Publications for 2017

2017

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A Novel Long Non-Coding RNA in the hTERT Promoter Region Regulates hTERT Expression.
Malhotra S, Freeberg MA, Winans SJ, Taylor J, Beemon KL. Non-coding RNA Volume 4 (2017) DOI: 10.3390/ncrna4010001
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Genome-wide evolutionary dynamics of influenza B viruses on a global scale.
Langat P, Raghwani J, Dudas G, Bowden TA, Edwards S, Gall A, Bedford T, Rambaut A, Daniels RS, Russell CA, Pybus OG, McCauley J, Kellam P, Watson SJ. PLoS pathogens Volume 13 (2017) p.e1006749 DOI: 10.1371/journal.ppat.1006749
Phenotype inference in an Escherichia coli strain panel.
Galardini M, Koumoutsi A, Herrera-Dominguez L, Cordero Varela JA, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P. eLife Volume 6 (2017) DOI: 10.7554/elife.31035
A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it.
Spicer RA, Steinbeck C. Metabolomics : Official journal of the Metabolomic Society Volume 14 (2018) p.16 DOI: 10.1007/s11306-017-1309-5
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Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes
Rheinbay E, Nielsen MM, Abascal F, Tiao G, Hornshøj H, Hess JM, Pedersen RI, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bertl J, Dhingra P, Diamanti K, Gonzalez-Perez A, Guo Q, Haradhvala NJ, Isaev K, Juul M, Komorowski J, Kumar S, Lee D, Lochovsky L, Liu EM, Pich O, Tamborero D, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Zhang J, Boroevich KA, Carlevaro-Fita J, Chakravarty D, Chan CW, Fonseca NA, Hamilton MP, Hong C, Kahles A, Kim Y, Lehmann K, Johnson TA, Kahraman A, Park K, Saksena G, Sieverling L, Sinnott-Armstrong NA, Campbell PJ, Hobolth A, Kellis M, Lawrence MS, Raphael B, Rubin MA, Sander C, Stein L, Stuart J, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein MB, Khurana E, López-Bigas N, Martincorena I, Pedersen JS, Getz G. Preprint DOI: 10.1101/237313
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CYRI1-mediated inhibition of RAC1 signalling restricts Salmonella Typhimurium infection
Yuki KE, Marei H, Fiskin E, Eva MM, Gopal AA, Schwartzentruber JA, Majewski J, Cellier M, Mandl JN, Vidal SM, Malo D, Dikic I. Preprint DOI: 10.1101/238733
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat.
Martín-Gálvez D, Dunoyer de Segonzac D, Ma MCJ, Kwitek AE, Thybert D, Flicek P. BMC genomics Volume 18 (2017) p.986 DOI: 10.1186/s12864-017-4351-9
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Comparative analysis of neutrophil and monocyte epigenomes
Rico D, Martens JH, Downes K, Carrillo-de-Santa-Pau E, Pancaldi V, Breschi A, Richardson D, Heath S, Saeed S, Frontini M, Chen L, Watt S, Müller F, Clarke L, Kerstens HH, Wilder SP, Palumbo E, Djebali S, Raineri E, Merkel A, Esteve-Codina A, Sultan M, van Bommel A, Gut M, Yaspo M, Rubio M, Fernandez JM, Attwood A, de la Torre V, Royo R, Fragkogianni S, Gelpí JL, Torrents D, Iotchkova V, Logie C, Aghajanirefah A, Singh AA, Janssen-Megens EM, Berentsen K, Erber W, Rendon A, Kostadima M, Loos R, van der Ent MA, Kaan A, Sharifi N, Paul DS, Ifrim DC, Quintin J, Love MI, Pisano DG, Burden F, Foad N, Farrow S, Zerbino DR, Dunham I, Kuijpers T, Lehrach H, Lengauer T, Bertone P, Netea MG, Vingron M, Beck S, Flicek P, Gut I, Ouwehand WH, Bock C, Soranzo N, Guigo R, Valencia A, Stunnenberg HG. Preprint DOI: 10.1101/237784
Cell ontology in an age of data-driven cell classification.
Osumi-Sutherland D. BMC bioinformatics Volume 18 (2017) p.558 DOI: 10.1186/s12859-017-1980-6
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Usage of cell nomenclature in biomedical literature.
Kafkas Ş, Sarntivijai S, Hoehndorf R. BMC bioinformatics Volume 18 (2017) p.561 DOI: 10.1186/s12859-017-1978-0
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RNA-Seq Analysis of an Antisense Sequence Optimized for Exon Skipping in Duchenne Patients Reveals No Off-Target Effect.
Domenger C, Allais M, François V, Léger A, Lecomte E, Montus M, Servais L, Voit T, Moullier P, Audic Y, Le Guiner C. Molecular therapy. Nucleic acids Volume 10 (2018) p.277-291 DOI: 10.1016/j.omtn.2017.12.008
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Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions.
Tang J, Tanoli ZU, Ravikumar B, Alam Z, Rebane A, Vähä-Koskela M, Peddinti G, van Adrichem AJ, Wakkinen J, Jaiswal A, Karjalainen E, Gautam P, He L, Parri E, Khan S, Gupta A, Ali M, Yetukuri L, Gustavsson AL, Seashore-Ludlow B, Hersey A, Leach AR, Overington JP, Repasky G, Wennerberg K, Aittokallio T. Cell chemical biology Volume 25 (2018) p.224-229.e2 DOI: 10.1016/j.chembiol.2017.11.009
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Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses.
Ong E, Xie J, Ni Z, Liu Q, Sarntivijai S, Lin Y, Cooper D, Terryn R, Stathias V, Chung C, Schürer S, He Y. BMC bioinformatics Volume 18 (2017) p.556 DOI: 10.1186/s12859-017-1981-5
Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge.
Sarntivijai S, Diehl AD, He Y. BMC bioinformatics Volume 18 (2017) p.560 DOI: 10.1186/s12859-017-1976-2
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Comparison, alignment, and synchronization of cell line information between CLO and EFO.
Ong E, Sarntivijai S, Jupp S, Parkinson H, He Y. BMC bioinformatics Volume 18 (2017) p.557 DOI: 10.1186/s12859-017-1979-z
Accurate and fast feature selection workflow for high-dimensional omics data.
Perez-Riverol Y, Kuhn M, Vizcaíno JA, Hitz MP, Audain E. PloS one Volume 12 (2017) p.e0189875 DOI: 10.1371/journal.pone.0189875
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Single molecule real-time DNA sequencing of HLA genes at ultra-high resolution from 126 International HLA and Immunogenetics Workshop cell lines.
Turner TR, Hayhurst JD, Hayward DR, Bultitude WP, Barker DJ, Robinson J, Madrigal JA, Mayor NP, Marsh SGE. HLA Volume 91 (2018) p.88-101 DOI: 10.1111/tan.13184
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A protein standard that emulates homology for the characterization of protein inference algorithms
The M, Edfors F, Perez-Riverol Y, Payne SH, Hoopmann MR, Palmblad M, Forsström B, Käll L. Preprint DOI: 10.1101/236471
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Severe infections emerge from commensal bacteria by adaptive evolution.
Young BC, Wu CH, Gordon NC, Cole K, Price JR, Liu E, Sheppard AE, Perera S, Charlesworth J, Golubchik T, Iqbal Z, Bowden R, Massey RC, Paul J, Crook DW, Peto TE, Walker AS, Llewelyn MJ, Wyllie DH, Wilson DJ. eLife Volume 6 (2017) DOI: 10.7554/elife.30637
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MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go.
Muth T, Kohrs F, Heyer R, Benndorf D, Rapp E, Reichl U, Martens L, Renard BY. Analytical chemistry Volume 90 (2018) p.685-689 DOI: 10.1021/acs.analchem.7b03544
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Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast.
Aslanzadeh V, Huang Y, Sanguinetti G, Beggs JD. Genome research Volume 28 (2018) p.203-213 DOI: 10.1101/gr.225615.117
Expression Atlas: Quick tour
Huerta L. DOI: 10.6019/tol.exatlas-qt.2017.00001.1
Open Targets: Mining gene and disease associations for improved drug target identification
Carvalho-Silva D. DOI: 10.6019/tol.opentargets-w.2017.00001.1
Finding the best data for your needs in the PDB archive
Conroy M. DOI: 10.6019/tol.pdbenov17-w.2017.00001.1
Enzymes in UniProt
Zaru R. DOI: 10.6019/tol.unip-enzymes-w.2017.00001.1
GWAS Catalog: Exploring SNP-trait associations
Emery L, MacArthur J. DOI: 10.6019/tol.gwas-t.2017.00001.1
Navigating the data-rich literature: finding evidence in biomedical publications
Levchenko M. DOI: 10.6019/tol.epmc_oct-w.2017.00001.1
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The IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation
Pramanik J, Chen X, Kar G, Gomes T, Henriksson J, Miao Z, Natarajan K, McKenzie ANJ, Mahata B, Teichmann SA. Preprint DOI: 10.1101/235010
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Real-time search of all bacterial and viral genomic data
Bradley P, Den Bakker HC, Rocha EPC, McVean G, Iqbal Z. Preprint DOI: 10.1101/234955
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Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging
Severo MS, Landry JJ, Lindquist RL, Goosmann C, Brinkmann V, Collier P, Hauser AE, Benes V, Henriksson J, Teichmann SA, Levashina EA. Preprint DOI: 10.1101/234492
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Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis
Stojic L, Lun A, Mangei J, Mascalchi P, Quarantotti V, Barr AR, Bakal C, Marioni JC, Gergely F, Odom DT. Preprint DOI: 10.1101/234930
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The Metabolic Response of Skeletal Muscle to Endurance Exercise Is Modified by the ACE-I/D Gene Polymorphism and Training State.
Valdivieso P, Vaughan D, Laczko E, Brogioli M, Waldron S, Rittweger J, Flück M. Frontiers in physiology Volume 8 (2017) p.993 DOI: 10.3389/fphys.2017.00993
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Sharing and reuse of individual participant data from clinical trials: principles and recommendations.
Ohmann C, Banzi R, Canham S, Battaglia S, Matei M, Ariyo C, Becnel L, Bierer B, Bowers S, Clivio L, Dias M, Druml C, Faure H, Fenner M, Galvez J, Ghersi D, Gluud C, Groves T, Houston P, Karam G, Kalra D, Knowles RL, Krleža-Jerić K, Kubiak C, Kuchinke W, Kush R, Lukkarinen A, Marques PS, Newbigging A, O'Callaghan J, Ravaud P, Schlünder I, Shanahan D, Sitter H, Spalding D, Tudur-Smith C, van Reusel P, van Veen EB, Visser GR, Wilson J, Demotes-Mainard J. BMJ open Volume 7 (2017) p.e018647 DOI: 10.1136/bmjopen-2017-018647
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nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.
Schober D, Jacob D, Wilson M, Cruz JA, Marcu A, Grant JR, Moing A, Deborde C, de Figueiredo LF, Haug K, Rocca-Serra P, Easton J, Ebbels TMD, Hao J, Ludwig C, Günther UL, Rosato A, Klein MS, Lewis IA, Luchinat C, Jones AR, Grauslys A, Larralde M, Yokochi M, Kobayashi N, Porzel A, Griffin JL, Viant MR, Wishart DS, Steinbeck C, Salek RM, Neumann S. Analytical chemistry Volume 90 (2018) p.649-656 DOI: 10.1021/acs.analchem.7b02795
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In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering.
Wu Q, Ferry QRV, Baeumler TA, Michaels YS, Vitsios DM, Habib O, Arnold R, Jiang X, Maio S, Steinkraus BR, Tapia M, Piazza P, Xu N, Holländer GA, Milne TA, Kim JS, Enright AJ, Bassett AR, Fulga TA. Nature communications Volume 8 (2017) p.2109 DOI: 10.1038/s41467-017-00686-2
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Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling.
Tresadern G, Trabanco AA, Pérez-Benito L, Overington JP, van Vlijmen HWT, van Westen GJP. Journal of chemical information and modeling Volume 57 (2017) p.2976-2985 DOI: 10.1021/acs.jcim.7b00338
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Molecular and functional variation in iPSC-derived sensory neurons.
Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, Patel M, Goncalves A, Ferreira R, Benn CL, Wilbrey A, Bictash M, Impey E, Cao L, Lainez S, Loucif AJ, Whiting PJ, HIPSCI Consortium, Gutteridge A, Gaffney DJ. Nature genetics Volume 50 (2018) p.54-61 DOI: 10.1038/s41588-017-0005-8
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History-driven population structure and asymmetric gene flow in a recovering large carnivore at the rear-edge of its European range.
Karamanlidis AA, Skrbinšek T, de Gabriel Hernando M, Krambokoukis L, Munoz-Fuentes V, Bailey Z, Nowak C, Stronen AV. Heredity Volume 120 (2018) p.168-182 DOI: 10.1038/s41437-017-0031-4
Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.
Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Peat G, Pignatelli M, Falcone F, Benes CH, Dunham I, Bignell G, McDade SS, Garnett MJ, Saez-Rodriguez J. Cancer research Volume 78 (2018) p.769-780 DOI: 10.1158/0008-5472.can-17-1679
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Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing.
Bach K, Pensa S, Grzelak M, Hadfield J, Adams DJ, Marioni JC, Khaled WT. Nature communications Volume 8 (2017) p.2128 DOI: 10.1038/s41467-017-02001-5
The HMMER Web Server for Protein Sequence Similarity Search.
Prakash A, Jeffryes M, Bateman A, Finn RD. Current protocols in bioinformatics Volume 60 (2017) p.3.15.1-3.15.23 DOI: 10.1002/cpbi.40
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Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation
Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B. Preprint DOI: 10.1101/231118
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Acquisition of functions on the outer capsid surface during evolution of double-stranded RNA fungal viruses.
Mata CP, Luque D, Gómez-Blanco J, Rodríguez JM, González JM, Suzuki N, Ghabrial SA, Carrascosa JL, Trus BL, Castón JR. PLoS pathogens Volume 13 (2017) p.e1006755 DOI: 10.1371/journal.ppat.1006755
Immuno-oncology from the perspective of somatic evolution.
González S, Volkova N, Beer P, Gerstung M. Seminars in cancer biology Volume 52 (2018) p.75-85 DOI: 10.1016/j.semcancer.2017.12.001
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Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines.
Blattmann P, Henriques D, Zimmermann M, Frommelt F, Sauer U, Saez-Rodriguez J, Aebersold R. Cell systems Volume 5 (2017) p.604-619.e7 DOI: 10.1016/j.cels.2017.11.002
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Structural Mapping of Adenosine Receptor Mutations: Ligand Binding and Signaling Mechanisms.
Jespers W, Schiedel AC, Heitman LH, Cooke RM, Kleene L, van Westen GJP, Gloriam DE, Müller CE, Sotelo E, Gutiérrez-de-Terán H. Trends in pharmacological sciences Volume 39 (2018) p.75-89 DOI: 10.1016/j.tips.2017.11.001
Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the "Gene-Battery" Model.
Sundaram V, Wang T. BioEssays : news and reviews in molecular, cellular and developmental biology Volume 40 (2018) DOI: 10.1002/bies.201700155
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Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes.
Sancho R, Cantalapiedra CP, López-Alvarez D, Gordon SP, Vogel JP, Catalán P, Contreras-Moreira B. The New phytologist Volume 218 (2018) p.1631-1644 DOI: 10.1111/nph.14926
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The Human Cell Atlas.
Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N, Human Cell Atlas Meeting Participants. eLife Volume 6 (2017) DOI: 10.7554/elife.27041
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Target and Tissue Selectivity Prediction by Integrated Mechanistic Pharmacokinetic-Target Binding and Quantitative Structure Activity Modeling.
Vlot AHC, de Witte WEA, Danhof M, van der Graaf PH, van Westen GJP, de Lange ECM. The AAPS journal Volume 20 (2017) p.11 DOI: 10.1208/s12248-017-0172-7
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Functional SNP allele discovery (fSNPd): an approach to find highly penetrant, environmental-triggered genotypes underlying complex human phenotypes.
Stouffer K, Nahorski M, Moreno P, Sarveswaran N, Menon D, Lee M, Geoffrey Woods C. BMC genomics Volume 18 (2017) p.944 DOI: 10.1186/s12864-017-4325-y
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clustComp, a bioconductor package for the comparison of clustering results.
Torrente A, Brazma A. Bioinformatics (Oxford, England) Volume 33 (2017) p.4001-4003 DOI: 10.1093/bioinformatics/btx532
Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.
Vitsios DM, Kentepozidou E, Quintais L, Benito-Gutiérrez E, van Dongen S, Davis MP, Enright AJ. Nucleic acids research Volume 45 (2017) p.e177 DOI: 10.1093/nar/gkx836
Editorial overview: Catalysis and regulation.
Thornton J, Orengo C. Current opinion in structural biology Volume 47 (2017) p.vi-viii DOI: 10.1016/j.sbi.2017.11.005
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Using bio.tools to generate and annotate workbench tool descriptions.
Hillion KH, Kuzmin I, Khodak A, Rasche E, Crusoe M, Peterson H, Ison J, Ménager H. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.12974.1
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DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation.
Richard MA, Huan T, Ligthart S, Gondalia R, Jhun MA, Brody JA, Irvin MR, Marioni R, Shen J, Tsai PC, Montasser ME, Jia Y, Syme C, Salfati EL, Boerwinkle E, Guan W, Mosley TH, Bressler J, Morrison AC, Liu C, Mendelson MM, Uitterlinden AG, van Meurs JB, BIOS Consortium, Franco OH, Zhang G, Li Y, Stewart JD, Bis JC, Psaty BM, Chen YI, Kardia SLR, Zhao W, Turner ST, Absher D, Aslibekyan S, Starr JM, McRae AF, Hou L, Just AC, Schwartz JD, Vokonas PS, Menni C, Spector TD, Shuldiner A, Damcott CM, Rotter JI, Palmas W, Liu Y, Paus T, Horvath S, O'Connell JR, Guo X, Pausova Z, Assimes TL, Sotoodehnia N, Smith JA, Arnett DK, Deary IJ, Baccarelli AA, Bell JT, Whitsel E, Dehghan A, Levy D, Fornage M. American journal of human genetics Volume 101 (2017) p.888-902 DOI: 10.1016/j.ajhg.2017.09.028
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Nbeal2 interacts with Dock7, Sec16a, and Vac14.
Mayer L, Jasztal M, Pardo M, Aguera de Haro S, Collins J, Bariana TK, Smethurst PA, Grassi L, Petersen R, Nurden P, Favier R, Yu L, Meacham S, Astle WJ, Choudhary J, Yue WW, Ouwehand WH, Guerrero JA. Blood Volume 131 (2018) p.1000-1011 DOI: 10.1182/blood-2017-08-800359
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Genetic diversity of the African malaria vector Anopheles gambiae.
Anopheles gambiae 1000 Genomes Consortium, Data analysis group, Partner working group, Sample collections—Angola:, Burkina Faso:, Cameroon:, Gabon:, Guinea:, Guinea-Bissau:, Kenya:, Uganda:, Crosses:, Sequencing and data production, Web application development, Project coordination. Nature Volume 552 (2017) p.96-100 DOI: 10.1038/nature24995
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Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.
Shahbazi MN, Scialdone A, Skorupska N, Weberling A, Recher G, Zhu M, Jedrusik A, Devito LG, Noli L, Macaulay IC, Buecker C, Khalaf Y, Ilic D, Voet T, Marioni JC, Zernicka-Goetz M. Nature Volume 552 (2017) p.239-243 DOI: 10.1038/nature24675
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Assessing the Gene Regulatory Landscape in 1,188 Human Tumors
Calabrese C, Lehmann K, Urban L, Liu F, Erkek S, Fonseca N, Kahles A, Kilpinen H, Markowski J, Waszak S, Korbel J, Zhang Z, Brazma A, Rätsch G, Schwarz R, Stegle O, PCAWG Group 3. Preprint DOI: 10.1101/225441
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Community-driven data analysis training for biology
Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz H, Houwaart T, Jagtap P, Larivière D, Corguillé GL, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D, Network GT, Backofen R, Taylor J, Nekrutenko A, Grüning B. Preprint DOI: 10.1101/225680
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Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants.
Rifaioglu AS, Doğan T, Saraç ÖS, Ersahin T, Saidi R, Atalay MV, Martin MJ, Cetin-Atalay R. Proteins Volume 86 (2018) p.135-151 DOI: 10.1002/prot.25416
Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells.
Gonçalves E, Sciacovelli M, Costa ASH, Tran MGB, Johnson TI, Machado D, Frezza C, Saez-Rodriguez J. Metabolic engineering Volume 45 (2018) p.149-157 DOI: 10.1016/j.ymben.2017.11.011
Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression.
Berthelot C, Villar D, Horvath JE, Odom DT, Flicek P. Nature ecology & evolution Volume 2 (2018) p.152-163 DOI: 10.1038/s41559-017-0377-2
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NumtS colonization in mammalian genomes.
Calabrese FM, Balacco DL, Preste R, Diroma MA, Forino R, Ventura M, Attimonelli M. Scientific reports Volume 7 (2017) p.16357 DOI: 10.1038/s41598-017-16750-2
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The challenge of modeling protein assemblies: the CASP12-CAPRI experiment.
Lensink MF, Velankar S, Baek M, Heo L, Seok C, Wodak SJ. Proteins Volume 86 Suppl 1 (2018) p.257-273 DOI: 10.1002/prot.25419
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Is systems pharmacology ready to impact upon therapy development? A study on the cholesterol biosynthesis pathway.
Benson HE, Watterson S, Sharman JL, Mpamhanga CP, Parton A, Southan C, Harmar AJ, Ghazal P. British journal of pharmacology Volume 174 (2017) p.4362-4382 DOI: 10.1111/bph.14037
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Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.
Griffiths JA, Scialdone A, Marioni JC. BMC genomics Volume 18 (2017) p.904 DOI: 10.1186/s12864-017-4253-x
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Automated evaluation of quaternary structures from protein crystals
Bliven S, Lafita A, Parker A, Capitani G, Duarte JM. Preprint DOI: 10.1101/224717
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5-Formylcytosine controls nucleosome positioning through covalent histone-DNA interaction
Raiber E, Portella G, Cuesta SM, Hardisty R, Murat P, Li Z, Iurlaro M, Dean W, Spindel J, Beraldi D, Dawson MA, Reik W, Balasubramanian S. Preprint DOI: 10.1101/224444
Validation of Structures in the Protein Data Bank.
Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ. Structure (London, England : 1993) Volume 25 (2017) p.1916-1927 DOI: 10.1016/j.str.2017.10.009
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NCBI will no longer make taxonomy identifiers for individual influenza strains on January 15, 2018
Hatcher E, Bao Y, Amedeo P, Blinkova O, Cochrane G, Fedorova N, Gruner W, Leipe D, Nakamura Y, Ostapchuk Y, Palanigobu V, Sanders R, Schoch C, Smith C, Wentworth D, Yankie L, Zhdanov S, Karsch-Mizrachi I, Brister JR. Preprint DOI: 10.7287/peerj.preprints.3428v1
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DNA methylation markers associated with type 2 diabetes, fasting glucose and HbA1c levels: a systematic review and replication in a case-control sample of the Lifelines study.
Walaszczyk E, Luijten M, Spijkerman AMW, Bonder MJ, Lutgers HL, Snieder H, Wolffenbuttel BHR, van Vliet-Ostaptchouk JV. Diabetologia Volume 61 (2018) p.354-368 DOI: 10.1007/s00125-017-4497-7
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Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast
Stirparo GG, Boroviak T, Guo G, Nichols J, Smith A, Bertone P. Preprint DOI: 10.1101/222760
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The global distribution and spread of the mobilized colistin resistance gene mcr-1
Wang R, van Dorp L, Shaw L, Bradley P, Wang Q, Wang X, Jin L, Zhang Q, Liu Y, Rieux A, Dorai-Schneiders T, Weinert LA, Iqbal Z, Didelot X, Wang H, Balloux F. Preprint DOI: 10.1101/220921
The Gene Ontology of eukaryotic cilia and flagella.
Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J. Cilia Volume 6 (2017) p.10 DOI: 10.1186/s13630-017-0054-8
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Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.
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Reduced hepatitis B and D viral entry using clinically applied drugs as novel inhibitors of the bile acid transporter NTCP.
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Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani.
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Scipion web tools: Easy to use cryo-EM image processing over the web.
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A novel multi SNP based method for the identification of subspecies and associated lineages and sub-lineages of the Mycobacterium tuberculosis complex by whole genome sequencing
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Whole Exome Sequencing allows the identification of two novel groups of Xeroderma pigmentosum in Tunisia, XP-D and XP-E: Impact on molecular diagnosis.
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Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean.
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StUbEx PLUS-A Modified Stable Tagged Ubiquitin Exchange System for Peptide Level Purification and In-Depth Mapping of Ubiquitination Sites.
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On expert curation and scalability: UniProtKB/Swiss-Prot as a case study.
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PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.
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Wagih O. Bioinformatics (Oxford, England) Volume 33 (2017) p.3645-3647 DOI: 10.1093/bioinformatics/btx469
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Germline determinants of the somatic mutation landscape in 2,642 cancer genomes
Waszak SM, Tiao G, Zhu B, Rausch T, Muyas F, Rodríguez-Martín B, Rabionet R, Yakneen S, Escaramis G, Li Y, Saini N, Roberts SA, Demidov GM, Pitkänen E, Delaneau O, Heredia-Genestar JM, Weischenfeldt J, Shringarpure SS, Chen J, Nakagawa H, Alexandrov LB, Drechsel O, Dursi LJ, Segre AV, Garrison E, Erkek S, Habermann N, Urban L, Khurana E, Cafferkey A, Hayashi S, Imoto S, Aaltonen LA, Alvarez EG, Baez-Ortega A, Bailey M, Bosio M, Bruzos AL, Buchhalter I, Bustamante CD, Calabrese C, DiBiase A, Gerstein M, Holik AZ, Hua X, Huang K, Letunic I, Klimczak LJ, Koster R, Kumar S, McLellan M, Mashl J, Mirabello L, Newhouse S, Prasad A, Rätsch G, Schlesner M, Schwarz R, Sharma P, Shmaya T, Sidiropoulos N, Song L, Susak H, Tanskanen T, Tojo M, Wedge DC, Wright M, Wu Y, Ye K, Yellapantula VD, Zamora J, Butte AJ, Getz G, Simpson J, Ding L, Marques-Bonet T, Navarro A, Brazma A, Campbell P, Chanock SJ, Chatterjee N, Stegle O, Siebert R, Ossowski S, Harismendy O, Gordenin DA, Tubio JM, Vega FMDL, Easton DF, Estivill X, Korbel JO, on behalf of the PCAWG Germline Working group%, and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/208330
Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells.
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ComplexViewer: visualization of curated macromolecular complexes.
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An epigenome-wide association study meta-analysis of educational attainment.
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Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.
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The future of metabolomics in ELIXIR
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Genetically defined elevated homocysteine levels do not result in widespread changes of DNA methylation in leukocytes.
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PDBsum: Structural summaries of PDB entries.
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Activation of the Aryl Hydrocarbon Receptor Interferes with Early Embryonic Development.
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Terminal uridylyltransferases target RNA viruses as part of the innate immune system in animals
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Report of the International Stem Cell Banking Initiative Workshop Activity: Current Hurdles and Progress in Seed-Stock Banking of Human Pluripotent Stem Cells.
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Comprehensive Pharmacogenomic Profiling of Malignant Pleural Mesothelioma Identifies a Subgroup Sensitive to FGFR Inhibition.
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Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
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Biological and functional relevance of CASP predictions.
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Developing data interoperability using standards: A wheat community use case.
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Genomics in healthcare: GA4GH looks to 2022
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Legacy data sharing to improve drug safety assessment: the eTOX project.
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Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data.
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RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit.
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A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction.
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DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.
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Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
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Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis.
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Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer.
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SourceData: a semantic platform for curating and searching figures.
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Kelsey G, Stegle O, Reik W. Science (New York, N.Y.) Volume 358 (2017) p.69-75 DOI: 10.1126/science.aan6826
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A screen for combination therapies in BRAF/NRAS wild type melanoma identifies nilotinib plus MEK inhibitor as a synergistic combination
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Target Identification of Mycobacterium tuberculosis Phenotypic Hits Using a Concerted Chemogenomic, Biophysical, and Structural Approach.
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Spicer RA, Salek R, Steinbeck C. Scientific data Volume 4 (2017) p.170137 DOI: 10.1038/sdata.2017.137
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Spicer RA, Salek R, Steinbeck C. Scientific data Volume 4 (2017) p.170138 DOI: 10.1038/sdata.2017.138
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Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome.
Pasquier J, Braasch I, Batzel P, Cabau C, Montfort J, Nguyen T, Jouanno E, Berthelot C, Klopp C, Journot L, Postlethwait JH, Guiguen Y, Bobe J. Journal of experimental zoology. Part B, Molecular and developmental evolution Volume 328 (2017) p.709-721 DOI: 10.1002/jez.b.22770
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Perspectives from the NanoSafety Modelling Cluster on the validation criteria for (Q)SAR models used in nanotechnology.
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Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.
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Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles.
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PharmML in Action: an Interoperable Language for Modeling and Simulation.
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Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.
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Uncovering novel repositioning opportunities using the Open Targets platform.
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clusterSeq: methods for identifying co-expression in high-throughput sequencing data
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Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets.
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Avoiding ascertainment bias in the maximum likelihood inference of phylogenies based on truncated data
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Understanding enzyme function evolution from a computational perspective.
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BraCeR: Reconstruction of B-cell receptor sequences and clonality inference from single-cell RNA-sequencing
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Assessing SNP genotyping of noninvasively collected wildlife samples using microfluidic arrays.
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The future of metabolomics in ELIXIR.
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WormJam: A consensus Metabolic Reconstruction and Metabolomics Community and Workshop Series.
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Parallel Evolution of Group B Streptococcus Hypervirulent Clonal Complex 17 Unveils New Pathoadaptive Mutations.
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Societal challenges of precision medicine: Bringing order to chaos.
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PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models.
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Best practice data life cycle approaches for the life sciences.
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Structural and Functional View of Polypharmacology.
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The RNA m6A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence.
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Absence of Selection for Quantum Coherence in the Fenna-Matthews-Olson Complex: A Combined Evolutionary and Excitonic Study.
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Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
Seaton DD, Graf A, Baerenfaller K, Stitt M, Millar AJ, Gruissem W. Preprint DOI: 10.1101/182071
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A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity.
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The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training.
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A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.
Haque A, Engel J, Teichmann SA, Lönnberg T. Genome medicine Volume 9 (2017) p.75 DOI: 10.1186/s13073-017-0467-4
The application of project-based learning in bioinformatics training.
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Exploring protein interactions with UniProt
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Human genetic variation (I): an introduction
Armstrong D, Burke M, Emery L, MacArthur J, Nightingale A, Perry E, Pundir S, Saunders G. DOI: 10.6019/tol.hugenvar_1-t.2017.00001.1
10th Anniversary Treasure Hunt
Armstrong D, Burke M, Huerta L, Levchenko M, Mitchell A, Morgan S, Mugumbate G, Mutowo P, Orchard S, Perry E, Pundir S, Richardson L, Tang A. DOI: 10.6019/tol.treasure-t.2017.00001.1
User experience design for more user-friendly applications
Ide-Smith M, Karamanis N. DOI: 10.6019/tol.uxapp-w.2017.00001.1
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Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data
Zhang C, Bijlard J, Staiger C, Scollen S, van Enckevort D, Hoogstrate Y, Senf A, Hiltemann S, Repo S, Pipping W, Bierkens M, Payralbe S, Stringer B, Heringa J, Stubbs A, Bonino Da Silva Santos LO, Belien J, Weistra W, Azevedo R, van Bochove K, Meijer G, Boiten J, Rambla J, Fijneman R, Spalding JD, Abeln S. Preprint DOI: 10.12688/f1000research.12168.1
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Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data.
Zhang C, Bijlard J, Staiger C, Scollen S, van Enckevort D, Hoogstrate Y, Senf A, Hiltemann S, Repo S, Pipping W, Bierkens M, Payralbe S, Stringer B, Heringa J, Stubbs A, Bonino Da Silva Santos LO, Belien J, Weistra W, Azevedo R, van Bochove K, Meijer G, Boiten JW, Rambla J, Fijneman R, Spalding JD, Abeln S. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.12168.1
QuickGO - Gene ontology annotation
Georghiou G. DOI: 10.6019/tol.quickgo-w.2017.00001.1
How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.
Marioni JC, Arendt D. Annual review of cell and developmental biology Volume 33 (2017) p.537-553 DOI: 10.1146/annurev-cellbio-100616-060818
Reactome: Tools for analysis of biological pathways
Jupe S. DOI: 10.6019/tol.reactome_tools-t.2017.00001.1
Europe PMC: Quick tour
Parkin M. DOI: 10.6019/tol.epmc-qt.2017.00001.2
UniChem: EMBL-EBI’s mapping tool for small molecule database identifiers: webinar
Chambers J, Hersey A. DOI: 10.6019/tol.unichem-w.2017.00001.1
Ensembl tools: webinar
Perry E. DOI: 10.6019/tol.ens-too-w.2017.00001.2
ChEMBL walkthrough: webinar
Mutowo P. DOI: 10.6019/tol.chemblwalk-w.2017.00001.1
Reactome: Exploring biological pathways
Jupe S. DOI: 10.6019/tol.reactome_exbp-t.2017.00001.1
Human genetic variation (II): exploring publicly available data
Armstrong D, Burke M, Emery L, MacArthur J, Nightingale A, Perry E, Pundir S, Saunders G. DOI: 10.6019/tol.hugenvar_2-t.2017.00001.1
EMBL-EBI, programmatically: take a REST from manual searches
Burke M, Armstrong D, Carvalho-Silva D, Castro L, Cowley A, Finn R, Foix A, Katuri J, Laird M, Lee J, Levchenko M, Lopez R, Nightingale A, Nightingale A, Nowotka M, Perry E, Pichler K, Pundir S, Morgan S, Saunders G, Garcia P, Squizzato S. DOI: 10.6019/tol.ebiprogrammatically-w.2017.00001.1
Europe PMC: get the most from literature searches
Parkin M. DOI: 10.6019/tol.epmcsearch-w.2017.00001.1
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Detection and removal of barcode swapping in single-cell RNA-seq data
Griffiths JA, Richard AC, Bach K, Lun AT, Marioni JC. Preprint DOI: 10.1101/177048
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A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology.
Penas DR, Henriques D, González P, Doallo R, Saez-Rodriguez J, Banga JR. PloS one Volume 12 (2017) p.e0182186 DOI: 10.1371/journal.pone.0182186
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A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters
Demircioğlu D, Kindermans M, Nandi T, Cukuroglu E, Calabrese C, Fonseca NA, Kahles A, Lehmann K, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J, on behalf of the PCAWG Transcriptome Working Group, and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/176487
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Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set.
Lenselink EB, Ten Dijke N, Bongers B, Papadatos G, van Vlijmen HWT, Kowalczyk W, IJzerman AP, van Westen GJP. Journal of cheminformatics Volume 9 (2017) p.45 DOI: 10.1186/s13321-017-0232-0
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mRNA 3' uridylation and poly(A) tail length sculpt the mammalian maternal transcriptome.
Morgan M, Much C, DiGiacomo M, Azzi C, Ivanova I, Vitsios DM, Pistolic J, Collier P, Moreira PN, Benes V, Enright AJ, O'Carroll D. Nature Volume 548 (2017) p.347-351 DOI: 10.1038/nature23318
Navigating freely-available software tools for metabolomics analysis.
Spicer R, Salek RM, Moreno P, Cañueto D, Steinbeck C. Metabolomics : Official journal of the Metabolomic Society Volume 13 (2017) p.106 DOI: 10.1007/s11306-017-1242-7
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Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient.
Jiménez-Sánchez A, Memon D, Pourpe S, Veeraraghavan H, Li Y, Vargas HA, Gill MB, Park KJ, Zivanovic O, Konner J, Ricca J, Zamarin D, Walther T, Aghajanian C, Wolchok JD, Sala E, Merghoub T, Snyder A, Miller ML. Cell Volume 170 (2017) p.927-938.e20 DOI: 10.1016/j.cell.2017.07.025
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mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.
Larralde M, Lawson TN, Weber RJM, Moreno P, Haug K, Rocca-Serra P, Viant MR, Steinbeck C, Salek RM. Bioinformatics (Oxford, England) Volume 33 (2017) p.2598-2600 DOI: 10.1093/bioinformatics/btx169
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BioCIDER: a Contextualisation InDEx for biological Resources discovery.
Horro C, Cook M, Attwood TK, Brazas MD, Hancock JM, Palagi P, Corpas M, Jimenez R. Bioinformatics (Oxford, England) Volume 33 (2017) p.2607-2608 DOI: 10.1093/bioinformatics/btx213
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Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Genoscope Technical Team, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Tara Oceans Consortium Coordinators, Pesant S, Karsenti E, Wincker P. Scientific data Volume 4 (2017) p.170093 DOI: 10.1038/sdata.2017.93
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Epigenetic resetting of human pluripotency.
Guo G, von Meyenn F, Rostovskaya M, Clarke J, Dietmann S, Baker D, Sahakyan A, Myers S, Bertone P, Reik W, Plath K, Smith A. Development (Cambridge, England) Volume 144 (2017) p.2748-2763 DOI: 10.1242/dev.146811
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BioContainers: an open-source and community-driven framework for software standardization.
da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y. Bioinformatics (Oxford, England) Volume 33 (2017) p.2580-2582 DOI: 10.1093/bioinformatics/btx192
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Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.
Mohammed H, Hernando-Herraez I, Savino A, Scialdone A, Macaulay I, Mulas C, Chandra T, Voet T, Dean W, Nichols J, Marioni JC, Reik W. Cell reports Volume 20 (2017) p.1215-1228 DOI: 10.1016/j.celrep.2017.07.009
The metagenomic data life-cycle: standards and best practices.
Ten Hoopen P, Finn RD, Bongo LA, Corre E, Fosso B, Meyer F, Mitchell A, Pelletier E, Pesole G, Santamaria M, Willassen NP, Cochrane G. GigaScience Volume 6 (2017) p.1-11 DOI: 10.1093/gigascience/gix047
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A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine.
Vamathevan J, Birney E. Yearbook of medical informatics Volume 26 (2017) p.178-187 DOI: 10.15265/iy-2017-017
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Impact of Alternative Splicing on the Human Proteome.
Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. Cell reports Volume 20 (2017) p.1229-1241 DOI: 10.1016/j.celrep.2017.07.025
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Genomic Evolution of Breast Cancer Metastasis and Relapse.
Yates LR, Knappskog S, Wedge D, Farmery JHR, Gonzalez S, Martincorena I, Alexandrov LB, Van Loo P, Haugland HK, Lilleng PK, Gundem G, Gerstung M, Pappaemmanuil E, Gazinska P, Bhosle SG, Jones D, Raine K, Mudie L, Latimer C, Sawyer E, Desmedt C, Sotiriou C, Stratton MR, Sieuwerts AM, Lynch AG, Martens JW, Richardson AL, Tutt A, Lønning PE, Campbell PJ. Cancer cell Volume 32 (2017) p.169-184.e7 DOI: 10.1016/j.ccell.2017.07.005
Automated assembly of species metabolomes through data submission into a public repository.
Salek RM, Conesa P, Cochrane K, Haug K, Williams M, Kale N, Moreno P, Jayaseelan KV, Macias JR, Nainala VC, Hall RD, Reed LK, Viant MR, O'Donovan C, Steinbeck C. GigaScience Volume 6 (2017) p.1-4 DOI: 10.1093/gigascience/gix062
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Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS. Cell reports Volume 20 (2017) p.2201-2214 DOI: 10.1016/j.celrep.2017.08.010
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Flipping the odds of drug development success through human genomics
Hingorani AD, Kuan V, Finan C, Kruger FA, Gaulton A, Chopade S, Sofat R, MacAllister RJ, Overington JP, Hemingway H, Denaxas S, Prieto D, Casas JP. Preprint DOI: 10.1101/170142
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Logic Modeling in Quantitative Systems Pharmacology.
Traynard P, Tobalina L, Eduati F, Calzone L, Saez-Rodriguez J. CPT: pharmacometrics & systems pharmacology Volume 6 (2017) p.499-511 DOI: 10.1002/psp4.12225
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Beyond the Hype: Deep Neural Networks Outperform Established Methods Using A ChEMBL Bioactivity Benchmark Set
Lenselink EB, Dijke Nt, Bongers B, Papadatos G, van Vlijmen HW, Kowalczyk W, IJzerman AP, van Westen GJ. Preprint DOI: 10.1101/168914
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Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat
Martín-Gálvez D, de Segonzac DD, John Ma MC, Kwitek AE, Thybert D, Flicek P. Preprint DOI: 10.1101/169748
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Very low depth whole genome sequencing in complex trait association studies
Gilly A, Southam L, Suveges D, Suveges D, Kuchenbaecker K, Moore R, Melloni GE, Hatzikotoulas K, Farmaki A, Ritchie G, Schwartzentruber J, Danecek P, Kilian B, Pollard MO, Ge X, Tsafantakis E, Dedoussis G, Zeggini E. Preprint DOI: 10.1101/169789
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Designing an intuitive web application for drug discovery scientists
Karamanis N, Carvalho-Silva D, Cham JA, Fumis L, Hasan S, Hulcoop D, Koscielny G, Maguire M, Newell W, Ong C, Papa E, Pierleoni A, Pignatelli M, Pundir S, Rowland F, Vamathevan J, Watkins X, Barrett JC, Dunham I. Preprint DOI: 10.1101/169193
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PIsCO: A Performance indicators framework for collection of bioinformatics resource metrics
Artaza H, Hancock JM, Jimenez RC, Corpas M. Preprint DOI: 10.7287/peerj.preprints.3112v1
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Whole-body single-cell sequencing of the Platynereis larva reveals a subdivision into apical versus non-apical tissues
Achim K, Eling N, Martinez Vergara H, Bertucci PY, Brunet T, Collier P, Benes V, Marioni JC, Arendt D. Preprint DOI: 10.1101/167742
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Best Practice Data Life Cycle Approaches for the Life Sciences
Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. Preprint DOI: 10.1101/167619
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GDSCTools for Mining Pharmacogenomic Interactions in Cancer
Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ. Preprint DOI: 10.1101/166223
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Digoxin reveals a functional connection between HIV-1 integration preference and T-cell activation.
Zhyvoloup A, Melamed A, Anderson I, Planas D, Lee CH, Kriston-Vizi J, Ketteler R, Merritt A, Routy JP, Ancuta P, Bangham CRM, Fassati A. PLoS pathogens Volume 13 (2017) p.e1006460 DOI: 10.1371/journal.ppat.1006460
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Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity.
Dönertaş HM, İzgi H, Kamacıoğlu A, He Z, Khaitovich P, Somel M. Scientific reports Volume 7 (2017) p.5894 DOI: 10.1038/s41598-017-05927-4
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A Bright Future for Serial Femtosecond Crystallography with XFELs.
Johansson LC, Stauch B, Ishchenko A, Cherezov V. Trends in biochemical sciences Volume 42 (2017) p.749-762 DOI: 10.1016/j.tibs.2017.06.007
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Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours
Haghverdi L, Lun ATL, Morgan MD, Marioni JC. Preprint DOI: 10.1101/165118
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A user’s guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)
Goldman M, Zhang J, Fonseca NA, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, O’Connor BD, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, Haussler D, Weinstein JN, Huber W, Valencia A, Park PJ, Papatheodorou I, Zhu J, Ferretti V, Vazquez M, on behalf of the PCAWG Portals and Visualization Working Group, the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/163907
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Platelet function is modified by common sequence variation in megakaryocyte super enhancers.
Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts AS, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide ME, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M, Ouwehand WH, Astle WJ, Downes K, Kostadima M, Frontini M. Nature communications Volume 8 (2017) p.16058 DOI: 10.1038/ncomms16058
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An "on-matrix" digestion procedure for AP-MS experiments dissects the interplay between complex-conserved and serotype-specific reactivities in Dengue virus-human plasma interactome.
Ramos Y, Huerta V, Martín D, Palomares S, Yero A, Pupo D, Gallien S, Martín AM, Pérez-Riverol Y, Sarría M, Guirola O, Chinea G, Domon B, González LJ. Journal of proteomics Volume 193 (2019) p.71-84 DOI: 10.1016/j.jprot.2017.07.004
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Correction: Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.
Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C, BEEHIVE collaboration. PLoS biology Volume 15 (2017) p.e1002608 DOI: 10.1371/journal.pbio.1002608
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The yeast noncoding RNA interaction network.
Panni S, Prakash A, Bateman A, Orchard S. RNA (New York, N.Y.) Volume 23 (2017) p.1479-1492 DOI: 10.1261/rna.060996.117
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General guidelines for biomedical software development
Silva LB, Jimenez RC, Blomberg N, Luis Oliveira J. Preprint DOI: 10.12688/f1000research.10750.2
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Model Description Language (MDL): A Standard for Modeling and Simulation.
Smith MK, Moodie SL, Bizzotto R, Blaudez E, Borella E, Carrara L, Chan P, Chenel M, Comets E, Gieschke R, Harling K, Harnisch L, Hartung N, Hooker AC, Karlsson MO, Kaye R, Kloft C, Kokash N, Lavielle M, Lestini G, Magni P, Mari A, Mentré F, Muselle C, Nordgren R, Nyberg HB, Parra-Guillén ZP, Pasotti L, Rode-Kristensen N, Sardu ML, Smith GR, Swat MJ, Terranova N, Yngman G, Yvon F, Holford N, DDMoRe consortium. CPT: pharmacometrics & systems pharmacology Volume 6 (2017) p.647-650 DOI: 10.1002/psp4.12222
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Sequanix: A Dynamic Graphical Interface for Snakemake Workflows
Desvillechabrol D, Legendre R, Rioualen C, Bouchier C, Helden Jv, Kennedy S, Cokelaer T. Preprint DOI: 10.1101/162701
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The evolutionary history of 2,658 cancers
Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Loo PV, on behalf of the PCAWG Evolution and Heterogeneity Working Group, the PCAWG network. Preprint DOI: 10.1101/161562
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SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data
Venkatesan A, Kim J, Talo F, Ide-Smith M, Gobeill J, Carter J, Batista-Navarro R, Ananiadou S, Ruch P, McEntyre J. Preprint DOI: 10.12688/wellcomeopenres.10210.2
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Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments
Yung CK, O’Connor BD, Yakneen S, Zhang J, Ellrott K, Kleinheinz K, Miyoshi N, Raine KM, Royo R, Saksena GB, Schlesner M, Shorser SI, Vazquez M, Weischenfeldt J, Yuen D, Butler AP, Davis-Dusenbery BN, Eils R, Ferretti V, Grossman RL, Harismendy O, Kim Y, Nakagawa H, Newhouse SJ, Torrents D, Stein LD, Rodriguez JB, Boroevich KA, Boyce R, Brooks AN, Buchanan A, Buchhalter I, Byrne NJ, Cafferkey A, Campbell PJ, Chen Z, Cho S, Choi W, Clapham P, De La Vega FM, Demeulemeester J, Dow MT, Dursi LJ, Eils J, Farcas C, Favero F, Fayzullaev N, Flicek P, Fonseca NA, Gelpi JL, Getz G, Gibson B, Heinold MC, Hess JM, Hofmann O, Hong JH, Hudson TJ, Huebschmann D, Hutter B, Hutter CM, Imoto S, Ivkovic S, Jeon S, Jiao W, Jung J, Kabbe R, Kahles A, Kerssemakers J, Kim H, Kim H, Kim J, Korbel JO, Koscher M, Koures A, Kovacevic M, Lawerenz C, Leshchiner I, Livitz DG, Mihaiescu GL, Mijalkovic S, Lazic AM, Miyano S, Nahal HK, Nastic M, Nicholson J, Ocana D, Ohi K, Ohno-Machado L, Omberg L, Francis Ouellette B, Paramasivam N, Perry MD, Pihl TD, Prinz M, Puiggròs M, Radovic P, Rheinbay E, Rosenberg MW, Short C, Sofia HJ, Spring J, Struck AJ, Tiao G, Tijanic N, Loo PV, Vicente D, Wala JA, Wang Z, Werner J, Williams A, Woo Y, Wright AJ, Xiang Q, on behalf of the PCAWG Technical Working Group, the PCAWG Network. Preprint DOI: 10.1101/161638
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Quantification of transmission risk in a male patient with a FLNB mosaic mutation causing Larsen syndrome: Implications for genetic counseling in postzygotic mosaicism cases.
Bernkopf M, Hunt D, Koelling N, Morgan T, Collins AL, Fairhurst J, Robertson SP, Douglas AGL, Goriely A. Human mutation Volume 38 (2017) p.1360-1364 DOI: 10.1002/humu.23281
Building bridges between cellular and molecular structural biology.
Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M, Kleywegt GJ. eLife Volume 6 (2017) DOI: 10.7554/elife.25835
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Genetics of Cerebellar and Neocortical Expansion in Anthropoid Primates: A Comparative Approach.
Harrison PW, Montgomery SH. Brain, behavior and evolution Volume 89 (2017) p.274-285 DOI: 10.1159/000477432
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Linking functions: an additional role for an intrinsically disordered linker domain in the transcriptional coactivator CBP.
Contreras-Martos S, Piai A, Kosol S, Varadi M, Bekesi A, Lebrun P, Volkov AN, Gevaert K, Pierattelli R, Felli IC, Tompa P. Scientific reports Volume 7 (2017) p.4676 DOI: 10.1038/s41598-017-04611-x
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Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia.
Wang L, Fan J, Francis JM, Georghiou G, Hergert S, Li S, Gambe R, Zhou CW, Yang C, Xiao S, Cin PD, Bowden M, Kotliar D, Shukla SA, Brown JR, Neuberg D, Alessi DR, Zhang CZ, Kharchenko PV, Livak KJ, Wu CJ. Genome research Volume 27 (2017) p.1300-1311 DOI: 10.1101/gr.217331.116
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Classification and analysis of a large collection of in vivo bioassay descriptions.
Zwierzyna M, Overington JP. PLoS computational biology Volume 13 (2017) p.e1005641 DOI: 10.1371/journal.pcbi.1005641
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Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action.
Pawlik A, van Gelder CWG, Nenadic A, Palagi PM, Korpelainen E, Lijnzaad P, Marek D, Sansone SA, Hancock J, Goble C. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.11718.1
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Extracellular vesicles are independent metabolic units with asparaginase activity.
Iraci N, Gaude E, Leonardi T, Costa ASH, Cossetti C, Peruzzotti-Jametti L, Bernstock JD, Saini HK, Gelati M, Vescovi AL, Bastos C, Faria N, Occhipinti LG, Enright AJ, Frezza C, Pluchino S. Nature chemical biology Volume 13 (2017) p.951-955 DOI: 10.1038/nchembio.2422
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Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
Thybert D, Roller M, Navarro FC, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin A, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Quail MA, Sisu C, Stanke M, Stefflova K, Oosterhout CV, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams D, Brazma A, Gerstein M, Paten B, Pham S, Keane T, Odom DT, Flicek P. Preprint DOI: 10.1101/158659
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Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks.
Raisaro JL, Tramèr F, Ji Z, Bu D, Zhao Y, Carey K, Lloyd D, Sofia H, Baker D, Flicek P, Shringarpure S, Bustamante C, Wang S, Jiang X, Ohno-Machado L, Tang H, Wang X, Hubaux JP. Journal of the American Medical Informatics Association : JAMIA Volume 24 (2017) p.799-805 DOI: 10.1093/jamia/ocw167
ProtVista: visualization of protein sequence annotations.
Watkins X, Garcia LJ, Pundir S, Martin MJ, UniProt Consortium. Bioinformatics (Oxford, England) Volume 33 (2017) p.2040-2041 DOI: 10.1093/bioinformatics/btx120
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IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.
Bertelli C, Laird MR, Williams KP, Simon Fraser University Research Computing Group, Lau BY, Hoad G, Winsor GL, Brinkman FSL. Nucleic acids research Volume 45 (2017) p.W30-W35 DOI: 10.1093/nar/gkx343
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Chojnacki S, Cowley A, Lee J, Foix A, Lopez R. Nucleic acids research Volume 45 (2017) p.W550-W553 DOI: 10.1093/nar/gkx273
The EBI search engine: EBI search as a service-making biological data accessible for all.
Park YM, Squizzato S, Buso N, Gur T, Lopez R. Nucleic acids research Volume 45 (2017) p.W545-W549 DOI: 10.1093/nar/gkx359
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Petryszak R, Fonseca NA, Füllgrabe A, Huerta L, Keays M, Tang YA, Brazma A. Bioinformatics (Oxford, England) Volume 33 (2017) p.2218-2220 DOI: 10.1093/bioinformatics/btx143
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Zheng-Bradley X, Streeter I, Fairley S, Richardson D, Clarke L, Flicek P, 1000 Genomes Project Consortium. GigaScience Volume 6 (2017) p.1-8 DOI: 10.1093/gigascience/gix038
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Glycolytic Enzymes Coalesce in G Bodies under Hypoxic Stress.
Jin M, Fuller GG, Han T, Yao Y, Alessi AF, Freeberg MA, Roach NP, Moresco JJ, Karnovsky A, Baba M, Yates JR, Gitler AD, Inoki K, Klionsky DJ, Kim JK. Cell reports Volume 20 (2017) p.895-908 DOI: 10.1016/j.celrep.2017.06.082
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Natarajan KN, Teichmann SA, Kolodziejczyk AA. Current opinion in genetics & development Volume 46 (2017) p.66-76 DOI: 10.1016/j.gde.2017.06.003
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Pandurangan AP, Ochoa-Montaño B, Ascher DB, Blundell TL. Nucleic acids research Volume 45 (2017) p.W229-W235 DOI: 10.1093/nar/gkx439
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Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data.
Lun ATL, Marioni JC. Biostatistics (Oxford, England) Volume 18 (2017) p.451-464 DOI: 10.1093/biostatistics/kxw055
The Proteins API: accessing key integrated protein and genome information.
Nightingale A, Antunes R, Alpi E, Bursteinas B, Gonzales L, Liu W, Luo J, Qi G, Turner E, Martin M. Nucleic acids research Volume 45 (2017) p.W539-W544 DOI: 10.1093/nar/gkx237
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Galgonek J, Vymetal J, Jakubec D, Vondrášek J. Nucleic acids research Volume 45 (2017) p.W388-W392 DOI: 10.1093/nar/gkx352
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PHYLOSCANNER: Inferring Transmission from Within‐ and Between-Host Pathogen Genetic Diversity
Wymant C, Hall M, Ratmann O, Bonsall D, Golubchik T, de Cesare M, Gall A, Cornelissen M, Fraser C. Preprint DOI: 10.1101/157768
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Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.
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Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity.
Hendricks AE, Bochukova EG, Marenne G, Keogh JM, Atanassova N, Bounds R, Wheeler E, Mistry V, Henning E, Körner A, Muddyman D, McCarthy S, Hinney A, Hebebrand J, Scott RA, Langenberg C, Wareham NJ, Surendran P, Howson JM, Butterworth AS, Danesh J, Nordestgaard BG, Nielsen SF, Afzal S, Papadia S, Ashford S, Garg S, Millhauser GL, Palomino RI, Kwasniewska A, Tachmazidou I, O'Rahilly S, Zeggini E, Barroso I, Farooqi IS, Understanding Society Scientific Group, EPIC-CVD Consortium, UK10K Consortium. Scientific reports Volume 7 (2017) p.4394 DOI: 10.1038/s41598-017-03054-8
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SIGNOR: A Database of Causal Relationships Between Biological Entities-A Short Guide to Searching and Browsing.
Lo Surdo P, Calderone A, Cesareni G, Perfetto L. Current protocols in bioinformatics Volume 58 (2017) p.8.23.1-8.23.16 DOI: 10.1002/cpbi.28
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BRIE: transcriptome-wide splicing quantification in single cells.
Huang Y, Sanguinetti G. Genome biology Volume 18 (2017) p.123 DOI: 10.1186/s13059-017-1248-5
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ScipionCloud: An integrative and interactive gateway for large scale cryo electron microscopy image processing on commercial and academic clouds.
Cuenca-Alba J, Del Cano L, Gómez Blanco J, de la Rosa Trevín JM, Conesa Mingo P, Marabini R, S Sorzano CO, Carazo JM. Journal of structural biology Volume 200 (2017) p.20-27 DOI: 10.1016/j.jsb.2017.06.004
Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.
Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Torlai Triglia E, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA. Nature communications Volume 8 (2017) p.36 DOI: 10.1038/s41467-017-00052-2
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Prevalence of sexual dimorphism in mammalian phenotypic traits.
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LARP1 functions as a molecular switch for mTORC1-mediated translation of an essential class of mRNAs.
Hong S, Freeberg MA, Han T, Kamath A, Yao Y, Fukuda T, Suzuki T, Kim JK, Inoki K. eLife Volume 6 (2017) DOI: 10.7554/elife.25237
Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.
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The Genetic Epidemiology of Developmental Dysplasia of the Hip: A Genome-Wide Association Study Harnessing National Clinical Audit Data
Hatzikotoulas K, Roposch A, Shah K, Clark M, Bratherton S, Limbani V, Steinberg J, Zengini E, Warsame K, Ratnayake M, Tselepi M, Schwartzentruber J, Loughlin J, Eastwood D, Zeggini E, Wilkinson JM. Preprint DOI: 10.1101/154013
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High-Throughput Phenotypic Screening of Kinase Inhibitors to Identify Drug Targets for Polycystic Kidney Disease.
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ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.
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De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms.
Giordano F, Aigrain L, Quail MA, Coupland P, Bonfield JK, Davies RM, Tischler G, Jackson DK, Keane TM, Li J, Yue JX, Liti G, Durbin R, Ning Z. Scientific reports Volume 7 (2017) p.3935 DOI: 10.1038/s41598-017-03996-z
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Differential gene expression at different stages of mesocarp development in high- and low-yielding oil palm.
Wong YC, Teh HF, Mebus K, Ooi TEK, Kwong QB, Koo KL, Ong CK, Mayes S, Chew FT, Appleton DR, Kulaveerasingam H. BMC genomics Volume 18 (2017) p.470 DOI: 10.1186/s12864-017-3855-7
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Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study.
Suchan T, Espíndola A, Rutschmann S, Emerson BC, Gori K, Dessimoz C, Arrigo N, Ronikier M, Alvarez N. Molecular phylogenetics and evolution Volume 114 (2017) p.189-198 DOI: 10.1016/j.ympev.2017.06.012
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Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1.
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The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
Menschaert G, Wang X, Jones AR, Ghali F, Fenyö D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaíno JA. Preprint DOI: 10.1101/152579
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The Image Data Resource: A Bioimage Data Integration and Publication Platform.
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR. Nature methods Volume 14 (2017) p.775-781 DOI: 10.1038/nmeth.4326
Drug repurposing for aging research using model organisms.
Ziehm M, Kaur S, Ivanov DK, Ballester PJ, Marcus D, Partridge L, Thornton JM. Aging cell Volume 16 (2017) p.1006-1015 DOI: 10.1111/acel.12626
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Four simple recommendations to encourage best practices in research software.
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A community proposal to integrate proteomics activities in ELIXIR.
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Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery.
Nowotka MM, Gaulton A, Mendez D, Bento AP, Hersey A, Leach A. Expert opinion on drug discovery Volume 12 (2017) p.757-767 DOI: 10.1080/17460441.2017.1339032
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Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.
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Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer
Fonseca NA, He Y, Greger L, Brazma A, Zhang Z, PCAWG3. Preprint DOI: 10.1101/148684
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Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches.
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OWL Reasoning: Subsumption Test Hardness and Modularity.
Matentzoglu N, Parsia B, Sattler U. Journal of automated reasoning Volume 60 (2018) p.385-419 DOI: 10.1007/s10817-017-9414-8
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Integrating long-range connectivity information into de Bruijn graphs
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Literature evidence in open targets - a target validation platform.
Kafkas Ş, Dunham I, McEntyre J. Journal of biomedical semantics Volume 8 (2017) p.20 DOI: 10.1186/s13326-017-0131-3
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An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures
Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Berna J, Tubio JM, McMurran CE, Young AM, Young MD, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson MD, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott MW, Kirollos RW, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U. Preprint DOI: 10.1101/146811
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The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.
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Epigenetic resetting of human pluripotency
Guo G, Meyenn Fv, Rostovskaya M, Clarke J, Dietmann S, Baker D, Sahakyan A, Myers S, Bertone P, Reik W, Plath K, Smith A. Preprint DOI: 10.1101/146712
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Accurate and Fast feature selection workflow for high-dimensional omics data
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Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance.
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PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance.
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Benchmarking substrate-based kinase activity inference using phosphoproteomic data.
Hernandez-Armenta C, Ochoa D, Gonçalves E, Saez-Rodriguez J, Beltrao P. Bioinformatics (Oxford, England) Volume 33 (2017) p.1845-1851 DOI: 10.1093/bioinformatics/btx082
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Cylindromatosis Tumor Suppressor Protein (CYLD) Deubiquitinase is Necessary for Proper Ubiquitination and Degradation of the Epidermal Growth Factor Receptor.
Sanchez-Quiles V, Akimov V, Osinalde N, Francavilla C, Puglia M, Barrio-Hernandez I, Kratchmarova I, Olsen JV, Blagoev B. Molecular & cellular proteomics : MCP Volume 16 (2017) p.1433-1446 DOI: 10.1074/mcp.m116.066423
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ReGaTE: Registration of Galaxy Tools in Elixir.
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Structural Variation Shapes the Landscape of Recombination in Mouse.
Morgan AP, Gatti DM, Najarian ML, Keane TM, Galante RJ, Pack AI, Mott R, Churchill GA, de Villena FP. Genetics Volume 206 (2017) p.603-619 DOI: 10.1534/genetics.116.197988
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MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry.
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MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry
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SpatialDE - Identification of spatially variable genes
Svensson V, Teichmann SA, Stegle O. Preprint DOI: 10.1101/143321
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OpenMS - A platform for reproducible analysis of mass spectrometry data.
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A novel community driven software for functional enrichment analysis of extracellular vesicles data.
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Whole genome sequencing and imputation in isolated populations identify genetic associations with medically-relevant complex traits.
Southam L, Gilly A, Süveges D, Farmaki AE, Schwartzentruber J, Tachmazidou I, Matchan A, Rayner NW, Tsafantakis E, Karaleftheri M, Xue Y, Dedoussis G, Zeggini E. Nature communications Volume 8 (2017) p.15606 DOI: 10.1038/ncomms15606
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HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.
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Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.
Joseph AP, Lagerstedt I, Patwardhan A, Topf M, Winn M. Journal of structural biology Volume 199 (2017) p.12-26 DOI: 10.1016/j.jsb.2017.05.007
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Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.
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Phenotype prediction in an Escherichia coli strain panel
Galardin M, Koumoutsi A, Herrera-Dominguez L, Varela JAC, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P. Preprint DOI: 10.1101/141879
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MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni.
Protasio AV, van Dongen S, Collins J, Quintais L, Ribeiro DM, Sessler F, Hunt M, Rinaldi G, Collins JJ, Enright AJ, Berriman M. PLoS neglected tropical diseases Volume 11 (2017) p.e0005559 DOI: 10.1371/journal.pntd.0005559
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Two forms of death in ageing Caenorhabditis elegans.
Zhao Y, Gilliat AF, Ziehm M, Turmaine M, Wang H, Ezcurra M, Yang C, Phillips G, McBay D, Zhang WB, Partridge L, Pincus Z, Gems D. Nature communications Volume 8 (2017) p.15458 DOI: 10.1038/ncomms15458
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SNP in human ARHGEF3 promoter is associated with DNase hypersensitivity, transcript level and platelet function, and Arhgef3 KO mice have increased mean platelet volume.
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Speed D, Cai N, UCLEB Consortium, Johnson MR, Nejentsev S, Balding DJ. Nature genetics Volume 49 (2017) p.986-992 DOI: 10.1038/ng.3865
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Platelet proteome reveals novel pathways of platelet activation and platelet-mediated immunoregulation in dengue.
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PGBD5 promotes site-specific oncogenic mutations in human tumors.
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Testing for differential abundance in mass cytometry data.
Lun ATL, Richard AC, Marioni JC. Nature methods Volume 14 (2017) p.707-709 DOI: 10.1038/nmeth.4295
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Gabryś HS, Buettner F, Sterzing F, Hauswald H, Bangert M. Acta oncologica (Stockholm, Sweden) Volume 56 (2017) p.1197-1203 DOI: 10.1080/0284186x.2017.1324209
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Common sequence variants affect molecular function more than rare variants?
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The Human Cell Atlas
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ImmunoNodes - graphical development of complex immunoinformatics workflows.
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TwiMed: Twitter and PubMed Comparable Corpus of Drugs, Diseases, Symptoms, and Their Relations.
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MORC-1 Integrates Nuclear RNAi and Transgenerational Chromatin Architecture to Promote Germline Immortality.
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Fifty important research questions in microbial ecology.
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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.
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Identification of Gene Loci That Overlap Between Schizophrenia and Educational Attainment.
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PCSK9 monoclonal antibodies for the primary and secondary prevention of cardiovascular disease.
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Bridging the translational innovation gap through good biomarker practice.
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Gli1+ Mesenchymal Stromal Cells Are a Key Driver of Bone Marrow Fibrosis and an Important Cellular Therapeutic Target.
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The Profile and Dynamics of RNA Modifications in Animals.
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Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
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A suite of essential biodiversity variables for detecting critical biodiversity change.
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A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog
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Expansion of the clinical phenotype of the distal 10q26.3 deletion syndrome to include ataxia and hyperemia of the hands and feet.
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UniEuk: Time to Speak a Common Language in Protistology!
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Trends in the Electron Microscopy Data Bank (EMDB).
Patwardhan A. Acta crystallographica. Section D, Structural biology Volume 73 (2017) p.503-508 DOI: 10.1107/s2059798317004181
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Effect of pistachio consumption on the modulation of urinary gut microbiota-related metabolites in prediabetic subjects.
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A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining.
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Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data.
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Exploring models for human disease with UniProt
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Sub-minute phosphoregulation of cell-cycle systems during Plasmodium gamete formation
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EBI Metagenomics: analysing and exploring metagenomic data
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Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
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Decoding the functional Fes kinase signaling network topology in a lymphocyte model
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Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression
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Literature Evidence in Open Targets – a target validation platform
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Short template switch events explain mutation clusters in the human genome.
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Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold.
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Updates in Rhea - an expert curated resource of biochemical reactions.
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Identifying genes for neurobehavioural traits in rodents: progress and pitfalls.
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Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method.
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Novel 25 kb Deletion of MERTK Causes Retinitis Pigmentosa With Severe Progression.
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Towards Coordinated International Support of Core Data Resources for the Life Sciences
Anderson W, Apweiler R, Bateman A, Bauer G, Berman H, Blake J, Blomberg N, Burley S, Cochrane G, Di Francesco V, Donohue T, Durinx C, Game A, Green E, Gojobori T, Goodhand P, Hamosh A, Hermjakob H, Kanehisa M, Kiley R, McEntyre J, McKibbin R, Miyano S, Pauly B, Perrimon N, Ragan M, Richards G, Teo Y, Westerfield M, Westhof E, Lasko P. Preprint DOI: 10.1101/110825
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Antibiotic Resistance Determinant-Focused Acinetobacter baumannii Vaccine Designed Using Reverse Vaccinology.
Ni Z, Chen Y, Ong E, He Y. International journal of molecular sciences Volume 18 (2017) DOI: 10.3390/ijms18020458
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A computational protocol to evaluate the effects of protein mutants in the kinase gatekeeper position on the binding of ATP substrate analogues.
Romano V, de Beer TA, Schwede T. BMC research notes Volume 10 (2017) p.104 DOI: 10.1186/s13104-017-2428-9
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Prospective identification of hematopoietic lineage choice by deep learning.
Buggenthin F, Buettner F, Hoppe PS, Endele M, Kroiss M, Strasser M, Schwarzfischer M, Loeffler D, Kokkaliaris KD, Hilsenbeck O, Schroeder T, Theis FJ, Marr C. Nature methods Volume 14 (2017) p.403-406 DOI: 10.1038/nmeth.4182
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New drug candidates for liposomal delivery identified by computer modeling of liposomes' remote loading and leakage.
Cern A, Marcus D, Tropsha A, Barenholz Y, Goldblum A. Journal of controlled release : official journal of the Controlled Release Society Volume 252 (2017) p.18-27 DOI: 10.1016/j.jconrel.2017.02.015
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The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection.
Hulo C, Masson P, de Castro E, Auchincloss AH, Foulger R, Poux S, Lomax J, Bougueleret L, Xenarios I, Le Mercier P. PloS one Volume 12 (2017) p.e0171746 DOI: 10.1371/journal.pone.0171746
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11,670 whole-genome sequences representative of the Han Chinese population from the CONVERGE project.
Cai N, Bigdeli TB, Kretzschmar WW, Li Y, Liang J, Hu J, Peterson RE, Bacanu S, Webb BT, Riley B, Li Q, Marchini J, Mott R, Kendler KS, Flint J. Scientific data Volume 4 (2017) p.170011 DOI: 10.1038/sdata.2017.11
Promoter shape varies across populations and affects promoter evolution and expression noise.
Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE. Nature genetics Volume 49 (2017) p.550-558 DOI: 10.1038/ng.3791
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Structure of the Escherichia coli ProQ RNA-binding protein.
Gonzalez GM, Hardwick SW, Maslen SL, Skehel JM, Holmqvist E, Vogel J, Bateman A, Luisi BF, Broadhurst RW. RNA (New York, N.Y.) Volume 23 (2017) p.696-711 DOI: 10.1261/rna.060343.116
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Genetic regulatory signatures underlying islet gene expression and type 2 diabetes.
Varshney A, Scott LJ, Welch RP, Erdos MR, Chines PS, Narisu N, Albanus RD, Orchard P, Wolford BN, Kursawe R, Vadlamudi S, Cannon ME, Didion JP, Hensley J, Kirilusha A, NISC Comparative Sequencing Program, Bonnycastle LL, Taylor DL, Watanabe R, Mohlke KL, Boehnke M, Collins FS, Parker SC, Stitzel ML. Proceedings of the National Academy of Sciences of the United States of America Volume 114 (2017) p.2301-2306 DOI: 10.1073/pnas.1621192114
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A high-resolution mRNA expression time course of embryonic development in zebrafish
White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Hourlier T, Füllgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. Preprint DOI: 10.1101/107631
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Nuclear RNA Decay Pathways Aid Rapid Remodeling of Gene Expression in Yeast.
Bresson S, Tuck A, Staneva D, Tollervey D. Molecular cell Volume 65 (2017) p.787-800.e5 DOI: 10.1016/j.molcel.2017.01.005
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OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.
Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK. Structure (London, England : 1993) Volume 25 (2017) p.536-545 DOI: 10.1016/j.str.2017.01.004
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Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.
Koo BM, Kritikos G, Farelli JD, Todor H, Tong K, Kimsey H, Wapinski I, Galardini M, Cabal A, Peters JM, Hachmann AB, Rudner DZ, Allen KN, Typas A, Gross CA. Cell systems Volume 4 (2017) p.291-305.e7 DOI: 10.1016/j.cels.2016.12.013
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Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations.
Brammeld JS, Petljak M, Martincorena I, Williams SP, Alonso LG, Dalmases A, Bellosillo B, Robles-Espinoza CD, Price S, Barthorpe S, Tarpey P, Alifrangis C, Bignell G, Vidal J, Young J, Stebbings L, Beal K, Stratton MR, Saez-Rodriguez J, Garnett M, Montagut C, Iorio F, McDermott U. Genome research Volume 27 (2017) p.613-625 DOI: 10.1101/gr.213546.116
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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. Development (Cambridge, England) Volume 144 (2017) p.1221-1234 DOI: 10.1242/dev.142711
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Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.
Imprialou M, Kahles A, Steffen JG, Osborne EJ, Gan X, Lempe J, Bhomra A, Belfield E, Visscher A, Greenhalgh R, Harberd NP, Goram R, Hein J, Robert-Seilaniantz A, Jones J, Stegle O, Kover P, Tsiantis M, Nordborg M, Rätsch G, Clark RM, Mott R. Genetics Volume 205 (2017) p.1425-1441 DOI: 10.1534/genetics.116.192823
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Linking circadian time to growth rate quantitatively via carbon metabolism
Chew YH, Seaton DD, Mengin V, Flis A, Mugford ST, Smith AM, Stitt M, Millar AJ. Preprint DOI: 10.1101/105437
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Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.
Henriques D, Villaverde AF, Rocha M, Saez-Rodriguez J, Banga JR. PLoS computational biology Volume 13 (2017) p.e1005379 DOI: 10.1371/journal.pcbi.1005379
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Interactions between genetic variation and cellular environment in skeletal muscle gene expression
Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Paolo Casale F, Wolford BN, Guan L, Varshney A, Oliveira Albanus R, Parker SC, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS. Preprint DOI: 10.1101/105429
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Correction: Mitochondrial Complex I Is a Global Regulator of Secondary Metabolism, Virulence and Azole Sensitivity in Fungi.
Bromley M, Johns A, Davies E, Fraczek M, Gilsenan JM, Kurbatova N, Keays M, Kapushesky M, Gut M, Gut I, Denning DW, Bowyer P. PloS one Volume 12 (2017) p.e0171787 DOI: 10.1371/journal.pone.0171787
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A Comparative Analysis of Drug-Induced Hepatotoxicity in Clinically Relevant Situations.
Thiel C, Cordes H, Fabbri L, Aschmann HE, Baier V, Smit I, Atkinson F, Blank LM, Kuepfer L. PLoS computational biology Volume 13 (2017) p.e1005280 DOI: 10.1371/journal.pcbi.1005280
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eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis.
Armit C, Richardson L, Venkataraman S, Graham L, Burton N, Hill B, Yang Y, Baldock RA. Developmental biology Volume 423 (2017) p.1-11 DOI: 10.1016/j.ydbio.2017.01.023
Synthetic human proteomes for accelerating protein research.
Perez-Riverol Y, Vizcaíno JA. Nature methods Volume 14 (2017) p.240-242 DOI: 10.1038/nmeth.4191
Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders.
Evers JM, Laskowski RA, Bertolli M, Clayton-Smith J, Deshpande C, Eason J, Elmslie F, Flinter F, Gardiner C, Hurst JA, Kingston H, Kini U, Lampe AK, Lim D, Male A, Naik S, Parker MJ, Price S, Robert L, Sarkar A, Straub V, Woods G, Thornton JM, DDD Study, Wright CF. Human molecular genetics Volume 26 (2017) p.519-526 DOI: 10.1093/hmg/ddw409
Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis.
Vitsios DM, Davis MP, van Dongen S, Enright AJ. Nucleic acids research Volume 45 (2017) p.1079-1090 DOI: 10.1093/nar/gkw1031
From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB.
Zaru R, Magrane M, O'Donovan C, UniProt Consortium. The Biochemical journal Volume 474 (2017) p.493-515 DOI: 10.1042/bcj20160991
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The Genetic Architecture of Major Depressive Disorder in Han Chinese Women.
Peterson RE, Cai N, Bigdeli TB, Li Y, Reimers M, Nikulova A, Webb BT, Bacanu SA, Riley BP, Flint J, Kendler KS. JAMA psychiatry Volume 74 (2017) p.162-168 DOI: 10.1001/jamapsychiatry.2016.3578
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RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.
Miao Z, Adamiak RW, Antczak M, Batey RT, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J, Sarzynska J, Szachniuk M, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B, Xiao Y, Xu X, Xu X, Zhang D, Zok T, Westhof E. RNA (New York, N.Y.) Volume 23 (2017) p.655-672 DOI: 10.1261/rna.060368.116
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Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.
Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP, Sidiropoulos N, Rapin N, Merkel A, BLUEPRINT Consortium, Stunnenberg HG, Stegle O, Frontini M, Downes K, Pastinen T, Kuijpers TW, Rico D, Valencia A, Beck S, Soranzo N, Paul DS. Genome biology Volume 18 (2017) p.18 DOI: 10.1186/s13059-017-1156-8
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Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration.
Arno G, Carss KJ, Hull S, Zihni C, Robson AG, Fiorentino A, UK Inherited Retinal Disease Consortium, Hardcastle AJ, Holder GE, Cheetham ME, Plagnol V, NIHR Bioresource - Rare Diseases Consortium, Moore AT, Raymond FL, Matter K, Balda MS, Webster AR. American journal of human genetics Volume 100 (2017) p.334-342 DOI: 10.1016/j.ajhg.2016.12.014
Genetic Variation in the Social Environment Contributes to Health and Disease.
Baud A, Mulligan MK, Casale FP, Ingels JF, Bohl CJ, Callebert J, Launay JM, Krohn J, Legarra A, Williams RW, Stegle O. PLoS genetics Volume 13 (2017) p.e1006498 DOI: 10.1371/journal.pgen.1006498
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The Nucleosome Remodelling and Deacetylation complex restricts Mediator access to enhancers to control transcription
Xenophontos M, Reynolds N, Gharbi S, Johnstone E, Signolet J, Floyd R, Ralser M, Bornelöv S, Dietmann S, Loos R, Bertone P, Hendrich B. Preprint DOI: 10.1101/103192
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The influence of proton pump inhibitors and other commonly used medication on the gut microbiota.
Imhann F, Vich Vila A, Bonder MJ, Lopez Manosalva AG, Koonen DPY, Fu J, Wijmenga C, Zhernakova A, Weersma RK. Gut microbes Volume 8 (2017) p.351-358 DOI: 10.1080/19490976.2017.1284732
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Application of a Dot Blot Hybridization Platform to Assess Streptococcus uberis Population Structure in Dairy Herds.
Albuquerque P, Ribeiro N, Almeida A, Panschin I, Porfirio A, Vales M, Diniz F, Madeira H, Tavares F. Frontiers in microbiology Volume 8 (2017) p.54 DOI: 10.3389/fmicb.2017.00054
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ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services.
Robertsen EM, Denise H, Mitchell A, Finn RD, Bongo LA, Willassen NP. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.10443.1
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A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.
Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, Nik-Zainal S. Nature genetics Volume 49 (2017) p.341-348 DOI: 10.1038/ng.3771
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A Golden Age for Working with Public Proteomics Data.
Martens L, Vizcaíno JA. Trends in biochemical sciences Volume 42 (2017) p.333-341 DOI: 10.1016/j.tibs.2017.01.001
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Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti.
Maringer K, Yousuf A, Heesom KJ, Fan J, Lee D, Fernandez-Sesma A, Bessant C, Matthews DA, Davidson AD. BMC genomics Volume 18 (2017) p.101 DOI: 10.1186/s12864-016-3432-5
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First Complete Providencia rettgeri Genome Sequence, the NDM-1-Producing Clinical Strain RB151.
Marquez-Ortiz RA, Haggerty L, Sim EM, Duarte C, Castro-Cardozo BE, Beltran M, Saavedra S, Vanegas N, Escobar-Perez J, Petty NK. Genome announcements Volume 5 (2017) DOI: 10.1128/genomea.01472-16
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Unique Triphenylphosphonium Derivatives for Enhanced Mitochondrial Uptake and Photodynamic Therapy.
Hu Z, Sim Y, Kon OL, Ng WH, Ribeiro AJ, Ramos MJ, Fernandes PA, Ganguly R, Xing B, García F, Yeow EK. Bioconjugate chemistry Volume 28 (2017) p.590-599 DOI: 10.1021/acs.bioconjchem.6b00682
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Uniform resolution of compact identifiers for biomedical data
Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T. Preprint DOI: 10.1101/101279
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Urinary Exosomes Contain MicroRNAs Capable of Paracrine Modulation of Tubular Transporters in Kidney.
Gracia T, Wang X, Su Y, Norgett EE, Williams TL, Moreno P, Micklem G, Karet Frankl FE. Scientific reports Volume 7 (2017) p.40601 DOI: 10.1038/srep40601
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Precision oncology for acute myeloid leukemia using a knowledge bank approach.
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. Nature genetics Volume 49 (2017) p.332-340 DOI: 10.1038/ng.3756
Global open data management in metabolomics.
Haug K, Salek RM, Steinbeck C. Current opinion in chemical biology Volume 36 (2017) p.58-63 DOI: 10.1016/j.cbpa.2016.12.024
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Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.
Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJ, Cvejic A, Gfeller D. Genome research Volume 27 (2017) p.451-461 DOI: 10.1101/gr.207704.116
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Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, Creighton CJ, on behalf of the PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/099861
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.
Gonçalves E, Raguz Nakic Z, Zampieri M, Wagih O, Ochoa D, Sauer U, Beltrao P, Saez-Rodriguez J. PLoS computational biology Volume 13 (2017) p.e1005297 DOI: 10.1371/journal.pcbi.1005297
System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.
Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M, Vaga S, Vitek O, Saez-Rodriguez J, Aebersold R. Journal of proteome research Volume 16 (2017) p.831-841 DOI: 10.1021/acs.jproteome.6b00815
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New insights into the GINS complex explain the controversy between existing structural models.
Carroni M, De March M, Medagli B, Krastanova I, Taylor IA, Amenitsch H, Araki H, Pisani FM, Patwardhan A, Onesti S. Scientific reports Volume 7 (2017) p.40188 DOI: 10.1038/srep40188
The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying Neurodegeneration: Evolving Dimensions and Future Directions.
Lloret-Villas A, Varusai TM, Juty N, Laibe C, Le NovÈre N, Hermjakob H, Chelliah V. CPT: pharmacometrics & systems pharmacology Volume 6 (2017) p.73-86 DOI: 10.1002/psp4.12155
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Molecular and functional variation in iPSC-derived sensory neurons
Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, Patel M, Goncalves A, Ferreira R, Benn CL, Wilbrey A, Bictash M, Impey E, Cao L, Lainez S, Loucif AJ, Whiting PJ, Gutteridge A, Gaffney DJ, HIPSCI Consortium (www.hipsci.org). Preprint DOI: 10.1101/095943
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Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes.
Stasyuk OA, Jakubec D, Vondrášek J, Hobza P. Journal of chemical theory and computation Volume 13 (2017) p.877-885 DOI: 10.1021/acs.jctc.6b00775
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Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex.
Holinski A, Heyn K, Merkl R, Sterner R. Proteins Volume 85 (2017) p.312-321 DOI: 10.1002/prot.25225
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The emerging landscape of dynamic DNA methylation in early childhood.
Xu CJ, Bonder MJ, Söderhäll C, Bustamante M, Baïz N, Gehring U, Jankipersadsing SA, van der Vlies P, van Diemen CC, van Rijkom B, Just J, Kull I, Kere J, Antó JM, Bousquet J, Zhernakova A, Wijmenga C, Annesi-Maesano I, Sunyer J, Melén E, Li Y, Postma DS, Koppelman GH. BMC genomics Volume 18 (2017) p.25 DOI: 10.1186/s12864-016-3452-1
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The use of novel selectivity metrics in kinase research.
Bosc N, Meyer C, Bonnet P. BMC bioinformatics Volume 18 (2017) p.17 DOI: 10.1186/s12859-016-1413-y
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PDLIM5 links kidney anion exchanger 1 (kAE1) to ILK and is required for membrane targeting of kAE1.
Su Y, Hiemstra TF, Yan Y, Li J, Karet HI, Rosen L, Moreno P, Karet Frankl FE. Scientific reports Volume 7 (2017) p.39701 DOI: 10.1038/srep39701
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Prediction of Protein Kinase-Ligand Interactions through 2.5D Kinochemometrics.
Bosc N, Wroblowski B, Meyer C, Bonnet P. Journal of chemical information and modeling Volume 57 (2017) p.93-101 DOI: 10.1021/acs.jcim.6b00520
Primer on Ontologies.
Hastings J. Methods in molecular biology (Clifton, N.J.) Volume 1446 (2017) p.3-13 DOI: 10.1007/978-1-4939-3743-1_1
UniProt Protein Knowledgebase.
Pundir S, Martin MJ, O'Donovan C. Methods in molecular biology (Clifton, N.J.) Volume 1558 (2017) p.41-55 DOI: 10.1007/978-1-4939-6783-4_2
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Annotation Extensions.
Huntley RP, Lovering RC. Methods in molecular biology (Clifton, N.J.) Volume 1446 (2017) p.233-243 DOI: 10.1007/978-1-4939-3743-1_17
ODE-Based Modeling of Complex Regulatory Circuits.
Seaton DD. Methods in molecular biology (Clifton, N.J.) Volume 1629 (2017) p.317-330 DOI: 10.1007/978-1-4939-7125-1_20
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Equipping Physiologists with an Informatics Tool Chest: Toward an Integerated Mitochondrial Phenome.
Garlid AO, Polson JS, Garlid KD, Hermjakob H, Ping P. Handbook of experimental pharmacology Volume 240 (2017) p.377-401 DOI: 10.1007/164_2016_93
Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data.
Bolser DM, Staines DM, Perry E, Kersey PJ. Methods in molecular biology (Clifton, N.J.) Volume 1533 (2017) p.1-31 DOI: 10.1007/978-1-4939-6658-5_1
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High-Throughput Mapping and Clonal Quantification of Retroviral Integration Sites.
Gillet NA, Melamed A, Bangham CR. Methods in molecular biology (Clifton, N.J.) Volume 1582 (2017) p.127-141 DOI: 10.1007/978-1-4939-6872-5_10
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MicroRNA Biomarkers and Platelet Reactivity: The Clot Thickens.
Sunderland N, Skroblin P, Barwari T, Huntley RP, Lu R, Joshi A, Lovering RC, Mayr M. Circulation research Volume 120 (2017) p.418-435 DOI: 10.1161/circresaha.116.309303
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TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species.
Malhotra S, Mugumbate G, Blundell TL, Higueruelo AP. Database : the journal of biological databases and curation Volume 2017 (2017) DOI: 10.1093/database/bax041
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.
Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird M, Longden I, Proctor G, Searle S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P. Database : the journal of biological databases and curation Volume 2017 (2017) DOI: 10.1093/database/bax020
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Complementary Sources of Protein Functional Information: The Far Side of GO.
Furnham N. Methods in molecular biology (Clifton, N.J.) Volume 1446 (2017) p.263-274 DOI: 10.1007/978-1-4939-3743-1_19
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Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149.
Tkavc R, Matrosova VY, Grichenko OE, Gostinčar C, Volpe RP, Klimenkova P, Gaidamakova EK, Zhou CE, Stewart BJ, Lyman MG, Malfatti SA, Rubinfeld B, Courtot M, Singh J, Dalgard CL, Hamilton T, Frey KG, Gunde-Cimerman N, Dugan L, Daly MJ. Frontiers in Microbiology Volume 8 (2017) p.2528 DOI: 10.3389/fmicb.2017.02528
Using the MEROPS Database for Investigation of Lysosomal Peptidases, Their Inhibitors, and Substrates.
Rawlings ND. Methods in molecular biology (Clifton, N.J.) Volume 1594 (2017) p.213-226 DOI: 10.1007/978-1-4939-6934-0_14
The ProFunc Function Prediction Server.
Laskowski RA. Methods in molecular biology (Clifton, N.J.) Volume 1611 (2017) p.75-95 DOI: 10.1007/978-1-4939-7015-5_7
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Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.
Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. Methods in molecular biology (Clifton, N.J.) Volume 1607 (2017) p.627-641 DOI: 10.1007/978-1-4939-7000-1_26
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Profiling Phosphopeptide-Binding Domain Recognition Specificity Using Peptide Microarrays.
Tinti M, Panni S, Cesareni G. Methods in molecular biology (Clifton, N.J.) Volume 1518 (2017) p.177-193 DOI: 10.1007/978-1-4939-6584-7_12
Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways.
Saidi R, Boudellioua I, Martin MJ, Solovyev V. Methods in molecular biology (Clifton, N.J.) Volume 1613 (2017) p.311-331 DOI: 10.1007/978-1-4939-7027-8_12