Publications for 2019

2019

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scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation.
Madissoon E, Wilbrey-Clark A, Miragaia RJ, Saeb-Parsy K, Mahbubani KT, Georgakopoulos N, Harding P, Polanski K, Huang N, Nowicki-Osuch K, Fitzgerald RC, Loudon KW, Ferdinand JR, Clatworthy MR, Tsingene A, van Dongen S, Dabrowska M, Patel M, Stubbington MJT, Teichmann SA, Stegle O, Meyer KB. Genome biology Volume 21 (2019) p.1 DOI: 10.1186/s13059-019-1906-x
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Bringing data from curated pathway resources to Cytoscape with OmniPath.
Ceccarelli F, Turei D, Gabor A, Saez-Rodriguez J. Bioinformatics (Oxford, England) Volume 36 (2020) p.2632-2633 DOI: 10.1093/bioinformatics/btz968
Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project.
Lowy-Gallego E, Fairley S, Zheng-Bradley X, Ruffier M, Clarke L, Flicek P, 1000 Genomes Project Consortium. Wellcome open research Volume 4 (2019) p.50 DOI: 10.12688/wellcomeopenres.15126.2
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Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project
Lowy-Gallego E, Fairley S, Zheng-Bradley X, Ruffier M, Clarke L, Flicek P, The 1000 Genomes Project Consortium. Preprint DOI: 10.12688/wellcomeopenres.15126.2
The neurocognitive gains of diagnostic reasoning training using simulated interactive veterinary cases.
Nassar M. Scientific reports Volume 9 (2019) p.19878 DOI: 10.1038/s41598-019-56404-z
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Publisher Correction: In silico prediction of housekeeping long intergenic non-coding RNAs reveals HKlincR1 as an essential player in lung cancer cell survival.
Memon D, Bi J, Miller CJ. Scientific reports Volume 9 (2019) p.20211 DOI: 10.1038/s41598-019-55753-z
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Prioritization of novel ADPKD drug candidates from disease-stage specific gene expression profiles.
Malas TB, Leonhard WN, Bange H, Granchi Z, Hettne KM, Van Westen GJP, Price LS, 't Hoen PAC, Peters DJM. EBioMedicine Volume 51 (2020) p.102585 DOI: 10.1016/j.ebiom.2019.11.046
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A partial genome assembly of the miniature parasitoid wasp, Megaphragma amalphitanum.
Sharko FS, Nedoluzhko AV, Lê BM, Tsygankova SV, Boulygina ES, Rastorguev SM, Sokolov AS, Rodriguez F, Mazur AM, Polilov AA, Benton R, Evgen'ev MB, Arkhipova IR, Prokhortchouk EB, Skryabin KG. PloS one Volume 14 (2019) p.e0226485 DOI: 10.1371/journal.pone.0226485
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A map of transcriptional heterogeneity and regulatory variation in human microglia
Young AM, Kumasaka N, Calvert F, Hammond TR, Knights A, Panousis N, Schwartzentruber J, Liu J, Kundu K, Segel M, Murphy N, McMurran CE, Bulstrode H, Correia J, Budohoski KP, Joannides A, Guilfoyle MR, Trivedi R, Kirollos R, Morris R, Garnett MR, Fernandes H, Timofeev I, Jalloh I, Holland K, Mannion R, Mair R, Watts C, Price SJ, Kirkpatrick PJ, Santarius T, Soranzo N, Stevens B, Hutchinson PJ, Franklin RJ, Gaffney DJ. Preprint DOI: 10.1101/2019.12.20.874099
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Estimating the quality of eukaryotic genomes recovered from metagenomic analysis
Saary P, Mitchell AL, Finn RD. Preprint DOI: 10.1101/2019.12.19.882753
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Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets.
Dempster JM, Pacini C, Pantel S, Behan FM, Green T, Krill-Burger J, Beaver CM, Younger ST, Zhivich V, Najgebauer H, Allen F, Gonçalves E, Shepherd R, Doench JG, Yusa K, Vazquez F, Parts L, Boehm JS, Golub TR, Hahn WC, Root DE, Garnett MJ, Tsherniak A, Iorio F. Nature communications Volume 10 (2019) p.5817 DOI: 10.1038/s41467-019-13805-y
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Genomic analysis of carbapenemase-producing Enterobacteriaceae in Queensland reveals widespread transmission of bla IMP-4 on an IncHI2 plasmid.
Roberts LW, Catchpoole E, Jennison AV, Bergh H, Hume A, Heney C, George N, Paterson DL, Schembri MA, Beatson SA, Harris PNA. Microbial genomics Volume 6 (2020) DOI: 10.1099/mgen.0.000321
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Integrative analysis of the plasma proteome and polygenic risk of cardiometabolic diseases
Ritchie SC, Liu Y, Lambert SA, Teo SM, Scepanovic P, Marten J, Zahid S, Chaffin M, Abraham G, Ouwehand WH, Roberts DJ, Watkins NA, Di Angelantonio E, Soranzo N, Burgess S, Drew BG, Kathiresan S, Calkin AC, Khera AV, Danesh J, Butterworth AS, Inouye M. Preprint DOI: 10.1101/2019.12.14.876474
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A roadmap for gene functional characterisation in wheat
Adamski NM, Borrill P, Brinton J, Harrington S, Marchal C, Bentley AR, Bovill WD, Cattivelli L, Cockram J, Contreras-Moreira B, Ford B, Ghosh S, Harwood W, Hassani-Pak K, Hayta S, Hickey LT, Kanyuka K, King J, Maccaferri M, Naamati G, Pozniak CJ, Ramirez-Gonzalez RH, Sansaloni C, Trevaskis B, Wingen LU, Wulff BB, Uauy C. Preprint DOI: 10.7287/peerj.preprints.26877v2
Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines.
Perez-Riverol Y, Moreno P. Proteomics Volume 20 (2020) p.e1900147 DOI: 10.1002/pmic.201900147
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Blood transcriptome profile induced by an efficacious vaccine formulated with salivary antigens from cattle ticks.
Maruyama SR, Carvalho B, González-Porta M, Rung J, Brazma A, Gustavo Gardinassi L, Ferreira BR, Banin TM, Veríssimo CJ, Katiki LM, de Miranda-Santos IKF. NPJ vaccines Volume 4 (2019) p.53 DOI: 10.1038/s41541-019-0145-1
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Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system.
Crispell J, Benton CH, Balaz D, De Maio N, Ahkmetova A, Allen A, Biek R, Presho EL, Dale J, Hewinson G, Lycett SJ, Nunez-Garcia J, Skuce RA, Trewby H, Wilson DJ, Zadoks RN, Delahay RJ, Kao RR. eLife Volume 8 (2019) DOI: 10.7554/elife.45833
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High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation.
Abeler-Dörner L, Laing AG, Lorenc A, Ushakov DS, Clare S, Speak AO, Duque-Correa MA, White JK, Ramirez-Solis R, Saran N, Bull KR, Morón B, Iwasaki J, Barton PR, Caetano S, Hng KI, Cambridge E, Forman S, Crockford TL, Griffiths M, Kane L, Harcourt K, Brandt C, Notley G, Babalola KO, Warren J, Mason JC, Meeniga A, Karp NA, Melvin D, Cawthorne E, Weinrick B, Rahim A, Drissler S, Meskas J, Yue A, Lux M, Song-Zhao GX, Chan A, Ballesteros Reviriego C, Abeler J, Wilson H, Przemska-Kosicka A, Edmans M, Strevens N, Pasztorek M, Meehan TF, Powrie F, Brinkman R, Dougan G, Jacobs W, Lloyd CM, Cornall RJ, Maloy KJ, Grencis RK, Griffiths GM, Adams DJ, Hayday AC. Nature immunology Volume 21 (2020) p.86-100 DOI: 10.1038/s41590-019-0549-0
ChEMBL: Quick tour
Hersey A. DOI: 10.6019/tol.chembl-qt.2019.00001.1
A guide to UniProt for students
Bye-A-Jee H, Pundir S. DOI: 10.6019/tol.uniprotguide-w.2019.00001.1
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Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma.
Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Dorado Garcia H, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Nature genetics Volume 52 (2020) p.29-34 DOI: 10.1038/s41588-019-0547-z
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Cancer Risks Associated With Germline PALB2 Pathogenic Variants: An International Study of 524 Families.
Yang X, Leslie G, Doroszuk A, Schneider S, Allen J, Decker B, Dunning AM, Redman J, Scarth J, Plaskocinska I, Luccarini C, Shah M, Pooley K, Dorling L, Lee A, Adank MA, Adlard J, Aittomäki K, Andrulis IL, Ang P, Barwell J, Bernstein JL, Bobolis K, Borg Å, Blomqvist C, Claes KBM, Concannon P, Cuggia A, Culver JO, Damiola F, de Pauw A, Diez O, Dolinsky JS, Domchek SM, Engel C, Evans DG, Fostira F, Garber J, Golmard L, Goode EL, Gruber SB, Hahnen E, Hake C, Heikkinen T, Hurley JE, Janavicius R, Kleibl Z, Kleiblova P, Konstantopoulou I, Kvist A, Laduca H, Lee ASG, Lesueur F, Maher ER, Mannermaa A, Manoukian S, McFarland R, McKinnon W, Meindl A, Metcalfe K, Mohd Taib NA, Moilanen J, Nathanson KL, Neuhausen S, Ng PS, Nguyen-Dumont T, Nielsen SM, Obermair F, Offit K, Olopade OI, Ottini L, Penkert J, Pylkäs K, Radice P, Ramus SJ, Rudaitis V, Side L, Silva-Smith R, Silvestri V, Skytte AB, Slavin T, Soukupova J, Tondini C, Trainer AH, Unzeitig G, Usha L, van Overeem Hansen T, Whitworth J, Wood M, Yip CH, Yoon SY, Yussuf A, Zogopoulos G, Goldgar D, Hopper JL, Chenevix-Trench G, Pharoah P, George SHL, Balmaña J, Houdayer C, James P, El-Haffaf Z, Ehrencrona H, Janatova M, Peterlongo P, Nevanlinna H, Schmutzler R, Teo SH, Robson M, Pal T, Couch F, Weitzel JN, Elliott A, Southey M, Winqvist R, Easton DF, Foulkes WD, Antoniou AC, Tischkowitz M. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Volume 38 (2020) p.674-685 DOI: 10.1200/jco.19.01907
Ensembl gene annotation for clinical genomics
Perry E, Morales J. DOI: 10.6019/tol.ensembl_clingen-w.2019.00001.1
Genome3D annotations in InterPro
Paysan-Lafosse T. DOI: 10.6019/tol.genome3dinterpro-w.2019.00001.1
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Induced aneuploidy disrupts MCF10A acini formation and CCND1 expression
Waschow M, Wang Q, Saary P, Klein C, Aschenbrenner S, Jechow K, Maier L, Tirier S, Schoell B, Chudoba I, Dietz C, Dreidax D, Jauch A, Sprick M, Herrmann C, Eils R, Conrad C. Preprint DOI: 10.1101/2019.12.15.876763
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Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.
Huang Y, McCarthy DJ, Stegle O. Genome biology Volume 20 (2019) p.273 DOI: 10.1186/s13059-019-1865-2
Twenty-five years of nomenclature and classification of proteolytic enzymes.
Rawlings ND. Biochimica et biophysica acta. Proteins and proteomics Volume 1868 (2020) p.140345 DOI: 10.1016/j.bbapap.2019.140345
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Phosphoproteomic profiling reveals a defined genetic program for osteoblastic lineage commitment of human bone marrow-derived stromal stem cells.
Barrio-Hernandez I, Jafari A, Rigbolt KTG, Hallenborg P, Sanchez-Quiles V, Skovrind I, Akimov V, Kratchmarova I, Dengjel J, Kassem M, Blagoev B. Genome Research Volume 30 (2020) p.127-137 DOI: 10.1101/gr.248286.119
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Bayesian inference associates rare KDR variants with specific phenotypes in pulmonary arterial hypertension
Swietlik EM, Greene D, Zhu N, Megy K, Cogliano M, Rajaram S, Pandya D, Tilly T, Lutz KA, Welch CCL, Pauciulo MW, Southgate L, Martin JM, Treacy CM, Penkett CJ, Stephens JC, Bogaard HJ, Church C, Coghlan G, Coleman AW, Condliffe R, Eyries M, Gall H, Ghio S, Girerd B, Holden S, Howard L, Humbert M, Kiely DG, Kovacs G, Lordan J, Machado RD, Ross RVM, McCabe C, Moledina S, Montani D, Olschewski H, Pepke-Zaba J, Price L, Rhodes CJ, Seeger W, Soubrier F, Suntharalingam J, Toshner MR, Noordegraaf AV, Wharton J, Wild J, Wort SJ, Lawrie A, Wilkins MR, Trembath RC, Shen Y, Chung WK, Swift AJ, Nichols WC, Morrell NW, Gräf S, NIHR BioResource for Translational Research - Rare Diseases, National Cohort Study of Idiopathic and Heritable PAH, PAH Biobank Enrolling Centers’ Investigators. Preprint DOI: 10.1101/2019.12.11.871210
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Development of a Retinal-Based Probe for the Profiling of Retinaldehyde Dehydrogenases in Cancer Cells.
Koenders STA, Wijaya LS, Erkelens MN, Bakker AT, van der Noord VE, van Rooden EJ, Burggraaff L, Putter PC, Botter E, Wals K, van den Elst H, den Dulk H, Florea BI, van de Water B, van Westen GJP, Mebius RE, Overkleeft HS, Le Dévédec SE, van der Stelt M. ACS Central Science Volume 5 (2019) p.1965-1974 DOI: 10.1021/acscentsci.9b01022
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BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology.
Xavier BB, Mysara M, Bolzan M, Ribeiro-Gonçalves B, Alako BTF, Harrison P, Lammens C, Kumar-Singh S, Goossens H, Carriço JA, Cochrane G, Malhotra-Kumar S. iScience Volume 23 (2020) p.100769 DOI: 10.1016/j.isci.2019.100769
Multi-omics profiling of mouse gastrulation at single-cell resolution.
Argelaguet R, Clark SJ, Mohammed H, Stapel LC, Krueger C, Kapourani CA, Imaz-Rosshandler I, Lohoff T, Xiang Y, Hanna CW, Smallwood S, Ibarra-Soria X, Buettner F, Sanguinetti G, Xie W, Krueger F, Göttgens B, Rugg-Gunn PJ, Kelsey G, Dean W, Nichols J, Stegle O, Marioni JC, Reik W. Nature Volume 576 (2019) p.487-491 DOI: 10.1038/s41586-019-1825-8
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Towards a systematic map of the functional role of protein phosphorylation
Viéitez C, Busby BP, Ochoa D, Mateus A, Galardini M, Jawed A, Memon D, Potel CM, Vonesch SC, Tu CS, Shahraz M, Stein F, Steinmetz LM, Savitski MM, Typas A, Beltrao P. Preprint DOI: 10.1101/872770
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Improving the odds of drug development success through human genomics: modelling study.
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. Scientific reports Volume 9 (2019) p.18911 DOI: 10.1038/s41598-019-54849-w
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The epigenomic landscape of transposable elements across normal human development and anatomy.
Pehrsson EC, Choudhary MNK, Sundaram V, Wang T. Nature communications Volume 10 (2019) p.5640 DOI: 10.1038/s41467-019-13555-x
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Metabolic rewiring of the hypertensive kidney.
Rinschen MM, Palygin O, Guijas C, Palermo A, Palacio-Escat N, Domingo-Almenara X, Montenegro-Burke R, Saez-Rodriguez J, Staruschenko A, Siuzdak G. Science signaling Volume 12 (2019) DOI: 10.1126/scisignal.aax9760
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A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information.
Vitale O, Preste R, Palmisano D, Attimonelli M. Molecular genetics & genomic medicine Volume 8 (2020) p.e1085 DOI: 10.1002/mgg3.1085
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Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer.
Berndt N, Egners A, Mastrobuoni G, Vvedenskaya O, Fragoulis A, Dugourd A, Bulik S, Pietzke M, Bielow C, van Gassel R, Damink SWO, Erdem M, Saez-Rodriguez J, Holzhütter HG, Kempa S, Cramer T. British journal of cancer Volume 122 (2020) p.233-244 DOI: 10.1038/s41416-019-0659-3
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Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum.
Bortnov V, Tonelli M, Lee W, Lin Z, Annis DS, Demerdash ON, Bateman A, Mitchell JC, Ge Y, Markley JL, Mosher DF. Nature communications Volume 10 (2019) p.5612 DOI: 10.1038/s41467-019-13577-5
The functional landscape of the human phosphoproteome.
Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, Beltrao P. Nature biotechnology Volume 38 (2020) p.365-373 DOI: 10.1038/s41587-019-0344-3
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Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
The Anopheles gambiae 1000 Genomes Consortium, Clarkson CS, Miles A, Harding NJ, Lucas ER, Battey CJ, Amaya-Romero JE, Cano J, Diabate A, Constant E, Nwakanma DC, Jawara M, Essandoh J, Dinis J, Le Goff G, Robert V, Troco AD, Costantini C, Rohatgi KR, Elissa N, Coulibaly B, Midega J, Mbogo C, Mawejje HD, Stalker J, Rockett KA, Drury E, Mead D, Jeffreys AE, Hubbart C, Rowlands K, Isaacs AT, Jyothi D, Malangone C, Kamali M, Henrichs C, Simpson V, Ayala D, Besansky NJ, Burt A, Caputo B, della Torre A, Fontaine M, Godfray HCJ, Hahn MW, Kern AD, Lawniczak MKN, O’Loughlin S, Pinto J, Riehle MM, Sharakhov I, Schrider DR, Vernick KD, White BJ, Donnelly MJ, Kwiatkowski DP. Preprint DOI: 10.1101/864314
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Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection.
Whelan F, Lafita A, Griffiths SC, Cooper REM, Whittingham JL, Turkenburg JP, Manfield IW, St John AN, Paci E, Bateman A, Potts JR. Proceedings of the National Academy of Sciences of the United States of America (2019) DOI: 10.1073/pnas.1911776116
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A comprehensive resource for retrieving, visualizing, and integrating functional genomics data.
Blum M, Cholley PE, Malysheva V, Nicaise S, Moehlin J, Gronemeyer H, Mendoza-Parra MA. Life science alliance Volume 3 (2020) DOI: 10.26508/lsa.201900546
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Pervasive lesion segregation shapes cancer genome evolution
Aitken SJ, Anderson CJ, Connor F, Pich O, Sundaram V, Feig C, Rayner TF, Lukk M, Aitken S, Luft J, Kentepozidou E, Arnedo-Pac C, Beentjes S, Davies SE, Drews RM, Ewing A, Kaiser VB, Khamseh A, López-Arribillaga E, Redmond AM, Santoyo-Lopez J, Sentís I, Talmane L, Yates AD, Semple CA, López-Bigas N, Flicek P, Odom DT, Taylor MS. Preprint DOI: 10.1101/868679
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The tuatara genome: insights into vertebrate evolution from the sole survivor of an ancient reptilian order
Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, Martin FJ, Flicek P, Petersen B, Kang L, Michalak P, Buckley TR, Wilson M, Cheng Y, Miller H, Schott RK, Jordan M, Newcomb R, Arroyo JI, Valenzuela N, Hore TA, Renart J, Peona V, Peart CR, Warmuth VM, Zeng L, Kortschak RD, Raison JM, Zapata VV, Wu Z, Santesmasses D, Mariotti M, Guigó R, Rupp SM, Twort VG, Dussex N, Taylor H, Abe H, Paterson JM, Mulcahy DG, Gonzalez VL, Barbieri CG, DeMeo DP, Pabinger S, Ryder O, Edwards SV, Salzberg SL, Mickelson L, Nelson N, Stone C, Board NT. Preprint DOI: 10.1101/867069
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Data structures based on k-mers for querying large collections of sequencing datasets
Marchet C, Boucher C, Puglisi SJ, Medvedev P, Salson M, Chikhi R. Preprint DOI: 10.1101/866756
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Transposable element landscape in Drosophila populations selected for longevity
Fabian DK, Dönertaş HM, Fuentealba M, Partridge L, Thornton JM. Preprint DOI: 10.1101/867838
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ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion.
Hulstaert N, Shofstahl J, Sachsenberg T, Walzer M, Barsnes H, Martens L, Perez-Riverol Y. Journal of proteome research Volume 19 (2020) p.537-542 DOI: 10.1021/acs.jproteome.9b00328
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Setting Our Sights on Infectious Diseases.
De Rycker M, Horn D, Aldridge B, Amewu RK, Barry CE, Buckner FS, Cook S, Ferguson MAJ, Gobeau N, Herrmann J, Herrling P, Hope W, Keiser J, Lafuente-Monasterio MJ, Leeson PD, Leroy D, Manjunatha UH, McCarthy J, Miles TJ, Mizrahi V, Moshynets O, Niles J, Overington JP, Pottage J, Rao SPS, Read KD, Ribeiro I, Silver LL, Southern J, Spangenberg T, Sundar S, Taylor C, Van Voorhis W, White NJ, Wyllie S, Wyatt PG, Gilbert IH. ACS infectious diseases Volume 6 (2020) p.3-13 DOI: 10.1021/acsinfecdis.9b00371
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Conditional Hfq Association with Small Noncoding RNAs in Pseudomonas aeruginosa Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing.
Chihara K, Bischler T, Barquist L, Monzon VA, Noda N, Vogel J, Tsuneda S. mSystems Volume 4 (2019) DOI: 10.1128/msystems.00590-19
A global analysis of function and conservation of catalytic residues in enzymes.
Ribeiro AJM, Tyzack JD, Borkakoti N, Holliday GL, Thornton JM. The Journal of biological chemistry Volume 295 (2020) p.314-324 DOI: 10.1074/jbc.rev119.006289
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Influence of Liver Fibrosis on Lobular Zonation.
Ghallab A, Myllys M, Holland CH, Zaza A, Murad W, Hassan R, Ahmed YA, Abbas T, Abdelrahim EA, Schneider KM, Matz-Soja M, Reinders J, Gebhardt R, Berres ML, Hatting M, Drasdo D, Saez-Rodriguez J, Trautwein C, Hengstler JG. Cells Volume 8 (2019) DOI: 10.3390/cells8121556
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Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe
Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler P, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, Soolingen Dv, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook DW, Iqbal Z. Preprint DOI: 10.12688/wellcomeopenres.15603.1
Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.
Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler P, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, van Soolingen D, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook DW, Iqbal Z. Wellcome open research Volume 4 (2019) p.191 DOI: 10.12688/wellcomeopenres.15603.1
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Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A.
Steward CA, Roovers J, Suner MM, Gonzalez JM, Uszczynska-Ratajczak B, Pervouchine D, Fitzgerald S, Viola M, Stamberger H, Hamdan FF, Ceulemans B, Leroy P, Nava C, Lepine A, Tapanari E, Keiller D, Abbs S, Sanchis-Juan A, Grozeva D, Rogers AS, Diekhans M, Guigó R, Petryszak R, Minassian BA, Cavalleri G, Vitsios D, Petrovski S, Harrow J, Flicek P, Lucy Raymond F, Lench NJ, Jonghe P, Mudge JM, Weckhuysen S, Sisodiya SM, Frankish A. NPJ genomic medicine Volume 4 (2019) p.31 DOI: 10.1038/s41525-019-0106-7
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Cohesin-dependent regulation of gene expression during differentiation is lost in cohesin-mutated myeloid malignancies.
Sasca D, Yun H, Giotopoulos G, Szybinski J, Evan T, Wilson NK, Gerstung M, Gallipoli P, Green AR, Hills R, Russell N, Osborne CS, Papaemmanuil E, Göttgens B, Campbell P, Huntly BJP. Blood Volume 134 (2019) p.2195-2208 DOI: 10.1182/blood.2019001553
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Germline mutations in the transcription factor IKZF5 cause thrombocytopenia.
Lentaigne C, Greene D, Sivapalaratnam S, Favier R, Seyres D, Thys C, Grassi L, Mangles S, Sibson K, Stubbs M, Burden F, Bordet JC, Armari-Alla C, Erber W, Farrow S, Gleadall N, Gomez K, Megy K, Papadia S, Penkett CJ, Sims MC, Stefanucci L, Stephens JC, Read RJ, Stirrups KE, Ouwehand WH, Laffan MA, NIHR BioResource, Frontini M, Freson K, Turro E. Blood Volume 134 (2019) p.2070-2081 DOI: 10.1182/blood.2019000782
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Diagnostic high-throughput sequencing of 2396 patients with bleeding, thrombotic, and platelet disorders.
Downes K, Megy K, Duarte D, Vries M, Gebhart J, Hofer S, Shamardina O, Deevi SVV, Stephens J, Mapeta R, Tuna S, Al Hasso N, Besser MW, Cooper N, Daugherty L, Gleadall N, Greene D, Haimel M, Martin H, Papadia S, Revel-Vilk S, Sivapalaratnam S, Symington E, Thomas W, Thys C, Tolios A, Penkett CJ, NIHR BioResource, Ouwehand WH, Abbs S, Laffan MA, Laffan MA, Turro E, Simeoni I, Mumford AD, Henskens YMC, Pabinger I, Gomez K, Freson K. Blood Volume 134 (2019) p.2082-2091 DOI: 10.1182/blood.2018891192
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Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.
Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, Gruca A, Grynberg M, Kajava AV, Promponas VJ, Anisimova M, Jakobsen KS, Linke D. Nucleic acids research Volume 47 (2019) p.10994-11006 DOI: 10.1093/nar/gkz841
The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae.
Galardini M, Busby BP, Vieitez C, Dunham AS, Typas A, Beltrao P. Molecular systems biology Volume 15 (2019) p.e8831 DOI: 10.15252/msb.20198831
*
Sequence tube maps: making graph genomes intuitive to commuters.
Beyer W, Novak AM, Hickey G, Chan J, Tan V, Paten B, Zerbino DR. Bioinformatics (Oxford, England) Volume 35 (2019) p.5318-5320 DOI: 10.1093/bioinformatics/btz597
*
Parallel Evolution of Complex Centipede Venoms Revealed by Comparative Proteotranscriptomic Analyses.
Jenner RA, von Reumont BM, Campbell LI, Undheim EAB. Molecular biology and evolution Volume 36 (2019) p.2748-2763 DOI: 10.1093/molbev/msz181
The authors reply.
Saez-Rodriguez J, Rinschen MM, Floege J, Kramann R. Kidney international Volume 96 (2019) p.1422-1423 DOI: 10.1016/j.kint.2019.09.011
*
CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels.
Vavra O, Filipovic J, Plhak J, Bednar D, Marques SM, Brezovsky J, Stourac J, Matyska L, Damborsky J. Bioinformatics (Oxford, England) Volume 35 (2019) p.4986-4993 DOI: 10.1093/bioinformatics/btz386
*
A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses.
Etherington GJ, Soranzo N, Mohammed S, Haerty W, Davey RP, Palma FD. GigaScience Volume 8 (2019) DOI: 10.1093/gigascience/giz144
*
Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases.
Priyam A, Woodcroft BJ, Rai V, Moghul I, Munagala A, Ter F, Chowdhary H, Pieniak I, Maynard LJ, Gibbins MA, Moon H, Davis-Richardson A, Uludag M, Watson-Haigh NS, Challis R, Nakamura H, Favreau E, Gómez EA, Pluskal T, Leonard G, Rumpf W, Wurm Y. Molecular biology and evolution Volume 36 (2019) p.2922-2924 DOI: 10.1093/molbev/msz185
*
Genomic characterisation and context of the blaNDM-1 carbapenemase in Escherichia coli ST101
Ashcroft MM, Forde BM, Phan M, Peters KM, Henderson A, Hancock SJ, Roberts LW, White RT, White RT, Chan K, Chong TM, Yin W, Paterson DL, Walsh TR, Schembri MA, Beatson SA. Preprint DOI: 10.1101/860726
*
Intensive infection control responses and whole genome sequencing to interrupt and resolve widespread transmission of OXA-181 Escherichia coli in a hospital setting
Roberts LW, Forde BM, Henderson A, Playford EG, Runnegar N, Henderson B, Watson C, Lindsay M, Bursle E, Douglas J, Paterson DL, Schembri MA, Harris PN, Beatson SA. Preprint DOI: 10.1101/850628
*
Brain DNA Methylation Patterns in CLDN5 Associated With Cognitive Decline
Hüls A, Robins C, Conneely KN, Edgar R, De Jager PL, Bennett DA, Wingo AP, Epstein MP, Wingo TS. Preprint DOI: 10.1101/857953
*
The Dundee Resource for Sequence Analysis and Structure Prediction.
MacGowan SA, Madeira F, Britto-Borges T, Warowny M, Drozdetskiy A, Procter JB, Barton GJ. Protein science : a publication of the Protein Society Volume 29 (2020) p.277-297 DOI: 10.1002/pro.3783
*
Whole genome sequencing analysis of the cardiometabolic proteome
Gilly A, Park Y, Png G, Barysenka A, Fischer I, Bjornland T, Southam L, Suveges D, Neumeyer S, Rayner NW, Tsafantakis E, Karaleftheri M, Dedoussis G, Zeggini E. Preprint DOI: 10.1101/854752
*
Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly.
Í Kongsstovu S, Mikalsen SO, Homrum EÍ, Jacobsen JA, Flicek P, Dahl HA. Scientific reports Volume 9 (2019) p.17716 DOI: 10.1038/s41598-019-54151-9
*
Characterization of gallium resistance induced in a Pseudomonas aeruginosa cystic fibrosis isolate.
Tovar-García A, Angarita-Zapata V, Cazares A, Jasso-Chávez R, Belmont-Díaz J, Sanchez-Torres V, López-Jacome LE, Coria-Jiménez R, Maeda T, García-Contreras R. Archives of microbiology Volume 202 (2020) p.617-622 DOI: 10.1007/s00203-019-01777-y
*
Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry.
Walker JA, Jordan VE, Storer JM, Steely CJ, Gonzalez-Quiroga P, Beckstrom TO, Rewerts LC, St Romain CP, Rockwell CE, Rogers J, Jolly CJ, Konkel MK, Baboon Genome Analysis Consortium, Batzer MA. Mobile DNA Volume 10 (2019) p.46 DOI: 10.1186/s13100-019-0187-y
*
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.
Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A. Structure (London, England : 1993) Volume 27 (2019) p.1745-1759 DOI: 10.1016/j.str.2019.11.002
*
Phoenix Enhancer: proteomics data mining using clustered spectra
Bai M, Qin C, Shu K, Griss J, Perez-Riverol Y, Zhu W, Hermjakob H. Preprint DOI: 10.1101/846303
*
Prediction of impacts of mutations on protein structure and interactions: SDM, a statistical approach, and mCSM, using machine learning.
Pandurangan AP, Blundell TL. Protein science : a publication of the Protein Society Volume 29 (2020) p.247-257 DOI: 10.1002/pro.3774
*
Improved inference and prediction of bacterial genotype-phenotype associations using pangenome-spanning regressions
Lees JA, Tien Mai T, Galardini M, Wheeler NE, Corander J. Preprint DOI: 10.1101/852426
*
A resource of targeted mutant mouse lines for 5,061 genes
Birling M, Yoshiki A, Adams DJ, Ayabe S, Beaudet AL, Bottomley J, Bradley A, Brown SD, Bürger A, Bushell W, Chiani F, Chin HG, Christou S, Codner GF, DeMayo FJ, Dickinson ME, Doe B, Donahue LR, Fray MD, Gambadoro A, Gao X, Gertsenstein M, Gomez-Segura A, Goodwin LO, Heaney JD, Hérault Y, de Angelis MH, Jiang S, Justice MJ, Kasparek P, King RE, Kühn R, Lee H, Lee YJ, Liu Z, Kent Lloyd KC, Lorenzo I, Mallon A, McKerlie C, Meehan TF, Newman S, Nutter LM, Oh GT, Pavlovic G, Ramirez-Solis R, Rosen B, Ryder EJ, Santos LA, Schick J, Seavitt JR, Sedlacek R, Seisenberger C, Seong JK, Skarnes WC, Sorg T, Steel KP, Tamura M, Tocchini-Valentini GP, Leo Wang C, Wardle-Jones H, Wattenhofer-Donzé M, Wells S, Willis BJ, Wood JA, Wurst W, Xu Y, Teboul L, Murray SA, IMPC Consortium. Preprint DOI: 10.1101/844092
*
Learning mutational signatures and their multidimensional genomic properties with TensorSignatures
Vöhringer H, van Hoeck A, van Hoeck A, Cuppen E, Gerstung M. Preprint DOI: 10.1101/850453
*
Minimal genome-wide human CRISPR-Cas9 library
Gonçalves E, Thomas M, Behan FM, Picco G, Pacini C, Allen F, Sharma M, Jackson DA, Price S, Beaver CM, Dovey O, Parry-Smith D, Iorio F, Parts L, Yusa K, Garnett MJ. Preprint DOI: 10.1101/848895
*
Comparison Study of Computational Prediction Tools for Drug-Target Binding Affinities.
Thafar M, Raies AB, Albaradei S, Essack M, Bajic VB. Frontiers in chemistry Volume 7 (2019) p.782 DOI: 10.3389/fchem.2019.00782
*
Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease.
D'Antonio M, Reyna J, Jakubosky D, Donovan MK, Bonder MJ, Matsui H, Stegle O, Nariai N, D'Antonio-Chronowska A, Frazer KA. eLife Volume 8 (2019) DOI: 10.7554/elife.48476
*
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I. Genome biology Volume 20 (2019) p.244 DOI: 10.1186/s13059-019-1835-8
The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases.
Vizcaíno JA, Kubiniok P, Kovalchik KA, Ma Q, Duquette JD, Mongrain I, Deutsch EW, Peters B, Sette A, Sirois I, Caron E. Molecular & cellular proteomics : MCP Volume 19 (2020) p.31-49 DOI: 10.1074/mcp.r119.001743
Identifying pseudoenzymes using functional annotation: pitfalls of common practice.
Ribeiro AJM, Tyzack JD, Borkakoti N, Thornton JM. The FEBS journal (2019) DOI: 10.1111/febs.15142
*
RNA modifications detection by comparative Nanopore direct RNA sequencing
Leger A, Amaral PP, Pandolfini L, Capitanchik C, Capraro F, Barbieri I, Migliori V, Luscombe NM, Enright AJ, Tzelepis K, Ule J, Fitzgerald T, Birney E, Leonardi T, Kouzarides T. Preprint DOI: 10.1101/843136
*
BlobToolKit – Interactive quality assessment of genome assemblies
Challis R, Richards E, Rajan J, Cochrane G, Blaxter M. Preprint DOI: 10.1101/844852
*
Investigating higher order interactions in single cell data with scHOT
Ghazanfar S, Lin Y, Su X, Lin DM, Patrick E, Han ZG, Marioni JC, Yang JYH. Preprint DOI: 10.1101/841593
Mouse protein coding diversity: What's left to discover?
Lilue J, Shivalikanjli A, Adams DJ, Keane TM. PLoS genetics Volume 15 (2019) p.e1008446 DOI: 10.1371/journal.pgen.1008446
*
A Functional Landscape of CKD Entities From Public Transcriptomic Data.
Tajti F, Kuppe C, Antoranz A, Ibrahim MM, Kim H, Ceccarelli F, Holland CH, Olauson H, Floege J, Alexopoulos LG, Kramann R, Saez-Rodriguez J. Kidney international reports Volume 5 (2020) p.211-224 DOI: 10.1016/j.ekir.2019.11.005
*
Blood pressure-related electrocardiographic findings in healthy young individuals.
Hassing GJ, van der Wall HEC, van Westen GJP, Kemme MJB, Adiyaman A, Elvan A, Burggraaf J, Gal P. Blood pressure Volume 29 (2020) p.113-122 DOI: 10.1080/08037051.2019.1673149
*
How common are single gene mutations as a cause for lacunar stroke? A targeted gene panel study.
Tan RYY, Traylor M, Megy K, Duarte D, Deevi SVV, Shamardina O, Mapeta RP, NIHR BioResource: Rare Diseases Consortium, Ouwehand WH, Gräf S, Downes K, Markus HS. Neurology Volume 93 (2019) p.e2007-e2020 DOI: 10.1212/wnl.0000000000008544
*
From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL.
Liu A, Trairatphisan P, Gjerga E, Didangelos A, Barratt J, Saez-Rodriguez J. NPJ systems biology and applications Volume 5 (2019) p.40 DOI: 10.1038/s41540-019-0118-z
*
MOFA+: a probabilistic framework for comprehensive integration of structured single-cell data
Argelaguet R, Arnol D, Bredikhin D, Deloro Y, Velten B, Marioni JC, Stegle O. Preprint DOI: 10.1101/837104
*
RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding.
Santana-Garcia W, Rocha-Acevedo M, Ramirez-Navarro L, Mbouamboua Y, Thieffry D, Thomas-Chollier M, Contreras-Moreira B, van Helden J, Medina-Rivera A. Computational and structural biotechnology journal Volume 17 (2019) p.1415-1428 DOI: 10.1016/j.csbj.2019.09.009
Collaborative Annotation Redefines Gene Sets for Crucial Phytopathogens.
Pedro H, Yates AD, Kersey PJ, De Silva NH. Frontiers in microbiology Volume 10 (2019) p.2477 DOI: 10.3389/fmicb.2019.02477
*
Automatic annotation of protein residues in published papers.
Firth R, Talo F, Venkatesan A, Mukhopadhyay A, McEntyre J, Velankar S, Morris C. Acta crystallographica. Section F, Structural biology communications Volume 75 (2019) p.665-672 DOI: 10.1107/s2053230x1901210x
Exploring Chemical Biosynthetic Design Space with Transform-MinER.
Tyzack JD, Ribeiro AJM, Borkakoti N, Thornton JM. ACS synthetic biology Volume 8 (2019) p.2494-2506 DOI: 10.1021/acssynbio.9b00105
*
Genetic structure at national and regional scale in a long-distance dispersing pest organism, the bird cherry–oat aphid Rhopalosiphum padi
Morales-Hojas R, Gonzalez-Uriarte A, Iraizoz FA, Jenkins T, Alderson L, Kruger T, Hall MJ, Greenslade A, Shortall CR, Bell JR. Preprint DOI: 10.1101/829986
*
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.
Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Tara Oceans Coordinators, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S. Cell Volume 179 (2019) p.1068-1083.e21 DOI: 10.1016/j.cell.2019.10.014
*
Global Trends in Marine Plankton Diversity across Kingdoms of Life.
Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahé F, Rigonato J, Royo-Llonch M, Salazar G, Sanz-Sáez I, Scalco E, Soviadan D, Zayed AA, Zingone A, Labadie K, Ferland J, Marec C, Kandels S, Picheral M, Dimier C, Poulain J, Pisarev S, Carmichael M, Pesant S, Tara Oceans Coordinators, Babin M, Boss E, Iudicone D, Jaillon O, Acinas SG, Ogata H, Pelletier E, Stemmann L, Sullivan MB, Sunagawa S, Bopp L, de Vargas C, Karp-Boss L, Wincker P, Lombard F, Bowler C, Zinger L. Cell Volume 179 (2019) p.1084-1097.e21 DOI: 10.1016/j.cell.2019.10.008
*
Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction.
Szalai B, Subramanian V, Holland CH, Alföldi R, Puskás LG, Saez-Rodriguez J. Nucleic acids research Volume 47 (2019) p.10010-10026 DOI: 10.1093/nar/gkz805
VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations.
Stephenson JD, Laskowski RA, Nightingale A, Hurles ME, Thornton JM. Bioinformatics (Oxford, England) Volume 35 (2019) p.4854-4856 DOI: 10.1093/bioinformatics/btz482
*
Towards clinical utility of polygenic risk scores.
Lambert SA, Abraham G, Inouye M. Human molecular genetics Volume 28 (2019) p.R133-R142 DOI: 10.1093/hmg/ddz187
*
Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022.
Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Heringa J, Holub P, Hooyberghs J, Juty N, Keane TM, Korbel JO, Lappalainen I, Leskosek B, Matthijs G, Mayrhofer MT, Metspalu A, Navarro A, Newhouse S, Nyrönen T, Page A, Persson B, Palotie A, Parkinson H, Rambla J, Salgado D, Steinfelder E, Swertz MA, Valencia A, Varma S, Blomberg N, Scollen S. Nature reviews. Genetics Volume 20 (2019) p.702 DOI: 10.1038/s41576-019-0178-3
*
A decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery.
Watson OP, Cortes-Ciriano I, Taylor AR, Watson JA. Bioinformatics (Oxford, England) Volume 35 (2019) p.4656-4663 DOI: 10.1093/bioinformatics/btz293
*
PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations.
Kamat MA, Blackshaw JA, Young R, Surendran P, Burgess S, Danesh J, Butterworth AS, Staley JR. Bioinformatics (Oxford, England) Volume 35 (2019) p.4851-4853 DOI: 10.1093/bioinformatics/btz469
*
PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels.
Martin AR, Williams E, Foulger RE, Leigh S, Daugherty LC, Niblock O, Leong IUS, Smith KR, Gerasimenko O, Haraldsdottir E, Thomas E, Scott RH, Baple E, Tucci A, Brittain H, de Burca A, Ibañez K, Kasperaviciute D, Smedley D, Caulfield M, Rendon A, McDonagh EM. Nature genetics Volume 51 (2019) p.1560-1565 DOI: 10.1038/s41588-019-0528-2
*
eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data.
Breeze CE, Reynolds AP, van Dongen J, Dunham I, Lazar J, Neph S, Vierstra J, Bourque G, Teschendorff AE, Stamatoyannopoulos JA, Beck S. Bioinformatics (Oxford, England) Volume 35 (2019) p.4767-4769 DOI: 10.1093/bioinformatics/btz456
*
Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines.
Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Ori A, Iskar M, Gillet L, Bi R, Zhang J, Zhang H, Yu C, Zhong Q, Varma S, Schmitt U, Qiu P, Zhang Q, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Liu K, Saez-Rodriguez J, Elloumi F, Reinhold WC, Sander C, Pommier Y, Aebersold R. iScience Volume 21 (2019) p.664-680 DOI: 10.1016/j.isci.2019.10.059
*
Life beyond the bench: Scientific writing.
Hatch VL. Developmental biology Volume 459 (2020) p.17-18 DOI: 10.1016/j.ydbio.2019.10.015
*
Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders.
Manica M, Oskooei A, Born J, Subramanian V, Sáez-Rodríguez J, Rodríguez Martínez M. Molecular pharmaceutics Volume 16 (2019) p.4797-4806 DOI: 10.1021/acs.molpharmaceut.9b00520
*
Human-specific tandem repeat expansion and differential gene expression during primate evolution.
Sulovari A, Li R, Audano PA, Porubsky D, Vollger MR, Logsdon GA, Human Genome Structural Variation Consortium, Warren WC, Pollen AA, Chaisson MJP, Eichler EE. Proceedings of the National Academy of Sciences of the United States of America Volume 116 (2019) p.23243-23253 DOI: 10.1073/pnas.1912175116
VarSite: Disease variants and protein structure.
Laskowski RA, Stephenson JD, Sillitoe I, Orengo CA, Thornton JM. Protein science : a publication of the Protein Society Volume 29 (2020) p.111-119 DOI: 10.1002/pro.3746
*
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.
Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subraman SR, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, Chauvot de Beauchêne I, Maigret B, Devignes MD, Ruiz Echartea ME, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkūnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Ryan Merideth B, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Honorato RV, Bonvin AMJJ, Wodak SJ. Proteins Volume 87 (2019) p.1200-1221 DOI: 10.1002/prot.25838
*
Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis
Fu Y, Jung AW, Torne RV, Gonzalez S, Vöhringer H, Shmatko A, Yates L, Jimenez-Linan M, Moore L, Gerstung M. Preprint DOI: 10.1101/813543
*
Caenorhabditis elegans AF4/FMR2 family homolog affl-2 is required for heat shock induced gene expression
Walton SJ, Wang H, Quintero-Cadena P, Bateman A, Sternberg PW. Preprint DOI: 10.1101/817833
*
A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.
Pettersson ME, Rochus CM, Han F, Chen J, Hill J, Wallerman O, Fan G, Hong X, Xu Q, Zhang H, Liu S, Liu X, Haggerty L, Hunt T, Martin FJ, Flicek P, Bunikis I, Folkvord A, Andersson L. Genome research Volume 29 (2019) p.1919-1928 DOI: 10.1101/gr.253435.119
*
Wikidata as a FAIR knowledge graph for the life sciences
Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith O, Hanspers K, Hermjakob H, Hudson TS, Hybiske K, Hybiske K, Keating SM, Manske M, Mayers M, Mietchen D, Mitraka E, Pico AR, Putman T, Riutta A, Queralt-Rosinach N, Schriml LM, Shafee T, Slenter D, Stephan R, Thornton K, Tsueng G, Tu R, Ul-Hasan S, Willighagen E, Wu C, Su AI. Preprint DOI: 10.1101/799684
*
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0.
Deutsch EW, Lane L, Overall CM, Bandeira N, Baker MS, Pineau C, Moritz RL, Corrales F, Orchard S, Van Eyk JE, Paik YK, Weintraub ST, Vandenbrouck Y, Omenn GS. Journal of proteome research Volume 18 (2019) p.4108-4116 DOI: 10.1021/acs.jproteome.9b00542
*
Hematopoietic Npc1 mutation shifts gut microbiota composition in Ldlr-/- mice on a high-fat, high-cholesterol diet.
Houben T, Penders J, Oligschlaeger Y, Dos Reis IAM, Bonder MJ, Koonen DP, Fu J, Hofker MH, Shiri-Sverdlov R. Scientific reports Volume 9 (2019) p.14956 DOI: 10.1038/s41598-019-51525-x
*
Sodium dodecyl sulfate free gel electrophoresis/electroelution sorting for peptide fractionation.
Ramos Y, González A, Sosa-Acosta P, Perez-Riverol Y, García Y, Castellanos-Serra L, Gil J, Sánchez A, González LJ, Besada V. Journal of separation science Volume 42 (2019) p.3712-3717 DOI: 10.1002/jssc.201900495
Challenges in the annotation of pseudoenzymes in databases: the UniProtKB approach.
Zaru R, Magrane M, Orchard S, UniProt Consortium. The FEBS journal (2019) DOI: 10.1111/febs.15100
*
CLICK-enabled analogues reveal pregnenolone interactomes in cancer and immune cells
Roy S, Sipthorp J, Mahata B, Pramanik J, Hennrich ML, Gavin A, Ley SV, Teichmann SA. Preprint DOI: 10.1101/800649
*
Next-generation sequencing for the diagnosis of MYH9-RD: Predicting pathogenic variants.
Bury L, Megy K, Stephens JC, Grassi L, Greene D, Gleadall N, Althaus K, Allsup D, Bariana TK, Bonduel M, Butta NV, Collins P, Curry N, Deevi SVV, Downes K, Duarte D, Elliott K, Falcinelli E, Furie B, Keeling D, Lambert MP, Linger R, Mangles S, Mapeta R, Millar CM, Penkett C, Perry DJ, Stirrups KE, Turro E, Westbury SK, Wu J, BioResource N, Gomez K, Freson K, Ouwehand WH, Gresele P, Simeoni I. Human mutation Volume 41 (2020) p.277-290 DOI: 10.1002/humu.23927
*
An intrinsically disordered proteins community for ELIXIR
Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE. Preprint DOI: 10.12688/f1000research.20136.1
*
An intrinsically disordered proteins community for ELIXIR.
Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE. F1000Research Volume 8 (2019) DOI: 10.12688/f1000research.20136.1
*
The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells.
McEwen LM, O'Donnell KJ, McGill MG, Edgar RD, Jones MJ, MacIsaac JL, Lin DTS, Ramadori K, Morin A, Gladish N, Garg E, Unternaehrer E, Pokhvisneva I, Karnani N, Kee MZL, Klengel T, Adler NE, Barr RG, Letourneau N, Giesbrecht GF, Reynolds JN, Czamara D, Armstrong JM, Essex MJ, de Weerth C, Beijers R, Tollenaar MS, Bradley B, Jovanovic T, Ressler KJ, Steiner M, Entringer S, Wadhwa PD, Buss C, Bush NR, Binder EB, Boyce WT, Meaney MJ, Horvath S, Kobor MS. Proceedings of the National Academy of Sciences of the United States of America Volume 117 (2020) p.23329-23335 DOI: 10.1073/pnas.1820843116
*
Curating the gnomAD database: Report of novel variants in the globin-coding genes and bioinformatics analysis.
Scheps KG, Hasenahuer MA, Parisi G, Targovnik HM, Fornasari MS. Human mutation Volume 41 (2020) p.81-102 DOI: 10.1002/humu.23925
*
Ambiguity coding allows accurate inference of evolutionary parameters from alignments in an aggregated state-space
Weber CC, Perron U, Casey D, Yang Z, Goldman N. Preprint DOI: 10.1101/802603
*
Predicting cellular position in the Drosophila embryo from Single-Cell Transcriptomics data
Tanevski J, Nguyen T, Truong B, Karaiskos N, Ahsen ME, Zhang X, Shu C, Xu K, Liang X, Hu Y, Pham HV, Xiaomei L, Le TD, Tarca AL, Bhatti G, Romero R, Karathanasis N, Loher P, Chen Y, Ouyang Z, Mao D, Zhang Y, Zand M, Ruan J, Hafemeister C, Qiu P, Tran D, Nguyen T, Gabor A, Yu T, Glaab E, Krause R, Banda P, Stolovitzky G, Rajewsky N, Saez-Rodriguez J, Meyer P, DREAM SCTC Consortium. Preprint DOI: 10.1101/796029
*
Novel functional proteins coded by the human genome discovered in metastases of melanoma patients.
Sanchez A, Kuras M, Murillo JR, Pla I, Pawlowski K, Szasz AM, Gil J, Nogueira FCS, Perez-Riverol Y, Eriksson J, Appelqvist R, Miliotis T, Kim Y, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Ekedahl H, Horvatovich P, Sugihara Y, Welinder C, Wieslander E, Kwon HJ, Domont GB, Malm J, Rezeli M, Betancourt LH, Marko-Varga G. Cell biology and toxicology Volume 36 (2020) p.261-272 DOI: 10.1007/s10565-019-09494-4
*
Decoding human fetal liver haematopoiesis.
Popescu DM, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K, Goh I, Efremova M, Acres M, Maunder D, Vegh P, Gitton Y, Park JE, Vento-Tormo R, Miao Z, Dixon D, Rowell R, McDonald D, Fletcher J, Poyner E, Reynolds G, Mather M, Moldovan C, Mamanova L, Greig F, Young MD, Meyer KB, Lisgo S, Bacardit J, Fuller A, Millar B, Innes B, Lindsay S, Stubbington MJT, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Filby A, Carey P, Villani AC, Roy A, Regev A, Chédotal A, Roberts I, Göttgens B, Behjati S, Laurenti E, Teichmann SA, Haniffa M. Nature Volume 574 (2019) p.365-371 DOI: 10.1038/s41586-019-1652-y
*
Resolving the fibrotic niche of human liver cirrhosis at single-cell level.
Ramachandran P, Dobie R, Wilson-Kanamori JR, Dora EF, Henderson BEP, Luu NT, Portman JR, Matchett KP, Brice M, Marwick JA, Taylor RS, Efremova M, Vento-Tormo R, Carragher NO, Kendall TJ, Fallowfield JA, Harrison EM, Mole DJ, Wigmore SJ, Newsome PN, Weston CJ, Iredale JP, Tacke F, Pollard JW, Ponting CP, Marioni JC, Teichmann SA, Henderson NC. Nature Volume 575 (2019) p.512-518 DOI: 10.1038/s41586-019-1631-3
*
HLA-DQA1*05 Carriage Associated With Development of Anti-Drug Antibodies to Infliximab and Adalimumab in Patients With Crohn's Disease.
Sazonovs A, Kennedy NA, Moutsianas L, Heap GA, Rice DL, Reppell M, Bewshea CM, Chanchlani N, Walker GJ, Perry MH, McDonald TJ, Lees CW, Cummings JRF, Parkes M, Mansfield JC, Irving PM, Barrett JC, McGovern D, Goodhand JR, Anderson CA, Ahmad T, PANTS Consortium. Gastroenterology Volume 158 (2020) p.189-199 DOI: 10.1053/j.gastro.2019.09.041
*
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases
Chen Q, Britto R, Erill I, J. Jeffery C, Liberzon A, Magrane M, Onami J, Robinson-Rechavi M, Sponarova J, Zobel J, Verspoor K. Preprint DOI: 10.1101/788034
*
The midbody interactome reveals unexpected roles for PP1 phosphatases in cytokinesis.
Capalbo L, Bassi ZI, Geymonat M, Todesca S, Copoiu L, Enright AJ, Callaini G, Riparbelli MG, Yu L, Choudhary JS, Ferrero E, Wheatley S, Douglas ME, Mishima M, D'Avino PP. Nature communications Volume 10 (2019) p.4513 DOI: 10.1038/s41467-019-12507-9
*
Exploring genetic variation that influences brain methylation in attention-deficit/hyperactivity disorder.
Pineda-Cirera L, Shivalikanjli A, Cabana-Domínguez J, Demontis D, Rajagopal VM, Børglum AD, Faraone SV, Cormand B, Fernàndez-Castillo N. Translational psychiatry Volume 9 (2019) p.242 DOI: 10.1038/s41398-019-0574-7
*
CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets
Fleming SJ, Marioni JC, Babadi M. Preprint DOI: 10.1101/791699
*
Metabolic dysregulation of the lysophospholipid/autotaxin axis in the chromosome 9p21 gene SNP rs10757274
Meckelmann SW, Hawksworth JI, White D, Andrews R, Rodrigues P, O’Connor A, Alvarez-Jarreta J, Tyrrell VJ, Hinz C, Zhou Y, Williams J, Aldrovandi M, Watkins WJ, Engler AJ, Slatter DA, Allen SM, Acharya J, Mitchell J, Cooper J, Aoki J, Kano K, Humphries SE, O’Donnell VB. Preprint DOI: 10.1101/789768
Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis.
Arnol D, Schapiro D, Bodenmiller B, Saez-Rodriguez J, Stegle O. Cell reports Volume 29 (2019) p.202-211.e6 DOI: 10.1016/j.celrep.2019.08.077
*
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.
Perfetto L, Acencio ML, Bradley G, Cesareni G, Del Toro N, Fazekas D, Hermjakob H, Korcsmaros T, Kuiper M, Lægreid A, Lo Surdo P, Lovering RC, Orchard S, Porras P, Thomas PD, Touré V, Zobolas J, Licata L. Bioinformatics (Oxford, England) Volume 35 (2019) p.3779-3785 DOI: 10.1093/bioinformatics/btz132
*
Interoperable and scalable data analysis with microservices: applications in metabolomics.
Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran AN, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O. Bioinformatics (Oxford, England) Volume 35 (2019) p.3752-3760 DOI: 10.1093/bioinformatics/btz160
*
Advances and Applications in the Quest for Orthologs.
Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, da Silva AS, Wang Y, Sonnhammer E, Thomas PD. Molecular biology and evolution Volume 36 (2019) p.2157-2164 DOI: 10.1093/molbev/msz150
*
Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems.
Thomas PD, Hill DP, Mi H, Osumi-Sutherland D, Van Auken K, Carbon S, Balhoff JP, Albou LP, Good B, Gaudet P, Lewis SE, Mungall CJ. Nature genetics Volume 51 (2019) p.1429-1433 DOI: 10.1038/s41588-019-0500-1
*
Body mass index related electrocardiographic findings in healthy young individuals with a normal body mass index.
Hassing GJ, van der Wall HEC, van Westen GJP, Kemme MJB, Adiyaman A, Elvan A, Burggraaf J, Gal P. Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation Volume 27 (2019) p.506-512 DOI: 10.1007/s12471-019-1282-x
*
Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data.
Eling N, Richard AC, Richardson S, Marioni JC, Vallejos CA. Cell systems Volume 9 (2019) p.401-413 DOI: 10.1016/j.cels.2019.08.003
*
A five-level classification system for proteoform identifications.
Smith LM, Thomas PM, Shortreed MR, Schaffer LV, Fellers RT, LeDuc RD, Tucholski T, Ge Y, Agar JN, Anderson LC, Chamot-Rooke J, Gault J, Loo JA, Paša-Tolić L, Robinson CV, Schlüter H, Tsybin YO, Vilaseca M, Vizcaíno JA, Danis PO, Kelleher NL. Nature methods Volume 16 (2019) p.939-940 DOI: 10.1038/s41592-019-0573-x
*
A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes.
Mostajo NF, Lataretu M, Krautwurst S, Mock F, Desirò D, Lamkiewicz K, Collatz M, Schoen A, Weber F, Marz M, Hölzer M. NAR genomics and bioinformatics Volume 2 (2020) p.lqz006 DOI: 10.1093/nargab/lqz006
*
Systematic assessment of regulatory effects of human disease variants in pluripotent cells
Bonder MJ, Smail C, Gloudemans MJ, Frésard L, Jakubosky D, D’Antonio M, Li X, Ferraro NM, Carcamo-Orive I, Mirauta B, Seaton DD, Cai N, Horta D, Smith EN, Frazer KA, Montgomery SB, Stegle O, HipSci Consortium, iPSCORE Consortium, GENESiPS Consortium, PhLiPS Consortium. Preprint DOI: 10.1101/784967
*
Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration.
Palma A, Cerquone Perpetuini A, Ferrentino F, Fuoco C, Gargioli C, Giuliani G, Iannuccelli M, Licata L, Micarelli E, Paoluzi S, Perfetto L, Petrilli LL, Reggio A, Rosina M, Sacco F, Vumbaca S, Zuccotti A, Castagnoli L, Cesareni G. Frontiers in physiology Volume 10 (2019) p.1216 DOI: 10.3389/fphys.2019.01216
*
The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid.
Canals R, Chaudhuri RR, Steiner RE, Owen SV, Quinones-Olvera N, Gordon MA, Baym M, Ibba M, Hinton JCD. PLoS pathogens Volume 15 (2019) p.e1007948 DOI: 10.1371/journal.ppat.1007948
*
COPO: a metadata platform for brokering FAIR data in the life sciences
Etuk A, Shaw F, Gonzalez-Beltran A, Johnson D, Laporte M, Rocca-Serra P, Arnaud E, Devare M, Kersey PJ, Sansone S, Davey RP. Preprint DOI: 10.1101/782771
*
MSqRob takes the missing hurdle: uniting intensity- and count-based proteomics
Goeminne LJ, Sticker A, Martens L, Gevaert K, Clement L. Preprint DOI: 10.1101/782466
*
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
Katayama T, Kawashima S, Micklem G, Kawano S, Kim J, Kocbek S, Okamoto S, Wang Y, Wu H, Yamaguchi A, Yamamoto Y, Antezana E, Aoki-Kinoshita KF, Arakawa K, Banno M, Baran J, Bolleman JT, Bonnal RJP, Bono H, Fernández-Breis JT, Buels R, Campbell MP, Chiba H, Cock PJA, Cohen KB, Dumontier M, Fujisawa T, Fujiwara T, Garcia L, Gaudet P, Hattori E, Hoehndorf R, Itaya K, Ito M, Jamieson D, Jupp S, Juty N, Kalderimis A, Kato F, Kawaji H, Kawashima T, Kinjo AR, Komiyama Y, Kotera M, Kushida T, Malone J, Matsubara M, Mizuno S, Mizutani S, Mori H, Moriya Y, Murakami K, Nakazato T, Nishide H, Nishimura Y, Ogishima S, Ohta T, Okuda S, Ono H, Perez-Riverol Y, Shinmachi D, Splendiani A, Strozzi F, Suzuki S, Takehara J, Thompson M, Tokimatsu T, Uchiyama I, Verspoor K, Wilkinson MD, Wimalaratne S, Yamada I, Yamamoto N, Yarimizu M, Kawamoto S, Takagi T. Preprint DOI: 10.12688/f1000research.18238.1
*
Thrombospondin module 1 domain (TSP1) of the matricellular protein CCN3 shows an atypical disulfide pattern and incomplete CWR layers
Xu E, Lafita A, Bateman A, Hyvönen M. Preprint DOI: 10.1101/779553
*
Detection of Cell Surface Ligands for Human Synovial γδ T Cells.
Collins C, Lui Y, Santos AM, Ballif BA, Gogerly-Moragoda AM, Brouwer H, Ross R, Balagurunathan K, Sharma S, Wright GJ, Davis S, Budd RC. Journal of immunology (Baltimore, Md. : 1950) Volume 203 (2019) p.2369-2376 DOI: 10.4049/jimmunol.1900451
*
Smad7 Binds Differently to Individual and Tandem WW3 and WW4 Domains of WWP2 Ubiquitin Ligase Isoforms.
Wahl LC, Watt JE, Yim HTT, De Bourcier D, Tolchard J, Soond SM, Blumenschein TMA, Chantry A. International journal of molecular sciences Volume 20 (2019) DOI: 10.3390/ijms20194682
FAIR adoption, assessment and challenges at UniProt.
Garcia L, Bolleman J, Gehant S, Redaschi N, Martin M, UniProt Consortium. Scientific data Volume 6 (2019) p.175 DOI: 10.1038/s41597-019-0180-9
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.
Mudge JM, Jungreis I, Hunt T, Gonzalez JM, Wright JC, Kay M, Davidson C, Fitzgerald S, Seal R, Tweedie S, He L, Waterhouse RM, Li Y, Bruford E, Choudhary JS, Frankish A, Kellis M. Genome research Volume 29 (2019) p.2073-2087 DOI: 10.1101/gr.246462.118
*
A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome
Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, Pollard KS, Parks DH, Hugenholtz P, Segata N, Kyrpides NC, Finn RD. Preprint DOI: 10.1101/762682
*
Expert Curation of the Human and Mouse Olfactory Receptor Gene Repertoires Identifies Conserved Coding Regions Split Across Two Exons
Barnes IHA, Ibarra-Soria X, Fitzgerald S, Gonzalez JM, Davidson C, Hardy MP, Manthravadi D, Van Gerven L, Jorissen M, Zeng Z, Khan M, Mombaerts P, Harrow J, Logan DW, Frankish A. Preprint DOI: 10.1101/774612
*
Ontology based mining of pathogen-disease associations from literature.
Kafkas Ş, Hoehndorf R. Journal of biomedical semantics Volume 10 (2019) p.15 DOI: 10.1186/s13326-019-0208-2
*
Sequencing-based microsatellite instability testing using as few as six markers for high-throughput clinical diagnostics.
Gallon R, Sheth H, Hayes C, Redford L, Alhilal G, O'Brien O, Spiewak H, Waltham A, McAnulty C, Izuogu OG, Arends MJ, Oniscu A, Alonso AM, Laguna SM, Borthwick GM, Santibanez-Koref M, Jackson MS, Burn J. Human mutation Volume 41 (2020) p.332-341 DOI: 10.1002/humu.23906
*
Transfer of regulatory knowledge from human to mouse for functional genomics analysis.
Holland CH, Szalai B, Saez-Rodriguez J. Biochimica et biophysica acta. Gene regulatory mechanisms Volume 1863 (2020) p.194431 DOI: 10.1016/j.bbagrm.2019.194431
*
Understanding life sciences data curation practices via user research
Venkatesan A, Karamanis N, Ide-Smith M, Hickford J, McEntyre J. Preprint DOI: 10.12688/f1000research.19427.1
*
Cell type specific novel lincRNAs and circRNAs in the BLUEPRINT haematopoietic transcriptomes atlas
Grassi L, Izuogu OG, Jorge NA, Seyres D, Bustamante M, Burden F, Farrow S, Farahi N, Martin FJ, Frankish A, Mudge JM, Kostadima M, Petersen R, Lambourne JJ, Rowlston S, Martin-Rendon E, Clarke L, Downes K, Estivill X, Flicek P, Martens JH, Yaspo M, Stunnenberg HG, Ouwehand WH, Passetti F, Turro E, Frontini M. Preprint DOI: 10.1101/764613
*
Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges.
Ellrott K, Buchanan A, Creason A, Mason M, Schaffter T, Hoff B, Eddy J, Chilton JM, Yu T, Stuart JM, Saez-Rodriguez J, Stolovitzky G, Boutros PC, Guinney J. Genome biology Volume 20 (2019) p.195 DOI: 10.1186/s13059-019-1794-0
*
Integrated evolutionary and structural analysis reveals xenobiotics and pathogens as the major drivers of mammalian adaptation
Slodkowicz G, Goldman N. Preprint DOI: 10.1101/762690
*
An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity.
Benjelloun B, Boyer F, Streeter I, Zamani W, Engelen S, Alberti A, Alberto FJ, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Rezaei HR, Naderi S, Stella A, Chikhi A, Clarke L, Kijas J, Flicek P, Taberlet P, Pompanon F. Molecular ecology resources Volume 19 (2019) p.1497-1515 DOI: 10.1111/1755-0998.13070
*
p13CMFA: Parsimonious 13C metabolic flux analysis.
Foguet C, Jayaraman A, Marin S, Selivanov VA, Moreno P, Messeguer R, de Atauri P, Cascante M. PLoS computational biology Volume 15 (2019) p.e1007310 DOI: 10.1371/journal.pcbi.1007310
*
DCAF8, a novel MuRF1 interaction partner, promotes muscle atrophy.
Nowak M, Suenkel B, Porras P, Migotti R, Schmidt F, Kny M, Zhu X, Wanker EE, Dittmar G, Fielitz J, Sommer T. Journal of cell science Volume 132 (2019) DOI: 10.1242/jcs.233395
*
Methylation Warfare: Interaction of Pneumococcal Bacteriophages with Their Host.
Furi L, Crawford LA, Rangel-Pineros G, Manso AS, De Ste Croix M, Haigh RD, Kwun MJ, Engelsen Fjelland K, Gilfillan GD, Bentley SD, Croucher NJ, Clokie MR, Oggioni MR. Journal of bacteriology Volume 201 (2019) DOI: 10.1128/jb.00370-19
*
Similarities and differences in patterns of germline mutation between mice and humans.
Lindsay SJ, Rahbari R, Kaplanis J, Keane T, Hurles ME. Nature communications Volume 10 (2019) p.4053 DOI: 10.1038/s41467-019-12023-w
*
Geleophysic dysplasia: novel missense variants and insights into ADAMTSL2 intracellular trafficking.
Piccolo P, Sabatino V, Mithbaokar P, Polishchuck E, Law SK, Magraner-Pardo L, Pons T, Polishchuck R, Brunetti-Pierri N. Molecular genetics and metabolism reports Volume 21 (2019) p.100504 DOI: 10.1016/j.ymgmr.2019.100504
*
Non-coding RNA regulatory networks.
Panni S, Lovering RC, Porras P, Orchard S. Biochimica et biophysica acta. Gene regulatory mechanisms Volume 1863 (2020) p.194417 DOI: 10.1016/j.bbagrm.2019.194417
*
Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads.
Yang A, Tang JYS, Troup M, Ho JWK. F1000Research Volume 8 (2019) p.1587 DOI: 10.12688/f1000research.19426.1
*
Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants.
Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, De Baets G, Bromberg Y, Cao C, Capriotti E, Casadio R, Van Durme J, Giollo M, Karchin R, Katsonis P, Leonardi E, Lichtarge O, Martelli PL, Masica D, Mooney SD, Olatubosun A, Radivojac P, Rousseau F, Pal LR, Savojardo C, Schymkowitz J, Thusberg J, Tosatto SCE, Vihinen M, Väliaho J, Repo S, Moult J, Brenner SE, Friedberg I. Human mutation Volume 40 (2019) p.1530-1545 DOI: 10.1002/humu.23868
*
Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes.
Attardo GM, Abd-Alla AMM, Acosta-Serrano A, Allen JE, Bateta R, Benoit JB, Bourtzis K, Caers J, Caljon G, Christensen MB, Farrow DW, Friedrich M, Hua-Van A, Jennings EC, Larkin DM, Lawson D, Lehane MJ, Lenis VP, Lowy-Gallego E, Macharia RW, Malacrida AR, Marco HG, Masiga D, Maslen GL, Matetovici I, Meisel RP, Meki I, Michalkova V, Miller WJ, Minx P, Mireji PO, Ometto L, Parker AG, Rio R, Rose C, Rosendale AJ, Rota-Stabelli O, Savini G, Schoofs L, Scolari F, Swain MT, Takáč P, Tomlinson C, Tsiamis G, Van Den Abbeele J, Vigneron A, Wang J, Warren WC, Waterhouse RM, Weirauch MT, Weiss BL, Wilson RK, Zhao X, Aksoy S. Genome biology Volume 20 (2019) p.187 DOI: 10.1186/s13059-019-1768-2
*
Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers.
Shome S, Parra RG, Fatima N, Monzon AM, Cuypers B, Moosa Y, Coimbra NDR, Assis J, Giner-Delgado C, Dönertaş HM, Cuesta-Astroz Y, Saarunya G, Allali I, Gupta S, Srivastava A, Kalsan M, Valdivia C, J Olguin-Orellana G, Papadimitriou S, Parisi D, Kristensen NP, Rib L, Guebila MB, Bauer E, Zaffaroni G, Bekkar A, Ashano E, Paladin L, Necci M, Moreyra NN, Rydén M, Villalobos-Solís J, Papadopoulos N, Rafael C, Karakulak T, Kaya Y, Gladbach Y, Dhanda SK, Šoštarić N, Alex A, DeBlasio D, Rahman F. F1000Research Volume 8 (2019) DOI: 10.12688/f1000research.20408.1
*
Reduced stomatal density in bread wheat leads to increased water-use efficiency.
Dunn J, Hunt L, Afsharinafar M, Meselmani MA, Mitchell A, Howells R, Wallington E, Fleming AJ, Gray JE. Journal of experimental botany Volume 70 (2019) p.4737-4748 DOI: 10.1093/jxb/erz248
Know Thy PDX Model.
Meehan TF. Cancer research Volume 79 (2019) p.4324-4325 DOI: 10.1158/0008-5472.can-19-2023
A new reference genome sequence for Caenorhabditis elegans?
Howe KL. Lab animal Volume 48 (2019) p.267-268 DOI: 10.1038/s41684-019-0371-1
*
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases.
Rifaioglu AS, Atas H, Martin MJ, Cetin-Atalay R, Atalay V, Doğan T. Briefings in bioinformatics Volume 20 (2019) p.1878-1912 DOI: 10.1093/bib/bby061
Author Correction: Challenges in measuring and understanding biological noise.
Eling N, Morgan MD, Marioni JC. Nature reviews. Genetics Volume 20 (2019) p.562 DOI: 10.1038/s41576-019-0142-2
Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States.
Perron U, Kozlov AM, Stamatakis A, Goldman N, Moal IH. Molecular biology and evolution Volume 36 (2019) p.2086-2103 DOI: 10.1093/molbev/msz122
Challenges in measuring and understanding biological noise.
Eling N, Morgan MD, Marioni JC. Nature reviews. Genetics Volume 20 (2019) p.536-548 DOI: 10.1038/s41576-019-0130-6
*
A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.
Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J. Cell Volume 178 (2019) p.1465-1477.e17 DOI: 10.1016/j.cell.2019.08.018
Finding enzyme cofactors in Protein Data Bank.
Mukhopadhyay A, Borkakoti N, Pravda L, Tyzack JD, Thornton JM, Velankar S. Bioinformatics (Oxford, England) Volume 35 (2019) p.3510-3511 DOI: 10.1093/bioinformatics/btz115
*
Correction to: The official unified nomenclature adopted by the HGNC calls for the use of the acronyms, CCN1-6, and discontinuation in the use of CYR61, CTGF, NOV and WISP 1-3 respectively.
Perbal B, Tweedie S, Bruford E. Journal of cell communication and signaling Volume 13 (2019) p.435 DOI: 10.1007/s12079-019-00532-8
*
Robustness and applicability of functional genomics tools on scRNA-seq data
Holland CH, Tanevski J, Gleixner J, Kumar MP, Mereu E, Perales-Patón J, Joughin BA, Stegle O, Lauffenburger DA, Heyn H, Szalai B, Saez-Rodriguez J. Preprint DOI: 10.1101/753319
*
Elucidating Compound Mechanism of Action and Predicting Cytotoxicity Using Machine Learning Approaches, Taking Prediction Confidence into Account.
Drakakis G, Cortés-Ciriano I, Alexander-Dann B, Bender A. Current protocols in chemical biology Volume 11 (2019) p.e73 DOI: 10.1002/cpch.73
*
Detection of Epidemic Scarlet Fever Group A Streptococcus in Australia.
Walker MJ, Brouwer S, Forde BM, Worthing KA, McIntyre L, Sundac L, Maloney S, Roberts LW, Barnett TC, Richter J, Cork AJ, Irwin AD, You Y, Zhang J, Dougan G, Yuen KY, Nizet V, Beatson SA, Grimwood K, Davies MR. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Volume 69 (2019) p.1232-1234 DOI: 10.1093/cid/ciz099
*
Spatiotemporal immune zonation of the human kidney.
Stewart BJ, Ferdinand JR, Young MD, Mitchell TJ, Loudon KW, Riding AM, Richoz N, Frazer GL, Staniforth JUL, Vieira Braga FA, Botting RA, Popescu DM, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Polanski K, Efremova M, Green K, Del Castillo Velasco-Herrera M, Guzzo C, Collord G, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Lindsay S, Bajenoff M, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Behjati S, Clatworthy MR. Science (New York, N.Y.) Volume 365 (2019) p.1461-1466 DOI: 10.1126/science.aat5031
*
Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes.
De Maio N, Shaw LP, Hubbard A, George S, Sanderson ND, Swann J, Wick R, AbuOun M, Stubberfield E, Hoosdally SJ, Crook DW, Peto TEA, Sheppard AE, Bailey MJ, Read DS, Anjum MF, Walker AS, Stoesser N, On Behalf Of The Rehab Consortium. Microbial genomics Volume 5 (2019) DOI: 10.1099/mgen.0.000294
*
Assessment of network module identification across complex diseases.
Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R, DREAM Module Identification Challenge Consortium, Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D. Nature methods Volume 16 (2019) p.843-852 DOI: 10.1038/s41592-019-0509-5
*
Structure Kinetics Relationships and Molecular Dynamics Show Crucial Role for Heterocycle Leaving Group in Irreversible Diacylglycerol Lipase Inhibitors.
Janssen APA, van Hengst JMA, Béquignon OJM, Deng H, van Westen GJP, van der Stelt M. Journal of medicinal chemistry Volume 62 (2019) p.7910-7922 DOI: 10.1021/acs.jmedchem.9b00686
*
scHLAcount: Allele-specific HLA expression from single-cell gene expression data
Darby CA, Stubbington MJT, Marks PJ, Barrio ÁM, Fiddes IT. Preprint DOI: 10.1101/750612
*
Development of Ubiquitin-Based Probe for Metalloprotease Deubiquitinases.
Hameed DS, Sapmaz A, Burggraaff L, Amore A, Slingerland CJ, van Westen GJP, Ovaa H. Angewandte Chemie (International ed. in English) Volume 58 (2019) p.14477-14482 DOI: 10.1002/anie.201906790
*
Leveraging European infrastructures to access 1 million human genomes by 2022.
Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Heringa J, Holub P, Hooyberghs J, Juty N, Keane TM, Korbel JO, Lappalainen I, Leskosek B, Matthijs G, Mayrhofer MT, Metspalu A, Navarro A, Newhouse S, Nyrönen T, Page A, Persson B, Palotie A, Parkinson H, Rambla J, Salgado D, Steinfelder E, Swertz MA, Valencia A, Varma S, Blomberg N, Scollen S. Nature reviews. Genetics Volume 20 (2019) p.693-701 DOI: 10.1038/s41576-019-0156-9
*
Assessment of protein assembly prediction in CASP13.
Guzenko D, Lafita A, Monastyrskyy B, Kryshtafovych A, Duarte JM. Proteins Volume 87 (2019) p.1190-1199 DOI: 10.1002/prot.25795
*
Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system.
Bruno L, Ramlall V, Studer RA, Sauer S, Bradley D, Dharmalingam G, Carroll T, Ghoneim M, Chopin M, Nutt SL, Elderkin S, Rueda DS, Fisher AG, Siggers T, Beltrao P, Merkenschlager M. Nature immunology Volume 20 (2019) p.1372-1380 DOI: 10.1038/s41590-019-0471-5
*
Genomic landscape and chronological reconstruction of driver events in multiple myeloma.
Maura F, Bolli N, Angelopoulos N, Dawson KJ, Leongamornlert D, Martincorena I, Mitchell TJ, Fullam A, Gonzalez S, Szalat R, Abascal F, Rodriguez-Martin B, Samur MK, Glodzik D, Roncador M, Fulciniti M, Tai YT, Minvielle S, Magrangeas F, Moreau P, Corradini P, Anderson KC, Tubio JMC, Wedge DC, Gerstung M, Avet-Loiseau H, Munshi N, Campbell PJ. Nature communications Volume 10 (2019) p.3835 DOI: 10.1038/s41467-019-11680-1
*
iTRAQ-Based Global Phosphoproteomics Reveals Novel Molecular Differences Between Toxoplasma gondii Strains of Different Genotypes.
Wang ZX, Zhou CX, Calderón-Mantilla G, Petsalaki E, He JJ, Song HY, Elsheikha HM, Zhu XQ. Frontiers in cellular and infection microbiology Volume 9 (2019) p.307 DOI: 10.3389/fcimb.2019.00307
*
12 Grand Challenges in Single-Cell Data Science
Laehnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Beerenwinkel N, Campbell KR, Mahfouz A, Pinello L, Skums P, Stamatakis A, Stephan-Otto Attolini C, Aparicio S, Baaijens J, Balvert M, de Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Jessurun Lobo T, Keizer EM, Khatri I, Kiełbasa SM, Korbel JO, Kozlov AM, Kuo T, Lelieveldt BP, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Rączkowski Ł, Reinders M, de Ridder J, Saliba A, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A. Preprint DOI: 10.7287/peerj.preprints.27885v3
*
Heparan sulfates are critical regulators of the inhibitory megakaryocyte-platelet receptor G6b-B.
Vögtle T, Sharma S, Mori J, Nagy Z, Semeniak D, Scandola C, Geer MJ, Smith CW, Lane J, Pollack S, Lassila R, Jouppila A, Barr AJ, Ogg DJ, Howard TD, McMiken HJ, Warwicker J, Geh C, Rowlinson R, Abbott WM, Eckly A, Schulze H, Wright GJ, Mazharian A, Fütterer K, Rajesh S, Douglas MR, Senis YA. eLife Volume 8 (2019) DOI: 10.7554/elife.46840
*
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis.
Viehweger A, Krautwurst S, Lamkiewicz K, Madhugiri R, Ziebuhr J, Hölzer M, Marz M. Genome research Volume 29 (2019) p.1545-1554 DOI: 10.1101/gr.247064.118
*
A Putative Type V Pilus Contributes to Bacteroides thetaiotaomicron Biofilm Formation Capacity.
Mihajlovic J, Bechon N, Ivanova C, Chain F, Almeida A, Langella P, Beloin C, Ghigo JM. Journal of bacteriology Volume 201 (2019) DOI: 10.1128/jb.00650-18
*
Comparison of Associations with Different Macular Inner Retinal Thickness Parameters in a Large Cohort: The UK Biobank.
Khawaja AP, Chua S, Hysi PG, Georgoulas S, Currant H, Fitzgerald TW, Birney E, Ko F, Yang Q, Reisman C, Garway-Heath DF, Hammond CJ, Khaw PT, Foster PJ, Patel PJ, Strouthidis N, UK Biobank Eye and Vision Consortium. Ophthalmology Volume 127 (2020) p.62-71 DOI: 10.1016/j.ophtha.2019.08.015
*
Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma
Ordoñez R, Kulis M, Russiñol N, Chapaprieta V, Beekman R, Meydan C, Duran-Ferrer M, Verdaguer-Dot N, Clot G, Vilarrasa-Blasi R, Garate L, Miranda E, Carrasco A, Ezponda T, Vilas-Zornoza A, Lara-Astiaso D, Dupéré-Richer D, Martens JH, Torrents D, El-Omri H, Taha RY, Calasanz MJ, Paiva B, Miguel JS, Flicek P, Gut I, Melnick A, Mitsiades CS, Licht JD, Campo E, Stunnenberg HG, Agirre X, Prosper F, Martin-Subero JI. Preprint DOI: 10.1101/740027
*
Getting the Entire Message: Progress in Isoform Sequencing.
Hardwick SA, Joglekar A, Flicek P, Frankish A, Tilgner HU. Frontiers in genetics Volume 10 (2019) p.709 DOI: 10.3389/fgene.2019.00709
*
HENA, heterogeneous network-based data set for Alzheimer's disease.
Sügis E, Dauvillier J, Leontjeva A, Adler P, Hindie V, Moncion T, Collura V, Daudin R, Loe-Mie Y, Herault Y, Lambert JC, Hermjakob H, Pupko T, Rain JC, Xenarios I, Vilo J, Simonneau M, Peterson H. Scientific data Volume 6 (2019) p.151 DOI: 10.1038/s41597-019-0152-0
Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1.
Martin-Herranz DE, Aref-Eshghi E, Bonder MJ, Stubbs TM, Choufani S, Weksberg R, Stegle O, Sadikovic B, Reik W, Thornton JM. Genome biology Volume 20 (2019) p.146 DOI: 10.1186/s13059-019-1753-9
*
Meta-Analysis of Cancer Triploidy: Rearrangements of Genome Complements in Male Human Tumors Are Characterized by XXY Karyotypes.
Vainshelbaum NM, Zayakin P, Kleina R, Giuliani A, Erenpreisa J. Genes Volume 10 (2019) DOI: 10.3390/genes10080613
Emerging concepts in pseudoenzyme classification, evolution, and signaling.
Ribeiro AJM, Das S, Dawson N, Zaru R, Orchard S, Thornton JM, Orengo C, Zeqiraj E, Murphy JM, Eyers PA. Science signaling Volume 12 (2019) DOI: 10.1126/scisignal.aat9797
*
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
Deutsch EW, Lane L, Overall CM, Bandeira N, Baker MS, Pineau C, Moritz RL, Corrales F, Orchard S, Van Eyk JE, Paik Y, Weintraub ST, Vandenbrouck Y, Omenn GS. Preprint DOI: 10.1101/733576
*
Population dynamics of an Escherichia coli ST131 lineage during recurrent urinary tract infection.
Forde BM, Roberts LW, Phan MD, Peters KM, Fleming BA, Russell CW, Lenherr SM, Myers JB, Barker AP, Fisher MA, Chong TM, Yin WF, Chan KG, Schembri MA, Mulvey MA, Beatson SA. Nature communications Volume 10 (2019) p.3643 DOI: 10.1038/s41467-019-11571-5
*
The bio.tools registry of software tools and data resources for the life sciences.
Ison J, Ienasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, Schwämmle V, Grüning B, Beard N, Lopez R, Duvaud S, Stockinger H, Persson B, Vařeková RS, Raček T, Vondrášek J, Peterson H, Salumets A, Jonassen I, Hooft R, Nyrönen T, Valencia A, Capella S, Gelpí J, Zambelli F, Savakis B, Leskošek B, Rapacki K, Blanchet C, Jimenez R, Oliveira A, Vriend G, Collin O, van Helden J, Løngreen P, Brunak S. Genome biology Volume 20 (2019) p.164 DOI: 10.1186/s13059-019-1772-6
*
Virus- and Interferon Alpha-Induced Transcriptomes of Cells from the Microbat Myotis daubentonii.
Hölzer M, Schoen A, Wulle J, Müller MA, Drosten C, Marz M, Weber F. iScience Volume 19 (2019) p.647-661 DOI: 10.1016/j.isci.2019.08.016
*
NaPLeS: a natural products likeness scorer-web application and database.
Sorokina M, Steinbeck C. Journal of Cheminformatics Volume 11 (2019) p.55 DOI: 10.1186/s13321-019-0378-z
*
Assembly of B4GALT1/ST6GAL1 heteromers in the Golgi membranes involves lateral interactions via highly charged surface domains.
Khoder-Agha F, Harrus D, Brysbaert G, Lensink MF, Harduin-Lepers A, Glumoff T, Kellokumpu S. The Journal of biological chemistry Volume 294 (2019) p.14383-14393 DOI: 10.1074/jbc.ra119.009539
*
Transcriptomic analysis of insecticide resistance in the lymphatic filariasis vector Culex quinquefasciatus.
Silva Martins WF, Wilding CS, Isaacs AT, Rippon EJ, Megy K, Donnelly MJ. Scientific reports Volume 9 (2019) p.11406 DOI: 10.1038/s41598-019-47850-w
*
A Report from a Workshop of the International Stem Cell Banking Initiative, Held in Collaboration of Global Alliance for iPSC Therapies and the Harvard Stem Cell Institute, Boston, 2017.
Kim JH, Alderton A, Crook JM, Benvenisty N, Brandsten C, Firpo M, Harrison PW, Kawamata S, Kawase E, Kurtz A, Loring JF, Ludwig T, Man J, Mountford JC, Turner ML, Oh S, da Veiga Pereira L, Pranke P, Sheldon M, Steeg R, Sullivan S, Yaffe M, Zhou Q, Stacey GN. Stem cells (Dayton, Ohio) Volume 37 (2019) p.1130-1135 DOI: 10.1002/stem.3003
*
Multi-targeted kinase inhibition alleviates mTOR inhibitor resistance in triple-negative breast cancer.
He J, McLaughlin RP, van der Noord V, Foekens JA, Martens JWM, van Westen G, Zhang Y, van de Water B. Breast cancer research and treatment Volume 178 (2019) p.263-274 DOI: 10.1007/s10549-019-05380-z
*
Novel plasma peptide markers involved in the pathology of CKD identified using mass spectrometric approach.
Gajjala PR, Bruck H, Noels H, Heinze G, Ceccarelli F, Kribben A, Saez-Rodriguez J, Marx N, Zidek W, Jankowski J, Jankowski V. Journal of molecular medicine (Berlin, Germany) Volume 97 (2019) p.1451-1463 DOI: 10.1007/s00109-019-01823-8
Quantifying the impact of public omics data.
Perez-Riverol Y, Zorin A, Dass G, Vu MT, Xu P, Glont M, Vizcaíno JA, Jarnuczak AF, Petryszak R, Ping P, Hermjakob H. Nature communications Volume 10 (2019) p.3512 DOI: 10.1038/s41467-019-11461-w
*
A Galaxy-based training resource for single-cell RNA-seq quality control and analyses
Etherington GJ, Soranzo N, Mohammed S, Haerty W, Davey RP, Di Palma F. Preprint DOI: 10.1101/724047
Origins of peptidases.
Rawlings ND, Bateman A. Biochimie Volume 166 (2019) p.4-18 DOI: 10.1016/j.biochi.2019.07.026
*
Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data.
Schäfer A, Gjerga E, Welford RW, Renz I, Lehembre F, Groenen PM, Saez-Rodriguez J, Aebersold R, Gstaiger M. Molecular systems biology Volume 15 (2019) p.e8828 DOI: 10.15252/msb.20198828
*
MapOptics: a light-weight, cross-platform visualization tool for optical mapping alignment.
Burgin J, Molitor C, Mohareb F. Bioinformatics (Oxford, England) Volume 35 (2019) p.2671-2673 DOI: 10.1093/bioinformatics/bty1013
*
Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation
Low WY, Tearle R, Liu R, Koren S, Rhie A, Bickhart DM, Rosen BD, Kronenberg ZN, Kingan SB, Tseng E, Thibaud-Nissen F, Martin FJ, Billis K, Ghurye J, Hastie AR, Lee J, Pang AW, Heaton MP, Phillippy AM, Hiendleder S, Smith TP, Williams JL. Preprint DOI: 10.1101/720797
*
PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping.
Sánchez LFH, Burger B, Horro C, Fabregat A, Johansson S, Njølstad PR, Barsnes H, Hermjakob H, Vaudel M. GigaScience Volume 8 (2019) DOI: 10.1093/gigascience/giz088
*
Visualization and analysis of RNA-Seq assembly graphs.
Nazarie FW, Shih B, Angus T, Barnett MW, Chen SH, Summers KM, Klein K, Faulkner GJ, Saini HK, Watson M, Dongen SV, Enright AJ, Freeman TC. Nucleic acids research Volume 47 (2019) p.7262-7275 DOI: 10.1093/nar/gkz599
*
The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle.
Howick VM, Russell AJC, Andrews T, Heaton H, Reid AJ, Natarajan K, Butungi H, Metcalf T, Verzier LH, Rayner JC, Berriman M, Herren JK, Billker O, Hemberg M, Talman AM, Lawniczak MKN. Science (New York, N.Y.) Volume 365 (2019) DOI: 10.1126/science.aaw2619
*
Contrasting gene expression patterns in grain of high and low asparagine wheat genotypes in response to sulphur supply.
Curtis TY, Raffan S, Wan Y, King R, Gonzalez-Uriarte A, Halford NG. BMC genomics Volume 20 (2019) p.628 DOI: 10.1186/s12864-019-5991-8
*
Genome-wide screening of mouse knockouts reveals novel genes required for normal integumentary and oculocutaneous structure and function.
Moore BA, Flenniken AM, Clary D, Moshiri AS, Nutter LMJ, Berberovic Z, Owen C, Newbigging S, Adissu H, Eskandarian M, McKerlie C, International Mouse Phenotyping Consortium, Thomasy SM, Lloyd KCK, Murphy CJ, Moshiri A. Scientific reports Volume 9 (2019) p.11211 DOI: 10.1038/s41598-019-47286-2
*
The RNA hairpin binder TRIM71 modulates alternative splicing by repressing MBNL1.
Welte T, Tuck AC, Papasaikas P, Carl SH, Flemr M, Knuckles P, Rankova A, Bühler M, Großhans H. Genes & development Volume 33 (2019) p.1221-1235 DOI: 10.1101/gad.328492.119
*
Very low-depth whole-genome sequencing in complex trait association studies.
Gilly A, Southam L, Suveges D, Kuchenbaecker K, Moore R, Melloni GEM, Hatzikotoulas K, Farmaki AE, Ritchie G, Schwartzentruber J, Danecek P, Kilian B, Pollard MO, Ge X, Tsafantakis E, Dedoussis G, Zeggini E. Bioinformatics (Oxford, England) Volume 35 (2019) p.2555-2561 DOI: 10.1093/bioinformatics/bty1032
*
Correction: IQSEC2-related encephalopathy in males and females: a comparative study including 37 novel patients.
Mignot C, McMahon AC, Bar C, Campeau PM, Davidson C, Buratti J, Nava C, Jacquemont ML, Tallot M, Milh M, Edery P, Marzin P, Barcia G, Barnerias C, Besmond C, Bienvenu T, Bruel AL, Brunga L, Ceulemans B, Coubes C, Cristancho AG, Cunningham F, Dehouck MB, Donner EJ, Duban-Bedu B, Dubourg C, Gardella E, Gauthier J, Geneviève D, Gobin-Limballe S, Goldberg EM, Hagebeuk E, Hamdan FF, Hančárová M, Hubert L, Ioos C, Ichikawa S, Janssens S, Journel H, Kaminska A, Keren B, Koopmans M, Lacoste C, Laššuthová P, Lederer D, Lehalle D, Marjanovic D, Métreau J, Michaud JL, Miller K, Minassian BA, Morales J, Moutard ML, Munnich A, Ortiz-Gonzalez XR, Pinard JM, Prchalová D, Putoux A, Quelin C, Rosen AR, Roume J, Rossignol E, Simon MEH, Smol T, Shur N, Shelihan I, Štěrbová K, Vyhnálková E, Vilain C, Soblet J, Smits G, Yang SP, van der Smagt JJ, van Hasselt PM, van Kempen M, Weckhuysen S, Helbig I, Villard L, Héron D, Koeleman B, Møller RS, Lesca G, Helbig KL, Nabbout R, Verbeek NE, Depienne C. Genetics in medicine : official journal of the American College of Medical Genetics Volume 21 (2019) p.1897-1898 DOI: 10.1038/s41436-018-0327-7
*
A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans.
Saraiva LR, Riveros-McKay F, Mezzavilla M, Abou-Moussa EH, Arayata CJ, Makhlouf M, Trimmer C, Ibarra-Soria X, Khan M, Van Gerven L, Jorissen M, Gibbs M, O'Flynn C, McGrane S, Mombaerts P, Marioni JC, Mainland JD, Logan DW. Science advances Volume 5 (2019) p.eaax0396 DOI: 10.1126/sciadv.aax0396
*
Novel natural and synthetic inhibitors of solute carriers SGLT1 and SGLT2.
Oranje P, Gouka R, Burggraaff L, Vermeer M, Chalet C, Duchateau G, van der Pijl P, Geldof M, de Roo N, Clauwaert F, Vanpaeschen T, Nicolaï J, de Bruyn T, Annaert P, IJzerman AP, van Westen GJP. Pharmacology research & perspectives Volume 7 (2019) p.e00504 DOI: 10.1002/prp2.504
*
Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors.
Segal JM, Kent D, Wesche DJ, Ng SS, Serra M, Oulès B, Kar G, Emerton G, Blackford SJI, Darmanis S, Miquel R, Luong TV, Yamamoto R, Bonham A, Jassem W, Heaton N, Vigilante A, King A, Sancho R, Teichmann S, Quake SR, Nakauchi H, Rashid ST. Nature communications Volume 10 (2019) p.3350 DOI: 10.1038/s41467-019-11266-x
*
Genomic properties of structural variants and short tandem repeats that impact gene expression and complex traits in humans
Jakubosky D, D’Antonio M, Bonder MJ, Smail C, Donovan MK, Greenwald WWY, D’Antonio-Chronowska A, Matsui H, Stegle O, Smith EN, Montgomery SB, DeBoever C, Frazer KA, i2QTL Consortium. Preprint DOI: 10.1101/714477
*
Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats
Jakubosky D, Smith EN, D’Antonio M, Bonder MJ, Greenwald WWY, D’Antonio-Chronowska A, Matsui H, Stegle O, Montgomery SB, DeBoever C, Frazer KA, i2QTL Consortium, HipSci Consortium. Preprint DOI: 10.1101/713198
*
Syntrophy emerges spontaneously in complex metabolic systems.
Libby E, Hébert-Dufresne L, Hosseini SR, Hosseini SR, Wagner A. PLoS computational biology Volume 15 (2019) p.e1007169 DOI: 10.1371/journal.pcbi.1007169
*
Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits.
Porcu E, Rüeger S, Lepik K, eQTLGen Consortium, BIOS Consortium, Santoni FA, Reymond A, Kutalik Z. Nature communications Volume 10 (2019) p.3300 DOI: 10.1038/s41467-019-10936-0
Benchmark and integration of resources for the estimation of human transcription factor activities.
Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J. Genome research Volume 29 (2019) p.1363-1375 DOI: 10.1101/gr.240663.118
*
Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study
Galardini M, Clermont O, Baron A, Busby B, Dion S, Schubert S, Beltrao P, Denamur E. Preprint DOI: 10.1101/712034
*
Transcriptome sequencing, molecular markers, and transcription factor discovery of Platanus acerifolia in the presence of Corythucha ciliata.
Li F, Wu C, Gao M, Jiao M, Qu C, Gonzalez-Uriarte A, Luo C. Scientific data Volume 6 (2019) p.128 DOI: 10.1038/s41597-019-0111-9
*
Rora regulates activated T helper cells during inflammation
Haim-Vilmovsky L, Henriksson J, Walker JA, Miao Z, Natan E, Kar G, Clare S, Barlow JL, Charidemou E, Mamanova L, Chen X, Proserpio V, Pramanik J, Woodhouse S, Protasio AV, Efremova M, Griffin JL, Berriman M, Dougan G, Fisher J, Marioni JC, McKenzie AN, Teichmann SA. Preprint DOI: 10.1101/709998
*
A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division
Stojic L, Lun ATL, Mascalchi P, Ernst C, Redmond AM, Mangei J, Barr AR, Bousgouni V, Bakal C, Marioni JC, Odom DT, Gergely F. Preprint DOI: 10.1101/709030
*
When Three Isn't a Crowd: A Digyny Concept for Treatment-Resistant, Near-Triploid Human Cancers.
Salmina K, Gerashchenko BI, Hausmann M, Vainshelbaum NM, Zayakin P, Erenpreiss J, Freivalds T, Cragg MS, Erenpreisa J. Genes Volume 10 (2019) DOI: 10.3390/genes10070551
*
Gene Expression Analyses in Non Muscle Invasive Bladder Cancer Reveals a Role for Alternative Splicing and Tp53 Status.
Dueñas M, Pérez-Figueroa A, Oliveira C, Suárez-Cabrera C, Sousa A, Oliveira P, Villacampa F, Paramio JM, Martínez-Fernández M. Scientific reports Volume 9 (2019) p.10362 DOI: 10.1038/s41598-019-46652-4
*
NFDI4Chem: Shaping a Digital and Cultural Change in Chemistry.
Herres-Pawlis S, Koepler O, Steinbeck C. Angewandte Chemie (International ed. in English) Volume 58 (2019) p.10766-10768 DOI: 10.1002/anie.201907260
*
Proteome-wide inference of protein kinase regulatory circuits
Invergo BM, Petursson B, Bradley D, Giudice G, Petsalaki E, Beltrao P. Preprint DOI: 10.1101/703157
*
A simple approach for accurate peptide quantification in MS-based proteomics
Maia TM, Staes A, Plasman K, Pauwels J, Boucher K, Argentini A, Martens L, Montoye T, Gevaert K, Impens F. Preprint DOI: 10.1101/703397
*
Automated structure prediction of trans-acyltransferase polyketide synthase products.
Helfrich EJN, Ueoka R, Dolev A, Rust M, Meoded RA, Bhushan A, Califano G, Costa R, Gugger M, Steinbeck C, Moreno P, Piel J. Nature chemical biology Volume 15 (2019) p.813-821 DOI: 10.1038/s41589-019-0313-7
*
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.
Schreiber F, Sommer B, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. Journal of integrative bioinformatics Volume 16 (2019) DOI: 10.1515/jib-2019-0035
*
Detection of simple and complex de novo mutations without, with, or with multiple reference sequences
Garimella KV, Iqbal Z, Krause MA, Campino S, Kekre M, Drury E, Kwiatkowski D, Sa JM, Wellems TE, McVean G. Preprint DOI: 10.1101/698910
*
Genetic interactions of G-quadruplexes in humans.
Zyner KG, Mulhearn DS, Adhikari S, Martínez Cuesta S, Di Antonio M, Erard N, Hannon GJ, Tannahill D, Balasubramanian S. eLife Volume 8 (2019) DOI: 10.7554/elife.46793
*
IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response.
Chen HC, Eling N, Martinez-Jimenez CP, O'Brien LM, Carbonaro V, Marioni JC, Odom DT, de la Roche M. EMBO reports Volume 20 (2019) p.e47379 DOI: 10.15252/embr.201847379
*
CYRI/FAM49B negatively regulates RAC1-driven cytoskeletal remodelling and protects against bacterial 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. Nature microbiology Volume 4 (2019) p.1516-1531 DOI: 10.1038/s41564-019-0484-8
*
Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer.
Tang J, Gautam P, Gupta A, He L, Timonen S, Akimov Y, Wang W, Szwajda A, Jaiswal A, Turei D, Yadav B, Kankainen M, Saarela J, Saez-Rodriguez J, Wennerberg K, Aittokallio T. NPJ systems biology and applications Volume 5 (2019) p.20 DOI: 10.1038/s41540-019-0098-z
*
DeviaTE: Assembly-free analysis and visualization of mobile genetic element composition.
Weilguny L, Kofler R. Molecular ecology resources Volume 19 (2019) p.1346-1354 DOI: 10.1111/1755-0998.13030
*
High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation
Abeler-Dörner L, Laing AG, Lorenc A, Ushakov DS, Clare S, Speak A, Duque M, White JK, Ramirez-Solis R, Saran N, Bull KR, Morón B, Iwasaki J, Barton PR, Caetano S, Hng KI, Cambridge E, Forman S, Crockford TL, Griffiths M, Kane L, Harcourt K, Brandt C, Notley G, Babalola KO, Warren J, Mason JC, Meeniga A, Karp NA, Melvin D, Cawthorne E, Weinrick B, Rahim A, Drissler S, Meskas J, Yue A, Lux M, Song-Zhao G, Chan A, Reviriego CB, Abeler J, Wilson H, Przemska-Kosicka A, Edmans M, Strevens N, Pasztorek M, Meehan TF, Powrie F, Brinkman R, Dougan G, Jacobs W, Lloyd C, Cornall RJ, Maloy K, Grencis R, Griffiths GM, Adams D, Hayday AC. Preprint DOI: 10.1101/688010
*
A polymorphic helix of a Salmonella needle protein relays signals defining distinct steps in type III secretion.
Guo EZ, Desrosiers DC, Zalesak J, Tolchard J, Berbon M, Habenstein B, Marlovits T, Loquet A, Galán JE. PLoS biology Volume 17 (2019) p.e3000351 DOI: 10.1371/journal.pbio.3000351
*
Autism-associated missense genetic variants impact locomotion and neurodevelopment in Caenorhabditis elegans.
Wong WR, Brugman KI, Maher S, Oh JY, Howe K, Kato M, Sternberg PW. Human molecular genetics Volume 28 (2019) p.2271-2281 DOI: 10.1093/hmg/ddz051
*
Publisher Correction: 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 51 (2019) p.1190 DOI: 10.1038/s41588-019-0445-4
*
New models of atherosclerosis and multi-drug therapeutic interventions.
Parton A, McGilligan V, Chemaly M, O'Kane M, Watterson S. Bioinformatics (Oxford, England) Volume 35 (2019) p.2449-2457 DOI: 10.1093/bioinformatics/bty980
The EMBL-EBI search and sequence analysis tools APIs in 2019.
Madeira F, Park YM, Lee J, Buso N, Gur T, Madhusoodanan N, Basutkar P, Tivey ARN, Potter SC, Finn RD, Lopez R. Nucleic acids research Volume 47 (2019) p.W636-W641 DOI: 10.1093/nar/gkz268
TADOSS: computational estimation of tandem domain swap stability.
Lafita A, Tian P, Best RB, Bateman A. Bioinformatics (Oxford, England) Volume 35 (2019) p.2507-2508 DOI: 10.1093/bioinformatics/bty974
*
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport.
Stourac J, Vavra O, Kokkonen P, Filipovic J, Pinto G, Brezovsky J, Damborsky J, Bednar D. Nucleic acids research Volume 47 (2019) p.W414-W422 DOI: 10.1093/nar/gkz378
*
Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques.
Gabriels R, Martens L, Degroeve S. Nucleic acids research Volume 47 (2019) p.W295-W299 DOI: 10.1093/nar/gkz299
*
ORVAL: a novel platform for the prediction and exploration of disease-causing oligogenic variant combinations.
Renaux A, Papadimitriou S, Versbraegen N, Nachtegael C, Boutry S, Nowé A, Smits G, Lenaerts T. Nucleic acids research Volume 47 (2019) p.W93-W98 DOI: 10.1093/nar/gkz437
*
A plugin for the Ensembl Variant Effect Predictor that uses MaxEntScan to predict variant spliceogenicity.
Shamsani J, Kazakoff SH, Armean IM, McLaren W, Parsons MT, Thompson BA, O'Mara TA, Hunt SE, Waddell N, Spurdle AB. Bioinformatics (Oxford, England) Volume 35 (2019) p.2315-2317 DOI: 10.1093/bioinformatics/bty960
*
Estimating the predictability of cancer evolution.
Hosseini SR, Diaz-Uriarte R, Markowetz F, Beerenwinkel N. Bioinformatics (Oxford, England) Volume 35 (2019) p.i389-i397 DOI: 10.1093/bioinformatics/btz332
*
The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid
Canals R, Chaudhuri RR, Steiner RE, Owen SV, Quinones-Olvera N, Gordon MA, Ibba M, Hinton JCD. Preprint DOI: 10.1101/689075
Tandem domain swapping: determinants of multidomain protein misfolding.
Lafita A, Tian P, Best RB, Bateman A. Current opinion in structural biology Volume 58 (2019) p.97-104 DOI: 10.1016/j.sbi.2019.05.012
*
Mutational signatures are jointly shaped by DNA damage and repair
Volkova NV, Meier B, González-Huici V, Bertolini S, Gonzalez S, Voeringer H, Abascal F, Martincorena I, Campbell PJ, Gartner A, Gerstung M. Preprint DOI: 10.1101/686295
*
From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training.
McGrath A, Champ K, Shang CA, van Dam E, Brooksbank C, Morgan SL. PLoS computational biology Volume 15 (2019) p.e1006923 DOI: 10.1371/journal.pcbi.1006923
*
A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass spectrometry: Application to the characterisation of metabolites in rat urine.
Nye LC, Williams JP, Munjoma NC, Letertre MPM, Coen M, Bouwmeester R, Martens L, Swann JR, Nicholson JK, Plumb RS, McCullagh M, Gethings LA, Lai S, Langridge JI, Vissers JPC, Wilson ID. Journal of chromatography. A Volume 1602 (2019) p.386-396 DOI: 10.1016/j.chroma.2019.06.056
*
Analyzing the heterogeneity of rule-based EHR phenotyping algorithms in CALIBER and the UK Biobank
Denaxas S, Parkinson H, Fitzpatrick N, Sudlow C, Hemingway H. Preprint DOI: 10.1101/685156
*
Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout.
Cortés-Ciriano I, Bender A. Journal of chemical information and modeling Volume 59 (2019) p.3330-3339 DOI: 10.1021/acs.jcim.9b00297
*
Removing the hidden data dependency of DIA with predicted spectral libraries
Van Puyvelde B, Willems S, Gabriels R, Daled S, De Clerck L, Vande Casteele S, Staes A, Impens F, Deforce D, Martens L, Degroeve S, Dhaenens M. Preprint DOI: 10.1101/681429
*
Common and distinct transcriptional signatures of mammalian embryonic lethality.
Collins JE, White RJ, Staudt N, Sealy IM, Packham I, Wali N, Tudor C, Mazzeo C, Green A, Siragher E, Ryder E, White JK, Papatheodoru I, Tang A, Füllgrabe A, Billis K, Geyer SH, Weninger WJ, Galli A, Hemberger M, Stemple DL, Robertson E, Smith JC, Mohun T, Adams DJ, Busch-Nentwich EM. Nature communications Volume 10 (2019) p.2792 DOI: 10.1038/s41467-019-10642-x
*
Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels.
Sousa A, Gonçalves E, Mirauta B, Ochoa D, Stegle O, Beltrao P. Molecular & cellular proteomics : MCP Volume 18 (2019) p.S114-S125 DOI: 10.1074/mcp.ra118.001280
*
Read correction for non-uniform coverages
Marchet C, Dufresne Y, Limasset A. Preprint DOI: 10.1101/673624
Evolution of protein kinase substrate recognition at the active site.
Bradley D, Beltrao P. PLoS biology Volume 17 (2019) p.e3000341 DOI: 10.1371/journal.pbio.3000341
*
Human and mouse essentiality screens as a resource for disease gene discovery
Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LM, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu C, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon A, Lloyd KK, Brown SD, Parkinson H, Meehan TF, Smedley D, on behalf of the Genomics England Research Consortium and the International Mouse Phenotyping Consortium. Preprint DOI: 10.1101/678250
*
The Impact of Population Variation in the Analysis of microRNA Target Sites.
Helmy M, Hatlen A, Marco A. Non-coding RNA Volume 5 (2019) DOI: 10.3390/ncrna5020042
*
Induction of Neural Crest Stem Cells From Bardet-Biedl Syndrome Patient Derived hiPSCs.
Barrell WB, Griffin JN, Harvey JL, HipSci Consortium, Danovi D, Beales P, Grigoriadis AE, Liu KJ. Frontiers in molecular neuroscience Volume 12 (2019) p.139 DOI: 10.3389/fnmol.2019.00139
*
Structural analysis of pathogenic missense mutations in GABRA2 and identification of a novel de novo variant in the desensitization gate
Sanchis-Juan A, Hasenahuer MA, Baker JA, McTague A, Barwick K, Kurian MA, Duarte ST, Thornton J, Raymond FL, NIHR BioResource. Preprint DOI: 10.1101/678219
*
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.
Hucka M, Bergmann FT, Chaouiya C, Dräger A, Hoops S, Keating SM, König M, Novère NL, Myers CJ, Olivier BG, Sahle S, Schaff JC, Sheriff R, Smith LP, Waltemath D, Wilkinson DJ, Zhang F. Journal of integrative bioinformatics Volume 16 (2019) DOI: 10.1515/jib-2019-0021
*
Chlamydia buteonis, a new Chlamydia species isolated from a red-shouldered hawk.
Laroucau K, Vorimore F, Aaziz R, Solmonson L, Hsia RC, Bavoil PM, Fach P, Hölzer M, Wuenschmann A, Sachse K. Systematic and applied microbiology Volume 42 (2019) p.125997 DOI: 10.1016/j.syapm.2019.06.002
*
KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images.
Cortés-Ciriano I, Bender A. Journal of cheminformatics Volume 11 (2019) p.41 DOI: 10.1186/s13321-019-0364-5
*
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.
Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J. Nature communications Volume 10 (2019) p.2674 DOI: 10.1038/s41467-019-09799-2
*
De novo variant in tyrosine kinase SRC causes thrombocytopenia: case report of a second family.
De Kock L, Thys C, Downes K, Duarte D, Megy K, Van Geet C, Freson K. Platelets Volume 30 (2019) p.931-934 DOI: 10.1080/09537104.2019.1628197
*
Sequencing abasic sites in DNA at single-nucleotide resolution.
Liu ZJ, Martínez Cuesta S, van Delft P, Balasubramanian S. Nature chemistry Volume 11 (2019) p.629-637 DOI: 10.1038/s41557-019-0279-9
*
A cellular census of human lungs identifies novel cell states in health and in asthma.
Vieira Braga FA, Kar G, Berg M, Carpaij OA, Polanski K, Simon LM, Brouwer S, Gomes T, Hesse L, Jiang J, Fasouli ES, Efremova M, Vento-Tormo R, Talavera-López C, Jonker MR, Affleck K, Palit S, Strzelecka PM, Firth HV, Mahbubani KT, Cvejic A, Meyer KB, Saeb-Parsy K, Luinge M, Brandsma CA, Timens W, Angelidis I, Strunz M, Koppelman GH, van Oosterhout AJ, Schiller HB, Theis FJ, van den Berge M, Nawijn MC, Teichmann SA. Nature medicine Volume 25 (2019) p.1153-1163 DOI: 10.1038/s41591-019-0468-5
*
Genome-wide association meta-analysis of cocaine dependence: Shared genetics with comorbid conditions.
Cabana-Domínguez J, Shivalikanjli A, Fernàndez-Castillo N, Cormand B. Progress in neuro-psychopharmacology & biological psychiatry Volume 94 (2019) p.109667 DOI: 10.1016/j.pnpbp.2019.109667
*
Robust summarization and inference in proteome-wide label-free quantification
Sticker A, Goeminne L, Martens L, Clement L. Preprint DOI: 10.1101/668863
*
Simulating multiple faceted variability in single cell RNA sequencing.
Zhang X, Xu C, Yosef N. Nature communications Volume 10 (2019) p.2611 DOI: 10.1038/s41467-019-10500-w
*
Soft Windowing Application to Improve Analysis of High-throughput Phenotyping Data
Haselimashhadi H, Jeremy MC, Munoz-Fuentes V, López-Gómez F, Babalola K, Acar EF, Kumar V, White J, Flenniken AM, King R, Straiton E, Seavitt JR, Gaspero A, Garza A, Christianson AE, Hsu C, Reynolds CL, Lanza DG, Lorenzo I, Green JR, Gallegos JJ, Bohat R, Samaco RC, Veeraragavan S, Kim JK, Miller G, Fuchs H, Garrett L, Becker L, Kang YK, Clary D, Cho SY, Tamura M, Tanaka N, Soo KD, Bezginov A, About GB, Champy M, Vasseur L, Leblanc S, Meziane H, Selloum M, Reilly PT, Spielmann N, Maier H, Gailus-Durner V, Sorg T, Hiroshi M, Yuichi O, Heaney JD, Dickinson ME, Wolfgang W, Tocchini-Valentini GP, Lloyd KCK, McKerlie C, Seong JK, Yann H, de Angelis MH, Brown SD, Smedley D, Flicek P, Mallon A, Parkinson H, Meehan TF. Preprint DOI: 10.1101/656678
*
An improved pig reference genome sequence to enable pig genetics and genomics research
Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, Girón CG, Griffin DK, Hall R, Hannum G, Hourlier T, Howe K, Hume DA, Izuogu O, Kim K, Koren S, Liu H, Manchanda N, Martin FJ, Nonneman DJ, O’Connor RE, Phillippy AM, Rohrer GA, Rosen BD, Rund LA, Sargent CA, Schook LB, Schroeder SG, Schwartz AS, Skinner BM, Talbot R, Tseng E, Tuggle CK, Watson M, Smith TPL, Archibald AL. Preprint DOI: 10.1101/668921
*
Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains
Kentepozidou E, Aitken SJ, Feig C, Stefflova K, Ibarra-Soria X, Odom DT, Roller M, Flicek P. Preprint DOI: 10.1101/668855
*
How well do we understand the basis of classic selective sweeps in humans?
Szpak M, Xue Y, Ayub Q, Tyler-Smith C. FEBS letters Volume 593 (2019) p.1431-1448 DOI: 10.1002/1873-3468.13447
*
A chromosome-level assembly of the Atlantic herring – detection of a supergene and other signals of selection
Pettersson ME, Rochus CM, Han F, Chen J, Hill J, Wallerman O, Fan G, Hong X, Xu Q, Zhang H, Liu S, Liu X, Haggerty L, Hunt T, Martin FJ, Flicek P, Bunikis I, Folkvord A, Andersson L. Preprint DOI: 10.1101/668384
*
An integrated landscape of protein expression in human cancer
Jarnuczak AF, Najgebauer H, Barzine M, Kundu DJ, Ghavidel F, Perez-Riverol Y, Papatheodorou I, Brazma A, Vizcaíno JA. Preprint DOI: 10.1101/665968
*
Phospho-peptide binding domains in S. cerevisiae model organism.
Panni S. Biochimie Volume 163 (2019) p.117-127 DOI: 10.1016/j.biochi.2019.06.005
*
Curated disease-causing genes for bleeding, thrombotic, and platelet disorders: Communication from the SSC of the ISTH.
Megy K, Downes K, Simeoni I, Bury L, Morales J, Mapeta R, Bellissimo DB, Bray PF, Goodeve AC, Gresele P, Lambert M, Reitsma P, Ouwehand WH, Freson K, Subcommittee on Genomics in Thrombosis and Hemostasis. Journal of thrombosis and haemostasis : JTH Volume 17 (2019) p.1253-1260 DOI: 10.1111/jth.14479
*
Integration of genomic variation and phenotypic data using HmtPhenome
Preste R, Attimonelli M. Preprint DOI: 10.1101/660282
*
ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK).
Fritsch S, Neumann S, Schaub J, Steinbeck C, Zielesny A. Journal of Cheminformatics Volume 11 (2019) p.37 DOI: 10.1186/s13321-019-0361-8
*
SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse.
Koopmans F, van Nierop P, Andres-Alonso M, Byrnes A, Cijsouw T, Coba MP, Cornelisse LN, Farrell RJ, Goldschmidt HL, Howrigan DP, Hussain NK, Imig C, de Jong APH, Jung H, Kohansalnodehi M, Kramarz B, Lipstein N, Lovering RC, MacGillavry H, Mariano V, Mi H, Ninov M, Osumi-Sutherland D, Pielot R, Smalla KH, Tang H, Tashman K, Toonen RFG, Verpelli C, Reig-Viader R, Watanabe K, van Weering J, Achsel T, Ashrafi G, Asi N, Brown TC, De Camilli P, Feuermann M, Foulger RE, Gaudet P, Joglekar A, Kanellopoulos A, Malenka R, Nicoll RA, Pulido C, de Juan-Sanz J, Sheng M, Südhof TC, Tilgner HU, Bagni C, Bayés À, Biederer T, Brose N, Chua JJE, Dieterich DC, Gundelfinger ED, Hoogenraad C, Huganir RL, Jahn R, Kaeser PS, Kim E, Kreutz MR, McPherson PS, Neale BM, O'Connor V, Posthuma D, Ryan TA, Sala C, Feng G, Hyman SE, Thomas PD, Smit AB, Verhage M. Neuron Volume 103 (2019) p.217-234.e4 DOI: 10.1016/j.neuron.2019.05.002
*
Establishment of porcine and human expanded potential stem cells.
Gao X, Nowak-Imialek M, Chen X, Chen D, Herrmann D, Ruan D, Chen ACH, Eckersley-Maslin MA, Ahmad S, Lee YL, Kobayashi T, Ryan D, Zhong J, Zhu J, Wu J, Lan G, Petkov S, Yang J, Antunes L, Campos LS, Fu B, Wang S, Yong Y, Wang X, Xue SG, Ge L, Liu Z, Huang Y, Nie T, Li P, Wu D, Pei D, Zhang Y, Lu L, Yang F, Kimber SJ, Reik W, Zou X, Shang Z, Lai L, Surani A, Tam PPL, Ahmed A, Yeung WSB, Teichmann SA, Niemann H, Liu P. Nature cell biology Volume 21 (2019) p.687-699 DOI: 10.1038/s41556-019-0333-2
*
The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.
Avsec Ž, Kreuzhuber R, Israeli J, Xu N, Cheng J, Shrikumar A, Banerjee A, Kim DS, Beier T, Urban L, Kundaje A, Stegle O, Gagneur J. Nature biotechnology Volume 37 (2019) p.592-600 DOI: 10.1038/s41587-019-0140-0
*
Structure-guided fragment-based drug discovery at the synchrotron: screening binding sites and correlations with hotspot mapping.
Thomas SE, Collins P, James RH, Mendes V, Charoensutthivarakul S, Radoux C, Abell C, Coyne AG, Floto RA, von Delft F, Blundell TL. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Volume 377 (2019) p.20180422 DOI: 10.1098/rsta.2018.0422
*
Footprint-based functional analysis of multiomic data.
Dugourd A, Saez-Rodriguez J. Current opinion in systems biology Volume 15 (2019) p.82-90 DOI: 10.1016/j.coisb.2019.04.002
*
Integrated omics profiling reveals novel patterns of epigenetic programming in cancer-associated myofibroblasts.
Najgebauer H, Liloglou T, Jithesh PV, Giger OT, Varro A, Sanderson CM. Carcinogenesis Volume 40 (2019) p.500-512 DOI: 10.1093/carcin/bgz001
Applications of machine learning in drug discovery and development.
Vamathevan J, Clark D, Czodrowski P, Dunham I, Ferran E, Lee G, Li B, Madabhushi A, Shah P, Spitzer M, Zhao S. Nature reviews. Drug discovery Volume 18 (2019) p.463-477 DOI: 10.1038/s41573-019-0024-5
*
Genomic diversity affects the accuracy of bacterial SNP calling pipelines
Bush SJ, Foster D, Eyre DW, Clark EL, De Maio N, Shaw LP, Stoesser N, Peto TEA, Crook DW, Walker AS. Preprint DOI: 10.1101/653774
*
Immune disease variants modulate gene expression in regulatory CD4+ T cells and inform drug targets
Bossini-Castillo L, Glinos DA, Kunowska N, Golda G, Lamikanra A, Spitzer M, Soskic B, Cano-Gamez E, Smyth DJ, Cattermole C, Alasoo K, Mann A, Kundu K, Soranzo N, Dunham I, Roberts D, Trynka G. Preprint DOI: 10.1101/654632
*
Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters - the case of phage λ.
Ruklisa D, Brazma A, Cerans K, Schlitt T, Viksna J. BMC bioinformatics Volume 20 (2019) p.296 DOI: 10.1186/s12859-019-2909-z
*
Stochastic semi-supervised learning to prioritise genes from high-throughput genomic screens
Vitsios D, Petrovski S. Preprint DOI: 10.1101/655449
*
Systematic re-annotation of 191 genes associated with early-onset epilepsy unmasks de novo variants linked to Dravet syndrome in novel SCN1A exons
Steward CA, Roovers J, Suner M, Gonzalez JM, Uszczynska-Ratajczak B, Pervouchine D, Fitzgerald S, Viola M, Stamberger H, Hamdan FF, Ceulemans B, Leroy P, Nava C, Lepine A, Tapanari E, Keiller D, Abbs S, Sanchis-Juan A, Grozeva D, Rogers AS, Wright J, Choudhary J, Diekhans M, Guigó R, Petryszak R, Minassian BA, Cavalleri G, Vitsios D, Petrovski S, Harrow J, Flicek P, Raymond FL, Lench NJ, De Jonghe P, Mudge JM, Weckhuysen S, Sisodiya SM, Frankish A. Preprint DOI: 10.1101/648576
Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP.
Thormann A, Halachev M, McLaren W, Moore DJ, Svinti V, Campbell A, Kerr SM, Tischkowitz M, Hunt SE, Dunlop MG, Hurles ME, Wright CF, Firth HV, Cunningham F, FitzPatrick DR. Nature communications Volume 10 (2019) p.2373 DOI: 10.1038/s41467-019-10016-3
*
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkiran A, Cetin-Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MR, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Hou J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi P, Tseng W, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Vesztrocy AW, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes M, Emily Koo DC, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SC, Carraro M, Piovesan D, Rehman HU, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Larsen DJ, Omdahl AR, Sagers LW, Suh E, Dayton JB, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang J, Liao W, Liu Y, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O’Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I. Preprint DOI: 10.1101/653105
*
A clinal polymorphism in the insulin signaling transcription factor foxo contributes to life-history adaptation in Drosophila.
Durmaz E, Rajpurohit S, Betancourt N, Fabian DK, Kapun M, Schmidt P, Flatt T. Evolution; international journal of organic evolution Volume 73 (2019) p.1774-1792 DOI: 10.1111/evo.13759
*
Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters.
Kallies R, Hölzer M, Brizola Toscan R, Nunes da Rocha U, Anders J, Marz M, Chatzinotas A. Viruses Volume 11 (2019) DOI: 10.3390/v11060484
*
Supervised learning to quantify amyloidosis in whole brains of an Alzheimer's disease mouse model acquired with optical projection tomography.
Nguyen D, Uhlmann V, Planchette AL, Marchand PJ, Van De Ville D, Lasser T, Radenovic A. Biomedical optics express Volume 10 (2019) p.3041-3060 DOI: 10.1364/boe.10.003041
*
The neurocognitive gains of diagnostic reasoning training using simulated interactive veterinary cases
Nassar M. Preprint DOI: 10.1101/650499
*
Similarity regression predicts evolution of transcription factor sequence specificity.
Lambert SA, Yang AWH, Sasse A, Cowley G, Albu M, Caddick MX, Morris QD, Weirauch MT, Hughes TR. Nature genetics Volume 51 (2019) p.981-989 DOI: 10.1038/s41588-019-0411-1
*
An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor.
Liu X, Ye K, van Vlijmen HWT, IJzerman AP, van Westen GJP. Journal of Cheminformatics Volume 11 (2019) p.35 DOI: 10.1186/s13321-019-0355-6
*
New models for human disease from the International Mouse Phenotyping Consortium.
Cacheiro P, Haendel MA, Smedley D, International Mouse Phenotyping Consortium and the Monarch Initiative. Mammalian genome : official journal of the International Mammalian Genome Society Volume 30 (2019) p.143-150 DOI: 10.1007/s00335-019-09804-5
*
Proteomics Standards Initiative Extended FASTA Format.
Binz PA, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp EA, Mendoza L, Baker PR, Collins A, Van Den Bossche T, Deutsch EW. Journal of proteome research Volume 18 (2019) p.2686-2692 DOI: 10.1021/acs.jproteome.9b00064
*
Germline selection shapes human mitochondrial DNA diversity.
Wei W, Tuna S, Keogh MJ, Smith KR, Aitman TJ, Beales PL, Bennett DL, Gale DP, Bitner-Glindzicz MAK, Black GC, Brennan P, Elliott P, Flinter FA, Floto RA, Houlden H, Irving M, Koziell A, Maher ER, Markus HS, Morrell NW, Newman WG, Roberts I, Sayer JA, Smith KGC, Taylor JC, Watkins H, Webster AR, Wilkie AOM, Williamson C, NIHR BioResource–Rare Diseases, 100,000 Genomes Project–Rare Diseases Pilot, Ashford S, Penkett CJ, Stirrups KE, Rendon A, Ouwehand WH, Bradley JR, Raymond FL, Caulfield M, Turro E, Chinnery PF. Science (New York, N.Y.) Volume 364 (2019) DOI: 10.1126/science.aau6520
*
Microbial community drivers of PK/NRP gene diversity in selected global soils.
Borsetto C, Amos GCA, da Rocha UN, Mitchell AL, Finn RD, Laidi RF, Vallin C, Pearce DA, Newsham KK, Wellington EMH. Microbiome Volume 7 (2019) p.78 DOI: 10.1186/s40168-019-0692-8
*
RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia
Fuller GG, Han T, Freeberg MA, Moresco JJ, Yates JR, Kim JK. Preprint DOI: 10.1101/638650
*
COSS: A fast and user-friendly tool for spectral library searching
Shiferaw GA, Vandermarliere E, Hulstaert N, Gabriels R, Martens L, Volders P. Preprint DOI: 10.1101/640458
*
Literature-Based Enrichment Insights into Redox Control of Vascular Biology.
Essack M, Salhi A, Stanimirovic J, Tifratene F, Bin Raies A, Hungler A, Uludag M, Van Neste C, Trpkovic A, Bajic VP, Bajic VB, Isenovic ER. Oxidative medicine and cellular longevity Volume 2019 (2019) p.1769437 DOI: 10.1155/2019/1769437
*
Structure and Hierarchy of Influenza Virus Models Revealed by Reaction Network Analysis.
Peter S, Hölzer M, Lamkiewicz K, di Fenizio PS, Al Hwaeer H, Marz M, Schuster S, Dittrich P, Ibrahim B. Viruses Volume 11 (2019) DOI: 10.3390/v11050449
*
Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening.
Picco G, Chen ED, Alonso LG, Behan FM, Gonçalves E, Bignell G, Matchan A, Fu B, Banerjee R, Anderson E, Butler A, Benes CH, McDermott U, Dow D, Iorio F, Stronach E, Yang F, Yusa K, Saez-Rodriguez J, Garnett MJ. Nature communications Volume 10 (2019) p.2198 DOI: 10.1038/s41467-019-09940-1
*
End-to-End Security for Local and Remote Human Genetic Data Applications at the EGA.
Senf A. IEEE/ACM transactions on computational biology and bioinformatics Volume 16 (2019) p.1324-1327 DOI: 10.1109/tcbb.2019.2916810
*
DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks.
Sureyya Rifaioglu A, Doğan T, Jesus Martin M, Cetin-Atalay R, Atalay V. Scientific reports Volume 9 (2019) p.7344 DOI: 10.1038/s41598-019-43708-3
*
Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling.
Lun XK, Szklarczyk D, Gábor A, Dobberstein N, Zanotelli VRT, Saez-Rodriguez J, von Mering C, Bodenmiller B. Molecular cell Volume 74 (2019) p.1086-1102.e5 DOI: 10.1016/j.molcel.2019.04.021
*
Control of Bacterial Sulfite Detoxification by Conserved and Species-Specific Regulatory Circuits.
Tan YJC, Zhao C, Nasreen M, O'Rourke L, Dhouib R, Roberts L, Wan Y, Beatson SA, Kappler U. Frontiers in microbiology Volume 10 (2019) p.960 DOI: 10.3389/fmicb.2019.00960
*
In silico prediction of housekeeping long intergenic non-coding RNAs reveals HKlincR1 as an essential player in lung cancer cell survival.
Memon D, Bi J, Miller CJ. Scientific reports Volume 9 (2019) p.7372 DOI: 10.1038/s41598-019-43758-7
*
AbRSA: A robust tool for antibody numbering.
Li L, Chen S, Miao Z, Liu Y, Liu X, Xiao ZX, Cao Y. Protein science : a publication of the Protein Society Volume 28 (2019) p.1524-1531 DOI: 10.1002/pro.3633
*
Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle.
Taylor DL, Jackson AU, Narisu N, Hemani G, Erdos MR, Chines PS, Swift A, Idol J, Didion JP, Welch RP, Kinnunen L, Saramies J, Lakka TA, Laakso M, Tuomilehto J, Parker SCJ, Koistinen HA, Davey Smith G, Boehnke M, Scott LJ, Birney E, Collins FS. Proceedings of the National Academy of Sciences of the United States of America Volume 116 (2019) p.10883-10888 DOI: 10.1073/pnas.1814263116
*
Exome sequencing identifies a novel missense variant in CTSC causing nonsyndromic aggressive periodontitis.
Molitor A, Prud'homme T, Miao Z, Conrad S, Bloch-Zupan A, Pichot A, Hanauer A, Isidor B, Bahram S, Carapito R. Journal of human genetics Volume 64 (2019) p.689-694 DOI: 10.1038/s10038-019-0615-3
*
Survival of an epidemic MDR strain of Mycobacterium tuberculosis and its non-prosperous variant within activated macrophages.
Yokobori N, Monteserin J, Rearte B, Paul R, Símboli N, López B, Ritacco V, Sasiain MDC. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases Volume 73 (2019) p.248-254 DOI: 10.1016/j.meegid.2019.05.005
*
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
Cuomo AS, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, Vallier L, Marioni JC, Chhatriwala M, Stegle O, HipSci Consortium. Preprint DOI: 10.1101/630996
*
IN VITRO 3D PHENOTYPIC DRUG SCREEN IDENTIFIES CELASTROL AS AN EFFECTIVE IN VIVO INHIBITOR OF POLYCYSTIC KIDNEY DISEASE.
Booij TH, Leonhard WN, Bange H, Yan K, Fokkelman M, Plugge AJ, Veraar KAM, Dauwerse JG, van Westen GJP, van de Water B, Price LS, Peters DJM. Journal of molecular cell biology (2019) DOI: 10.1093/jmcb/mjz029
*
Molecular footprint of Medawar's mutation accumulation process in mammalian aging.
Turan ZG, Parvizi P, Dönertaş HM, Tung J, Khaitovich P, Somel M. Aging cell Volume 18 (2019) p.e12965 DOI: 10.1111/acel.12965
*
Author Correction: Linking drug target and pathway activation for effective therapy using multi-task learning.
Yang M, Simm J, Lam CC, Zakeri P, van Westen GJP, Moreau Y, Saez-Rodriguez J. Scientific reports Volume 9 (2019) p.7106 DOI: 10.1038/s41598-019-43503-0
*
Ten quick tips for biocuration.
Tang YA, Pichler K, Füllgrabe A, Lomax J, Malone J, Munoz-Torres MC, Vasant DV, Williams E, Haendel M. PLoS computational biology Volume 15 (2019) p.e1006906 DOI: 10.1371/journal.pcbi.1006906
*
Proteomics Standards Initiative Extended FASTA Format (PEFF)
Binz P, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp EA, Mendoza L, Baker PR, Collins A, Van Den Bossche T, Deutsch EW. Preprint DOI: 10.1101/624494
*
MEK1/2 inhibitor withdrawal reverses acquired resistance driven by BRAFV600E amplification whereas KRASG13D amplification promotes EMT-chemoresistance.
Sale MJ, Balmanno K, Saxena J, Ozono E, Wojdyla K, McIntyre RE, Gilley R, Woroniuk A, Howarth KD, Hughes G, Dry JR, Arends MJ, Caro P, Oxley D, Ashton S, Adams DJ, Saez-Rodriguez J, Smith PD, Cook SJ. Nature communications Volume 10 (2019) p.2030 DOI: 10.1038/s41467-019-09438-w
*
Functional genomics of the stable fly, Stomoxys calcitrans, reveals mechanisms underlying reproduction, host interactions, and novel targets for pest control
Olafson PU, Aksoy S, Attardo GM, Buckmeier G, Chen X, Coates CJ, Davis M, Dykema J, Emrich SJ, Friedrich M, Holmes CJ, Ioannidis P, Jansen EN, Jennings EC, Lawson D, Martinson EO, Maslen GL, Meisel RP, Murphy TD, Nayduch D, Nelson DR, Oyen KJ, Raszick TJ, Ribeiro JMC, Robertson HM, Rosendale AJ, Sackton TB, Swiger SL, Sze S, Tarone AM, Taylor DB, Warren WC, Waterhouse RM, Weirauch MT, Werren JH, Wilson RK, Zdobnov EM, Benoit JB. Preprint DOI: 10.1101/623009
The Convergence of Research and Clinical Genomics.
Birney E. American journal of human genetics Volume 104 (2019) p.781-783 DOI: 10.1016/j.ajhg.2019.04.003
Proteomics and phosphoproteomics in precision medicine: applications and challenges.
Giudice G, Petsalaki E. Briefings in bioinformatics Volume 20 (2019) p.767-777 DOI: 10.1093/bib/bbx141
*
De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers.
Hölzer M, Marz M. GigaScience Volume 8 (2019) DOI: 10.1093/gigascience/giz039
*
Identification of a regeneration-organizing cell in the Xenopus tail.
Aztekin C, Hiscock TW, Marioni JC, Gurdon JB, Simons BD, Jullien J. Science (New York, N.Y.) Volume 364 (2019) p.653-658 DOI: 10.1126/science.aav9996
*
Consent insufficient for data release-Response.
Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Science (New York, N.Y.) Volume 364 (2019) p.446 DOI: 10.1126/science.aax7509
*
RSAT Var-tools: an accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding
Santana-Garcia W, Rocha-Acevedo M, Ramirez-Navarro L, Mbouamboua Y, Thieffry D, Thomas-Chollier M, Contreras-Moreira B, van Helden J, Medina-Rivera A. Preprint DOI: 10.1101/623090
*
Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis.
Schiebenhoefer H, Van Den Bossche T, Fuchs S, Renard BY, Muth T, Martens L. Expert review of proteomics Volume 16 (2019) p.375-390 DOI: 10.1080/14789450.2019.1609944
*
Characterization of the transcriptome of Haloferax volcanii, grown under four different conditions, with mixed RNA-Seq.
Laass S, Monzon VA, Kliemt J, Hammelmann M, Pfeiffer F, Förstner KU, Soppa J. PloS one Volume 14 (2019) p.e0215986 DOI: 10.1371/journal.pone.0215986
Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.
Madeira F, Madhusoodanan N, Lee J, Tivey ARN, Lopez R. Current protocols in bioinformatics Volume 66 (2019) p.e74 DOI: 10.1002/cpbi.74
*
ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion
Hulstaert N, Sachsenberg T, Walzer M, Barsnes H, Martens L, Perez-Riverol Y. Preprint DOI: 10.1101/622852
*
Variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility
Watt S, Vasquez L, Walter K, Mann AL, Kundu K, Chen L, Yan Y, Ecker S, Burden F, Farrow S, Farr B, Iotchkova V, Elding H, Mead D, Tardaguila M, Ponstingl H, Richardson D, Datta A, Flicek P, Clarke L, Downes K, Pastinen T, Fraser P, Frontini M, Javierre B, Spivakov M, Soranzo N. Preprint DOI: 10.1101/620260
Conserved phosphorylation hotspots in eukaryotic protein domain families.
Strumillo MJ, Oplová M, Viéitez C, Ochoa D, Shahraz M, Busby BP, Sopko R, Studer RA, Perrimon N, Panse VG, Beltrao P. Nature communications Volume 10 (2019) p.1977 DOI: 10.1038/s41467-019-09952-x
*
Marine DNA Viral Macro- and Microdiversity from Pole to Pole.
Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Domínguez-Huerta G, Ferland J, Kandels S, Liu Y, Marec C, Pesant S, Picheral M, Pisarev S, Poulain J, Tremblay JÉ, Vik D, Tara Oceans Coordinators, Babin M, Bowler C, Culley AI, de Vargas C, Dutilh BE, Iudicone D, Karp-Boss L, Roux S, Sunagawa S, Wincker P, Sullivan MB. Cell Volume 177 (2019) p.1109-1123.e14 DOI: 10.1016/j.cell.2019.03.040
*
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm.
Bliven SE, Lafita A, Rose PW, Capitani G, Prlić A, Bourne PE. PLoS computational biology Volume 15 (2019) p.e1006842 DOI: 10.1371/journal.pcbi.1006842
*
MAPK pathway and B cells overactivation in multiple sclerosis revealed by phosphoproteomics and genomic analysis.
Kotelnikova E, Kiani NA, Messinis D, Pertsovskaya I, Pliaka V, Bernardo-Faura M, Rinas M, Vila G, Zubizarreta I, Pulido-Valdeolivas I, Sakellaropoulos T, Faigle W, Silberberg G, Masso M, Stridh P, Behrens J, Olsson T, Martin R, Paul F, Alexopoulos LG, Saez-Rodriguez J, Tegner J, Villoslada P. Proceedings of the National Academy of Sciences of the United States of America Volume 116 (2019) p.9671-9676 DOI: 10.1073/pnas.1818347116
*
Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Nature communications Volume 10 (2019) p.1784 DOI: 10.1038/s41467-018-08148-z
*
Bcl-2 and IP3 compete for the ligand-binding domain of IP3Rs modulating Ca2+ signaling output.
Ivanova H, Wagner LE, Tanimura A, Vandermarliere E, Luyten T, Welkenhuyzen K, Alzayady KJ, Wang L, Hamada K, Mikoshiba K, De Smedt H, Martens L, Yule DI, Parys JB, Bultynck G. Cellular and molecular life sciences : CMLS Volume 76 (2019) p.3843-3859 DOI: 10.1007/s00018-019-03091-8
*
Detecting the mutational signature of homologous recombination deficiency in clinical samples.
Gulhan DC, Lee JJ, Melloni GEM, Cortés-Ciriano I, Park PJ. Nature genetics Volume 51 (2019) p.912-919 DOI: 10.1038/s41588-019-0390-2
*
Hybrid model for efficient prediction of poly(A) signals in human genomic DNA.
Albalawi F, Chahid A, Guo X, Albaradei S, Magana-Mora A, Jankovic BR, Uludag M, Van Neste C, Essack M, Laleg-Kirati TM, Bajic VB. Methods (San Diego, Calif.) Volume 166 (2019) p.31-39 DOI: 10.1016/j.ymeth.2019.04.001
*
Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia.
Gorman KM, Meyer E, Grozeva D, Spinelli E, McTague A, Sanchis-Juan A, Carss KJ, Bryant E, Reich A, Schneider AL, Pressler RM, Simpson MA, Debelle GD, Wassmer E, Morton J, Sieciechowicz D, Jan-Kamsteeg E, Paciorkowski AR, King MD, Cross JH, Poduri A, Mefford HC, Scheffer IE, Haack TB, McCullagh G, Deciphering Developmental Disorders Study, UK10K Consortium, NIHR BioResource, Millichap JJ, Carvill GL, Clayton-Smith J, Maher ER, Raymond FL, Kurian MA. American journal of human genetics Volume 104 (2019) p.948-956 DOI: 10.1016/j.ajhg.2019.03.005
*
Mouse screen reveals multiple new genes underlying mouse and human hearing loss.
Ingham NJ, Pearson SA, Vancollie VE, Rook V, Lewis MA, Chen J, Buniello A, Martelletti E, Preite L, Lam CC, Weiss FD, Powis Z, Suwannarat P, Lelliott CJ, Dawson SJ, White JK, Steel KP. PLoS biology Volume 17 (2019) p.e3000194 DOI: 10.1371/journal.pbio.3000194
*
Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk.
Kurilshikov A, van den Munckhof ICL, Chen L, Bonder MJ, Schraa K, Rutten JHW, Riksen NP, de Graaf J, Oosting M, Sanna S, Joosten LAB, van der Graaf M, Brand T, Koonen DPY, van Faassen M, LifeLines DEEP Cohort Study, BBMRI Metabolomics Consortium, Slagboom PE, Xavier RJ, Kuipers F, Hofker MH, Wijmenga C, Netea MG, Zhernakova A, Fu J. Circulation research Volume 124 (2019) p.1808-1820 DOI: 10.1161/circresaha.118.314642
*
Scalable data analysis in proteomics and metabolomics using BioContainers and workflows engines
Perez-Riverol Y, Moreno P. Preprint DOI: 10.1101/604413
*
Harnessing Novel Diversity From Landraces to Improve an Elite Barley Variety.
Monteagudo A, Casas AM, Cantalapiedra CP, Contreras-Moreira B, Gracia MP, Igartua E. Frontiers in plant science Volume 10 (2019) p.434 DOI: 10.3389/fpls.2019.00434
*
A data citation roadmap for scholarly data repositories.
Fenner M, Crosas M, Grethe JS, Kennedy D, Hermjakob H, Rocca-Serra P, Durand G, Berjon R, Karcher S, Martone M, Clark T. Scientific data Volume 6 (2019) p.28 DOI: 10.1038/s41597-019-0031-8
*
Human mitochondrial variant annotation with HmtNote
Preste R, Clima R, Attimonelli M. Preprint DOI: 10.1101/600619
Functional Annotation of Rare Genetic Variants
Ritchie GRS, Flicek P. Assessing Rare Variation in Complex Traits: Design and Analysis of Genetic Studies Springer, New York (NY)
*
Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens.
Behan FM, Iorio F, Picco G, Gonçalves E, Beaver CM, Migliardi G, Santos R, Rao Y, Sassi F, Pinnelli M, Ansari R, Harper S, Jackson DA, McRae R, Pooley R, Wilkinson P, van der Meer D, Dow D, Buser-Doepner C, Bertotti A, Trusolino L, Stronach EA, Saez-Rodriguez J, Yusa K, Garnett MJ. Nature Volume 568 (2019) p.511-516 DOI: 10.1038/s41586-019-1103-9
*
Comparative analysis of sequencing technologies for single-cell transcriptomics.
Natarajan KN, Miao Z, Jiang M, Huang X, Zhou H, Xie J, Wang C, Qin S, Zhao Z, Wu L, Yang N, Li B, Hou Y, Liu S, Teichmann SA. Genome biology Volume 20 (2019) p.70 DOI: 10.1186/s13059-019-1676-5
*
MuGVRE. A virtual research environment for 3D/4D genomics
Codó L, Bayarri G, Cid-Fuentes JA, Conejero J, Royo R, Repchevsky D, Pasi M, Meletiou A, McDowall MD, Reham F, Alcantara JA, Jimenez-Garcia B, Walther J, Illa R, Serra F, Goodstadt M, Castillo D, Sati S, Buitrago D, Brun-Heath I, Fernandez-Recio J, Cavalli G, Marti-Renom M, Yates A, Laughton CA, Badia RM, Orozco M, Gelpí JL, Adam Hospital. Preprint DOI: 10.1101/602474
*
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB).
Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY. Acta crystallographica. Section D, Structural biology Volume 75 (2019) p.451-454 DOI: 10.1107/s2059798319004522
*
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ. PLoS computational biology Volume 15 (2019) p.e1006650 DOI: 10.1371/journal.pcbi.1006650
*
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences
Drysdale R, Cook CE, Petryszak R, Baillie-Gerritsen V, Barlow M, Gasteiger E, Gruhl F, Haas J, Lanfear J, Lopez R, Redaschi N, Stockinger H, Teixeira D, Venkatesan A, Blomberg N, Durinx C, McEntyre J, ELIXIR Core Data Resource Forum. Preprint DOI: 10.1101/598318
*
Reverse GWAS: Using genetics to identify and model phenotypic subtypes.
Dahl A, Cai N, Ko A, Laakso M, Pajukanta P, Flint J, Zaitlen N. PLoS genetics Volume 15 (2019) p.e1008009 DOI: 10.1371/journal.pgen.1008009
*
MAGI: A Method for Metabolite Annotation and Gene Integration.
Erbilgin O, Rübel O, Louie KB, Trinh M, Raad M, Wildish T, Udwary D, Hoover C, Deutsch S, Northen TR, Bowen BP. ACS chemical biology Volume 14 (2019) p.704-714 DOI: 10.1021/acschembio.8b01107
*
Phospholipid membranes drive abdominal aortic aneurysm development through stimulating coagulation factor activity.
Allen-Redpath K, Aldrovandi M, Lauder SN, Gketsopoulou A, Tyrrell VJ, Slatter DA, Andrews R, Watkins WJ, Atkinson G, McNeill E, Gilfedder A, Protty M, Burston J, Johnson SRC, Rodrigues PRS, Jones DO, Lee R, Handa A, Channon K, Obaji S, Alvarez-Jarreta J, Krönke G, Ackermann J, Jenkins PV, Collins PW, O'Donnell VB. Proceedings of the National Academy of Sciences of the United States of America Volume 116 (2019) p.8038-8047 DOI: 10.1073/pnas.1814409116
*
UniProt genomic mapping for deciphering functional effects of missense variants.
McGarvey PB, Nightingale A, Luo J, Huang H, Martin MJ, Wu C, UniProt Consortium. Human mutation Volume 40 (2019) p.694-705 DOI: 10.1002/humu.23738
*
Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.
Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Berger CS, Chang CC, Chao H, Chen MM, Chen YT, Childers CP, Chipman AD, Cridge AG, Crumière AJJ, Dearden PK, Didion EM, Dinh H, Doddapaneni HV, Dolan A, Dugan S, Extavour CG, Febvay G, Friedrich M, Ginzburg N, Han Y, Heger P, Holmes CJ, Horn T, Hsiao YM, Jennings EC, Johnston JS, Jones TE, Jones JW, Khila A, Koelzer S, Kovacova V, Leask M, Lee SL, Lee CY, Lovegrove MR, Lu HL, Lu Y, Moore PJ, Munoz-Torres MC, Muzny DM, Palli SR, Parisot N, Pick L, Porter ML, Qu J, Refki PN, Richter R, Rivera-Pomar R, Rosendale AJ, Roth S, Sachs L, Santos ME, Seibert J, Sghaier E, Shukla JN, Stancliffe RJ, Tidswell O, Traverso L, van der Zee M, Viala S, Worley KC, Zdobnov EM, Gibbs RA, Richards S. Genome biology Volume 20 (2019) p.64 DOI: 10.1186/s13059-019-1660-0
*
Genetic association with high-resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula.
Contreras-Moreira B, Serrano-Notivoli R, Mohammed NE, Cantalapiedra CP, Beguería S, Casas AM, Igartua E. Molecular ecology Volume 28 (2019) p.1994-2012 DOI: 10.1111/mec.15009
*
Number of ECG Replicates and QT Correction Formula Influences the Estimated QT Prolonging Effect of a Drug.
van der Wall HEC, Gal P, Kemme MJB, van Westen GJP, Burggraaf J. Journal of cardiovascular pharmacology Volume 73 (2019) p.257-264 DOI: 10.1097/fjc.0000000000000657
*
Gene expression heterogeneity during brain development and aging: temporal changes and functional consequences
Işıldak U, Somel M, Thornton JM, Dönertaş HM. Preprint DOI: 10.1101/595249
*
Out of Transcaucasia: Origin of Western and Central Palearctic populations of Microthlaspi perfoliatum
Ali T, Muñoz-Fuentes V, Buch AK, Çelik A, Dutbayev A, Gabrielyan I, Glynou K, Kachour L, Khaliq I, Kitner M, Nigrelli L, Ploch S, Runge F, Solovyeva I, Schmuker A, Vakhrusheva L, Xia X, Maciá-Vicente JG, Nowak C, Thines M. Flora. Volume 253 (2019) p.127-141
The widespread increase in inter-individual variability of gene expression in the human brain with age.
Kedlian VR, Donertas HM, Thornton JM. Aging Volume 11 (2019) p.2253-2280 DOI: 10.18632/aging.101912
*
Assessing evolutionary risks of resistance for new antimicrobial therapies.
Brockhurst MA, Harrison F, Veening JW, Harrison E, Blackwell G, Iqbal Z, Maclean C. Nature ecology & evolution Volume 3 (2019) p.515-517 DOI: 10.1038/s41559-019-0854-x
*
Elastin imaging enables noninvasive staging and treatment monitoring of kidney fibrosis.
Sun Q, Baues M, Klinkhammer BM, Ehling J, Djudjaj S, Drude NI, Daniel C, Amann K, Kramann R, Kim H, Saez-Rodriguez J, Weiskirchen R, Onthank DC, Botnar RM, Kiessling F, Floege J, Lammers T, Boor P. Science translational medicine Volume 11 (2019) DOI: 10.1126/scitranslmed.aat4865
*
Publisher Correction: Federated discovery and sharing of genomic data using Beacons.
Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, Törnroos J, Linden M, Spalding JD, Ur-Rehman S, Page A, Flicek P, Sherry S, Haussler D, Varma S, Saunders G, Scollen S. Nature biotechnology Volume 37 (2019) p.480 DOI: 10.1038/s41587-019-0094-2
*
Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.
Ratmann O, Grabowski MK, Hall M, Golubchik T, Wymant C, Abeler-Dörner L, Bonsall D, Hoppe A, Brown AL, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C, PANGEA Consortium and Rakai Health Sciences Program. Nature communications Volume 10 (2019) p.1411 DOI: 10.1038/s41467-019-09139-4
*
Structural and Functional Characterization of the Type Three Secretion System (T3SS) Needle of Pseudomonas aeruginosa.
Lombardi C, Tolchard J, Bouillot S, Signor L, Gebus C, Liebl D, Fenel D, Teulon JM, Brock J, Habenstein B, Pellequer JL, Faudry E, Loquet A, Attrée I, Dessen A, Job V. Frontiers in microbiology Volume 10 (2019) p.573 DOI: 10.3389/fmicb.2019.00573
*
Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets.
Wiwie C, Kuznetsova I, Mostafa A, Rauch A, Haakonsson A, Barrio-Hernandez I, Blagoev B, Mandrup S, Schmidt HHHW, Pleschka S, Röttger R, Baumbach J. Systems medicine (New Rochelle, N.Y.) Volume 2 (2019) p.1-9 DOI: 10.1089/sysm.2018.0013
*
An analysis and metric of reusable data licensing practices for biomedical resources.
Carbon S, Champieux R, McMurry JA, Winfree L, Wyatt LR, Haendel MA. PloS one Volume 14 (2019) p.e0213090 DOI: 10.1371/journal.pone.0213090
*
CaverDock: A Novel Method for the Fast Analysis of Ligand Transport.
Filipovic J, Vavra O, Plhak J, Bednar D, Marques SM, Brezovsky J, Matyska L, Damborsky J. IEEE/ACM transactions on computational biology and bioinformatics (2019) DOI: 10.1109/tcbb.2019.2907492
*
Heparan sulfates are critical regulators of the inhibitory megakaryocyte-platelet receptor G6b-B
Vögtle T, Sharma S, Mori J, Nagy Z, Semeniak D, Geer MJ, Smith CW, Lane J, Pollack S, Lassila R, Jouppila A, Barr AJ, Ogg DJ, Howard TD, McMiken HJ, Warwicker J, Geh C, Rowlinson R, Mark Abbott W, Schulze H, Wright GJ, Mazharian A, Fütterer K, Rajesh S, Douglas MR, Senis YA. Preprint DOI: 10.1101/584698
*
Fine-tuning of the flowering time control in winter barley: the importance of HvOS2 and HvVRN2 in non-inductive conditions.
Monteagudo A, Igartua E, Contreras-Moreira B, Gracia MP, Ramos J, Karsai I, Casas AM. BMC plant biology Volume 19 (2019) p.113 DOI: 10.1186/s12870-019-1727-9
*
Stratification and prediction of drug synergy based on target functional similarity
Yang M, Menden MP, Jaaks P, Dry J, Garnett M, Saez-Rodriguez J. Preprint DOI: 10.1101/586123
*
EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data.
Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T, participants in the 1st Human Cell Atlas Jamboree, Marioni JC. Genome biology Volume 20 (2019) p.63 DOI: 10.1186/s13059-019-1662-y
*
Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins.
Griss J, Stanek F, Hudecz O, Dürnberger G, Perez-Riverol Y, Vizcaíno JA, Mechtler K. Journal of proteome research Volume 18 (2019) p.1477-1485 DOI: 10.1021/acs.jproteome.8b00377
*
SUMOylation promotes survival and integration of neural stem cell grafts in ischemic stroke.
Bernstock JD, Peruzzotti-Jametti L, Leonardi T, Vicario N, Ye D, Lee YJ, Maric D, Johnson KR, Mou Y, Van Den Bosch A, Winterbone M, Friedman GK, Franklin RJM, Hallenbeck JM, Pluchino S. EBioMedicine Volume 42 (2019) p.214-224 DOI: 10.1016/j.ebiom.2019.03.035
*
Recommendations for the packaging and containerizing of bioinformatics software
Gruening B, Sallou O, Moreno P, da Veiga Leprevost F, Ménager H, Søndergaard D, Röst H, Sachsenberg T, O'Connor B, Madeira F, Dominguez Del Angel V, Crusoe MR, Varma S, Blankenberg D, Jimenez RC, Perez-Riverol Y, BioContainers Community. Preprint DOI: 10.12688/f1000research.15140.2
Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis.
Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC, Odom DT. Nature communications Volume 10 (2019) p.1251 DOI: 10.1038/s41467-019-09182-1
*
Linked-read analysis identifies mutations in single-cell DNA-sequencing data.
Bohrson CL, Barton AR, Lodato MA, Rodin RE, Luquette LJ, Viswanadham VV, Gulhan DC, Cortés-Ciriano I, Sherman MA, Kwon M, Coulter ME, Galor A, Walsh CA, Park PJ. Nature genetics Volume 51 (2019) p.749-754 DOI: 10.1038/s41588-019-0366-2
*
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage.
Hendriksen RS, Munk P, Njage P, van Bunnik B, McNally L, Lukjancenko O, Röder T, Nieuwenhuijse D, Pedersen SK, Kjeldgaard J, Kaas RS, Clausen PTLC, Vogt JK, Leekitcharoenphon P, van de Schans MGM, Zuidema T, de Roda Husman AM, Rasmussen S, Petersen B, Global Sewage Surveillance project consortium, Amid C, Cochrane G, Sicheritz-Ponten T, Schmitt H, Alvarez JRM, Aidara-Kane A, Pamp SJ, Lund O, Hald T, Woolhouse M, Koopmans MP, Vigre H, Petersen TN, Aarestrup FM. Nature communications Volume 10 (2019) p.1124 DOI: 10.1038/s41467-019-08853-3
*
Whole genome sequencing reveals that genetic conditions are frequent in intensively ill children.
French CE, Delon I, Dolling H, Sanchis-Juan A, Shamardina O, Mégy K, Abbs S, Austin T, Bowdin S, Branco RG, Firth H, NIHR BioResource—Rare Disease, Next Generation Children Project, Rowitch DH, Raymond FL. Intensive care medicine Volume 45 (2019) p.627-636 DOI: 10.1007/s00134-019-05552-x
*
The midbody interactome reveals new unexpected roles for PP1 phosphatases in cytokinesis
Capalbo L, Bassi ZI, Geymonat M, Todesca S, Copoiu L, Enright A, Callaini G, Riparbelli MG, Yu L, Choudhary J, Ferrero E, Wheatley S, Douglas ME, Mishima M, D’Avino PP. Preprint DOI: 10.1101/569459
*
Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts.
Moore BA, Leonard BC, Sebbag L, Edwards SG, Cooper A, Imai DM, Straiton E, Santos L, Reilly C, Griffey SM, Bower L, Clary D, Mason J, Roux MJ, Meziane H, Herault Y, International Mouse Phenotyping Consortium, McKerlie C, Flenniken AM, Nutter LMJ, Berberovic Z, Owen C, Newbigging S, Adissu H, Eskandarian M, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gallegos JJ, Seavitt JR, Heaney JD, Beaudet AL, Dickinson ME, Justice MJ, Philip V, Kumar V, Svenson KL, Braun RE, Wells S, Cater H, Stewart M, Clementson-Mobbs S, Joynson R, Gao X, Suzuki T, Wakana S, Smedley D, Seong JK, Tocchini-Valentini G, Moore M, Fletcher C, Karp N, Ramirez-Solis R, White JK, de Angelis MH, Wurst W, Thomasy SM, Flicek P, Parkinson H, Brown SDM, Meehan TF, Nishina PM, Murray SA, Krebs MP, Mallon AM, Kent Lloyd KC, Murphy CJ, Moshiri A. Communications biology Volume 2 (2019) p.97 DOI: 10.1038/s42003-019-0349-y
*
Author Correction: Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates.
Webster P, Dawes JC, Dewchand H, Takacs K, Iadarola B, Bolt BJ, Caceres JJ, Kaczor J, Dharmalingam G, Dore M, Game L, Adejumo T, Elliott J, Naresh K, Karimi M, Rekopoulou K, Tan G, Paccanaro A, Uren AG. Nature communications Volume 10 (2019) p.1167 DOI: 10.1038/s41467-019-09109-w
*
Extracytoplasmic Function σ Factors Can Be Implemented as Robust Heterologous Genetic Switches in Bacillus subtilis.
Pinto D, Dürr F, Froriep F, Araújo D, Liu Q, Mascher T. iScience Volume 13 (2019) p.380-390 DOI: 10.1016/j.isci.2019.03.001
*
Genomic investigation reveals contaminated detergent as the source of an ESBL-producing Klebsiella michiganensis outbreak in a neonatal unit
Chapman P, Forde BM, Roberts LW, Bergh H, Vesey D, Jennison AV, Moss S, Paterson DL, Beatson SA, Harris PNA. Preprint DOI: 10.1101/568154
Big science and big data in nephrology.
Saez-Rodriguez J, Rinschen MM, Floege J, Kramann R. Kidney international Volume 95 (2019) p.1326-1337 DOI: 10.1016/j.kint.2018.11.048
*
Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.
IMEx Consortium contributing authors, Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P. Nature communications Volume 10 (2019) p.1098 DOI: 10.1038/s41467-019-08814-w
Microbial abundance, activity and population genomic profiling with mOTUs2.
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G, Sunagawa S. Nature communications Volume 10 (2019) p.1014 DOI: 10.1038/s41467-019-08844-4
*
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites.
Song J, Wang Y, Li F, Akutsu T, Rawlings ND, Webb GI, Chou KC. Briefings in bioinformatics Volume 20 (2019) p.638-658 DOI: 10.1093/bib/bby028
*
Epigenome-wide Association Study of Attention-Deficit/Hyperactivity Disorder Symptoms in Adults.
van Dongen J, Zilhão NR, Sugden K, BIOS Consortium, Hannon EJ, Mill J, Caspi A, Agnew-Blais J, Arseneault L, Corcoran DL, Moffitt TE, Poulton R, Franke B, Boomsma DI. Biological psychiatry Volume 86 (2019) p.599-607 DOI: 10.1016/j.biopsych.2019.02.016
*
Recipients Receiving Better HLA-Matched Hematopoietic Cell Transplantation Grafts, Uncovered by a Novel HLA Typing Method, Have Superior Survival: A Retrospective Study.
Mayor NP, Hayhurst JD, Turner TR, Szydlo RM, Shaw BE, Bultitude WP, Sayno JR, Tavarozzi F, Latham K, Anthias C, Robinson J, Braund H, Danby R, Perry J, Wilson MC, Bloor AJ, McQuaker IG, MacKinnon S, Marks DI, Pagliuca A, Potter MN, Potter VT, Russell NH, Thomson KJ, Madrigal JA, Marsh SGE. Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation Volume 25 (2019) p.443-450 DOI: 10.1016/j.bbmt.2018.12.768
*
Federated discovery and sharing of genomic data using Beacons.
Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, Törnroos J, Linden M, Spalding JD, Ur-Rehman S, Page A, Flicek P, Sherry S, Haussler D, Varma S, Saunders G, Scollen S. Nature biotechnology Volume 37 (2019) p.220-224 DOI: 10.1038/s41587-019-0046-x
*
A new pan-European Train-the-Trainer programme for bioinformatics: pilot results on feasibility, utility and sustainability of learning.
Via A, Attwood TK, Fernandes PL, Morgan SL, Schneider MV, Palagi PM, Rustici G, Tractenberg RE. Briefings in bioinformatics Volume 20 (2019) p.405-415 DOI: 10.1093/bib/bbx112
*
In-depth genetic analysis of 6p21.3 reveals insights into associations between HLA types and complex traits and disease
D’Antonio M, Reyna J, D’Antonio-Chronowska A, Bonder M, Jakubosky D, Matsui H, Smith EN, Stegle O, Nariai N, Frazer KA. Preprint DOI: 10.1101/564161
*
Advances and Challenges in Computational Target Prediction.
Sydow D, Burggraaff L, Szengel A, van Vlijmen HWT, IJzerman AP, van Westen GJP, Volkamer A. Journal of chemical information and modeling Volume 59 (2019) p.1728-1742 DOI: 10.1021/acs.jcim.8b00832
*
Human loss-of-function variants suggest that partial LRRK2 inhibition is a safe therapeutic strategy for Parkinson’s disease
Whiffin N, Armean IM, Kleinman A, Marshall JL, Minikel EV, Karczewski KJ, Cummings BB, Francioli L, Laricchia K, Wang Q, Guan A, Alipanahi B, Morrison P, Baptista MA, Merchant KM, Ware JS, Havulinna AS, Iliadou B, Lee J, Nadkarni GN, Whiteman C, Daly M, Esko T, Hultman C, Loos RJ, Milani L, Palotie A, Pato C, Pato M, Saleheen D, Sullivan PF, Alföldi J, Cannon P, MacArthur DG, Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, the 23andMe Research Team. Preprint DOI: 10.1101/561472
*
Intra-mitochondrial proteostasis is directly coupled to alpha-synuclein and Amyloid β 1-42 pathology
Lautenschläger J, Wagner-Valladolid S, Stephens AD, Fernández-Villegas A, Hockings C, Mishra A, Manton JD, Fantham MJ, Lu M, Rees EJ, Kaminski CF, Schierle GSK. Preprint DOI: 10.1101/561134
*
Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR/Cas9 screening
Picco G, Chen ED, Alonso LG, Behan FM, Gonçalves E, Bignell G, Matchan A, Fu B, Banerjee R, Anderson E, Butler A, Benes CH, McDermott U, Dow D, Iorio F, Stronach E, Yang F, Yusa K, Saez-Rodriguez J, Garnett MJ. Preprint DOI: 10.1101/559690
*
Integrative Omic Profiling Reveals Unique Hypoxia Induced Signatures in Gastric Cancer Associated Myofibroblasts.
Najgebauer H, Jarnuczak AF, Varro A, Sanderson CM. Cancers Volume 11 (2019) DOI: 10.3390/cancers11020263
*
Genomic analysis reveals a functional role for myocardial trabeculae in adults
Meyer HV, Dawes TJ, Serrani M, Bai W, Tokarczuk P, Cai J, de Marvao A, Rueckert D, Matthews PM, Costantino ML, Birney E, Cook SA, O’Regan DP. Preprint DOI: 10.1101/553651
*
Evaluation of Cross-Validation Strategies in Sequence-Based Binding Prediction Using Deep Learning.
Lopez-Del Rio A, Nonell-Canals A, Vidal D, Perera-Lluna A. Journal of chemical information and modeling Volume 59 (2019) p.1645-1657 DOI: 10.1021/acs.jcim.8b00663
*
Single-cell immune profiling reveals new insights into colorectal cancer.
Lönnberg T, Stubbington MJ. Immunology and cell biology Volume 97 (2019) p.241-243 DOI: 10.1111/imcb.12240
*
The COMPARE Data Hubs
Amid C, Pakseresht N, Silvester N, Jayathilaka S, Lund O, Dynovski LD, Pataki BÁ, Visontai D, Cotten M, Xavier BB, Alako B, Belka A, Cisneros JJL, Haringhuizen GB, Harrison PW, Höper D, Holt S, Hundahl C, Hussein A, Kaas RS, Malhotra-Kumar S, Leinonen R, Nieuwenhuijse DF, Rahman N, Ribeiro CdS, Skiby JE, Stéger J, Szalai-Gindl JM, Thomsen MCF, Csabai I, Koopmans M, Aarestrup F, Cochrane G. Preprint DOI: 10.1101/555938
*
A single-cell molecular map of mouse gastrulation and early organogenesis.
Pijuan-Sala B, Griffiths JA, Guibentif C, Hiscock TW, Jawaid W, Calero-Nieto FJ, Mulas C, Ibarra-Soria X, Tyser RCV, Ho DLL, Reik W, Srinivas S, Simons BD, Nichols J, Marioni JC, Göttgens B. Nature Volume 566 (2019) p.490-495 DOI: 10.1038/s41586-019-0933-9
*
Update on the human and mouse lipocalin (LCN) gene family, including evidence the mouse Mup cluster is result of an "evolutionary bloom".
Charkoftaki G, Wang Y, McAndrews M, Bruford EA, Thompson DC, Vasiliou V, Nebert DW. Human genomics Volume 13 (2019) p.11 DOI: 10.1186/s40246-019-0191-9
*
Multi-omic measurements of heterogeneity in HeLa cells across laboratories.
Liu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Frank M, Germain PL, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, Bena FS, Zhou H, Dehio C, Testa G, Saez-Rodriguez J, Antonarakis SE, Hardt WD, Aebersold R. Nature biotechnology Volume 37 (2019) p.314-322 DOI: 10.1038/s41587-019-0037-y
*
Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling.
Burggraaff L, Oranje P, Gouka R, van der Pijl P, Geldof M, van Vlijmen HWT, IJzerman AP, van Westen GJP. Journal of Cheminformatics Volume 11 (2019) p.15 DOI: 10.1186/s13321-019-0337-8
*
Bioinformatics calls the school: Use of smartphones to introduce Python for bioinformatics in high schools.
Velez Rueda AJ, Benítez GI, Marchetti J, Hasenahuer MA, Fornasari MS, Palopoli N, Parisi G. PLoS computational biology Volume 15 (2019) p.e1006473 DOI: 10.1371/journal.pcbi.1006473
*
Comprehensive and Empirical Evaluation of Machine Learning Algorithms for Small Molecule LC Retention Time Prediction.
Bouwmeester R, Martens L, Degroeve S. Analytical chemistry Volume 91 (2019) p.3694-3703 DOI: 10.1021/acs.analchem.8b05820
*
mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics.
Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O, Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y, Vizcaíno JA, Salek RM, Neumann S, Jones AR. Analytical chemistry Volume 91 (2019) p.3302-3310 DOI: 10.1021/acs.analchem.8b04310
*
Efficient exact associative structure for sequencing data
Marchet C, Kerbiriou M, Limasset A. Preprint DOI: 10.1101/546309
*
CONSENT: Scalable long read self-correction and assembly polishing with multiple sequence alignment
Morisse P, Marchet C, Limasset A, Lecroq T, Lefebvre A. Preprint DOI: 10.1101/546630
Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity.
Linker SM, Urban L, Clark SJ, Chhatriwala M, Amatya S, McCarthy DJ, Ebersberger I, Vallier L, Reik W, Stegle O, Bonder MJ. Genome biology Volume 20 (2019) p.30 DOI: 10.1186/s13059-019-1644-0
A new genomic blueprint of the human gut microbiota.
Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB, Tarkowska A, Lawley TD, Finn RD. Nature Volume 568 (2019) p.499-504 DOI: 10.1038/s41586-019-0965-1
*
Screening for genes that accelerate the epigenetic ageing clock in humans reveals a role for the H3K36 methyltransferase NSD1
Martin-Herranz DE, Aref-Eshghi E, Bonder MJ, Stubbs TM, Stegle O, Sadikovic B, Reik W, Thornton JM. Preprint DOI: 10.1101/545830
*
Updated MS2PIP web server delivers fast and accurate MS2 peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques
Gabriels R, Martens L, Degroeve S. Preprint DOI: 10.1101/544965
BioJava 5: A community driven open-source bioinformatics library.
Lafita A, Bliven S, Prlić A, Guzenko D, Rose PW, Bradley A, Pavan P, Myers-Turnbull D, Valasatava Y, Heuer M, Larson M, Burley SK, Duarte JM. PLoS computational biology Volume 15 (2019) p.e1006791 DOI: 10.1371/journal.pcbi.1006791
*
Comparison of Human and Murine Enteroendocrine Cells by Transcriptomic and Peptidomic Profiling.
Roberts GP, Larraufie P, Richards P, Kay RG, Galvin SG, Miedzybrodzka EL, Leiter A, Li HJ, Glass LL, Ma MKL, Lam B, Yeo GSH, Scharfmann R, Chiarugi D, Hardwick RH, Reimann F, Gribble FM. Diabetes Volume 68 (2019) p.1062-1072 DOI: 10.2337/db18-0883
*
Characterising the loss-of-function impact of 5’ untranslated region variants in whole genome sequence data from 15,708 individuals
Whiffin N, Karczewski KJ, Zhang X, Chothani S, Smith MJ, Evans DG, Roberts AM, Quaife NM, Schafer S, Rackham O, Alföldi J, O’Donnell-Luria AH, Francioli LC, Alföldi J, Armean IM, Banks E, Bergelson L, Cibulskis K, Collins RL, Connolly KM, Covarrubias M, Cummings B, Daly MJ, Donnelly S, Farjoun Y, Ferriera S, Francioli L, Gabriel S, Gauthier LD, Gentry J, Gupta N, Jeandet T, Kaplan D, Karczewski KJ, Laricchia KM, Llanwarne C, Minikel EV, Munshi R, Neale BM, Novod S, O’Donnell-Luria AH, Petrillo N, Poterba T, Roazen D, Ruano-Rubio V, Saltzman A, Samocha KE, Schleicher M, Seed C, Solomonson M, Soto J, Tiao G, Tibbetts K, Tolonen C, Vittal C, Wade G, Wang A, Wang Q, Ware JS, Watts NA, Weisburd B, Whiffin N, Salinas CAA, Ahmad T, Albert CM, Ardissino D, Atzmon G, Barnard J, Beaugerie L, Benjamin EJ, Boehnke M, Bonnycastle LL, Bottinger EP, Bowden DW, Bown MJ, Chambers JC, Chan JC, Chasman D, Cho J, Chung MK, Cohen B, Correa A, Dabelea D, Daly MJ, Darbar D, Duggirala R, Dupuis J, Ellinor PT, Elosua R, Erdmann J, Esko T, Färkkilä M, Florez J, Franke A, Getz G, Glaser B, Glatt SJ, Goldstein D, Gonzalez C, Groop L, Haiman C, Hanis C, Harms M, Hiltunen M, Holi MM, Hultman CM, Kallela M, Kaprio J, Kathiresan S, Kim B, Kim YJ, Kirov G, Kooner J, Koskinen S, Krumholz HM, Kugathasan S, Kwak SH, Laakso M, Lehtimäki T, Loos RJ, Lubitz SA, Ma RC, MacArthur DG, Marrugat J, Mattila KM, McCarroll S, McCarthy MI, McGovern D, McPherson R, Meigs JB, Melander O, Metspalu A, Neale BM, Nilsson PM, O’Donovan MC, Ongur D, Orozco L, Owen MJ, Palmer CN, Palotie A, Park KS, Pato C, Pulver AE, Rahman N, Remes AM, Rioux JD, Ripatti S, Roden DM, Saleheen D, Salomaa V, Samani NJ, Scharf J, Schunkert H, Shoemaker MB, Sklar P, Soininen H, Soko H, Spector T, Sullivan PF, Suvisaari J, Tai ES, Teo YY, Tiinamaija T, Tsuang M, Turner D, Tusie-Luna T, Vartiainen E, Ware JS, Watkins H, Weersma RK, Wessman M, Wilson JG, Xavier RJ, Cook SA, Barton PJR, MacArthur DG, Ware JS, Genome Aggregation Database (gnomAD) Production Team, Genome Aggregation Database (gnomAD) Consortium. Preprint DOI: 10.1101/543504
*
Sequence analysis allows functional annotation of tyrosine recombinases in prokaryotic genomes
Smyshlyaev G, Barabas O, Bateman A. Preprint DOI: 10.1101/542381
*
Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects.
Gonçalves E, Behan FM, Louzada S, Arnol D, Stronach EA, Yang F, Yusa K, Stegle O, Iorio F, Garnett MJ. Genome biology Volume 20 (2019) p.27 DOI: 10.1186/s13059-019-1637-z
*
Prediction of combination therapies based on topological modeling of the immune signaling network in Multiple Sclerosis
Bernardo-Faura M, Rinas M, Wirbel J, Pertsovskaya I, Pliaka V, Messinis DE, Vila G, Sakellaropoulos T, Faigle W, Stridh P, Behrens JR, Olsson T, Martin R, Paul F, Alexopoulos LG, Villoslada P, Saez-Rodriguez J. Preprint DOI: 10.1101/541458
*
The functional landscape of the human phosphoproteome
Ochoa D, Jarnuczak AF, Gehre M, Soucheray M, Kleefeldt AA, Viéitez C, Hill A, Garcia-Alonso L, Swaney DL, Vizcaíno JA, Noh K, Beltrao P. Preprint DOI: 10.1101/541656
*
From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL
Liu A, Trairatphisan P, Gjerga E, Didangelos A, Barratt J, Saez-Rodriguez J. Preprint DOI: 10.1101/541888
*
A human gut bacterial genome and culture collection for improved metagenomic analyses.
Forster SC, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, Dunn M, Mkandawire TT, Zhu A, Shao Y, Pike LJ, Louie T, Browne HP, Mitchell AL, Neville BA, Finn RD, Lawley TD. Nature biotechnology Volume 37 (2019) p.186-192 DOI: 10.1038/s41587-018-0009-7
*
Ultrafast search of all deposited bacterial and viral genomic data.
Bradley P, den Bakker HC, Rocha EPC, McVean G, Iqbal Z. Nature biotechnology Volume 37 (2019) p.152-159 DOI: 10.1038/s41587-018-0010-1
*
Correction to: The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation
Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Beaudet AL, Brown SDM, Dickinson ME, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Heaney JD, Hrabě de Angelis M, Kim JK, Lloyd KCK, McKerlie C, Morgan H, Murray SA, Nutter LMJ, Reilly PT, Seavitt JR, Seong JK, Simon M, Wardle-Jones H, Mallon AM, Smedley D, Parkinson HE, the IMPC consortium. Conservation genetics (Print) Volume 20 (2019) p.135-136 DOI: 10.1007/s10592-019-01144-w
*
Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences.
Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GKJ, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, Van't Veer L, Tutt A, Knappskog S, Tan BKT, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR. Nature Volume 566 (2019) p.E1 DOI: 10.1038/s41586-019-0883-2
*
LipidFinder on LIPID MAPS: peak filtering, MS searching and statistical analysis for lipidomics.
Fahy E, Alvarez-Jarreta J, Brasher CJ, Nguyen A, Hawksworth JI, Rodrigues P, Meckelmann S, Allen SM, O'Donnell VB. Bioinformatics (Oxford, England) Volume 35 (2019) p.685-687 DOI: 10.1093/bioinformatics/bty679
*
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations.
Tang H, Finn RD, Thomas PD. Bioinformatics (Oxford, England) Volume 35 (2019) p.518-520 DOI: 10.1093/bioinformatics/bty625
Large-scale datasets uncovering cell signalling networks in cancer: context matters.
Sharma S, Petsalaki E. Current opinion in genetics & development Volume 54 (2019) p.118-124 DOI: 10.1016/j.gde.2019.05.001
*
SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation.
Jankauskaite J, Jiménez-García B, Dapkunas J, Fernández-Recio J, Moal IH. Bioinformatics (Oxford, England) Volume 35 (2019) p.462-469 DOI: 10.1093/bioinformatics/bty635
*
PhenoMeNal: processing and analysis of metabolomics data in the cloud.
Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Günther UL, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JTM, Peluso A, Piras ME, Pireddu L, Reed MAC, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C. GigaScience Volume 8 (2019) DOI: 10.1093/gigascience/giy149
Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors.
Vigilante A, Laddach A, Moens N, Meleckyte R, Leha A, Ghahramani A, Culley OJ, Kathuria A, Hurling C, Vickers A, Wiseman E, Tewary M, Zandstra PW, HipSci Consortium, Durbin R, Fraternali F, Stegle O, Birney E, Luscombe NM, Danovi D, Watt FM. Cell reports Volume 26 (2019) p.2078-2087.e3 DOI: 10.1016/j.celrep.2019.01.094
*
Endorsing and extending the repertory of nutraceutical and antioxidant sources in mangoes during postharvest shelf life.
Monribot-Villanueva JL, Elizalde-Contreras JM, Aluja M, Segura-Cabrera A, Birke A, Guerrero-Analco JA, Ruiz-May E. Food chemistry Volume 285 (2019) p.119-129 DOI: 10.1016/j.foodchem.2019.01.136
*
Minocycline and the risk of acute psychiatric events in adolescence: A self-controlled case series.
Brauer R, Herrero-Zazo M, Barlow DJ, Gaughran F, Taylor D, Howard LM. Journal of psychopharmacology (Oxford, England) Volume 33 (2019) p.466-471 DOI: 10.1177/0269881118821852
*
The comparative genomics and complex population history of Papio baboons.
Rogers J, Raveendran M, Harris RA, Mailund T, Leppälä K, Athanasiadis G, Schierup MH, Cheng J, Munch K, Walker JA, Konkel MK, Jordan V, Steely CJ, Beckstrom TO, Bergey C, Burrell A, Schrempf D, Noll A, Kothe M, Kopp GH, Liu Y, Murali S, Billis K, Martin FJ, Muffato M, Cox L, Else J, Disotell T, Muzny DM, Phillips-Conroy J, Aken B, Eichler EE, Marques-Bonet T, Kosiol C, Batzer MA, Hahn MW, Tung J, Zinner D, Roos C, Jolly CJ, Gibbs RA, Worley KC, Baboon Genome Analysis Consortium. Science advances Volume 5 (2019) p.eaau6947 DOI: 10.1126/sciadv.aau6947
*
An integrated transcriptional analysis of the developing human retina.
Mellough CB, Bauer R, Collin J, Dorgau B, Zerti D, Dolan DWP, Jones CM, Izuogu OG, Yu M, Hallam D, Steyn JS, White K, Steel DH, Santibanez-Koref M, Elliott DJ, Jackson MS, Lindsay S, Grellscheid S, Lako M. Development (Cambridge, England) Volume 146 (2019) DOI: 10.1242/dev.169474
*
Transfer of regulatory knowledge from human to mouse for functional genomic analysis
Holland CH, Szalai B, Saez-Rodriguez J. Preprint DOI: 10.1101/532739
*
Accelerating surveillance and research of antimicrobial resistance – an online repository for sharing of antimicrobial susceptibility data associated with whole genome sequences
Matamoros S, Hendriksen RS, Pataki B, Pakseresht N, Rossello M, Silvester N, Amid C, Cochrane G, Csabai I, Lund O, Schultsz C, COMPARE ML- AMR group. Preprint DOI: 10.1101/532267
*
GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals.
Iotchkova V, Ritchie GRS, Geihs M, Morganella S, Min JL, Walter K, Timpson NJ, UK10K Consortium, Dunham I, Birney E, Soranzo N. Nature genetics Volume 51 (2019) p.343-353 DOI: 10.1038/s41588-018-0322-6
*
The mutational constraint spectrum quantified from variation in 141,456 humans
Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP, Gauthier LD, Brand H, Solomonson M, Watts NA, Rhodes D, Singer-Berk M, England EM, Seaby EG, Kosmicki JA, Walters RK, Tashman K, Farjoun Y, Banks E, Poterba T, Wang A, Seed C, Whiffin N, Chong JX, Samocha KE, Pierce-Hoffman E, Zappala Z, O’Donnell-Luria AH, Minikel EV, Weisburd B, Lek M, Ware JS, Vittal C, Armean IM, Bergelson L, Cibulskis K, Connolly KM, Covarrubias M, Donnelly S, Ferriera S, Gabriel S, Gentry J, Gupta N, Jeandet T, Kaplan D, Llanwarne C, Munshi R, Novod S, Petrillo N, Roazen D, Ruano-Rubio V, Saltzman A, Schleicher M, Soto J, Tibbetts K, Tolonen C, Wade G, Talkowski ME, Neale BM, Daly MJ, MacArthur DG, Genome Aggregation Database (gnomAD) Consortium. Preprint DOI: 10.1101/531210
*
The Glossina Genome Cluster: Comparative Genomic Analysis of the Vectors of African Trypanosomes
Attardo GM, Abd-Alla AM, Acosta-Serrano A, Allen JE, Bateta R, Benoit J, Bourtzis K, Caers J, Caljon G, Christensen MB, Farrow DW, Friedrich M, Hua-Van A, Jennings EC, Larkin DM, Lawson D, Lehane MJ, Lenis VP, Lowy-Gallego E, Macharia RW, Malacrida AR, Marco HG, Masiga D, Maslen GL, Matetovici I, Meisel RP, Meki I, Michalkova V, Miller WJ, Minx P, Mireji PO, Ometto L, Parker AG, Rio R, Rose C, Rosendale AJ, Rota Stabelli O, Savini G, Schoofs L, Scolari F, Swain MT, Takáč P, Tomlinson C, Tsiamis G, Van Den Abbeele J, Vigneron A, Wang J, Warren WC, Waterhouse RM, Weirauch MT, Weiss BL, Wilson RK, Zhao X, Aksoy S. Preprint DOI: 10.1101/531749
*
Modelling structural constraints on protein evolution via side-chain conformational states
Perron U, Kozlov AM, Stamatakis A, Goldman N, Moal IH. Preprint DOI: 10.1101/530634
*
Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
De Maio N, Shaw LP, Hubbard A, George S, Sanderson N, Swann J, Wick R, AbuOun M, Stubberfield E, Hoosdally SJ, Crook DW, Peto TEA, Sheppard AE, Bailey MJ, Read DS, Anjum MF, Walker AS, Stoesser N, on behalf of the REHAB consortium. Preprint DOI: 10.1101/530824
*
Implementation and relevance of FAIR data principles in biopharmaceutical R&D.
Wise J, de Barron AG, Splendiani A, Balali-Mood B, Vasant D, Little E, Mellino G, Harrow I, Smith I, Taubert J, van Bochove K, Romacker M, Walgemoed P, Jimenez RC, Winnenburg R, Plasterer T, Gupta V, Hedley V. Drug discovery today Volume 24 (2019) p.933-938 DOI: 10.1016/j.drudis.2019.01.008
*
Protein Structure Databases
Armstrong DA, Berrisford JM, Conroy MJ, Clark AR, Gupta D, Mukhopadhyay A. Encyclopedia of Bioinformatics and Computational Biology Elsevier, Waltham, MA (2 edition) DOI: 10.1016/b978-0-12-809633-8.20280-x
*
The variability of expression of many genes and most functional pathways is observed to increase with age in brain transcriptome data
Kedlian VR, Donertas HM, Thornton JM. Preprint DOI: 10.1101/526491
*
Low-frequency variation in TP53 has large effects on head circumference and intracranial volume.
Haworth S, Shapland CY, Hayward C, Prins BP, Felix JF, Medina-Gomez C, Rivadeneira F, Wang C, Ahluwalia TS, Vrijheid M, Guxens M, Sunyer J, Tachmazidou I, Walter K, Iotchkova V, Jackson A, Cleal L, Huffmann J, Min JL, Sass L, Timmers PRHJ, UK10K consortium, Davey Smith G, Fisher SE, Wilson JF, Cole TJ, Fernandez-Orth D, Bønnelykke K, Bisgaard H, Pennell CE, Jaddoe VWV, Dedoussis G, Timpson N, Zeggini E, Vitart V, St Pourcain B. Nature communications Volume 10 (2019) p.357 DOI: 10.1038/s41467-018-07863-x
*
Activity-Based Protein Profiling Identifies α-Ketoamides as Inhibitors for Phospholipase A2 Group XVI.
Zhou J, Mock ED, Martella A, Kantae V, Di X, Burggraaff L, Baggelaar MP, Al-Ayed K, Bakker A, Florea BI, Grimm SH, den Dulk H, Li CT, Mulder L, Overkleeft HS, Hankemeier T, van Westen GJP, van der Stelt M. ACS chemical biology Volume 14 (2019) p.164-169 DOI: 10.1021/acschembio.8b00969
*
Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords
GUR T. Preprint DOI: 10.1101/520841
*
Fine-mapping of 150 breast cancer risk regions identifies 178 high confidence target genes
Fachal L, Aschard H, Beesley J, Barnes D, Allen J, Kar S, Pooley K, Dennis J, Michailidou K, Turman C, Soucy P, Lemacon A, Lush M, Tyrer J, Ghoussaini M, Moradi Marjaneh M, Jiang X, Agata S, Aittomaki K, Alonso MR, Andrulis I, Anton-Culver H, Antonenkova N, Arason A, Arndt V, Aronson K, Arun B, Auber B, Auer P, Azzollini J, Balmana J, Barkardottir R, Barrowdale D, Beeghly-Fadiel A, Benitez J, Bermisheva M, Bialkowska K, Blanco A, Blomqvist C, Blot W, Bogdanova N, Bojesen S, Bolla M, Bonanni B, Borg A, Bosse K, Brauch H, Brenner H, Briceno I, Brock I, Brooks-Wilson A, Bruning T, Burwinkel B, Buys S, Cai Q, Caldes T, Caligo M, Camp N, Campbell I, Canzian F, Carroll J, Carter B, Castelao J, Chiquette J, Christiansen H, Chung W, Claes K, Clarke C, Collee JM, Cornelissen S, Couch F, Cox A, Cross S, Cybulski C, Czene K, Daly M, de la Hoya M, Devilee P, Diez O, Ding YC, Dite G, Domchek S, Dork T, dos-Santos-Silva I, Droit A, Dubois S, Dumont M, Duran M, Durcan L, Dwek M, Eccles D, Engel C, Eriksson M, Evans DG, Fasching P, Fletcher O, Floris G, Flyger H, Foretova L, Foulkes W, Friedman E, Fritschi L, Frost D, Gabrielson M, Gago-Dominguez M, Gambino G, Ganz P, Gapstur S, Garber J, Garcia-Saenz J, Gaudet M, Georgoulias V, Giles G, Glendon G, Godwin A, Goldberg M, Goldgar D, Gonzalez-Neira A, Greene M, Grip M, Gronwald J, Grundy A, Guenel P, Hahnen E, Haiman C, Hakansson N, Hall P, Hamann U, Harrington P, Hartikainen J, Hartman M, He W, Healey C, Heemskerk-Gerritsen B, Heyworth J, Hillemanns P, Hogervorst F, Hollestelle A, Hooning M, Hopper J, Howell A, Huang G, Hulick P, Imyanitov E, Isaacs C, Iwasaki M, Jager A, Jakimovska M, Jakubowska A, James P, Janavicius R, Jankowitz R, John E, Johnson N, Jones M, Jukkola-Vuorinen A, Jung A, Kaaks R, Kang D, Karlan B, Keeman R, Kerin M, Khusnutdinova E, Kiiski J, Kirk J, Kitahara C, Ko Y, Konstantopoulou I, Kosma V, Koutros S, Kubelka-Sabit K, Kwong A, Kyriacou K, Laitman Y, Lambrechts D, Lee E, Leslie G, Lester J, Lesueur F, Lindblom A, Lo W, Long J, Lophatananon A, Loud J, Lubinski J, MacInnis R, Maishman T, Makalic E, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Matsuo K, Maurer T, Mavroudis D, Mayes R, McGuffog L, McLean C, Mebirouk N, Meindl A, Middha P, Miller N, Miller A, Montagna M, Moreno F, Mulligan AM, Munoz-Garzon V, Muranen T, Narod S, Nassir R, Nathanson K, Neuhausen S, Nevanlinna H, Neven P, Nielsen F, Nikitina-Zake L, Norman A, Offit K, Olah E, Olopade O, Olsson H, Orr N, Osorio A, Pankratz VS, Papp J, Park S, Park-Simon T, Parsons M, Paul J, Pedersen IS, Peissel B, Peshkin B, Peterlongo P, Peto J, Plaseska-Karanfilska D, Prajzendanz K, Prentice R, Presneau N, Prokofyeva D, Pujana MA, Pylkas K, Radice P, Ramus S, Rantala J, Rau-Murthy R, Renn G. Preprint DOI: 10.1101/521054
*
Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation.
Dhar R, Missarova AM, Lehner B, Carey LB. eLife Volume 8 (2019) DOI: 10.7554/elife.38904
*
Comprehensive structure-activity-relationship of azaindoles as highly potent FLT3 inhibitors.
Grimm SH, Gagestein B, Keijzer JF, Liu N, Wijdeven RH, Lenselink EB, Tuin AW, van den Nieuwendijk AMCH, van Westen GJP, van Boeckel CAA, Overkleeft HS, Neefjes J, van der Stelt M. Bioorganic & medicinal chemistry Volume 27 (2019) p.692-699 DOI: 10.1016/j.bmc.2019.01.006
*
CDH1 somatic alterations in Mexican patients with diffuse and mixed sporadic gastric cancer.
Bustos-Carpinteyro AR, Oliveira C, Sousa A, Oliveira P, Pinheiro H, Carvalho J, Magaña-Torres MT, Flores-Miramontes MG, Aguilar-Lemarroy A, Jave-Suárez LF, Peregrina-Sandoval J, Cruz-Ramos JA, Sánchez-López JY. BMC cancer Volume 19 (2019) p.69 DOI: 10.1186/s12885-019-5294-0
*
Targeted Resequencing of the Coding Sequence of 38 Genes Near Breast Cancer GWAS Loci in a Large Case-Control Study.
Decker B, Allen J, Luccarini C, Pooley KA, Shah M, Bolla MK, Wang Q, Ahmed S, Baynes C, Conroy DM, Brown J, Luben R, Ostrander EA, Pharoah PDP, Dunning AM, Easton DF. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology Volume 28 (2019) p.822-825 DOI: 10.1158/1055-9965.epi-18-0298
*
Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification: Supplementary Figures
Argelaguet R, Mohammed H, Clark S, Stapel C, Krueger C, Kapourani CA, Xiang Y, Hanna C, Smallwood S, Ibarra Soria X, Buettner F, Sanguinetti G, Krueger F, Xie W, Rugg-Gunn P, Kelsey G, Dean W, Nichols J, Stegle O, Marioni JC, Reik W. Preprint DOI: 10.1101/519207
Large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery.
Bosc N, Atkinson F, Felix E, Gaulton A, Hersey A, Leach AR. Journal of cheminformatics Volume 11 (2019) p.4 DOI: 10.1186/s13321-018-0325-4
*
Using the drug-protein interactome to identify anti-ageing compounds for humans.
Fuentealba M, Dönertaş HM, Williams R, Labbadia J, Thornton JM, Partridge L. PLoS computational biology Volume 15 (2019) p.e1006639 DOI: 10.1371/journal.pcbi.1006639
*
PROREPAIR-B: A Prospective Cohort Study of the Impact of Germline DNA Repair Mutations on the Outcomes of Patients With Metastatic Castration-Resistant Prostate Cancer.
Castro E, Romero-Laorden N, Del Pozo A, Lozano R, Medina A, Puente J, Piulats JM, Lorente D, Saez MI, Morales-Barrera R, Gonzalez-Billalabeitia E, Cendón Y, García-Carbonero I, Borrega P, Mendez Vidal MJ, Montesa A, Nombela P, Fernández-Parra E, Gonzalez Del Alba A, Villa-Guzmán JC, Ibáñez K, Rodriguez-Vida A, Magraner-Pardo L, Perez-Valderrama B, Vallespín E, Gallardo E, Vazquez S, Pritchard CC, Lapunzina P, Olmos D. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Volume 37 (2019) p.490-503 DOI: 10.1200/jco.18.00358
*
Copy number aberrations drive kinase re-wiring leading to genetic vulnerabilities in cancer
Memon D, Gill MG, Papachristou E, Ochoa D, D'Santos C, Miller ML, Beltrao P. Preprint DOI: 10.1101/515932
*
iProteinDB: An Integrative Database of Drosophila Post-translational Modifications.
Hu Y, Sopko R, Chung V, Foos M, Studer RA, Landry SD, Liu D, Rabinow L, Gnad F, Beltrao P, Perrimon N. G3 (Bethesda, Md.) Volume 9 (2019) p.1-11 DOI: 10.1534/g3.118.200637
*
Matching the genetics of released and local Aedes aegypti populations is critical to assure Wolbachia invasion.
Garcia GA, Sylvestre G, Aguiar R, da Costa GB, Martins AJ, Lima JBP, Petersen MT, Lourenço-de-Oliveira R, Shadbolt MF, Rašić G, Hoffmann AA, Villela DAM, Dias FBS, Dong Y, O'Neill SL, Moreira LA, Maciel-de-Freitas R. PLoS neglected tropical diseases Volume 13 (2019) p.e0007023 DOI: 10.1371/journal.pntd.0007023
*
ELECTOR: Evaluator for long reads correction methods
Marchet C, Morisse P, Lecompte L, Lefebvre A, Lecroq T, Peterlongo P, Limasset A. Preprint DOI: 10.1101/512889
*
A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesis.
Morgan M, Kabayama Y, Much C, Ivanova I, Di Giacomo M, Auchynnikava T, Monahan JM, Vitsios DM, Vasiliauskaitė L, Comazzetto S, Rappsilber J, Allshire RC, Porse BT, Enright AJ, O'Carroll D. Cell research Volume 29 (2019) p.221-232 DOI: 10.1038/s41422-018-0128-1
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Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.
Gardner PP, Watson RJ, Morgan XC, Draper JL, Finn RD, Morales SE, Stott MB. PeerJ Volume 7 (2019) p.e6160 DOI: 10.7717/peerj.6160
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What Makes a Kinase Promiscuous for Inhibitors?
Hanson SM, Georghiou G, Thakur MK, Miller WT, Rest JS, Chodera JD, Seeliger MA. Cell chemical biology Volume 26 (2019) p.390-399.e5 DOI: 10.1016/j.chembiol.2018.11.005
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Towards quality assurance and quality control in untargeted metabolomics studies.
Beger RD, Dunn WB, Bandukwala A, Bethan B, Broadhurst D, Clish CB, Dasari S, Derr L, Evans A, Fischer S, Flynn T, Hartung T, Herrington D, Higashi R, Hsu PC, Jones C, Kachman M, Karuso H, Kruppa G, Lippa K, Maruvada P, Mosley J, Ntai I, O'Donovan C, Playdon M, Raftery D, Shaughnessy D, Souza A, Spaeder T, Spalholz B, Tayyari F, Ubhi B, Verma M, Walk T, Wilson I, Witkin K, Bearden DW, Zanetti KA. Metabolomics : Official journal of the Metabolomic Society Volume 15 (2019) p.4 DOI: 10.1007/s11306-018-1460-7
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Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.
IMEx Consortium Curators, Del-Toro N, Duesbury M, Koch M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Hermjakob H, Orchard S, Porras P. Nature communications Volume 10 (2019) p.10 DOI: 10.1038/s41467-018-07709-6
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Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes.
Yi G, Wierenga ATJ, Petraglia F, Narang P, Janssen-Megens EM, Mandoli A, Merkel A, Berentsen K, Kim B, Matarese F, Singh AA, Habibi E, Prange KHM, Mulder AB, Jansen JH, Clarke L, Heath S, van der Reijden BA, Flicek P, Yaspo ML, Gut I, Bock C, Schuringa JJ, Altucci L, Vellenga E, Stunnenberg HG, Martens JHA. Cell reports Volume 26 (2019) p.1059-1069.e6 DOI: 10.1016/j.celrep.2018.12.098
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3DPatch: fast 3D structure visualization with residue conservation.
Jakubec D, Vondrášek J, Finn RD. Bioinformatics (Oxford, England) Volume 35 (2019) p.332-334 DOI: 10.1093/bioinformatics/bty464
GENCODE reference annotation for the human and mouse genomes.
Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P. Nucleic acids research Volume 47 (2019) p.D766-D773 DOI: 10.1093/nar/gky955
Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.
Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM. Methods in molecular biology (Clifton, N.J.) Volume 1851 (2019) p.263-275 DOI: 10.1007/978-1-4939-8736-8_14
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CATH: expanding the horizons of structure-based functional annotations for genome sequences.
Sillitoe I, Dawson N, Lewis TE, Das S, Lees JG, Ashford P, Tolulope A, Scholes HM, Senatorov I, Bujan A, Ceballos Rodriguez-Conde F, Dowling B, Thornton J, Orengo CA. Nucleic acids research Volume 47 (2019) p.D280-D284 DOI: 10.1093/nar/gky1097
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Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine?
Berthelot C, Clarke J, Desvignes T, William Detrich H, Flicek P, Peck LS, Peters M, Postlethwait JH, Clark MS. Genome biology and evolution Volume 11 (2019) p.220-231 DOI: 10.1093/gbe/evy262
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Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.
Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Osumi-Sutherland D, Cipriani V, Balhoff JP, Conlin T, Blau H, Baynam G, Palmer R, Gratian D, Dawkins H, Segal M, Jansen AC, Muaz A, Chang WH, Bergerson J, Laulederkind SJF, Yüksel Z, Beltran S, Freeman AF, Sergouniotis PI, Durkin D, Storm AL, Hanauer M, Brudno M, Bello SM, Sincan M, Rageth K, Wheeler MT, Oegema R, Lourghi H, Della Rocca MG, Thompson R, Castellanos F, Priest J, Cunningham-Rundles C, Hegde A, Lovering RC, Hajek C, Olry A, Notarangelo L, Similuk M, Zhang XA, Gómez-Andrés D, Lochmüller H, Dollfus H, Rosenzweig S, Marwaha S, Rath A, Sullivan K, Smith C, Milner JD, Leroux D, Boerkoel CF, Klion A, Carter MC, Groza T, Smedley D, Haendel MA, Mungall C, Robinson PN. Nucleic acids research Volume 47 (2019) p.D1018-D1027 DOI: 10.1093/nar/gky1105
Ensembl 2019.
Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, Bennett R, Bhai J, Billis K, Boddu S, Cummins C, Davidson C, Dodiya KJ, Gall A, Girón CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Laird MR, Lavidas I, Liu Z, Loveland JE, Marugán JC, Maurel T, McMahon AC, Moore B, Morales J, Mudge JM, Nuhn M, Ogeh D, Parker A, Parton A, Patricio M, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sparrow H, Stapleton E, Szuba M, Taylor K, Threadgold G, Thormann A, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Yates AD, Zerbino DR, Flicek P. Nucleic acids research Volume 47 (2019) p.D745-D751 DOI: 10.1093/nar/gky1113
Using BRIE to Detect and Analyze Splicing Isoforms in scRNA-Seq Data.
Huang Y, Sanguinetti G. Methods in molecular biology (Clifton, N.J.) Volume 1935 (2019) p.175-185 DOI: 10.1007/978-1-4939-9057-3_12
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.
Dana JM, Gutmanas A, Tyagi N, Qi G, O'Donovan C, Martin M, Velankar S. Nucleic acids research Volume 47 (2019) p.D482-D489 DOI: 10.1093/nar/gky1114
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Integration of macromolecular complex data into the Saccharomyces Genome Database.
Wong ED, Skrzypek MS, Weng S, Binkley G, Meldal BHM, Perfetto L, Orchard SE, Engel SR, Cherry JM, SGD Project. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz008
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes.
Meldal BHM, Bye-A-Jee H, Gajdoš L, Hammerová Z, Horácková A, Melicher F, Perfetto L, Pokorný D, Lopez MR, Türková A, Wong ED, Xie Z, Casanova EB, Del-Toro N, Koch M, Porras P, Hermjakob H, Orchard S. Nucleic acids research Volume 47 (2019) p.D550-D558 DOI: 10.1093/nar/gky1001
The COMPARE Data Hubs.
Amid C, Pakseresht N, Silvester N, Jayathilaka S, Lund O, Dynovski LD, Pataki BÁ, Visontai D, Xavier BB, Alako BTF, Belka A, Cisneros JLB, Cotten M, Haringhuizen GB, Harrison PW, Höper D, Holt S, Hundahl C, Hussein A, Kaas RS, Liu X, Leinonen R, Malhotra-Kumar S, Nieuwenhuijse DF, Rahman N, Dos S Ribeiro C, Skiby JE, Schmitz D, Stéger J, Szalai-Gindl JM, Thomsen MCF, Cacciò SM, Csabai I, Kroneman A, Koopmans M, Aarestrup F, Cochrane G. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz136
Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities.
Jarnuczak AF, Ternent T, Vizcaíno JA. Methods in molecular biology (Clifton, N.J.) Volume 1977 (2019) p.217-235 DOI: 10.1007/978-1-4939-9232-4_14
Reply to “Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery”
Bosc N, Atkinson F, Félix E, Gaulton A, Hersey A, Leach A. Journal of cheminformatics Volume 11 (2019)
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htsget: a protocol for securely streaming genomic data.
Kelleher J, Lin M, Albach CH, Birney E, Davies R, Gourtovaia M, Glazer D, Gonzalez CY, Jackson DK, Kemp A, Marshall J, Nowak A, Senf A, Tovar-Corona JM, Vikhorev A, Keane TM, GA4GH Streaming Task Team. Bioinformatics (Oxford, England) Volume 35 (2019) p.119-121 DOI: 10.1093/bioinformatics/bty492
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Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D.
Yang M, Zhang W, Yao G, Zhang H, Li W. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz092
PDX Finder: A portal for patient-derived tumor xenograft model discovery.
Conte N, Mason JC, Halmagyi C, Neuhauser S, Mosaku A, Yordanova G, Chatzipli A, Begley DA, Krupke DM, Parkinson H, Meehan TF, Bult CC. Nucleic acids research Volume 47 (2019) p.D1073-D1079 DOI: 10.1093/nar/gky984
Reactome and ORCID-fine-grained credit attribution for community curation.
Viteri G, Matthews L, Varusai T, Gillespie M, Milacic M, Cook J, Weiser J, Shorser S, Sidiropoulos K, Fabregat A, Haw R, Wu G, Stein L, D'Eustachio P, Hermjakob H. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz123
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COSMIC: the Catalogue Of Somatic Mutations In Cancer.
Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, Boutselakis H, Cole CG, Creatore C, Dawson E, Fish P, Harsha B, Hathaway C, Jupe SC, Kok CY, Noble K, Ponting L, Ramshaw CC, Rye CE, Speedy HE, Stefancsik R, Thompson SL, Wang S, Ward S, Campbell PJ, Forbes SA. Nucleic acids research Volume 47 (2019) p.D941-D947 DOI: 10.1093/nar/gky1015
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Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate.
Korlević P, Meyer M. Methods in molecular biology (Clifton, N.J.) Volume 1963 (2019) p.15-19 DOI: 10.1007/978-1-4939-9176-1_2
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De novo clustering of long reads by gene from transcriptomics data.
Marchet C, Lecompte L, Silva CD, Cruaud C, Aury JM, Nicolas J, Peterlongo P. Nucleic acids research Volume 47 (2019) p.e2 DOI: 10.1093/nar/gky834
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RNAcentral: a hub of information for non-coding RNA sequences.
The RNAcentral Consortium. Nucleic acids research Volume 47 (2019) p.D1250-D1251 DOI: 10.1093/nar/gky1206
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Annotation of gene product function from high-throughput studies using the Gene Ontology.
Attrill H, Gaudet P, Huntley RP, Lovering RC, Engel SR, Poux S, Van Auken KM, Georghiou G, Chibucos MC, Berardini TZ, Wood V, Drabkin H, Fey P, Garmiri P, Harris MA, Sawford T, Reiser L, Tauber R, Toro S, Gene Ontology Consortium. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz007
ChEMBL: towards direct deposition of bioassay data.
Mendez D, Gaulton A, Bento AP, Chambers J, De Veij M, Félix E, Magariños MP, Mosquera JF, Mutowo P, Nowotka M, Gordillo-Marañón M, Hunter F, Junco L, Mugumbate G, Rodriguez-Lopez M, Atkinson F, Bosc N, Radoux CJ, Segura-Cabrera A, Hersey A, Leach AR. Nucleic acids research Volume 47 (2019) p.D930-D940 DOI: 10.1093/nar/gky1075
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Toward unrestricted use of public genomic data.
Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Science (New York, N.Y.) Volume 363 (2019) p.350-352 DOI: 10.1126/science.aaw1280
The European Bioinformatics Institute in 2018: tools, infrastructure and training.
Cook CE, Lopez R, Stroe O, Cochrane G, Brooksbank C, Birney E, Apweiler R. Nucleic acids research Volume 47 (2019) p.D15-D22 DOI: 10.1093/nar/gky1124
The Pfam protein families database in 2019.
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer ELL, Hirsh L, Paladin L, Piovesan D, Tosatto SCE, Finn RD. Nucleic acids research Volume 47 (2019) p.D427-D432 DOI: 10.1093/nar/gky995
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RNAcentral: a hub of information for non-coding RNA sequences.
The RNAcentral Consortium. Nucleic acids research Volume 47 (2019) p.D221-D229 DOI: 10.1093/nar/gky1034
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iProX: an integrated proteome resource.
Ma J, Chen T, Wu S, Yang C, Bai M, Shu K, Li K, Zhang G, Jin Z, He F, Hermjakob H, Zhu Y. Nucleic acids research Volume 47 (2019) p.D1211-D1217 DOI: 10.1093/nar/gky869
Open Targets Platform: new developments and updates two years on.
Carvalho-Silva D, Pierleoni A, Pignatelli M, Ong C, Fumis L, Karamanis N, Carmona M, Faulconbridge A, Hercules A, McAuley E, Miranda A, Peat G, Spitzer M, Barrett J, Hulcoop DG, Papa E, Koscielny G, Dunham I. Nucleic acids research Volume 47 (2019) p.D1056-D1065 DOI: 10.1093/nar/gky1133
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HmtVar: a new resource for human mitochondrial variations and pathogenicity data.
Preste R, Vitale O, Clima R, Gasparre G, Attimonelli M. Nucleic acids research Volume 47 (2019) p.D1202-D1210 DOI: 10.1093/nar/gky1024
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MoonDB 2.0: an updated database of extreme multifunctional and moonlighting proteins.
Ribeiro DM, Briere G, Bely B, Spinelli L, Brun C. Nucleic acids research Volume 47 (2019) p.D398-D402 DOI: 10.1093/nar/gky1039
The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019.
Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E, Suveges D, Vrousgou O, Whetzel PL, Amode R, Guillen JA, Riat HS, Trevanion SJ, Hall P, Junkins H, Flicek P, Burdett T, Hindorff LA, Cunningham F, Parkinson H. Nucleic acids research Volume 47 (2019) p.D1005-D1012 DOI: 10.1093/nar/gky1120
The European Nucleotide Archive in 2018.
Harrison PW, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Holt S, Hussein A, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Milano A, Pakseresht N, Rajan J, Reddy K, Richards E, Rosello M, Silvester N, Smirnov D, Toribio AL, Vijayaraja S, Cochrane G. Nucleic acids research Volume 47 (2019) p.D84-D88 DOI: 10.1093/nar/gky1078
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Integrating Genomics into Healthcare: A Global Responsibility.
Stark Z, Dolman L, Manolio TA, Ozenberger B, Hill SL, Caulfied MJ, Levy Y, Glazer D, Wilson J, Lawler M, Boughtwood T, Braithwaite J, Goodhand P, Birney E, North KN. American journal of human genetics Volume 104 (2019) p.13-20 DOI: 10.1016/j.ajhg.2018.11.014
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Updates in Rhea: SPARQLing biochemical reaction data.
Lombardot T, Morgat A, Axelsen KB, Aimo L, Hyka-Nouspikel N, Niknejad A, Ignatchenko A, Xenarios I, Coudert E, Redaschi N, Bridge A. Nucleic acids research Volume 47 (2019) p.D596-D600 DOI: 10.1093/nar/gky876
InterPro in 2019: improving coverage, classification and access to protein sequence annotations.
Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD. Nucleic acids research Volume 47 (2019) p.D351-D360 DOI: 10.1093/nar/gky1100
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes.
Richardson LJ, Rawlings ND, Salazar GA, Almeida A, Haft DR, Ducq G, Sutton GG, Finn RD. Nucleic acids research Volume 47 (2019) p.D564-D572 DOI: 10.1093/nar/gky1013
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PopTargs: a database for studying population evolutionary genetics of human microRNA target sites.
Hatlen A, Helmy M, Marco A. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz102
The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Pérez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaíno JA. Nucleic acids research Volume 47 (2019) p.D442-D450 DOI: 10.1093/nar/gky1106
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Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution.
Messmer T, von Meyenn F, Savino A, Santos F, Mohammed H, Lun ATL, Marioni JC, Reik W. Cell reports Volume 26 (2019) p.815-824.e4 DOI: 10.1016/j.celrep.2018.12.099
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Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery.
Gourdine JF, Brush MH, Vasilevsky NA, Shefchek K, Köhler S, Matentzoglu N, Munoz-Torres MC, McMurry JA, Zhang XA, Robinson PN, Haendel MA. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz114
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LNCipedia 5: towards a reference set of human long non-coding RNAs.
Volders PJ, Anckaert J, Verheggen K, Nuytens J, Martens L, Mestdagh P, Vandesompele J. Nucleic acids research Volume 47 (2019) p.D135-D139 DOI: 10.1093/nar/gky1031
BioSamples database: an updated sample metadata hub.
Courtot M, Cherubin L, Faulconbridge A, Vaughan D, Green M, Richardson D, Harrison P, Whetzel PL, Parkinson H, Burdett T. Nucleic acids research Volume 47 (2019) p.D1172-D1178 DOI: 10.1093/nar/gky1061
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Root colonizing and soil borne communities of arbuscular mycorrhizal fungi differ among soybean fields with contrasting historical land use
Faggioli VS, Fernanda Covacevich, Gabriel Grilli, Maarja Öpik, Marta Noemí Cabello, Martti Vasar. Agriculture, ecosystems & environment. Volume 269 (2019) p.174-182 DOI: 10.1016/j.agee.2018.10.002
ArrayExpress update - from bulk to single-cell expression data.
Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I, Sarkans U, Brazma A. Nucleic acids research Volume 47 (2019) p.D711-D715 DOI: 10.1093/nar/gky964
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The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver.
Pandurangan AP, Stahlhacke J, Oates ME, Smithers B, Gough J. Nucleic acids research Volume 47 (2019) p.D490-D494 DOI: 10.1093/nar/gky1130
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Single-Stranded DNA Virus Sequencing (SSV-Seq) for Characterization of Residual DNA and AAV Vector Genomes.
Lecomte E, Leger A, Penaud-Budloo M, Ayuso E. Methods in molecular biology (Clifton, N.J.) Volume 1950 (2019) p.85-106 DOI: 10.1007/978-1-4939-9139-6_5
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Sharing Programming Resources Between Bio* Projects.
Bonnal RJP, Yates A, Goto N, Gautier L, Willis S, Fields C, Katayama T, Prins P. Methods in molecular biology (Clifton, N.J.) Volume 1910 (2019) p.747-766 DOI: 10.1007/978-1-4939-9074-0_25
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Protein Data Bank: the single global archive for 3D macromolecular structure data.
wwPDB consortium. Nucleic acids research Volume 47 (2019) p.D520-D528 DOI: 10.1093/nar/gky949
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Literature-Based Enrichment Insights into Redox Control of Vascular Biology
Essack M, Salhi A, Stanimirovic J, Tifratene F, Raies A, Hungler A, Uludag M, Neste CV, Trpkovic A, Bajic VP, Bajic VB, Isenovic ER. Oxidative medicine and cellular longevity Volume 2019 (2019) DOI: 10.1155/2019/1769437
Genenames.org: the HGNC and VGNC resources in 2019.
Braschi B, Denny P, Gray K, Jones T, Seal R, Tweedie S, Yates B, Bruford E. Nucleic acids research Volume 47 (2019) p.D786-D792 DOI: 10.1093/nar/gky930