jenster G, J A Fijneman R, Boiten JW, A Meijer G, Stubbs A, Rambla J, Spalding D, Abeln S. F1000Research Volume 5 (2016) DOI: 10.12688/f1000research.10221.1
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Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate
Jasinska AJ, Zelaya I, Service SK, Peterson CB, Cantor RM, Choi O, DeYoung J, Eskin E, Fairbanks LA, Fears S, Furterer AE, Huang YS, Ramensky V, Schmitt CA, Svardal H, Jorgensen MJ, Kaplan JR, Villar D, Aken BL, Flicek P, Nag R, Wong ES, Blangero J, Dyer TD, Bogomolov M, Benjamini Y, Weinstock GM, Dewar K, Sabatti C, Wilson RK, Jentsch JD, Warren W, Coppola G, Woods RP, Freimer NB. Preprint DOI: 10.1101/092874
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Tracking the embryonic stem cell transition from ground state pluripotency
Kalkan T, Olova N, Roode M, Mulas C, Lee HJ, Nett I, Marks H, Walker R, Stunnenberg HG, Lilley KS, Nichols J, Reik W, Bertone P, Smith A. Preprint DOI: 10.1101/092510
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Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers.
Morgan AP, Didion JP, Doran AG, Holt JM, McMillan L, Keane TM, de Villena FP. G3 (Bethesda, Md.) Volume 6 (2016) p.4211-4216 DOI: 10.1534/g3.116.034751
Functional genomics (I): Introduction and designing experiments
Burke M, Huerta L. DOI: 10.6019/tol.fungeni-c.2016.00001.1
Ensembl browser webinar series
Perry E, Moore B, Sparrow H, Carvalho-Silva D, Newman V, Gall A, Haskell E. DOI: 10.6019/tol.ensbrows-w.2016.00001.1
UniProt peptide search and website updates: webinar
Pichler K. DOI: 10.6019/tol.unp-peptide-pub-w.2016.00001.1
Biocuration: An introduction
O'Donovan C. DOI: 10.6019/tol.biocur-w.2016.00001.1
Array Express: Exploring functional genomics data quickly and easily
Füllgrabe A. DOI: 10.6019/tol.aex-t.2016.00001.2
Functional genomics (II): Common technologies and data analysis methods
Huerta L, Burke M. DOI: 10.6019/tol.fungenii-c.2016.00001.1
EBI Metagenomics portal: Submitting metagenomics data to the European Nucleotide Archive
Denise H. DOI: 10.6019/tol.metagensubm-t.2016.00001.1
Functional genomics (III): Submiting your data and functional genomics databases
Burke M, Huerta L. DOI: 10.6019/tol.fungeniii-c.2016.00001.1
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Identification of context-dependent expression quantitative trait loci in whole blood.
Zhernakova DV, Deelen P, Vermaat M, van Iterson M, van Galen M, Arindrarto W, van 't Hof P, Mei H, van Dijk F, Westra HJ, Bonder MJ, van Rooij J, Verkerk M, Jhamai PM, Moed M, Kielbasa SM, Bot J, Nooren I, Pool R, van Dongen J, Hottenga JJ, Stehouwer CD, van der Kallen CJ, Schalkwijk CG, Zhernakova A, Li Y, Tigchelaar EF, de Klein N, Beekman M, Deelen J, van Heemst D, van den Berg LH, Hofman A, Uitterlinden AG, van Greevenbroek MM, Veldink JH, Boomsma DI, van Duijn CM, Wijmenga C, Slagboom PE, Swertz MA, Isaacs A, van Meurs JB, Jansen R, Heijmans BT, 't Hoen PA, Franke L. Nature genetics Volume 49 (2017) p.139-145 DOI: 10.1038/ng.3737
Drug repurposing
Overington JP. DOI: 10.6019/tol.drugrep-w.2016.00001.1
Network analysis of protein interaction data: an introduction
Porras P. DOI: 10.6019/tol.networks_t.2016.00001.1
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Disease variants alter transcription factor levels and methylation of their binding sites.
Bonder MJ, Luijk R, Zhernakova DV, Moed M, Deelen P, Vermaat M, van Iterson M, van Dijk F, van Galen M, Bot J, Slieker RC, Jhamai PM, Verbiest M, Suchiman HE, Verkerk M, van der Breggen R, van Rooij J, Lakenberg N, Arindrarto W, Kielbasa SM, Jonkers I, van 't Hof P, Nooren I, Beekman M, Deelen J, van Heemst D, Zhernakova A, Tigchelaar EF, Swertz MA, Hofman A, Uitterlinden AG, Pool R, van Dongen J, Hottenga JJ, Stehouwer CD, van der Kallen CJ, Schalkwijk CG, van den Berg LH, van Zwet EW, Mei H, Li Y, Lemire M, Hudson TJ, BIOS Consortium, Slagboom PE, Wijmenga C, Veldink JH, van Greevenbroek MM, van Duijn CM, Boomsma DI, Isaacs A, Jansen R, van Meurs JB, 't Hoen PA, Franke L, Heijmans BT. Nature genetics Volume 49 (2017) p.131-138 DOI: 10.1038/ng.3721
Pfam: Quick tour
El-Gebali S, Richardson L, Finn R. DOI: 10.6019/tol.pfam-qt.2016.00001.1
Introduction to 1000 Genomes Project and IGSR data resources
Fairley S. DOI: 10.6019/tol.isgr_w.2016.00001.1
Ensembl: Genomic features that regulate genes
Perry E. DOI: 10.6019/tol.ensreg-w.2016.00001.1
Ensembl Variant Effect Predictor (VEP): webinar
Moore B. DOI: 10.6019/tol.ensvep-w.2016.00001.1
Bioinformatics for the terrified
Brooksbank C, Cowley A. DOI: 10.6019/tol.bioinfter-c.2016.00001.1
Introduction to training with EMBL-EBI
Brooksbank C. DOI: 10.6019/tol.train-w.2016.00001.1
ArrayExpress: why and how to submit your data
Burke M. DOI: 10.6019/tol.aesub-w.2016.00001.1
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PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.
Urban M, Cuzick A, Rutherford K, Irvine A, Pedro H, Pant R, Sadanadan V, Khamari L, Billal S, Mohanty S, Hammond-Kosack KE. Nucleic acids research Volume 45 (2017) p.D604-D610 DOI: 10.1093/nar/gkw1089
A comprehensive map of molecular drug targets.
Santos R, Ursu O, Gaulton A, Bento AP, Donadi RS, Bologa CG, Karlsson A, Al-Lazikani B, Hersey A, Oprea TI, Overington JP. Nature reviews. Drug discovery Volume 16 (2017) p.19-34 DOI: 10.1038/nrd.2016.230
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Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition.
Lensink MF, Velankar S, Wodak SJ. Proteins Volume 85 (2017) p.359-377 DOI: 10.1002/prot.25215
An atlas of human kinase regulation.
Ochoa D, Jonikas M, Lawrence RT, El Debs B, Selkrig J, Typas A, Villén J, Santos SD, Beltrao P. Molecular systems biology Volume 12 (2016) p.888 DOI: 10.15252/msb.20167295
Plant specimen contextual data consensus.
Hoopen PT, Walls RL, Cannon EK, Cochrane G, Cole J, Johnston A, Karsch-Mizrachi I, Yilmaz P. GigaScience Volume 5 (2016) p.1-4 DOI: 10.1093/gigascience/giw002
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Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.
Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Cell Volume 167 (2016) p.1897 DOI: 10.1016/j.cell.2016.11.046
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Loss of the arginine methyltranserase PRMT7 causes syndromic intellectual disability with microcephaly and brachydactyly.
Kernohan KD, McBride A, Xi Y, Martin N, Schwartzentruber J, Dyment DA, Majewski J, Blaser S, Care4Rare Canada Consortium, Boycott KM, Chitayat D. Clinical genetics Volume 91 (2017) p.708-716 DOI: 10.1111/cge.12884
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A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree.
Eberle MA, Fritzilas E, Krusche P, Källberg M, Moore BL, Bekritsky MA, Iqbal Z, Chuang HY, Humphray SJ, Halpern AL, Kruglyak S, Margulies EH, McVean G, Bentley DR. Genome research Volume 27 (2017) p.157-164 DOI: 10.1101/gr.210500.116
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Open Targets: a platform for therapeutic target identification and validation.
Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I. Nucleic acids research Volume 45 (2017) p.D985-D994 DOI: 10.1093/nar/gkw1055
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The SWISS-MODEL Repository-new features and functionality.
Bienert S, Waterhouse A, de Beer TA, Tauriello G, Studer G, Bordoli L, Schwede T. Nucleic acids research Volume 45 (2017) p.D313-D319 DOI: 10.1093/nar/gkw1132
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MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.
Vallenet D, Calteau A, Cruveiller S, Gachet M, Lajus A, Josso A, Mercier J, Renaux A, Rollin J, Rouy Z, Roche D, Scarpelli C, Médigue C. Nucleic acids research Volume 45 (2017) p.D517-D528 DOI: 10.1093/nar/gkw1101
InterPro in 2017-beyond protein family and domain annotations.
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. Nucleic acids research Volume 45 (2017) p.D190-D199 DOI: 10.1093/nar/gkw1107
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Pharos: Collating protein information to shed light on the druggable genome.
Nguyen DT, Mathias S, Bologa C, Brunak S, Fernandez N, Gaulton A, Hersey A, Holmes J, Jensen LJ, Karlsson A, Liu G, Ma'ayan A, Mandava G, Mani S, Mehta S, Overington J, Patel J, Rouillard AD, Schürer S, Sheils T, Simeonov A, Sklar LA, Southall N, Ursu O, Vidovic D, Waller A, Yang J, Jadhav A, Oprea TI, Guha R. Nucleic acids research Volume 45 (2017) p.D995-D1002 DOI: 10.1093/nar/gkw1072
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Mutations at protein-protein interfaces: Small changes over big surfaces have large impacts on human health.
Jubb HC, Pandurangan AP, Turner MA, Ochoa-Montaño B, Blundell TL, Ascher DB. Progress in biophysics and molecular biology Volume 128 (2017) p.3-13 DOI: 10.1016/j.pbiomolbio.2016.10.002
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog).
MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H. Nucleic acids research Volume 45 (2017) p.D896-D901 DOI: 10.1093/nar/gkw1133
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Increased DNA methylation variability in type 1 diabetes across three immune effector cell types.
Paul DS, Teschendorff AE, Dang MA, Lowe R, Hawa MI, Ecker S, Beyan H, Cunningham S, Fouts AR, Ramelius A, Burden F, Farrow S, Rowlston S, Rehnstrom K, Frontini M, Downes K, Busche S, Cheung WA, Ge B, Simon MM, Bujold D, Kwan T, Bourque G, Datta A, Lowy E, Clarke L, Flicek P, Libertini E, Heath S, Gut M, Gut IG, Ouwehand WH, Pastinen T, Soranzo N, Hofer SE, Karges B, Meissner T, Boehm BO, Cilio C, Elding Larsson H, Lernmark Å, Steck AK, Rakyan VK, Beck S, Leslie RD. Nature communications Volume 7 (2016) p.13555 DOI: 10.1038/ncomms13555
European Nucleotide Archive in 2016.
Toribio AL, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Fairley S, Gibson R, Goodgame N, Ten Hoopen P, Jayathilaka S, Kay S, Leinonen R, Liu X, Martínez-Villacorta J, Pakseresht N, Rajan J, Reddy K, Rosello M, Silvester N, Smirnov D, Vaughan D, Zalunin V, Cochrane G. Nucleic acids research Volume 45 (2017) p.D32-D36 DOI: 10.1093/nar/gkw1106
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The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Lewis SE, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA. Nucleic acids research Volume 45 (2017) p.D712-D722 DOI: 10.1093/nar/gkw1128
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T Cell Receptor Vβ Staining Identifies the Malignant Clone in Adult T cell Leukemia and Reveals Killing of Leukemia Cells by Autologous CD8+ T cells.
Rowan AG, Witkover A, Melamed A, Tanaka Y, Cook LB, Fields P, Taylor GP, Bangham CR. PLoS pathogens Volume 12 (2016) p.e1006030 DOI: 10.1371/journal.ppat.1006030
Ensembl 2017.
Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Juettemann T, Keenan S, Laird MR, Lavidas I, Maurel T, McLaren W, Moore B, Murphy DN, Nag R, Newman V, Nuhn M, Ong CK, Parker A, Patricio M, Riat HS, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Wilder SP, Zadissa A, Kostadima M, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Cunningham F, Yates A, Zerbino DR, Flicek P. Nucleic acids research Volume 45 (2017) p.D635-D642 DOI: 10.1093/nar/gkw1104
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HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor.
Clima R, Preste R, Calabrese C, Diroma MA, Santorsola M, Scioscia G, Simone D, Shen L, Gasparre G, Attimonelli M. Nucleic acids research Volume 45 (2017) p.D698-D706 DOI: 10.1093/nar/gkw1066
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Uniclust databases of clustered and deeply annotated protein sequences and alignments.
Mirdita M, von den Driesch L, Galiez C, Martin MJ, Söding J, Steinegger M. Nucleic acids research Volume 45 (2017) p.D170-D176 DOI: 10.1093/nar/gkw1081
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IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex.
Maccari G, Robinson J, Ballingall K, Guethlein LA, Grimholt U, Kaufman J, Ho CS, de Groot NG, Flicek P, Bontrop RE, Hammond JA, Marsh SG. Nucleic acids research Volume 45 (2017) p.D860-D864 DOI: 10.1093/nar/gkw1050
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The Human Phenotype Ontology in 2017.
Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJ, DeMare LE, Devereau AD, de Vries BB, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MW, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JO, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN. Nucleic acids research Volume 45 (2017) p.D865-D876 DOI: 10.1093/nar/gkw1039
The ChEMBL database in 2017.
Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibrián-Uhalte E, Davies M, Dedman N, Karlsson A, Magariños MP, Overington JP, Papadatos G, Smit I, Leach AR. Nucleic acids research Volume 45 (2017) p.D945-D954 DOI: 10.1093/nar/gkw1074
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A scored human protein-protein interaction network to catalyze genomic interpretation.
Li T, Wernersson R, Hansen RB, Horn H, Mercer J, Slodkowicz G, Workman CT, Rigina O, Rapacki K, Stærfeldt HH, Brunak S, Jensen TS, Lage K. Nature methods Volume 14 (2017) p.61-64 DOI: 10.1038/nmeth.4083
WormBase ParaSite - a comprehensive resource for helminth genomics.
Howe KL, Bolt BJ, Shafie M, Kersey P, Berriman M. Molecular and biochemical parasitology Volume 215 (2017) p.2-10 DOI: 10.1016/j.molbiopara.2016.11.005
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Looking beyond the cancer cell for effective drug combinations.
Dry JR, Yang M, Saez-Rodriguez J. Genome medicine Volume 8 (2016) p.125 DOI: 10.1186/s13073-016-0379-8
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The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Dissemination
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Carazo Salas RE, Swedlow JR. Preprint DOI: 10.1101/089359
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Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.
Knijnenburg TA, Klau GW, Iorio F, Garnett MJ, McDermott U, Shmulevich I, Wessels LF. Scientific reports Volume 6 (2016) p.36812 DOI: 10.1038/srep36812
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Towards an open grapevine information system.
Adam-Blondon AF, Alaux M, Pommier C, Cantu D, Cheng ZM, Cramer GR, Davies C, Delrot S, Deluc L, Di Gaspero G, Grimplet J, Fennell A, Londo JP, Kersey P, Mattivi F, Naithani S, Neveu P, Nikolski M, Pezzotti M, Reisch BI, Töpfer R, Vivier MA, Ware D, Quesneville H. Horticulture research Volume 3 (2016) p.16056 DOI: 10.1038/hortres.2016.56
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The genome of Onchocerca volvulus, agent of river blindness.
Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JC, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, Ribeiro JM, Rogers MB, Stanley E, Swapna LS, Tsai IJ, Unnasch TR, Voronin D, Parkinson J, Nutman TB, Ghedin E, Berriman M, Lustigman S. Nature microbiology Volume 2 (2016) p.16216 DOI: 10.1038/nmicrobiol.2016.216
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Chromosome assembly of large and complex genomes using multiple references
Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane T, Thybert D, Paten B, Pham S. Preprint DOI: 10.1101/088435
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Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis.
Ernst C, Pike J, Aitken SJ, Long HK, Eling N, Stojic L, Ward MC, Connor F, Rayner TF, Lukk M, Klose RJ, Kutter C, Odom DT. eLife Volume 5 (2016) DOI: 10.7554/elife.20235
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Quantifying side-chain conformational variations in protein structure.
Miao Z, Cao Y. Scientific reports Volume 6 (2016) p.37024 DOI: 10.1038/srep37024
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Erratum to "Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient".
Löffler MW, Chandran PA, Laske K, Schroeder C, Bonzheim I, Walzer M, Hilke FJ, Trautwein N, Kowalewski DJ, Schuster H, Günder M, Carcamo Yañez VA, Mohr C, Sturm M, Nguyen HP, Riess O, Bauer P, Nahnsen S, Nadalin S, Zieker D, Glatzle J, Thiel K, Schneiderhan-Marra N, Clasen S, Bösmüller H, Fend F, Kohlbacher O, Gouttefangeas C, Stevanović S, Königsrainer A, Rammensee HG. Journal of hepatology Volume 66 (2017) p.252-253 DOI: 10.1016/j.jhep.2016.10.021
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Scalable latent-factor models applied to single-cell RNA-seq data separate biological drivers from confounding effects
Buettner F, Pratanwanich N, Marioni JC, Stegle O. Preprint DOI: 10.1101/087775
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The BLUEPRINT Data Analysis Portal.
Fernández JM, de la Torre V, Richardson D, Royo R, Puiggròs M, Moncunill V, Fragkogianni S, Clarke L, BLUEPRINT Consortium, Flicek P, Rico D, Torrents D, Carrillo de Santa Pau E, Valencia A. Cell systems Volume 3 (2016) p.491-495.e5 DOI: 10.1016/j.cels.2016.10.021
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Retroviruses integrate into a shared, non-palindromic DNA motif.
Kirk PD, Huvet M, Melamed A, Maertens GN, Bangham CR. Nature microbiology Volume 2 (2016) p.16212 DOI: 10.1038/nmicrobiol.2016.212
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Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation
Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird MR, Longden I, Proctor G, Steve S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P. Preprint DOI: 10.1101/087239
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Measures for interoperability of phenotypic data: minimum information requirements and formatting.
Ćwiek-Kupczyńska H, Altmann T, Arend D, Arnaud E, Chen D, Cornut G, Fiorani F, Frohmberg W, Junker A, Klukas C, Lange M, Mazurek C, Nafissi A, Neveu P, van Oeveren J, Pommier C, Poorter H, Rocca-Serra P, Sansone SA, Scholz U, van Schriek M, Seren Ü, Usadel B, Weise S, Kersey P, Krajewski P. Plant methods Volume 12 (2016) p.44 DOI: 10.1186/s13007-016-0144-4
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Transcriptome Profiling in Rat Inbred Strains and Experimental Cross Reveals Discrepant Genetic Architecture of Genome-Wide Gene Expression.
Kaisaki PJ, Otto GW, Argoud K, Collins SC, Wallis RH, Wilder SP, Yau ACY, Hue C, Calderari S, Bihoreau MT, Cazier JB, Mott R, Gauguier D. G3 (Bethesda, Md.) Volume 6 (2016) p.3671-3683 DOI: 10.1534/g3.116.033274
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GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
Iotchkova V, Ritchie GR, Geihs M, Morganella S, Min JL, Walter K, Timpson N, Dunham I, Birney E, Soranzo N, UK10K Consortium. Preprint DOI: 10.1101/085738
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Erratum to: Making sense of big data in health research: towards an EU action plan.
Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G. Genome medicine Volume 8 (2016) p.118 DOI: 10.1186/s13073-016-0376-y
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ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.
Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, Wishart DS. Journal of cheminformatics Volume 8 (2016) p.61 DOI: 10.1186/s13321-016-0174-y
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Genetic markers associated with dihydroartemisinin-piperaquine failure in Plasmodium falciparum malaria in Cambodia: a genotype-phenotype association study.
Amato R, Lim P, Miotto O, Amaratunga C, Dek D, Pearson RD, Almagro-Garcia J, Neal AT, Sreng S, Suon S, Drury E, Jyothi D, Stalker J, Kwiatkowski DP, Fairhurst RM. The Lancet. Infectious diseases Volume 17 (2017) p.164-173 DOI: 10.1016/s1473-3099(16)30409-1
The Mighty Fruit Fly Moves into Outbred Genetics.
Birney E. PLoS genetics Volume 12 (2016) p.e1006388 DOI: 10.1371/journal.pgen.1006388
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The Monarch Initiative: An integrative data and analytic platform connecting phenotypes to genotypes across species
Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine J, Jacobsen JO, Keith D, Laraway B, Lewis SE, Nguyen Xuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA. Preprint DOI: 10.1101/055756
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SPLASH, a hashed identifier for mass spectra.
Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O. Nature biotechnology Volume 34 (2016) p.1099-1101 DOI: 10.1038/nbt.3689
OmniPath: guidelines and gateway for literature-curated signaling pathway resources.
Türei D, Korcsmáros T, Saez-Rodriguez J. Nature methods Volume 13 (2016) p.966-967 DOI: 10.1038/nmeth.4077
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eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data.
Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JHA, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S. Cell reports Volume 17 (2016) p.2137-2150 DOI: 10.1016/j.celrep.2016.10.059
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Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.
Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N. Cell Volume 167 (2016) p.1398-1414.e24 DOI: 10.1016/j.cell.2016.10.026
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Single-cell analysis at the threshold.
Chen X, Love JC, Navin NE, Pachter L, Stubbington MJ, Svensson V, Sweedler JV, Teichmann SA. Nature biotechnology Volume 34 (2016) p.1111-1118 DOI: 10.1038/nbt.3721
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Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems.
Schuyler RP, Merkel A, Raineri E, Altucci L, Vellenga E, Martens JHA, Pourfarzad F, Kuijpers TW, Burden F, Farrow S, Downes K, Ouwehand WH, Clarke L, Datta A, Lowy E, Flicek P, Frontini M, Stunnenberg HG, Martín-Subero JI, Gut I, Heath S. Cell reports Volume 17 (2016) p.2101-2111 DOI: 10.1016/j.celrep.2016.10.054
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β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance.
Novakovic B, Habibi E, Wang SY, Arts RJW, Davar R, Megchelenbrink W, Kim B, Kuznetsova T, Kox M, Zwaag J, Matarese F, van Heeringen SJ, Janssen-Megens EM, Sharifi N, Wang C, Keramati F, Schoonenberg V, Flicek P, Clarke L, Pickkers P, Heath S, Gut I, Netea MG, Martens JHA, Logie C, Stunnenberg HG. Cell Volume 167 (2016) p.1354-1368.e14 DOI: 10.1016/j.cell.2016.09.034
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Gramene Database: Navigating Plant Comparative Genomics Resources.
Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P. Current plant biology Volume 7-8 (2016) p.10-15 DOI: 10.1016/j.cpb.2016.12.005
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The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.
Astle WJ, Elding H, Jiang T, Allen D, Ruklisa D, Mann AL, Mead D, Bouman H, Riveros-Mckay F, Kostadima MA, Lambourne JJ, Sivapalaratnam S, Downes K, Kundu K, Bomba L, Berentsen K, Bradley JR, Daugherty LC, Delaneau O, Freson K, Garner SF, Grassi L, Guerrero J, Haimel M, Janssen-Megens EM, Kaan A, Kamat M, Kim B, Mandoli A, Marchini J, Martens JHA, Meacham S, Megy K, O'Connell J, Petersen R, Sharifi N, Sheard SM, Staley JR, Tuna S, van der Ent M, Walter K, Wang SY, Wheeler E, Wilder SP, Iotchkova V, Moore C, Sambrook J, Stunnenberg HG, Di Angelantonio E, Kaptoge S, Kuijpers TW, Carrillo-de-Santa-Pau E, Juan D, Rico D, Valencia A, Chen L, Ge B, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yang Y, Guigo R, Beck S, Paul DS, Pastinen T, Bujold D, Bourque G, Frontini M, Danesh J, Roberts DJ, Ouwehand WH, Butterworth AS, Soranzo N. Cell Volume 167 (2016) p.1415-1429.e19 DOI: 10.1016/j.cell.2016.10.042
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RUNX1 mutations in acute myeloid leukemia are associated with distinct clinico-pathologic and genetic features.
Gaidzik VI, Teleanu V, Papaemmanuil E, Weber D, Paschka P, Hahn J, Wallrabenstein T, Kolbinger B, Köhne CH, Horst HA, Brossart P, Held G, Kündgen A, Ringhoffer M, Götze K, Rummel M, Gerstung M, Campbell P, Kraus JM, Kestler HA, Thol F, Heuser M, Schlegelberger B, Ganser A, Bullinger L, Schlenk RF, Döhner K, Döhner H. Leukemia Volume 30 (2016) p.2282 DOI: 10.1038/leu.2016.207
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Genome-wide association analysis of pain severity in dysmenorrhea identifies association at chromosome 1p13.2, near the nerve growth factor locus.
Jones AV, Hockley JR, Hyde C, Gorman D, Sredic-Rhodes A, Bilsland J, McMurray G, Furlotte NA, Hu Y, Hinds DA, Cox PJ, Scollen S. Pain Volume 157 (2016) p.2571-2581 DOI: 10.1097/j.pain.0000000000000678
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Sirtuin 1 stimulates the proliferation and the expression of glycolysis genes in pancreatic neoplastic lesions.
Pinho AV, Mawson A, Gill A, Arshi M, Warmerdam M, Giry-Laterriere M, Eling N, Lie T, Kuster E, Camargo S, Biankin AV, Wu J, Rooman I. Oncotarget Volume 7 (2016) p.74768-74778 DOI: 10.18632/oncotarget.11013
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Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.
Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F, BLUEPRINT Consortium, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P. Cell Volume 167 (2016) p.1369-1384.e19 DOI: 10.1016/j.cell.2016.09.037
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Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage.
Queirós AC, Beekman R, Vilarrasa-Blasi R, Duran-Ferrer M, Clot G, Merkel A, Raineri E, Russiñol N, Castellano G, Beà S, Navarro A, Kulis M, Verdaguer-Dot N, Jares P, Enjuanes A, Calasanz MJ, Bergmann A, Vater I, Salaverría I, van de Werken HJG, Wilson WH, Datta A, Flicek P, Royo R, Martens J, Giné E, Lopez-Guillermo A, Stunnenberg HG, Klapper W, Pott C, Heath S, Gut IG, Siebert R, Campo E, Martín-Subero JI. Cancer Cell Volume 30 (2016) p.806-821 DOI: 10.1016/j.ccell.2016.09.014
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Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium.
Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP, Moreno P, Verma D, Hill E, Drijkoningen J, Gilligan P, Esther CR, Noone PG, Giddings O, Bell SC, Thomson R, Wainwright CE, Coulter C, Pandey S, Wood ME, Stockwell RE, Ramsay KA, Sherrard LJ, Kidd TJ, Jabbour N, Johnson GR, Knibbs LD, Morawska L, Sly PD, Jones A, Bilton D, Laurenson I, Ruddy M, Bourke S, Bowler IC, Chapman SJ, Clayton A, Cullen M, Daniels T, Dempsey O, Denton M, Desai M, Drew RJ, Edenborough F, Evans J, Folb J, Humphrey H, Isalska B, Jensen-Fangel S, Jönsson B, Jones AM, Katzenstein TL, Lillebaek T, MacGregor G, Mayell S, Millar M, Modha D, Nash EF, O'Brien C, O'Brien D, Ohri C, Pao CS, Peckham D, Perrin F, Perry A, Pressler T, Prtak L, Qvist T, Robb A, Rodgers H, Schaffer K, Shafi N, van Ingen J, Walshaw M, Watson D, West N, Whitehouse J, Haworth CS, Harris SR, Ordway D, Parkhill J, Floto RA. Science (New York, N.Y.) Volume 354 (2016) p.751-757 DOI: 10.1126/science.aaf8156
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Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.
Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Cell Volume 167 (2016) p.1125-1136.e8 DOI: 10.1016/j.cell.2016.10.020
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The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.
Stunnenberg HG, International Human Epigenome Consortium, Hirst M. Cell Volume 167 (2016) p.1145-1149 DOI: 10.1016/j.cell.2016.11.007
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Genome-wide analysis identifies 12 loci influencing human reproductive behavior.
Barban N, Jansen R, de Vlaming R, Vaez A, Mandemakers JJ, Tropf FC, Shen X, Wilson JF, Chasman DI, Nolte IM, Tragante V, van der Laan SW, Perry JR, Kong A, BIOS Consortium, Ahluwalia TS, Albrecht E, Yerges-Armstrong L, Atzmon G, Auro K, Ayers K, Bakshi A, Ben-Avraham D, Berger K, Bergman A, Bertram L, Bielak LF, Bjornsdottir G, Bonder MJ, Broer L, Bui M, Barbieri C, Cavadino A, Chavarro JE, Turman C, Concas MP, Cordell HJ, Davies G, Eibich P, Eriksson N, Esko T, Eriksson J, Falahi F, Felix JF, Fontana MA, Franke L, Gandin I, Gaskins AJ, Gieger C, Gunderson EP, Guo X, Hayward C, He C, Hofer E, Huang H, Joshi PK, Kanoni S, Karlsson R, Kiechl S, Kifley A, Kluttig A, Kraft P, Lagou V, Lecoeur C, Lahti J, Li-Gao R, Lind PA, Liu T, Makalic E, Mamasoula C, Matteson L, Mbarek H, McArdle PF, McMahon G, Meddens SF, Mihailov E, Miller M, Missmer SA, Monnereau C, van der Most PJ, Myhre R, Nalls MA, Nutile T, Kalafati IP, Porcu E, Prokopenko I, Rajan KB, Rich-Edwards J, Rietveld CA, Robino A, Rose LM, Rueedi R, Ryan KA, Saba Y, Schmidt D, Smith JA, Stolk L, Streeten E, Tönjes A, Thorleifsson G, Ulivi S, Wedenoja J, Wellmann J, Willeit P, Yao J, Yengo L, Zhao JH, Zhao W, Zhernakova DV, Amin N, Andrews H, Balkau B, Barzilai N, Bergmann S, Biino G, Bisgaard H, Bønnelykke K, Boomsma DI, Buring JE, Campbell H, Cappellani S, Ciullo M, Cox SR, Cucca F, Toniolo D, Davey-Smith G, Deary IJ, Dedoussis G, Deloukas P, van Duijn CM, de Geus EJ, Eriksson JG, Evans DA, Faul JD, Sala CF, Froguel P, Gasparini P, Girotto G, Grabe HJ, Greiser KH, Groenen PJ, de Haan HG, Haerting J, Harris TB, Heath AC, Heikkilä K, Hofman A, Homuth G, Holliday EG, Hopper J, Hyppönen E, Jacobsson B, Jaddoe VW, Johannesson M, Jugessur A, Kähönen M, Kajantie E, Kardia SL, Keavney B, Kolcic I, Koponen P, Kovacs P, Kronenberg F, Kutalik Z, La Bianca M, Lachance G, Iacono WG, Lai S, Lehtimäki T, Liewald DC, LifeLines Cohort Study, Lindgren CM, Liu Y, Luben R, Lucht M, Luoto R, Magnus P, Magnusson PK, Martin NG, McGue M, McQuillan R, Medland SE, Meisinger C, Mellström D, Metspalu A, Traglia M, Milani L, Mitchell P, Montgomery GW, Mook-Kanamori D, de Mutsert R, Nohr EA, Ohlsson C, Olsen J, Ong KK, Paternoster L, Pattie A, Penninx BW, Perola M, Peyser PA, Pirastu M, Polasek O, Power C, Kaprio J, Raffel LJ, Räikkönen K, Raitakari O, Ridker PM, Ring SM, Roll K, Rudan I, Ruggiero D, Rujescu D, Salomaa V, Schlessinger D, Schmidt H, Schmidt R, Schupf N, Smit J, Sorice R, Spector TD, Starr JM, Stöckl D, Strauch K, Stumvoll M, Swertz MA, Thorsteinsdottir U, Thurik AR, Timpson NJ, Tung JY, Uitterlinden AG, Vaccargiu S, Viikari J, Vitart V, Völzke H, Vollenweider P, Vuckovic D, Waage J, Wagner GG, Wang JJ, Wareham NJ, Weir DR, Willemsen G, Willeit J, Wright AF, Zondervan KT, Stefansson K, Krueger RF, Lee JJ, Benjamin DJ, Cesarini D, Koellinger PD, den Hoed M, Snieder H, Mills MC. Nature genetics Volume 48 (2016) p.1462-1472 DOI: 10.1038/ng.3698
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Genome-wide genetic screening with chemically mutagenized haploid embryonic stem cells.
Forment JV, Herzog M, Coates J, Konopka T, Gapp BV, Nijman SM, Adams DJ, Keane TM, Jackson SP. Nature chemical biology Volume 13 (2017) p.12-14 DOI: 10.1038/nchembio.2226
Genenames.org: the HGNC and VGNC resources in 2017.
Yates B, Braschi B, Gray KA, Seal RL, Tweedie S, Bruford EA. Nucleic acids research Volume 45 (2017) p.D619-D625 DOI: 10.1093/nar/gkw1033
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Plant Reactome: a resource for plant pathways and comparative analysis.
Naithani S, Preece J, D'Eustachio P, Gupta P, Amarasinghe V, Dharmawardhana PD, Wu G, Fabregat A, Elser JL, Weiser J, Keays M, Fuentes AM, Petryszak R, Stein LD, Ware D, Jaiswal P. Nucleic acids research Volume 45 (2017) p.D1029-D1039 DOI: 10.1093/nar/gkw932
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RNAcentral: a comprehensive database of non-coding RNA sequences.
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Resolution of ab initio shapes determined from small-angle scattering.
Tuukkanen AT, Kleywegt GJ, Svergun DI. IUCrJ Volume 3 (2016) p.440-447 DOI: 10.1107/s2052252516016018
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Updates in Rhea - an expert curated resource of biochemical reactions.
Morgat A, Lombardot T, Axelsen KB, Aimo L, Niknejad A, Hyka-Nouspikel N, Coudert E, Pozzato M, Pagni M, Moretti S, Rosanoff S, Onwubiko J, Bougueleret L, Xenarios I, Redaschi N, Bridge A. Nucleic acids research Volume 45 (2017) p.D415-D418 DOI: 10.1093/nar/gkw990
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CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.
Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma AN, Doshi S, Courtot M, Lo R, Williams LE, Frye JG, Elsayegh T, Sardar D, Westman EL, Pawlowski AC, Johnson TA, Brinkman FS, Wright GD, McArthur AG. Nucleic acids research Volume 45 (2017) p.D566-D573 DOI: 10.1093/nar/gkw1004
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Evolutionary hallmarks of the human proteome: chasing the age and coregulation of protein-coding genes.
Lopes KP, Campos-Laborie FJ, Vialle RA, Ortega JM, De Las Rivas J. BMC genomics Volume 17 (2016) p.725 DOI: 10.1186/s12864-016-3062-y
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AAgAtlas 1.0: a human autoantigen database.
Wang D, Yang L, Zhang P, LaBaer J, Hermjakob H, Li D, Yu X. Nucleic acids research Volume 45 (2017) p.D769-D776 DOI: 10.1093/nar/gkw946
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The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.
Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA. Nucleic acids research Volume 45 (2017) p.D1100-D1106 DOI: 10.1093/nar/gkw936
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An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu F, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser D, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Di Palma F, Phillips A, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD. Preprint DOI: 10.1101/080796
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Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.
Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y. Nucleic acids research Volume 45 (2017) p.D347-D352 DOI: 10.1093/nar/gkw918
The human-induced pluripotent stem cell initiative-data resources for cellular genetics.
Streeter I, Harrison PW, Faulconbridge A, The HipSci Consortium, Flicek P, Parkinson H, Clarke L. Nucleic acids research Volume 45 (2017) p.D691-D697 DOI: 10.1093/nar/gkw928
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Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease.
Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RWF, Huttenhower C, Dijkstra G, Xavier RJ, Festen EAM, Wijmenga C, Zhernakova A, Weersma RK. Gut Volume 67 (2018) p.108-119 DOI: 10.1136/gutjnl-2016-312135
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The effect of host genetics on the gut microbiome.
Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, Deelen P, Vatanen T, Schirmer M, Smeekens SP, Zhernakova DV, Jankipersadsing SA, Jaeger M, Oosting M, Cenit MC, Masclee AA, Swertz MA, Li Y, Kumar V, Joosten L, Harmsen H, Weersma RK, Franke L, Hofker MH, Xavier RJ, Jonkers D, Netea MG, Wijmenga C, Fu J, Zhernakova A. Nature genetics Volume 48 (2016) p.1407-1412 DOI: 10.1038/ng.3663
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A multicenter study benchmarks software tools for label-free proteome quantification.
Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S. Nature biotechnology Volume 34 (2016) p.1130-1136 DOI: 10.1038/nbt.3685
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ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions.
Marenco L, Wang R, McDougal R, Olender T, Twik M, Bruford E, Liu X, Zhang J, Lancet D, Shepherd G, Crasto C. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw132
Evolution of protein phosphorylation across 18 fungal species.
Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Viéitez C, Solé C, Swaney DL, Stanford LB, Liachko I, Böttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villén J. Science (New York, N.Y.) Volume 354 (2016) p.229-232 DOI: 10.1126/science.aaf2144
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A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia.
Tzelepis K, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, Mupo A, Grinkevich V, Li M, Mazan M, Gozdecka M, Ohnishi S, Cooper J, Patel M, McKerrell T, Chen B, Domingues AF, Gallipoli P, Teichmann S, Ponstingl H, McDermott U, Saez-Rodriguez J, Huntly BJP, Iorio F, Pina C, Vassiliou GS, Yusa K. Cell reports Volume 17 (2016) p.1193-1205 DOI: 10.1016/j.celrep.2016.09.079
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A High-Density Map for Navigating the Human Polycomb Complexome.
Hauri S, Comoglio F, Seimiya M, Gerstung M, Glatter T, Hansen K, Aebersold R, Paro R, Gstaiger M, Beisel C. Cell reports Volume 17 (2016) p.583-595 DOI: 10.1016/j.celrep.2016.08.096
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Topological analysis of metabolic networks integrating co-segregating transcriptomes and metabolomes in type 2 diabetic rat congenic series.
Dumas ME, Domange C, Calderari S, Martínez AR, Ayala R, Wilder SP, Suárez-Zamorano N, Collins SC, Wallis RH, Gu Q, Wang Y, Hue C, Otto GW, Argoud K, Navratil V, Mitchell SC, Lindon JC, Holmes E, Cazier JB, Nicholson JK, Gauguier D. Genome medicine Volume 8 (2016) p.101 DOI: 10.1186/s13073-016-0352-6
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Identifying ELIXIR Core Data Resources.
Durinx C, McEntyre J, Appel R, Apweiler R, Barlow M, Blomberg N, Cook C, Gasteiger E, Kim JH, Lopez R, Redaschi N, Stockinger H, Teixeira D, Valencia A. F1000Research Volume 5 (2016) DOI: 10.12688/f1000research.9656.1
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Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs.
Zerbino DR, Ballinger T, Paten B, Hickey G, Haussler D. BMC bioinformatics Volume 17 (2016) p.400 DOI: 10.1186/s12859-016-1258-4
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.11033 DOI: 10.1093/nar/gkw880
A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL.
Mutowo P, Bento AP, Dedman N, Gaulton A, Hersey A, Lomax J, Overington JP. Journal of biomedical semantics Volume 7 (2016) p.59 DOI: 10.1186/s13326-016-0102-0
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Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening.
Lenselink EB, Jespers W, van Vlijmen HW, IJzerman AP, van Westen GJ. Journal of chemical information and modeling Volume 56 (2016) p.2053-2060 DOI: 10.1021/acs.jcim.6b00314
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Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.
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Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps.
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Native phasing of x-ray free-electron laser data for a G protein-coupled receptor.
Batyuk A, Galli L, Ishchenko A, Han GW, Gati C, Popov PA, Lee MY, Stauch B, White TA, Barty A, Aquila A, Hunter MS, Liang M, Boutet S, Pu M, Liu ZJ, Nelson G, James D, Li C, Zhao Y, Spence JC, Liu W, Fromme P, Katritch V, Weierstall U, Stevens RC, Cherezov V. Science advances Volume 2 (2016) p.e1600292 DOI: 10.1126/sciadv.1600292
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Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms.
Slieker RC, van Iterson M, Luijk R, Beekman M, Zhernakova DV, Moed MH, Mei H, van Galen M, Deelen P, Bonder MJ, Zhernakova A, Uitterlinden AG, Tigchelaar EF, Stehouwer CD, Schalkwijk CG, van der Kallen CJ, Hofman A, van Heemst D, de Geus EJ, van Dongen J, Deelen J, van den Berg LH, van Meurs J, Jansen R, 't Hoen PA, Franke L, Wijmenga C, Veldink JH, Swertz MA, van Greevenbroek MM, van Duijn CM, Boomsma DI, BIOS consortium, Slagboom PE, Heijmans BT. Genome biology Volume 17 (2016) p.191 DOI: 10.1186/s13059-016-1053-6
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Binding free energy calculations on E-selectin complexes with sLex oligosaccharide analogs.
Barra PA, Ribeiro AJ, Ramos MJ, Jiménez VA, Alderete JB, Fernandes PA. Chemical biology & drug design Volume 89 (2017) p.114-123 DOI: 10.1111/cbdd.12837
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Drug discovery and development in the era of Big Data.
Bajorath J, Overington J, Jenkins JL, Walters P. Future medicinal chemistry (2016) DOI: 10.4155/fmc-2014-0081
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Selenoprotein Gene Nomenclature.
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Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence.
Garin-Muga A, Odriozola L, Martínez-Val A, Del Toro N, Martínez R, Molina M, Cantero L, Rivera R, Garrido N, Dominguez F, Sanchez Del Pino MM, Vizcaíno JA, Corrales FJ, Segura V. Journal of proteome research Volume 15 (2016) p.4101-4115 DOI: 10.1021/acs.jproteome.6b00437
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First Draft Genome Sequence of a UK Strain (UK99) of Fusarium culmorum.
Urban M, King R, Andongabo A, Maheswari U, Pedro H, Kersey P, Hammond-Kosack K. Genome announcements Volume 4 (2016) DOI: 10.1128/genomea.00771-16
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A novel multisystem disease associated with recessive mutations in the tyrosyl-tRNA synthetase (YARS) gene.
Nowaczyk MJ, Huang L, Tarnopolsky M, Schwartzentruber J, Majewski J, Bulman DE, FORGE Canada Consortium, Care4Rare Canada Consortium, Hartley T, Boycott KM. American journal of medical genetics. Part A Volume 173 (2017) p.126-134 DOI: 10.1002/ajmg.a.37973
The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.
Clarke L, Fairley S, Zheng-Bradley X, Streeter I, Perry E, Lowy E, Tassé AM, Flicek P. Nucleic acids research Volume 45 (2017) p.D854-D859 DOI: 10.1093/nar/gkw829
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High-throughput discovery of novel developmental phenotypes.
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Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles.
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Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation
Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MSF, Fogg LG, Stubbington MJT, Otzen Bagger F, Zwiessele M, Lawrence N, Souza-Fonseca-Guimaraes F, Heath WR, Billker O, Stegle O, Haque A, Teichmann SA. Preprint DOI: 10.1101/074971
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Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.
Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A, GEUVADIS Consortium, Rosenstiel P, Strom TM, Lappalainen T, Guigó R, Sammeth M. Scientific reports Volume 6 (2016) p.32406 DOI: 10.1038/srep32406
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Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immunity
Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJ, Cvejic A, Gfeller D. Preprint DOI: 10.1101/074344
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Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.
Speranzini V, Rotili D, Ciossani G, Pilotto S, Marrocco B, Forgione M, Lucidi A, Forneris F, Mehdipour P, Velankar S, Mai A, Mattevi A. Science advances Volume 2 (2016) p.e1601017 DOI: 10.1126/sciadv.1601017
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A subset of RAB proteins modulates PP2A phosphatase activity.
Sacco F, Mattioni A, Boldt K, Panni S, Santonico E, Castagnoli L, Ueffing M, Cesareni G. Scientific reports Volume 6 (2016) p.32857 DOI: 10.1038/srep32857
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Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data
Lun ATL, Marioni JC. Preprint DOI: 10.1101/073973
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HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015).
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Power Analysis of Single Cell RNA-Sequencing Experiments
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Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts.
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An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
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Overview of the interactive task in BioCreative V.
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Warped Matrix Factorisation for Multi-view Data Integration
Pratanwanich N, Lió P, Stegle O. Machine Learning and Knowledge Discovery in Databases. ECML PKDD 2016. Springer , Cham (Lecture Notes in Computer Science, vol 9852) DOI: 10.1007/978-3-319-46227-1_49
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Structural and Biochemical Basis for Intracellular Kinase Inhibition by Src-specific Peptidic Macrocycles.
Aleem S, Georghiou G, Kleiner RE, Guja K, Craddock BP, Lyczek A, Chan AI, Garcia-Diaz M, Miller WT, Liu DR, Seeliger MA. Cell chemical biology Volume 23 (2016) p.1103-1112 DOI: 10.1016/j.chembiol.2016.07.017
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Intron retention-dependent gene regulation in Cryptococcus neoformans.
Gonzalez-Hilarion S, Paulet D, Lee KT, Hon CC, Lechat P, Mogensen E, Moyrand F, Proux C, Barboux R, Bussotti G, Hwang J, Coppée JY, Bahn YS, Janbon G. Scientific reports Volume 6 (2016) p.32252 DOI: 10.1038/srep32252
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How policy can help develop and sustain workforce capacity in UK dementia research: insights from a career tracking analysis and stakeholder interviews.
Marjanovic S, Lichten CA, Robin E, Parks S, Harte E, MacLure C, Walton C, Pickett J. BMJ open Volume 6 (2016) p.e012052 DOI: 10.1136/bmjopen-2016-012052
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A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.
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Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks
Muetze T, Goenawan IH, Wiencko HL, Bernal-Llinares M, Bryan K, Lynn DJ. Preprint DOI: 10.12688/f1000research.9118.2
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Impaired removal of H3K4 methylation affects cell fate determination and gene transcription.
Lussi YC, Mariani L, Friis C, Peltonen J, Myers TR, Krag C, Wong G, Salcini AE. Development (Cambridge, England) Volume 143 (2016) p.3751-3762 DOI: 10.1242/dev.139139
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Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design?
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Mitochondrial Complex I Is a Global Regulator of Secondary Metabolism, Virulence and Azole Sensitivity in Fungi.
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A High Density Map for Navigating the Human Polycomb Complexome
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PASP — a whole-transcriptome poly(A) tail length determination assay for the Illumina platform
Sipos B, Stütz AM, Slodkowicz G, Massingham T, Korbel J, Goldman N. Preprint DOI: 10.1101/060004
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Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.
Torrente A, Lukk M, Xue V, Parkinson H, Rung J, Brazma A. PloS one Volume 11 (2016) p.e0157484 DOI: 10.1371/journal.pone.0157484
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Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution
Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC, Odom DT, Flicek P. Preprint DOI: 10.1101/059873
Promiscuous or discriminating: Has the favored mRNA target of Fragile X Mental Retardation Protein been overlooked?
McMahon AC, Rosbash M. Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.7009-7011 DOI: 10.1073/pnas.1607665113
Databases and Archiving for CryoEM.
Patwardhan A, Lawson CL. Methods in enzymology Volume 579 (2016) p.393-412 DOI: 10.1016/bs.mie.2016.04.015
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QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni.
Melo-Filho CC, Dantas RF, Braga RC, Neves BJ, Senger MR, Valente WC, Rezende-Neto JM, Chaves WT, Muratov EN, Paveley RA, Furnham N, Kamentsky L, Carpenter AE, Silva-Junior FP, Andrade CH. Journal of chemical information and modeling Volume 56 (2016) p.1357-1372 DOI: 10.1021/acs.jcim.6b00055
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Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability.
Schiffthaler B, Kostadima M, NGS Trainer Consortium, Delhomme N, Rustici G. PLoS computational biology Volume 12 (2016) p.e1004937 DOI: 10.1371/journal.pcbi.1004937
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CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.
Cairns J, Freire-Pritchett P, Wingett SW, Várnai C, Dimond A, Plagnol V, Zerbino D, Schoenfelder S, Javierre BM, Osborne C, Fraser P, Spivakov M. Genome biology Volume 17 (2016) p.127 DOI: 10.1186/s13059-016-0992-2
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Navigating the phenotype frontier: The Monarch Initiative
McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine J, Jacobsen JO, Keith D, Laraway B, Lewis SE, Nguyen Xuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Mungall CJ, Groza T, Smedley D, Robinson PN, Haendel MA. Preprint DOI: 10.1101/059204
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Rising levels of atmospheric oxygen and evolution of Nrf2.
Gacesa R, Dunlap WC, Barlow DJ, Laskowski RA, Long PF. Scientific reports Volume 6 (2016) p.27740 DOI: 10.1038/srep27740
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Mixed Nodule Infection in Sinorhizobium meliloti-Medicago sativa Symbiosis Suggest the Presence of Cheating Behavior.
Checcucci A, Azzarello E, Bazzicalupo M, Galardini M, Lagomarsino A, Mancuso S, Marti L, Marzano MC, Mocali S, Squartini A, Zanardo M, Mengoni A. Frontiers in plant science Volume 7 (2016) p.835 DOI: 10.3389/fpls.2016.00835
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Strand-specific, high-resolution mapping of modified RNA polymerase II.
Milligan L, Huynh-Thu VA, Delan-Forino C, Tuck A, Petfalski E, Lombraña R, Sanguinetti G, Kudla G, Tollervey D. Molecular systems biology Volume 12 (2016) p.874 DOI: 10.15252/msb.20166869
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Combinatorial strategies for combating invasive fungal infections.
Spitzer M, Robbins N, Wright GD. Virulence Volume 8 (2017) p.169-185 DOI: 10.1080/21505594.2016.1196300
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Personally tailored cancer management based on knowledge banks of genomic and clinical data
Gerstung M, Papaemmanuil E, Martincorena I, Bullinger L, Gaidzik VI, Paschka P, Heuser M, Thol F, Bolli N, Ganly P, Ganser A, McDermott U, Döhner K, Schlenk RF, Döhner H, Campbell PJ. Preprint DOI: 10.1101/057497
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PhenoImageShare: an image annotation and query infrastructure.
Adebayo S, McLeod K, Tudose I, Osumi-Sutherland D, Burdett T, Baldock R, Burger A, Parkinson H. Journal of biomedical semantics Volume 7 (2016) p.35 DOI: 10.1186/s13326-016-0072-2
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HDTD: analyzing multi-tissue gene expression data.
Touloumis A, Marioni JC, Tavaré S. Bioinformatics (Oxford, England) Volume 32 (2016) p.2193-2195 DOI: 10.1093/bioinformatics/btw224
The Ensembl Variant Effect Predictor.
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. Genome biology Volume 17 (2016) p.122 DOI: 10.1186/s13059-016-0974-4
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Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.
Tripathi S, Vercruysse S, Chawla K, Christie KR, Blake JA, Huntley RP, Orchard S, Hermjakob H, Thommesen L, Lægreid A, Kuiper M. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw088
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Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS, Harrow J. Nature communications Volume 7 (2016) p.11778 DOI: 10.1038/ncomms11778
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Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination.
Bolland DJ, Koohy H, Wood AL, Matheson LS, Krueger F, Stubbington MJ, Baizan-Edge A, Chovanec P, Stubbs BA, Tabbada K, Andrews SR, Spivakov M, Corcoran AE. Cell reports Volume 15 (2016) p.2475-2487 DOI: 10.1016/j.celrep.2016.05.020
Genomic Classification and Prognosis in Acute Myeloid Leukemia.
Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, Potter NE, Heuser M, Thol F, Bolli N, Gundem G, Van Loo P, Martincorena I, Ganly P, Mudie L, McLaren S, O'Meara S, Raine K, Jones DR, Teague JW, Butler AP, Greaves MF, Ganser A, Döhner K, Schlenk RF, Döhner H, Campbell PJ. The New England journal of medicine Volume 374 (2016) p.2209-2221 DOI: 10.1056/nejmoa1516192
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Advancing vector biology research: a community survey for future directions, research applications and infrastructure requirements.
Kohl A, Pondeville E, Schnettler E, Crisanti A, Supparo C, Christophides GK, Kersey PJ, Maslen GL, Takken W, Koenraadt CJ, Oliva CF, Busquets N, Abad FX, Failloux AB, Levashina EA, Wilson AJ, Veronesi E, Pichard M, Arnaud Marsh S, Simard F, Vernick KD. Pathogens and global health Volume 110 (2016) p.164-172 DOI: 10.1080/20477724.2016.1211475
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Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Proteins Volume 84 Suppl 1 (2016) p.323-348 DOI: 10.1002/prot.25007
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A rule-based model of insulin signalling pathway.
Di Camillo B, Carlon A, Eduati F, Toffolo GM. BMC systems biology Volume 10 (2016) p.38 DOI: 10.1186/s12918-016-0281-4
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GENOMICS. A federated ecosystem for sharing genomic, clinical data.
Global Alliance for Genomics and Health. Science (New York, N.Y.) Volume 352 (2016) p.1278-1280 DOI: 10.1126/science.aaf6162
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Logical Modeling and Dynamical Analysis of Cellular Networks.
Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya C. Frontiers in genetics Volume 7 (2016) p.94 DOI: 10.3389/fgene.2016.00094
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RAFTS3: Rapid Alignment-Free Tool for Sequence Similarity Search
Vialle RA, Oliveira Pedrosa Fd, Weiss VA, Guizelini D, Tibaes JH, Marchaukoski JN, de Souza EM, Raittz RT. Preprint DOI: 10.1101/055269
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JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
Roll J, Zirbel CL, Sweeney B, Petrov AI, Leontis N. Nucleic acids research Volume 44 (2016) p.W320-7 DOI: 10.1093/nar/gkw453
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Polymorphism in a lincRNA Associates with a Doubled Risk of Pneumococcal Bacteremia in Kenyan Children.
Kenyan Bacteraemia Study Group, Wellcome Trust Case Control Consortium 2 (WTCCC2), Rautanen A, Pirinen M, Mills TC, Rockett KA, Strange A, Ndungu AW, Naranbhai V, Gilchrist JJ, Bellenguez C, Freeman C, Band G, Bumpstead SJ, Edkins S, Giannoulatou E, Gray E, Dronov S, Hunt SE, Langford C, Pearson RD, Su Z, Vukcevic D, Macharia AW, Uyoga S, Ndila C, Mturi N, Njuguna P, Mohammed S, Berkley JA, Mwangi I, Mwarumba S, Kitsao BS, Lowe BS, Morpeth SC, Khandwalla I, Kilifi Bacteraemia Surveillance Group, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CNA, Plomin R, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Deloukas P, Peltonen L, Williams TN, Scott JAG, Chapman SJ, Donnelly P, Hill AVS, Spencer CCA. American journal of human genetics Volume 98 (2016) p.1092-1100 DOI: 10.1016/j.ajhg.2016.03.025
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Common genetic variation drives molecular heterogeneity in human IPSCs
Kilpinen H, Goncalves A, Leha A, Afzal V, Ashford S, Bala S, Bensaddek D, Casale FP, Culley O, Danacek P, Faulconbridge A, Harrison P, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Preprint DOI: 10.1101/055160
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spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.
Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A. Nucleic acids research Volume 44 (2016) p.W176-80 DOI: 10.1093/nar/gkw443
The cellular microscopy phenotype ontology.
Jupp S, Malone J, Burdett T, Heriche JK, Williams E, Ellenberg J, Parkinson H, Rustici G. Journal of biomedical semantics Volume 7 (2016) p.28 DOI: 10.1186/s13326-016-0074-0
HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.
Bryan K, Jarboui MA, Raso C, Bernal-Llinares M, McCann B, Rauch J, Boldt K, Lynn DJ. Journal of proteome research Volume 15 (2016) p.2072-2079 DOI: 10.1021/acs.jproteome.5b01008
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LOGIQA: a database dedicated to long-range genome interactions quality assessment.
Mendoza-Parra MA, Blum M, Malysheva V, Cholley PE, Gronemeyer H. BMC genomics Volume 17 (2016) p.355 DOI: 10.1186/s12864-016-2642-1
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Multilevel models improve precision and speed of IC50 estimates.
Vis DJ, Bombardelli L, Lightfoot H, Iorio F, Garnett MJ, Wessels LF. Pharmacogenomics Volume 17 (2016) p.691-700 DOI: 10.2217/pgs.16.15
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Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).
Welch L, Brooksbank C, Schwartz R, Morgan SL, Gaeta B, Kilpatrick AM, Mietchen D, Moore BL, Mulder N, Pauley M, Pearson W, Radivojac P, Rosenberg N, Rosenwald A, Rustici G, Warnow T. PLoS computational biology Volume 12 (2016) p.e1004943 DOI: 10.1371/journal.pcbi.1004943
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Identification of a germline F692L drug resistance variant in cis with Flt3-internal tandem duplication in knock-in mice.
Dovey OM, Chen B, Mupo A, Friedrich M, Grove CS, Cooper JL, Lee B, Varela I, Huang Y, Vassiliou GS. Haematologica Volume 101 (2016) p.e328-31 DOI: 10.3324/haematol.2016.146159
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Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation.
Proserpio V, Piccolo A, Haim-Vilmovsky L, Kar G, Lönnberg T, Svensson V, Pramanik J, Natarajan KN, Zhai W, Zhang X, Donati G, Kayikci M, Kotar J, McKenzie AN, Montandon R, Billker O, Woodhouse S, Cicuta P, Nicodemi M, Teichmann SA. Genome biology Volume 17 (2016) p.103 DOI: 10.1186/s13059-016-0957-5
Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.
Rudolph KL, Schmitt BM, Villar D, White RJ, Marioni JC, Kutter C, Odom DT. PLoS genetics Volume 12 (2016) p.e1006024 DOI: 10.1371/journal.pgen.1006024
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Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns.
Digles D, Zdrazil B, Neefs JM, Van Vlijmen H, Herhaus C, Caracoti A, Brea J, Roibás B, Loza MI, Queralt-Rosinach N, Furlong LI, Gaulton A, Bartek L, Senger S, Chichester C, Engkvist O, Evelo CT, Franklin NI, Marren D, Ecker GF, Jacoby E. MedChemComm Volume 7 (2016) p.1237-1244 DOI: 10.1039/c6md00065g
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Subtype-specific micro-RNA expression signatures in breast cancer progression.
Haakensen VD, Nygaard V, Greger L, Aure MR, Fromm B, Bukholm IR, Lüders T, Chin SF, Git A, Caldas C, Kristensen VN, Brazma A, Børresen-Dale AL, Hovig E, Helland Å. International journal of cancer Volume 139 (2016) p.1117-1128 DOI: 10.1002/ijc.30142
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Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD).
Sousa SF, Sousa JF, Barbosa AC, Ferreira CE, Neves RP, Ribeiro AJ, Fernandes PA, Ramos MJ. The journal of physical chemistry. A Volume 120 (2016) p.5300-5306 DOI: 10.1021/acs.jpca.6b01536
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BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.
Ryu J, Lee M, Cha J, Laskowski RA, Ryu SE, Kim DS. Nucleic acids research Volume 44 (2016) p.W416-23 DOI: 10.1093/nar/gkw368
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RUNX1 mutations in acute myeloid leukemia are associated with distinct clinico-pathologic and genetic features.
Gaidzik VI, Teleanu V, Papaemmanuil E, Weber D, Paschka P, Hahn J, Wallrabenstein T, Kolbinger B, Köhne CH, Horst HA, Brossart P, Held G, Kündgen A, Ringhoffer M, Götze K, Rummel M, Gerstung M, Campbell P, Kraus JM, Kestler HA, Thol F, Heuser M, Schlegelberger B, Ganser A, Bullinger L, Schlenk RF, Döhner K, Döhner H. Leukemia Volume 30 (2016) p.2160-2168 DOI: 10.1038/leu.2016.126
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Effects of Pin1 Loss in Hdh(Q111) Knock-in Mice.
Agostoni E, Michelazzi S, Maurutto M, Carnemolla A, Ciani Y, Vatta P, Roncaglia P, Zucchelli S, Leanza G, Mantovani F, Gustincich S, Santoro C, Piazza S, Del Sal G, Persichetti F. Frontiers in cellular neuroscience Volume 10 (2016) p.110 DOI: 10.3389/fncel.2016.00110
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Landscape of somatic mutations in 560 breast cancer whole-genome sequences.
Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GK, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van't Veer L, Tutt A, Knappskog S, Tan BK, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR. Nature Volume 534 (2016) p.47-54 DOI: 10.1038/nature17676
The topography of mutational processes in breast cancer genomes.
Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H, Staaf J, Sieuwerts AM, Brinkman AB, Martin S, Ramakrishna M, Butler A, Kim HY, Borg Å, Sotiriou C, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Sale J, Rada C, Stratton MR, Birney E, Nik-Zainal S. Nature communications Volume 7 (2016) p.11383 DOI: 10.1038/ncomms11383
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Ensembl comparative genomics resources.
Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw053
Improved definition of the mouse transcriptome via targeted RNA sequencing.
Bussotti G, Leonardi T, Clark MB, Mercer TR, Crawford J, Malquori L, Notredame C, Dinger ME, Mattick JS, Enright AJ. Genome research Volume 26 (2016) p.705-716 DOI: 10.1101/gr.199760.115
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Proteotranscriptomic Analysis Reveals Stage Specific Changes in the Molecular Landscape of Clear-Cell Renal Cell Carcinoma.
Neely BA, Wilkins CE, Marlow LA, Malyarenko D, Kim Y, Ignatchenko A, Sasinowska H, Sasinowski M, Nyalwidhe JO, Kislinger T, Copland JA, Drake RR. PloS one Volume 11 (2016) p.e0154074 DOI: 10.1371/journal.pone.0154074
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The Ontology for Biomedical Investigations.
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. PloS one Volume 11 (2016) p.e0154556 DOI: 10.1371/journal.pone.0154556
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Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci
Amaral PP, Leonardi T, Han N, Viré E, Gascoigne DK, Arias-Carrasco R, Büscher M, Zhang A, Pluchino S, Maracaja-Coutinho V, Nakaya HI, Hemberg M, Shiekhattar R, Enright AJ, Kouzarides T. Preprint DOI: 10.1101/051052
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Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.
Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA, LifeLines cohort study, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J. Science (New York, N.Y.) Volume 352 (2016) p.565-569 DOI: 10.1126/science.aad3369
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Population-level analysis of gut microbiome variation.
Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D'hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J. Science (New York, N.Y.) Volume 352 (2016) p.560-564 DOI: 10.1126/science.aad3503
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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 JC, Soylemez O, Kondrashov F, Leptin M. Open biology Volume 6 (2016) p.160009 DOI: 10.1098/rsob.160009
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Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.
Lun AT, Bach K, Marioni JC. Genome biology Volume 17 (2016) p.75 DOI: 10.1186/s13059-016-0947-7
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From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.
Kılıç S, Sagitova DM, Wolfish S, Bely B, Courtot M, Ciufo S, Tatusova T, O'Donovan C, Chibucos MC, Martin MJ, Erill I. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw055
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Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome.
Zimmer F, Harrison PW, Dessimoz C, Mank JE. Genome biology and evolution Volume 8 (2016) p.1233-1242 DOI: 10.1093/gbe/evw075
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Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.
Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GR, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich Y, Handsaker RE, 1000 Genomes Project Consortium, Bustamante CD, Tyler-Smith C. Nature genetics Volume 48 (2016) p.593-599 DOI: 10.1038/ng.3559
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CHRONICITY OF DEPRESSION AND MOLECULAR MARKERS IN A LARGE SAMPLE OF HAN CHINESE WOMEN.
Edwards AC, Aggen SH, Cai N, Bigdeli TB, Peterson RE, Docherty AR, Webb BT, Bacanu SA, Flint J, Kendler KS. Depression and anxiety Volume 33 (2016) p.1048-1054 DOI: 10.1002/da.22517
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HIV-1 capsid is involved in post-nuclear entry steps.
Chen NY, Zhou L, Gane PJ, Opp S, Ball NJ, Nicastro G, Zufferey M, Buffone C, Luban J, Selwood D, Diaz-Griffero F, Taylor I, Fassati A. Retrovirology Volume 13 (2016) p.28 DOI: 10.1186/s12977-016-0262-0
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Organization, evolution and functions of the human and mouse Ly6/uPAR family genes.
Loughner CL, Bruford EA, McAndrews MS, Delp EE, Swamynathan S, Swamynathan SK. Human genomics Volume 10 (2016) p.10 DOI: 10.1186/s40246-016-0074-2
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The influence of a short-term gluten-free diet on the human gut microbiome.
Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, Zhong H, Vatanen T, Gevers D, Wijmenga C, Wang Y, Zhernakova A. Genome medicine Volume 8 (2016) p.45 DOI: 10.1186/s13073-016-0295-y
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SignaFish: A Zebrafish-Specific Signaling Pathway Resource.
Csályi K, Fazekas D, Kadlecsik T, Türei D, Gul L, Horváth B, Módos D, Demeter A, Pápai N, Lenti K, Csermely P, Vellai T, Korcsmáros T, Varga M. Zebrafish Volume 13 (2016) p.541-544 DOI: 10.1089/zeb.2016.1277
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Omics Discovery Index - Discovering and Linking Public ‘Omics’ Datasets
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RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.
Miao Z, Westhof E. Nucleic acids research Volume 44 (2016) p.W562-7 DOI: 10.1093/nar/gkw251
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A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic, and platelet disorders.
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Ten Simple Rules for Taking Advantage of git and GitHub
Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Veiga Leprevost Fd, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaino JA. Preprint DOI: 10.1101/048744
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Beyond comparisons of means: understanding changes in gene expression at the single-cell level.
Vallejos CA, Richardson S, Marioni JC. Genome biology Volume 17 (2016) p.70 DOI: 10.1186/s13059-016-0930-3
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Extending gene ontology in the context of extracellular RNA and vesicle communication.
Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC. Journal of biomedical semantics Volume 7 (2016) p.19 DOI: 10.1186/s13326-016-0061-5
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Cox26 is a novel stoichiometric subunit of the yeast cytochrome c oxidase.
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A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.
Patro R, Norel R, Prill RJ, Saez-Rodriguez J, Lorenz P, Steinbeck F, Ziems B, Luštrek M, Barbarini N, Tiengo A, Bellazzi R, Thiesen HJ, Stolovitzky G, Kingsford C. BMC bioinformatics Volume 17 (2016) p.155 DOI: 10.1186/s12859-016-1008-7
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CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.
Schofield EC, Carver T, Achuthan P, Freire-Pritchett P, Spivakov M, Todd JA, Burren OS. Bioinformatics (Oxford, England) Volume 32 (2016) p.2511-2513 DOI: 10.1093/bioinformatics/btw173
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Genetic and environmental influences interact with age and sex in shaping the human methylome.
van Dongen J, Nivard MG, Willemsen G, Hottenga JJ, Helmer Q, Dolan CV, Ehli EA, Davies GE, van Iterson M, Breeze CE, Beck S, BIOS Consortium, Suchiman HE, Jansen R, van Meurs JB, Heijmans BT, Slagboom PE, Boomsma DI. Nature communications Volume 7 (2016) p.11115 DOI: 10.1038/ncomms11115
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Mutational History of a Human Cell Lineage from Somatic to Induced Pluripotent Stem Cells.
Rouhani FJ, Nik-Zainal S, Wuster A, Li Y, Conte N, Koike-Yusa H, Kumasaka N, Vallier L, Yusa K, Bradley A. PLoS genetics Volume 12 (2016) p.e1005932 DOI: 10.1371/journal.pgen.1005932
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Lithium Promotes Longevity through GSK3/NRF2-Dependent Hormesis.
Castillo-Quan JI, Li L, Kinghorn KJ, Ivanov DK, Tain LS, Slack C, Kerr F, Nespital T, Thornton J, Hardy J, Bjedov I, Partridge L. Cell reports Volume 15 (2016) p.638-650 DOI: 10.1016/j.celrep.2016.03.041
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Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes.
Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB. PLoS computational biology Volume 12 (2016) p.e1004862 DOI: 10.1371/journal.pcbi.1004862
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The systems biology format converter.
Rodriguez N, Pettit JB, Dalle Pezze P, Li L, Henry A, van Iersel MP, Jalowicki G, Kutmon M, Natarajan KN, Tolnay D, Stefan MI, Evelo CT, Le Novère N. BMC bioinformatics Volume 17 (2016) p.154 DOI: 10.1186/s12859-016-1000-2
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Developing a web-based SKOS editor.
Conway M, Khojoyan A, Fana F, Scuba W, Castine M, Mowery D, Chapman W, Jupp S. Journal of biomedical semantics Volume 7 (2016) p.5 DOI: 10.1186/s13326-015-0043-z
ProbOnto: ontology and knowledge base of probability distributions.
Swat MJ, Grenon P, Wimalaratne S. Bioinformatics (Oxford, England) Volume 32 (2016) p.2719-2721 DOI: 10.1093/bioinformatics/btw170
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Divergence in gene expression within and between two closely related flycatcher species.
Uebbing S, Künstner A, Mäkinen H, Backström N, Bolivar P, Burri R, Dutoit L, Mugal CF, Nater A, Aken B, Flicek P, Martin FJ, Searle SM, Ellegren H. Molecular ecology Volume 25 (2016) p.2015-2028 DOI: 10.1111/mec.13596
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Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
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Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.
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TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins.
McMahon AC, Rahman R, Jin H, Shen JL, Fieldsend A, Luo W, Rosbash M. Cell Volume 165 (2016) p.742-753 DOI: 10.1016/j.cell.2016.03.007
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Association between DNA Methylation in Whole Blood and Measures of Glucose Metabolism: KORA F4 Study.
Kriebel J, Herder C, Rathmann W, Wahl S, Kunze S, Molnos S, Volkova N, Schramm K, Carstensen-Kirberg M, Waldenberger M, Gieger C, Peters A, Illig T, Prokisch H, Roden M, Grallert H. PloS one Volume 11 (2016) p.e0152314 DOI: 10.1371/journal.pone.0152314
UniProt Tools.
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Direct inhibition of osteoblastic Wnt pathway by fibroblast growth factor 23 contributes to bone loss in chronic kidney disease.
Carrillo-López N, Panizo S, Alonso-Montes C, Román-García P, Rodríguez I, Martínez-Salgado C, Dusso AS, Naves M, Cannata-Andía JB. Kidney international Volume 90 (2016) p.77-89 DOI: 10.1016/j.kint.2016.01.024
MetaboLights: An Open-Access Database Repository for Metabolomics Data.
Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P, Rocca-Serra P, Nainala VC, Spicer RA, Williams M, Li X, Salek RM, Griffin JL, Steinbeck C. Current protocols in bioinformatics Volume 53 (2016) p.14.13.1-14.13.18 DOI: 10.1002/0471250953.bi1413s53
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Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance.
Phelan J, Coll F, McNerney R, Ascher DB, Pires DE, Furnham N, Coeck N, Hill-Cawthorne GA, Nair MB, Mallard K, Ramsay A, Campino S, Hibberd ML, Pain A, Rigouts L, Clark TG. BMC medicine Volume 14 (2016) p.31 DOI: 10.1186/s12916-016-0575-9
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation.
Sarntivijai S, Vasant D, Jupp S, Saunders G, Bento AP, Gonzalez D, Betts J, Hasan S, Koscielny G, Dunham I, Parkinson H, Malone J. Journal of biomedical semantics Volume 7 (2016) p.8 DOI: 10.1186/s13326-016-0051-7
EMPIAR: a public archive for raw electron microscopy image data.
Iudin A, Korir PK, Salavert-Torres J, Kleywegt GJ, Patwardhan A. Nature methods Volume 13 (2016) p.387-388 DOI: 10.1038/nmeth.3806
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations.
Sangrador-Vegas A, Mitchell AL, Chang HY, Yong SY, Finn RD. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw027
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Exploring regulatory networks of miR-96 in the developing inner ear.
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Moya García A, Adeyelu T, Kruger FA, Dawson NL, Lees JG, Overington JP, Orengo C, Ranea JA. Preprint DOI: 10.1101/044289
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Synthesis of Chlorophyll-Binding Proteins in a Fully Segregated Δycf54 Strain of the Cyanobacterium Synechocystis PCC 6803.
Hollingshead S, Kopečná J, Armstrong DR, Bučinská L, Jackson PJ, Chen GE, Dickman MJ, Williamson MP, Sobotka R, Hunter CN. Frontiers in plant science Volume 7 (2016) p.292 DOI: 10.3389/fpls.2016.00292
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Evolutionary diversification of retinoic acid receptor ligand-binding pocket structure by molecular tinkering.
Gutierrez-Mazariegos J, Nadendla EK, Studer RA, Alvarez S, de Lera AR, Kuraku S, Bourguet W, Schubert M, Laudet V. Royal Society open science Volume 3 (2016) p.150484 DOI: 10.1098/rsos.150484
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The evolutionary fates of a large segmental duplication in mouse
Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AM, Didion JP, Yadgary L, Thybert D, Odom DT, Flicek P, McMillan L, de Villena FP. Preprint DOI: 10.1101/043687
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The FAIR Guiding Principles for scientific data management and stewardship.
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ncRNA orthologies in the vertebrate lineage.
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Proceedings of a Sickle Cell Disease Ontology workshop - Towards the first comprehensive ontology for Sickle Cell Disease.
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Transcriptional response networks for elucidating mechanisms of action of multitargeted agents.
Kibble M, Khan SA, Saarinen N, Iorio F, Saez-Rodriguez J, Mäkelä S, Aittokallio T. Drug discovery today Volume 21 (2016) p.1063-1075 DOI: 10.1016/j.drudis.2016.03.001
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Genetics of cortico-cerebellar expansion in anthropoid primates: a comparative approach
Harrison PW, Montgomery SH. Preprint DOI: 10.1101/043174
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Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design.
Smith JD, Suresh S, Schlecht U, Wu M, Wagih O, Peltz G, Davis RW, Steinmetz LM, Parts L, St Onge RP. Genome biology Volume 17 (2016) p.45 DOI: 10.1186/s13059-016-0900-9
T cell fate and clonality inference from single-cell transcriptomes.
Stubbington MJT, Lönnberg T, Proserpio V, Clare S, Speak AO, Dougan G, Teichmann SA. Nature methods Volume 13 (2016) p.329-332 DOI: 10.1038/nmeth.3800
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The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH. Nature genetics Volume 48 (2016) p.427-437 DOI: 10.1038/ng.3526
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB.
Doğan T, MacDougall A, Saidi R, Poggioli D, Bateman A, O'Donovan C, Martin MJ. Bioinformatics (Oxford, England) Volume 32 (2016) p.2264-2271 DOI: 10.1093/bioinformatics/btw114
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Genomic epidemiology of artemisinin resistant malaria.
MalariaGEN Plasmodium falciparum Community Project. eLife Volume 5 (2016) DOI: 10.7554/elife.08714
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The Ensembl Variant Effect Predictor
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Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass.
Guo G, von Meyenn F, Santos F, Chen Y, Reik W, Bertone P, Smith A, Nichols J. Stem cell reports Volume 6 (2016) p.437-446 DOI: 10.1016/j.stemcr.2016.02.005
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Advancing insect vector biology research: a community survey for future directions, research applications and infrastructure requirements
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An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway.
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A dominant gain-of-function mutation in universal tyrosine kinase SRC causes thrombocytopenia, myelofibrosis, bleeding, and bone pathologies.
Turro E, Greene D, Wijgaerts A, Thys C, Lentaigne C, Bariana TK, Westbury SK, Kelly AM, Selleslag D, Stephens JC, Papadia S, Simeoni I, Penkett CJ, Ashford S, Attwood A, Austin S, Bakchoul T, Collins P, Deevi SV, Favier R, Kostadima M, Lambert MP, Mathias M, Millar CM, Peerlinck K, Perry DJ, Schulman S, Whitehorn D, Wittevrongel C, BRIDGE-BPD Consortium, De Maeyer M, Rendon A, Gomez K, Erber WN, Mumford AD, Nurden P, Stirrups K, Bradley JR, Raymond FL, Laffan MA, Van Geet C, Richardson S, Freson K, Ouwehand WH. Science translational medicine Volume 8 (2016) p.328ra30 DOI: 10.1126/scitranslmed.aad7666
libChEBI: an API for accessing the ChEBI database.
Swainston N, Hastings J, Dekker A, Muthukrishnan V, May J, Steinbeck C, Mendes P. Journal of cheminformatics Volume 8 (2016) p.11 DOI: 10.1186/s13321-016-0123-9
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FlyBase portals to human disease research using Drosophila models.
Millburn GH, Crosby MA, Gramates LS, Tweedie S, FlyBase Consortium. Disease models & mechanisms Volume 9 (2016) p.245-252 DOI: 10.1242/dmm.023317
Cutting-edge single-cell genomics and modelling in immunology.
Proserpio V, Lönnberg T. Immunology and cell biology Volume 94 (2016) p.224 DOI: 10.1038/icb.2015.117
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Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells.
Kulbe H, Iorio F, Chakravarty P, Milagre CS, Moore R, Thompson RG, Everitt G, Canosa M, Montoya A, Drygin D, Braicu I, Sehouli J, Saez-Rodriguez J, Cutillas PR, Balkwill FR. Oncotarget Volume 7 (2016) p.15648-15661 DOI: 10.18632/oncotarget.7255
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The ORFeome Collaboration: a genome-scale human ORF-clone resource.
ORFeome Collaboration. Nature methods Volume 13 (2016) p.191-192 DOI: 10.1038/nmeth.3776
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Significant impact of miRNA-target gene networks on genetics of human complex traits.
Okada Y, Muramatsu T, Suita N, Kanai M, Kawakami E, Iotchkova V, Soranzo N, Inazawa J, Tanaka T. Scientific reports Volume 6 (2016) p.22223 DOI: 10.1038/srep22223
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transPLANT Resources for Triticeae Genomic Data.
Spannagl M, Alaux M, Lange M, Bolser DM, Bader KC, Letellier T, Kimmel E, Flores R, Pommier C, Kerhornou A, Walts B, Nussbaumer T, Grabmuller C, Chen J, Colmsee C, Beier S, Mascher M, Schmutzer T, Arend D, Thanki A, Ramirez-Gonzalez R, Ayling M, Ayling S, Caccamo M, Mayer KF, Scholz U, Steinbach D, Quesneville H, Kersey PJ. The plant genome Volume 9 (2016) DOI: 10.3835/plantgenome2015.06.0038
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Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.
Goolam M, Scialdone A, Graham SJL, Macaulay IC, Jedrusik A, Hupalowska A, Voet T, Marioni JC, Zernicka-Goetz M. Cell Volume 165 (2016) p.61-74 DOI: 10.1016/j.cell.2016.01.047
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The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome.
Satou Y, Miyazato P, Ishihara K, Yaguchi H, Melamed A, Miura M, Fukuda A, Nosaka K, Watanabe T, Rowan AG, Nakao M, Bangham CR. Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.3054-3059 DOI: 10.1073/pnas.1423199113
LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order.
Fontanesi L, Di Palma F, Flicek P, Smith AT, Thulin CG, Alves PC, Lagomorph Genomics Consortium. The Journal of heredity Volume 107 (2016) p.295-308 DOI: 10.1093/jhered/esw010
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Guidelines for the functional annotation of microRNAs using the Gene Ontology.
Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC. RNA (New York, N.Y.) Volume 22 (2016) p.667-676 DOI: 10.1261/rna.055301.115
Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression.
Rakitsch B, Stegle O. Genome biology Volume 17 (2016) p.33 DOI: 10.1186/s13059-016-0895-2
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A gain-of-function variant in DIAPH1 causes dominant macrothrombocytopenia and hearing loss.
Stritt S, Nurden P, Turro E, Greene D, Jansen SB, Westbury SK, Petersen R, Astle WJ, Marlin S, Bariana TK, Kostadima M, Lentaigne C, Maiwald S, Papadia S, Kelly AM, Stephens JC, Penkett CJ, Ashford S, Tuna S, Austin S, Bakchoul T, Collins P, Favier R, Lambert MP, Mathias M, Millar CM, Mapeta R, Perry DJ, Schulman S, Simeoni I, Thys C, BRIDGE-BPD Consortium, Gomez K, Erber WN, Stirrups K, Rendon A, Bradley JR, van Geet C, Raymond FL, Laffan MA, Nurden AT, Nieswandt B, Richardson S, Freson K, Ouwehand WH, Mumford AD. Blood Volume 127 (2016) p.2903-2914 DOI: 10.1182/blood-2015-10-675629
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Inferring causal molecular networks: empirical assessment through a community-based effort.
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Reaction Decoder Tool (RDT): extracting features from chemical reactions.
Rahman SA, Torrance G, Baldacci L, Martínez Cuesta S, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM. Bioinformatics (Oxford, England) Volume 32 (2016) p.2065-2066 DOI: 10.1093/bioinformatics/btw096
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A multiple-phenotype imputation method for genetic studies.
Dahl A, Iotchkova V, Baud A, Johansson Å, Gyllensten U, Soranzo N, Mott R, Kranis A, Marchini J. Nature genetics Volume 48 (2016) p.466-472 DOI: 10.1038/ng.3513
Ensembl comparative genomics resources.
Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/bav096
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The UniProtKB guide to the human proteome.
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Activation of the TGFβ pathway impairs endothelial to haematopoietic transition.
Vargel Ö, Zhang Y, Kosim K, Ganter K, Foehr S, Mardenborough Y, Shvartsman M, Enright AJ, Krijgsveld J, Lancrin C. Scientific reports Volume 6 (2016) p.21518 DOI: 10.1038/srep21518
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Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs.
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Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ, Marioni JC, Teichmann SA. Genome biology Volume 17 (2016) p.29 DOI: 10.1186/s13059-016-0888-1
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Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources.
Bousfield D, McEntyre J, Velankar S, Papadatos G, Bateman A, Cochrane G, Kim JH, Graef F, Vartak V, Alako B, Blomberg N. F1000Research Volume 5 (2016) DOI: 10.12688/f1000research.7911.1
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Malone J, Stevens R, Jupp S, Hancocks T, Parkinson H, Brooksbank C. PLoS computational biology Volume 12 (2016) p.e1004743 DOI: 10.1371/journal.pcbi.1004743
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Strømme Syndrome Is a Ciliary Disorder Caused by Mutations in CENPF.
Filges I, Bruder E, Brandal K, Meier S, Undlien DE, Waage TR, Hoesli I, Schubach M, de Beer T, Sheng Y, Hoeller S, Schulzke S, Røsby O, Miny P, Tercanli S, Oppedal T, Meyer P, Selmer KK, Strømme P. Human mutation Volume 37 (2016) p.359-363 DOI: 10.1002/humu.22960
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The Electron Microscopy eXchange (EMX) initiative.
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MOCCASIN: converting MATLAB ODE models to SBML.
Gómez HF, Hucka M, Keating SM, Nudelman G, Iber D, Sealfon SC. Bioinformatics (Oxford, England) Volume 32 (2016) p.1905-1906 DOI: 10.1093/bioinformatics/btw056
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Genomic insights into the Ixodes scapularis tick vector of Lyme disease.
Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayllón N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calderón GI, Grabowski JM, Jiang D, Khalil SMS, Kim D, Kocan KM, Koči J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, Sánchez-Gracia A, Severo MS, Silverman N, Šimo L, Tojo M, Tornador C, Van Zee JP, Vázquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio PV, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJP, Park Y, Rozas J, Benton R, Pedra JHF, Nelson DR, Unger MF, Tubio JMC, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, Nelson KE, Caler E, Hill CA. Nature communications Volume 7 (2016) p.10507 DOI: 10.1038/ncomms10507
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Focus on Extracellular Vesicles: Physiological Role and Signalling Properties of Extracellular Membrane Vesicles.
Iraci N, Leonardi T, Gessler F, Vega B, Pluchino S. International journal of molecular sciences Volume 17 (2016) p.171 DOI: 10.3390/ijms17020171
Exploring the chemistry and evolution of the isomerases.
Martínez Cuesta S, Rahman SA, Thornton JM. Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.1796-1801 DOI: 10.1073/pnas.1509494113
A review of the new HGNC gene family resource.
Gray KA, Seal RL, Tweedie S, Wright MW, Bruford EA. Human genomics Volume 10 (2016) p.6 DOI: 10.1186/s40246-016-0062-6
Characterising Complex Enzyme Reaction Data.
Dönertaş HM, Martínez Cuesta S, Rahman SA, Thornton JM. PloS one Volume 11 (2016) p.e0147952 DOI: 10.1371/journal.pone.0147952
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Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A.
Rohwer N, Bindel F, Grimm C, Lin SJ, Wappler J, Klinger B, Blüthgen N, Du Bois I, Schmeck B, Lehrach H, de Graauw M, Goncalves E, Saez-Rodriguez J, Tan P, Grabsch HI, Prigione A, Kempa S, Cramer T. Oncotarget Volume 7 (2016) p.6693-6710 DOI: 10.18632/oncotarget.6793
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The metabolic background is a global player in Saccharomyces gene expression epistasis.
Alam MT, Zelezniak A, Mülleder M, Shliaha P, Schwarz R, Capuano F, Vowinckel J, Radmanesfahar E, Krüger A, Calvani E, Michel S, Börno S, Christen S, Patil KR, Timmermann B, Lilley KS, Ralser M. Nature microbiology Volume 1 (2016) p.15030 DOI: 10.1038/nmicrobiol.2015.30
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Short template switch events explain mutation clusters in the human genome
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CPEB and miR-15/16 Co-Regulate Translation of Cyclin E1 mRNA during Xenopus Oocyte Maturation.
Wilczynska A, Git A, Argasinska J, Belloc E, Standart N. PloS one Volume 11 (2016) p.e0146792 DOI: 10.1371/journal.pone.0146792
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Scognamiglio R, Cabezas-Wallscheid N, Thier MC, Altamura S, Reyes A, Prendergast ÁM, Baumgärtner D, Carnevalli LS, Atzberger A, Haas S, von Paleske L, Boroviak T, Wörsdörfer P, Essers MA, Kloz U, Eisenman RN, Edenhofer F, Bertone P, Huber W, van der Hoeven F, Smith A, Trumpp A. Cell Volume 164 (2016) p.668-680 DOI: 10.1016/j.cell.2015.12.033
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Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs.
Juan D, Perner J, Carrillo de Santa Pau E, Marsili S, Ochoa D, Chung HR, Vingron M, Rico D, Valencia A. Cell reports Volume 14 (2016) p.1246-1257 DOI: 10.1016/j.celrep.2016.01.008
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Consolidating and Exploring Antibiotic Resistance Gene Data Resources.
Xavier BB, Das AJ, Cochrane G, De Ganck S, Kumar-Singh S, Aarestrup FM, Goossens H, Malhotra-Kumar S. Journal of clinical microbiology Volume 54 (2016) p.851-859 DOI: 10.1128/jcm.02717-15
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Genome wide association analysis of the heart using high-resolution 3D cardiac MRI identifies new genetic loci underlying cardiac structure and function.
Marvao Ad, Meyer HV, Dawes TJ, Shi W, Bai W, Rueckert D, Birney E, O'Regan DP, Cook S. Journal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance Volume 18 (2016) DOI: 10.1186/1532-429x-18-s1-q63
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Schwarz RF, Tamuri AU, Kultys M, King J, Godwin J, Florescu AM, Schultz J, Goldman N. Nucleic acids research Volume 44 (2016) p.e77 DOI: 10.1093/nar/gkw022
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De novo transcriptome assembly of Perkinsus olseni trophozoite stimulated in vitro with Manila clam (Ruditapes philippinarum) plasma.
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The H3K4me3/2 histone demethylase RBR-2 controls axon guidance by repressing the actin-remodeling gene wsp-1.
Mariani L, Lussi YC, Vandamme J, Riveiro A, Salcini AE. Development (Cambridge, England) Volume 143 (2016) p.851-863 DOI: 10.1242/dev.132985
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Leveraging Genomic Annotations and Pleiotropic Enrichment for Improved Replication Rates in Schizophrenia GWAS.
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Characterising granuloma regression and liver recovery in a murine model of schistosomiasis japonica.
Chuah C, Jones MK, McManus DP, Nawaratna SK, Burke ML, Owen HC, Ramm GA, Gobert GN. International journal for parasitology Volume 46 (2016) p.239-252 DOI: 10.1016/j.ijpara.2015.12.004
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Sudden Cardiac Arrest and Rare Genetic Variants in the Community.
Milano A, Blom MT, Lodder EM, van Hoeijen DA, Barc J, Koopmann TT, Bardai A, Beekman L, Lichtner P, van den Berg MP, Wilde AA, Bezzina CR, Tan HL. Circulation. Cardiovascular genetics Volume 9 (2016) p.147-153 DOI: 10.1161/circgenetics.115.001263
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Genetic and environmental risk for chronic pain and the contribution of risk variants for psychiatric disorders. Results from Generation Scotland: Scottish Family Health Study and UK Biobank
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Consent Codes: Upholding Standard Data Use Conditions.
Dyke SO, Philippakis AA, Rambla De Argila J, Paltoo DN, Luetkemeier ES, Knoppers BM, Brookes AJ, Spalding JD, Thompson M, Roos M, Boycott KM, Brudno M, Hurles M, Rehm HL, Matern A, Fiume M, Sherry ST. PLoS genetics Volume 12 (2016) p.e1005772 DOI: 10.1371/journal.pgen.1005772
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Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis.
Emwas AH, Roy R, McKay RT, Ryan D, Brennan L, Tenori L, Luchinat C, Gao X, Zeri AC, Gowda GA, Raftery D, Steinbeck C, Salek RM, Wishart DS. Journal of proteome research Volume 15 (2016) p.360-373 DOI: 10.1021/acs.jproteome.5b00885
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Regulatory and Functional Aspects of Indolic Metabolism in Plant Systemic Acquired Resistance.
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PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events.
Izuogu OG, Alhasan AA, Alafghani HM, Santibanez-Koref M, Elliott DJ, Jackson MS. BMC bioinformatics Volume 17 (2016) p.31 DOI: 10.1186/s12859-016-0881-4
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Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics.
Harper AL, McKinney LV, Nielsen LR, Havlickova L, Li Y, Trick M, Fraser F, Wang L, Fellgett A, Sollars ES, Janacek SH, Downie JA, Buggs RJ, Kjær ED, Bancroft I. Scientific reports Volume 6 (2016) p.19335 DOI: 10.1038/srep19335
The EMBL-EBI channel.
McEntyre J, Birney E. F1000Research Volume 5 (2016) p.52 DOI: 10.12688/f1000research.7764.1
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Antibody performance in ChIP-sequencing assays: From quality scores of public data sets to quantitative certification.
Mendoza-Parra MA, Saravaki V, Cholley PE, Blum M, Billoré B, Gronemeyer H. F1000Research Volume 5 (2016) p.54 DOI: 10.12688/f1000research.7637.1
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Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood S, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W. Nature methods Volume 13 (2016) p.229-232 DOI: 10.1038/nmeth.3728
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Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC. Nature communications Volume 7 (2016) p.10415 DOI: 10.1038/ncomms10415
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Rapid dissemination of human T-lymphotropic virus type 1 during primary infection in transplant recipients.
Cook LB, Melamed A, Demontis MA, Laydon DJ, Fox JM, Tosswill JH, de Freitas D, Price AD, Medcalf JF, Martin F, Neuberger JM, Bangham CR, Taylor GP. Retrovirology Volume 13 (2016) p.3 DOI: 10.1186/s12977-015-0236-7
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Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.
Kumar A, Beloglazova N, Bundalovic-Torma C, Phanse S, Deineko V, Gagarinova A, Musso G, Vlasblom J, Lemak S, Hooshyar M, Minic Z, Wagih O, Mosca R, Aloy P, Golshani A, Parkinson J, Emili A, Yakunin AF, Babu M. Cell reports Volume 14 (2016) p.648-661 DOI: 10.1016/j.celrep.2015.12.060
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A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases.
Berenstein AJ, Magariños MP, Chernomoretz A, Agüero F. PLoS neglected tropical diseases Volume 10 (2016) p.e0004300 DOI: 10.1371/journal.pntd.0004300
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Modelling-based experiment retrieval: a case study with gene expression clustering.
Blomstedt P, Dutta R, Seth S, Brazma A, Kaski S. Bioinformatics (Oxford, England) Volume 32 (2016) p.1388-1394 DOI: 10.1093/bioinformatics/btv762
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Lamin A is involved in the development of vascular calcification induced by chronic kidney failure and phosphorus load.
Quirós-González I, Román-García P, Alonso-Montes C, Barrio-Vázquez S, Carrillo-López N, Naves-Díaz M, Mora MI, Corrales FJ, López-Hernández FJ, Ruiz-Torres MP, Cannata-Andía JB, Fernández-Martín JL. Bone Volume 84 (2016) p.160-168 DOI: 10.1016/j.bone.2016.01.005
Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain.
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Beyond comparisons of means: understanding changes in gene expression at the single-cell level
Vallejos CA, Richardson S, Marioni JC. Preprint DOI: 10.1101/035949
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A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure.
Hebels DG, Rasche A, Herwig R, van Westen GJ, Jennen DG, Kleinjans JC. Methods in molecular biology (Clifton, N.J.) Volume 1425 (2016) p.339-359 DOI: 10.1007/978-1-4939-3609-0_15
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Homology-Based Annotation of Large Protein Datasets.
Punta M, Mistry J. Methods in molecular biology (Clifton, N.J.) Volume 1415 (2016) p.153-176 DOI: 10.1007/978-1-4939-3572-7_8
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The MIntAct Project and Molecular Interaction Databases.
Licata L, Orchard S. Methods in molecular biology (Clifton, N.J.) Volume 1415 (2016) p.55-69 DOI: 10.1007/978-1-4939-3572-7_3
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NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets.
Mendoza-Parra MA, Saleem MA, Blum M, Cholley PE, Gronemeyer H. Methods in molecular biology (Clifton, N.J.) Volume 1418 (2016) p.243-265 DOI: 10.1007/978-1-4939-3578-9_13
Protein Structure Databases.
Laskowski RA. Methods in molecular biology (Clifton, N.J.) Volume 1415 (2016) p.31-53 DOI: 10.1007/978-1-4939-3572-7_2
SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data.
Venkatesan A, Kim JH, Talo F, Ide-Smith M, Gobeill J, Carter J, Batista-Navarro R, Ananiadou S, Ruch P, McEntyre J. Wellcome open research Volume 1 (2016) p.25 DOI: 10.12688/wellcomeopenres.10210.2
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Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy.
Piai A, Calçada EO, Tarenzi T, Grande AD, Varadi M, Tompa P, Felli IC, Pierattelli R. Biophysical journal Volume 110 (2016) p.372-381 DOI: 10.1016/j.bpj.2015.11.3516
Ontology Lookup Service (OLS)
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Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.
Bolser D, Staines DM, Pritchard E, Kersey P. Methods in molecular biology (Clifton, N.J.) Volume 1374 (2016) p.115-140 DOI: 10.1007/978-1-4939-3167-5_6