Publications

Publications

2021

Learning mutational signatures and their multidimensional genomic properties with TensorSignatures.
Vöhringer H, Hoeck AV, Cuppen E, Gerstung M. Nature communications Volume 12 (2021) p.3628 DOI: 10.1038/s41467-021-23551-9
R2DT is a framework for predicting and visualising RNA secondary structure using templates.
Sweeney BA, Hoksza D, Nawrocki EP, Ribas CE, Madeira F, Cannone JJ, Gutell R, Maddala A, Meade CD, Williams LD, Petrov AS, Chan PP, Lowe TM, Finn RD, Petrov AI. Nature communications Volume 12 (2021) p.3494 DOI: 10.1038/s41467-021-23555-5
A map of transcriptional heterogeneity and regulatory variation in human microglia.
Young AMH, Kumasaka N, Calvert F, Hammond TR, Knights A, Panousis N, Park JS, Schwartzentruber J, Liu J, Kundu K, Segel M, Murphy NA, McMurran CE, Bulstrode H, Correia J, Budohoski KP, Joannides A, Guilfoyle MR, Trivedi R, Kirollos R, Morris R, Garnett MR, Timofeev I, Jalloh I, Holland K, Mannion R, Mair R, Watts C, Price SJ, Kirkpatrick PJ, Santarius T, Mountjoy E, Ghoussaini M, Soranzo N, Bayraktar OA, Stevens B, Hutchinson PJ, Franklin RJM, Gaffney DJ. Nature genetics Volume 53 (2021) p.861-868 DOI: 10.1038/s41588-021-00875-2
PDBe Aggregated API: Programmatic access to an integrative knowledge graph of molecular structure data.
Nair S, Váradi M, Nadzirin N, Pravda L, Anyango S, Mir S, Berrisford J, Armstrong D, Gutmanas A, Velankar S. Bioinformatics (Oxford, England) (2021) DOI: 10.1093/bioinformatics/btab424
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Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas
Börner K, Teichmann SA, Quardokus EM, Gee J, Browne K, Osumi-Sutherland D, Herr BW, Bueckle A, Paul H, Haniffa MA, Jardine L, Bernard A, Ding S, Miller JA, Lin S, Halushka M, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G. Preprint DOI: 10.1101/2021.05.31.446440
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Tracking the Ancestry of Known and ‘Ghost’ Homeologous Subgenomes in Model Grass Brachypodium Polyploids
Sancho R, Inda LA, Díaz-Pérez A, Des Marais DL, Gordon S, Vogel J, Lusinska J, Hasterok R, Contreras-Moreira B, Catalán P. Preprint DOI: 10.1101/2021.05.31.446465
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.
Harrison PW, Lopez R, Rahman N, Allen SG, Aslam R, Buso N, Cummins C, Fathy Y, Felix E, Glont M, Jayathilaka S, Kadam S, Kumar M, Lauer KB, Malhotra G, Mosaku A, Edbali O, Park YM, Parton A, Pearce M, Estrada Pena JF, Rossetto J, Russell C, Selvakumar S, Sitjà XP, Sokolov A, Thorne R, Ventouratou M, Walter P, Yordanova G, Zadissa A, Cochrane G, Blomberg N, Apweiler R. Nucleic acids research (2021) DOI: 10.1093/nar/gkab417
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Genomic reconstruction of the SARS-CoV-2 epidemic across England from September 2020 to May 2021
Vöhringer HS, Sanderson T, Sinnott M, De Maio N, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani C, Gonçalves S, Jackson D, Johnston I, Jung AW, Saint C, Sillitoe J, Suciu M, Goldman N, Birney E, Funk S, Volz E, Kwiatkowski D, Chand M, Martincorena I, Barrett JC, Gerstung M, The Wellcome Sanger Institute Covid-19 Surveillance Team, The COVID-19 Genomics UK (COG-UK) Consortium. Preprint DOI: 10.1101/2021.05.22.21257633
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A proteomics sample metadata representation for multiomics integration, and big data analysis
Dai C, Füllgrabe A, Pfeuffer J, Solovyeva E, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky L, Perez-Riverol Y. Preprint DOI: 10.1101/2021.05.21.445143
REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.
Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A. Nature methods (2021) DOI: 10.1038/s41592-021-01166-8
Mapping Rora expression in resting and activated CD4+ T cells.
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 ANJ, Teichmann SA. PloS one Volume 16 (2021) p.e0251233 DOI: 10.1371/journal.pone.0251233
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The Medaka Inbred Kiyosu-Karlsruhe (MIKK) Panel
Fitzgerald T, Brettell I, Leger A, Wolf N, Kusminski N, Monahan J, Barton C, Herder C, Aadepu N, Gierten J, Becker C, Hammouda OT, Hasel E, Lischik C, Lust K, Suzuki R, Tsingos E, Tavhelidse T, Thumberger T, Watson P, Welz B, Khouja N, Naruse K, Birney E, Wittbrodt J, Loosli F. Preprint DOI: 10.1101/2021.05.17.444412
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Attention-Guided Network with Densely Connected Convolution for Skin Lesion Segmentation.
Tao S, Jiang Y, Cao S, Wu C, Ma Z. Sensors (Basel, Switzerland) Volume 21 (2021) DOI: 10.3390/s21103462
Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images.
Currant H, Hysi P, Fitzgerald TW, Gharahkhani P, Bonnemaijer PWM, Senabouth A, Hewitt AW, UK Biobank Eye and Vision Consortium, International Glaucoma Genetics Consortium, Atan D, Aung T, Charng J, Choquet H, Craig J, Khaw PT, Klaver CCW, Kubo M, Ong JS, Pasquale LR, Reisman CA, Daniszewski M, Powell JE, Pébay A, Simcoe MJ, Thiadens AAHJ, van Duijn CM, Yazar S, Jorgenson E, MacGregor S, Hammond CJ, Mackey DA, Wiggs JL, Foster PJ, Patel PJ, Birney E, Khawaja AP. PLoS genetics Volume 17 (2021) p.e1009497 DOI: 10.1371/journal.pgen.1009497
Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei.
Hawkey J, Paranagama K, Baker KS, Bengtsson RJ, Weill FX, Thomson NR, Baker S, Cerdeira L, Iqbal Z, Hunt M, Ingle DJ, Dallman TJ, Jenkins C, Williamson DA, Holt KE. Nature communications Volume 12 (2021) p.2684 DOI: 10.1038/s41467-021-22700-4
Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison.
Schmidt T, Samaras P, Dorfer V, Panse C, Kockmann T, Bichmann L, van Puyvelde B, Perez-Riverol Y, Deutsch EW, Kuster B, Wilhelm M. Journal of proteome research Volume 20 (2021) p.3388-3394 DOI: 10.1021/acs.jproteome.1c00096
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Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature
Lange M, Alako BT, Cochrane G, Ghaffar M, Mascher M, Habekost P, Hillebrand U, Scholz U, Zunder F, Freitag J, Scholz AH. Preprint DOI: 10.1101/2021.05.10.443393
Modernized Uniform Representation of Carbohydrate Molecules in theProtein Data Bank.
Shao C, Feng Z, Westbrook JD, Peisach E, Berrisford J, Ikegawa Y, Kurisu G, Velankar S, Burley SK, Young JY. Glycobiology (2021) DOI: 10.1093/glycob/cwab039
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.
Sehnal D, Bittrich S, Deshpande M, Svobodová R, Berka K, Bazgier V, Velankar S, Burley SK, Koča J, Rose AS. Nucleic acids research (2021) DOI: 10.1093/nar/gkab314
Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities".
Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia JM, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, Galazka JM, Gibbons SM, Hays D, Hervey J, Hu B, Hurwitz BL, Jaiswal P, Joachimiak MP, Kinkel L, Ladau J, Martin SL, McCue LA, Miller K, Mouncey N, Mungall C, Pafilis E, Reddy TBK, Richardson L, Roux S, Schriml LM, Shaffer JP, Sundaramurthi JC, Thompson LR, Timme RE, Zheng J, Wood-Charlson EM, Eloe-Fadrosh EA. mSystems Volume 6 (2021) DOI: 10.1128/msystems.00273-21
A global view of standards for open image data formats and repositories.
Swedlow JR, Kankaanpää P, Sarkans U, Goscinski W, Galloway G, Malacrida L, Sullivan RP, Härtel S, Brown CM, Wood C, Keppler A, Paina F, Loos B, Zullino S, Longo DL, Aime S, Onami S. Nature methods (2021) DOI: 10.1038/s41592-021-01113-7
Computational principles and challenges in single-cell data integration.
Argelaguet R, Cuomo ASE, Stegle O, Marioni JC. Nature biotechnology (2021) DOI: 10.1038/s41587-021-00895-7
wwPDB biocuration: on the front line of structural biology.
Young JY, Berrisford J, Chen M. Nature methods Volume 18 (2021) p.431-432 DOI: 10.1038/s41592-021-01137-z
CONAN: a web application to detect specificity determinants and functional sites by amino acids co-variation network analysis.
Fonseca NJ, Afonso MQL, Carrijo L, Bleicher L. Bioinformatics (Oxford, England) Volume 37 (2021) p.1026-1028 DOI: 10.1093/bioinformatics/btaa713
Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2.
De Maio N, Walker CR, Turakhia Y, Lanfear R, Corbett-Detig R, Goldman N. Genome biology and evolution Volume 13 (2021) DOI: 10.1093/gbe/evab087
Copy number aberrations drive kinase rewiring, leading to genetic vulnerabilities in cancer.
Memon D, Gill MB, Papachristou EK, Ochoa D, D'Santos CS, Miller ML, Beltrao P. Cell reports Volume 35 (2021) p.109155 DOI: 10.1016/j.celrep.2021.109155
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Author Correction: Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts.
Woo XY, Giordano J, Srivastava A, Zhao ZM, Lloyd MW, de Bruijn R, Suh YS, Patidar R, Chen L, Scherer S, Bailey MH, Yang CH, Cortes-Sanchez E, Xi Y, Wang J, Wickramasinghe J, Kossenkov AV, Rebecca VW, Sun H, Mashl RJ, Davies SR, Jeon R, Frech C, Randjelovic J, Rosains J, Galimi F, Bertotti A, Lafferty A, O'Farrell AC, Modave E, Lambrechts D, Ter Brugge P, Serra V, Marangoni E, El Botty R, Kim H, Kim JI, Yang HK, Lee C, Dean DA, Davis-Dusenbery B, Evrard YA, Doroshow JH, Welm AL, Welm BE, Lewis MT, Fang B, Roth JA, Meric-Bernstam F, Herlyn M, Davies MA, Ding L, Li S, Govindan R, Isella C, Moscow JA, Trusolino L, Byrne AT, Jonkers J, Bult CJ, Medico E, Chuang JH, PDXNET Consortium, EurOPDX Consortium. Nature genetics Volume 53 (2021) p.761 DOI: 10.1038/s41588-021-00811-4
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes.
Smyshlyaev G, Bateman A, Barabas O. Molecular systems biology Volume 17 (2021) p.e9880 DOI: 10.15252/msb.20209880
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Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time.
von Mentzer A, Blackwell GA, Pickard D, Boinett CJ, Joffré E, Page AJ, Svennerholm AM, Dougan G, Sjöling Å. Scientific reports Volume 11 (2021) p.9256 DOI: 10.1038/s41598-021-88316-2
Somatic mutation landscapes at single-molecule resolution.
Abascal F, Harvey LMR, Mitchell E, Lawson ARJ, Lensing SV, Ellis P, Russell AJC, Alcantara RE, Baez-Ortega A, Wang Y, Kwa EJ, Lee-Six H, Cagan A, Coorens THH, Chapman MS, Olafsson S, Leonard S, Jones D, Machado HE, Davies M, Øbro NF, Mahubani KT, Allinson K, Gerstung M, Saeb-Parsy K, Kent DG, Laurenti E, Stratton MR, Rahbari R, Campbell PJ, Osborne RJ, Martincorena I. Nature Volume 593 (2021) p.405-410 DOI: 10.1038/s41586-021-03477-4
Towards complete and error-free genome assemblies of all vertebrate species.
Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Nature Volume 592 (2021) p.737-746 DOI: 10.1038/s41586-021-03451-0
Accessing Livestock Resources in Ensembl.
Martin FJ, Gall A, Szpak M, Flicek P. Frontiers in genetics Volume 12 (2021) p.650228 DOI: 10.3389/fgene.2021.650228
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Effects of concomitant obesity and diabetes on the aggressiveness and outcomes of differentiated thyroid cancer patients.
Elbasan O, Yavuz DG. Archives of endocrinology and metabolism (2021) DOI: 10.20945/2359-3997000000361
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Genetic variants in the SLC16A11 gene are associated with increased BMI and insulin levels in nondiabetic Chilean population.
Mardones L, Petermann-Rocha F, Martinez-Sanguinetti MA, Leiva AM, Troncoso-Pantoja C, Martorell M, Lasserre N, Ulloa N, Perez-Bravo F, Celis-Morales C, Villagran M, ELHOC group (Epidemiology of Lifestyle and Health Outcomes in Chile). Archives of endocrinology and metabolism (2021) DOI: 10.20945/2359-3997000000359
Adaptive introgression of the beta-globin cluster in two Andean waterfowl.
Graham AM, Peters JL, Wilson RE, Muñoz-Fuentes V, Green AJ, Dorfsman DA, Valqui TH, Winker K, McCracken KG. Heredity (2021) DOI: 10.1038/s41437-021-00437-6
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. Scientific data Volume 8 (2021) p.115 DOI: 10.1038/s41597-021-00890-2
Single-cell multi-omics analysis of the immune response in COVID-19.
Stephenson E, Reynolds G, Botting RA, Calero-Nieto FJ, Morgan MD, Tuong ZK, Bach K, Sungnak W, Worlock KB, Yoshida M, Kumasaka N, Kania K, Engelbert J, Olabi B, Spegarova JS, Wilson NK, Mende N, Jardine L, Gardner LCS, Goh I, Horsfall D, McGrath J, Webb S, Mather MW, Lindeboom RGH, Dann E, Huang N, Polanski K, Prigmore E, Gothe F, Scott J, Payne RP, Baker KF, Hanrath AT, Schim van der Loeff ICD, Barr AS, Sanchez-Gonzalez A, Bergamaschi L, Mescia F, Barnes JL, Kilich E, de Wilton A, Saigal A, Saleh A, Janes SM, Smith CM, Gopee N, Wilson C, Coupland P, Coxhead JM, Kiselev VY, van Dongen S, Bacardit J, King HW, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID-19 BioResource Collaboration, Rostron AJ, Simpson AJ, Hambleton S, Laurenti E, Lyons PA, Meyer KB, Nikolić MZ, Duncan CJA, Smith KGC, Teichmann SA, Clatworthy MR, Marioni JC, Göttgens B, Haniffa M. Nature medicine Volume 27 (2021) p.904-916 DOI: 10.1038/s41591-021-01329-2
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Sustainable data analysis with Snakemake
Mölder F, Jablonski KP, Letcher B, Hall MB, Tomkins-Tinch CH, Sochat V, Forster J, Lee S, Twardziok SO, Kanitz A, Wilm A, Holtgrewe M, Rahmann S, Nahnsen S, Köster J. Preprint DOI: 10.12688/f1000research.29032.2
Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data.
Saheb Kashaf S, Almeida A, Segre JA, Finn RD. Nature protocols Volume 16 (2021) p.2520-2541 DOI: 10.1038/s41596-021-00508-2
Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease.
Watt S, Vasquez L, Walter K, Mann AL, Kundu K, Chen L, Sims 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 BM, Spivakov M, Soranzo N. Nature communications Volume 12 (2021) p.2298 DOI: 10.1038/s41467-021-22548-8
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Visualization of loop extrusion by DNA nanoscale tracing in single human cells
Beckwith K, Ødegård-Fougner Ø, Morero N, Barton C, Schueder F, Alexander S, Jungmann R, Birney E, Ellenberg J. Preprint DOI: 10.1101/2021.04.12.439407
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Sensitive and specific spectral library searching with COSS and Percolator
Shiferaw GA, Gabriels R, Vandermarliere E, Martens L, Volders P. Preprint DOI: 10.1101/2021.04.09.438700
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Genomic sequence characteristics and the empiric accuracy of short-read sequencing
Marin M, Vargas R, Harris M, Jeffrey B, Epperson LE, Durbin D, Strong M, Salfinger M, Iqbal Z, Akhundova I, Vashakidze S, Crudu V, Rosenthal A, Farhat MR. Preprint DOI: 10.1101/2021.04.08.438862
Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19.
Gaziano L, Giambartolomei C, Pereira AC, Gaulton A, Posner DC, Swanson SA, Ho YL, Iyengar SK, Kosik NM, Vujkovic M, Gagnon DR, Bento AP, Barrio-Hernandez I, Rönnblom L, Hagberg N, Lundtoft C, Langenberg C, Pietzner M, Valentine D, Gustincich S, Tartaglia GG, Allara E, Surendran P, Burgess S, Zhao JH, Peters JE, Prins BP, Angelantonio ED, Devineni P, Shi Y, Lynch KE, DuVall SL, Garcon H, Thomann LO, Zhou JJ, Gorman BR, Huffman JE, O'Donnell CJ, Tsao PS, Beckham JC, Pyarajan S, Muralidhar S, Huang GD, Ramoni R, Beltrao P, Danesh J, Hung AM, Chang KM, Sun YV, Joseph J, Leach AR, Edwards TL, Cho K, Gaziano JM, Butterworth AS, Casas JP, VA Million Veteran Program COVID-19 Science Initiative. Nature medicine Volume 27 (2021) p.668-676 DOI: 10.1038/s41591-021-01310-z
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Linked electronic health records for research on a nationwide cohort of more than 54 million people in England: data resource.
Wood A, Denholm R, Hollings S, Cooper J, Ip S, Walker V, Denaxas S, Akbari A, Banerjee A, Whiteley W, Lai A, Sterne J, Sudlow C, CVD-COVID-UK consortium. BMJ (Clinical research ed.) Volume 373 (2021) p.n826 DOI: 10.1136/bmj.n826
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Cells of the human intestinal tract mapped across space and time
Elmentaite R, Kumasaka N, King H, Roberts K, Dabrowska M, Pritchard S, Bolt L, Vieira S, Mamanova L, Huang N, Goh Kai’En I, Stephenson E, Engelbert J, Botting R, Fleming A, Dann E, Lisgo S, Katan M, Leonard S, Oliver T, Hook C, Nayak K, Perrone F, Campos L, Dominguez-Conde C, Polanski K, Van Dongen S, Patel M, Morgan M, Marioni J, Bayraktar O, Meyer K, Zilbauer M, Uhlig H, Clatworthy M, Mahbubani K, Saeb Parsy K, Haniffa M, James K, Teichmann S. Preprint DOI: 10.1101/2021.04.07.438755
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matUtils: Tools to Interpret and Manipulate Mutation Annotated Trees
McBroome J, Thornlow B, Hinrichs AS, De Maio N, Goldman N, Haussler D, Corbett-Detig R, Turakhia Y. Preprint DOI: 10.1101/2021.04.03.438321
Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes.
Tagirdzhanova G, Saary P, Tingley JP, Díaz-Escandón D, Abbott DW, Finn RD, Spribille T. Genome biology and evolution Volume 13 (2021) DOI: 10.1093/gbe/evab047
The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation.
Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, McMahon A, Abraham G, Chapman M, Parkinson H, Danesh J, MacArthur JAL, Inouye M. Nature genetics Volume 53 (2021) p.420-425 DOI: 10.1038/s41588-021-00783-5
Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine.
Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni JC, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T, LifeTime Community Working Groups. Nature Volume 592 (2021) p.E8 DOI: 10.1038/s41586-021-03287-8
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).
Touré V, Vercruysse S, Acencio ML, Lovering RC, Orchard S, Bradley G, Casals-Casas C, Chaouiya C, Del-Toro N, Flobak Å, Gaudet P, Hermjakob H, Hoyt CT, Licata L, Lægreid A, Mungall CJ, Niknejad A, Panni S, Perfetto L, Porras P, Pratt D, Saez-Rodriguez J, Thieffry D, Thomas PD, Türei D, Kuiper M. Bioinformatics (Oxford, England) Volume 36 (2021) p.5712-5718 DOI: 10.1093/bioinformatics/btaa622
Author Correction: Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes.
Schwartzentruber J, Cooper S, Liu JZ, Barrio-Hernandez I, Bello E, Kumasaka N, Young AMH, Franklin RJM, Johnson T, Estrada K, Gaffney DJ, Beltrao P, Bassett A. Nature genetics Volume 53 (2021) p.585-586 DOI: 10.1038/s41588-021-00822-1
Analysing the yeast complexome-the Complex Portal rising to the challenge.
Meldal BHM, Pons C, Perfetto L, Del-Toro N, Wong E, Aloy P, Hermjakob H, Orchard S, Porras P. Nucleic acids research Volume 49 (2021) p.3156-3167 DOI: 10.1093/nar/gkab077
A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages.
Dellicour S, Durkin K, Hong SL, Vanmechelen B, Martí-Carreras J, Gill MS, Meex C, Bontems S, André E, Gilbert M, Walker C, Maio N, Faria NR, Hadfield J, Hayette MP, Bours V, Wawina-Bokalanga T, Artesi M, Baele G, Maes P. Molecular biology and evolution Volume 38 (2021) p.1608-1613 DOI: 10.1093/molbev/msaa284
User-friendly, scalable tools and workflows for single-cell RNA-seq analysis.
Moreno P, Huang N, Manning JR, Mohammed S, Solovyev A, Polanski K, Bacon W, Chazarra R, Talavera-López C, Doyle MA, Marnier G, Grüning B, Rasche H, George N, Fexova SK, Alibi M, Miao Z, Perez-Riverol Y, Haeussler M, Brazma A, Teichmann S, Meyer KB, Papatheodorou I. Nature methods Volume 18 (2021) p.327-328 DOI: 10.1038/s41592-021-01102-w
A resource of targeted mutant mouse lines for 5,061 genes.
Birling MC, Yoshiki A, Adams DJ, Ayabe S, Beaudet AL, Bottomley J, Bradley A, Brown SDM, 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 ST, Justice MJ, Kasparek P, King RE, Kühn R, Lee H, Lee YJ, Liu Z, Lloyd KCK, Lorenzo I, Mallon AM, McKerlie C, Meehan TF, Fuentes VM, Newman S, Nutter LMJ, 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, Wang CL, Wardle-Jones H, Wattenhofer-Donzé M, Wells S, Wiles MV, Willis BJ, Wood JA, Wurst W, Xu Y, International Mouse Phenotyping Consortium (IMPC), Teboul L, Murray SA. Nature genetics Volume 53 (2021) p.416-419 DOI: 10.1038/s41588-021-00825-y
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Brain Ependymoma in an African Grey Parrot (Psittacus erithacus erithacus).
Sailler A, Vanel M, Larrat S, Risi E. Journal of avian medicine and surgery Volume 35 (2021) p.75-79 DOI: 10.1647/1082-6742-35.1.75
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UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.
MacDougall A, Volynkin V, Saidi R, Poggioli D, Zellner H, Hatton-Ellis E, Joshi V, O'Donovan C, Orchard S, Auchincloss AH, Baratin D, Bolleman J, Coudert E, de Castro E, Hulo C, Masson P, Pedruzzi I, Rivoire C, Arighi C, Wang Q, Chen C, Huang H, Garavelli J, Vinayaka CR, Yeh LS, Natale DA, Laiho K, Martin MJ, Renaux A, Pichler K, The UniProt Consortium. Bioinformatics (Oxford, England) Volume 36 (2021) p.5562 DOI: 10.1093/bioinformatics/btaa663
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Biallelic mutations in cancer genomes reveal local mutational determinants
Demeulemeester J, Dentro SC, Gerstung M, Van Loo P. Preprint DOI: 10.1101/2021.03.29.437407
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GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning
Gröschel MI, Owens M, Freschi L, Vargas R, Marin MG, Phelan J, Iqbal Z, Dixit A, Farhat MR. Preprint DOI: 10.1101/2021.03.27.437319
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Efficient masking of plant genomes by combining kmer counting and curated repeats
Contreras-Moreira B, Filippi CV, Naamati G, Girón CG, Allen JE, Flicek P. Preprint DOI: 10.1101/2021.03.22.436504
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The SARS-CoV-2 replication-transcription complex is a priority target for broad-spectrum pan-coronavirus drugs
Yazdani S, De Maio N, Ding Y, Shahani V, Goldman N, Schapira M. Preprint DOI: 10.1101/2021.03.23.436637
Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research.
Kern C, Wang Y, Xu X, Pan Z, Halstead M, Chanthavixay G, Saelao P, Waters S, Xiang R, Chamberlain A, Korf I, Delany ME, Cheng HH, Medrano JF, Van Eenennaam AL, Tuggle CK, Ernst C, Flicek P, Quon G, Ross P, Zhou H. Nature communications Volume 12 (2021) p.1821 DOI: 10.1038/s41467-021-22100-8
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Deciphering Bedaquiline and Clofazimine Resistance in Tuberculosis: An Evolutionary Medicine Approach
Sonnenkalb L, Carter J, Spitaleri A, Iqbal Z, Hunt M, Malone K, Utpatel C, Cirillo DM, Rodrigues C, Nilgiriwala KS, Fowler PW, Merker M, Niemann S, the CRyPTIC Consortium. Preprint DOI: 10.1101/2021.03.19.436148
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A proteome-wide genetic investigation identifies several SARS-CoV-2-exploited host targets of clinical relevance
Karim MA, Shilts J, Schwartzentruber J, Hayhurst J, Buniello A, Mohammed ESE, Zheng J, Holmes MV, Ochoa D, Carmona M, Maranville J, Gaunt TR, Emilsson V, Gudnason V, McDonagh EM, Wright GJ, Ghoussaini M, Dunham I. Preprint DOI: 10.1101/2021.03.15.21253625
Suppression of insulin-induced gene 1 (INSIG1) function promotes hepatic lipid remodelling and restrains NASH progression.
Azzu V, Vacca M, Kamzolas I, Hall Z, Leslie J, Carobbio S, Virtue S, Davies SE, Lukasik A, Dale M, Bohlooly-Y M, Acharjee A, Lindén D, Bidault G, Petsalaki E, Griffin JL, Oakley F, Allison MED, Vidal-Puig A. Molecular metabolism Volume 48 (2021) p.101210 DOI: 10.1016/j.molmet.2021.101210
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phastSim: efficient simulation of sequence evolution for pandemic-scale datasets
De Maio N, Weilguny L, Walker CR, Turakhia Y, Corbett-Detig R, Goldman N. Preprint DOI: 10.1101/2021.03.15.435416
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DeepLC can predict retention times for peptides that carry as-yet unseen modifications
Martens L, Bouwmeester R, Gabriels R, Hulstaert N, Degroeve S. Preprint DOI: 10.21203/rs.3.rs-275246/v1
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Refget: standardised access to reference sequences
Yates AD, Adams J, Chaturvedi S, Davies RM, Laird M, Leinonen R, Nag R, Sheffield NC, Hofmann O, Keane T. Preprint DOI: 10.1101/2021.03.11.434800
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Posttranslational Modifications in Conserved Transcription Factors: A Survey of the TALE-Homeodomain Superclass in Human and Mouse.
Reichlmeir M, Elias L, Schulte D. Frontiers in cell and developmental biology Volume 9 (2021) p.648765 DOI: 10.3389/fcell.2021.648765
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Effects of Dangguixu-san in patients with acute lateral ankle sprain: a randomized controlled trial.
Kim JH, Lee CK, Lee EY, Cho MR, Lee YS, Lee JS. Trials Volume 22 (2021) p.184 DOI: 10.1186/s13063-021-05135-6
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation.
Jerber J, Seaton DD, Cuomo ASE, Kumasaka N, Haldane J, Steer J, Patel M, Pearce D, Andersson M, Bonder MJ, Mountjoy E, Ghoussaini M, Lancaster MA, HipSci Consortium, Marioni JC, Merkle FT, Gaffney DJ, Stegle O. Nature genetics Volume 53 (2021) p.304-312 DOI: 10.1038/s41588-021-00801-6
Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics.
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, Vakili D, Horta D, Zhao C, Zastrow DB, Bonner DE, HipSci Consortium, iPSCORE consortium, Undiagnosed Diseases Network, PhLiPS consortium, Wheeler MT, Kilpinen H, Knowles JW, Smith EN, Frazer KA, Montgomery SB, Stegle O. Nature genetics Volume 53 (2021) p.313-321 DOI: 10.1038/s41588-021-00800-7
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Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences
Blackwell GA, Hunt M, Malone KM, Lima L, Horesh G, Alako BT, Thomson NR, Iqbal Z. Preprint DOI: 10.1101/2021.03.02.433662
Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank.
Feng Z, Westbrook JD, Sala R, Smart OS, Bricogne G, Matsubara M, Yamada I, Tsuchiya S, Aoki-Kinoshita KF, Hoch JC, Kurisu G, Velankar S, Burley SK, Young JY. Structure (London, England : 1993) Volume 29 (2021) p.393-400.e1 DOI: 10.1016/j.str.2021.02.004
Iron limitation by transferrin promotes simultaneous cheating of pyoverdine and exoprotease in Pseudomonas aeruginosa.
Tostado-Islas O, Mendoza-Ortiz A, Ramírez-García G, Cabrera-Takane ID, Loarca D, Pérez-González C, Jasso-Chávez R, Jiménez-Cortés JG, Hoshiko Y, Maeda T, Cazares A, García-Contreras R. The ISME journal (2021) DOI: 10.1038/s41396-021-00938-6
Short-range template switching in great ape genomes explored using pair hidden Markov models.
Walker CR, Scally A, De Maio N, Goldman N. PLoS genetics Volume 17 (2021) p.e1009221 DOI: 10.1371/journal.pgen.1009221
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Triglia ET, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams T, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo ASE, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CGK, NHLBI LungMap Consortium, Human Cell Atlas Lung Biological Network. Nature medicine Volume 27 (2021) p.546-559 DOI: 10.1038/s41591-020-01227-z
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Drug-Resistant Tuberculosis in Pet Ring-Tailed Lemur, Madagascar.
LaFleur M, Reuter KE, Hall MB, Rasoanaivo HH, McKernan S, Ranaivomanana P, Michel A, Rabodoarivelo MS, Iqbal Z, Rakotosamimanana N, Lapierre SG. Emerging infectious diseases Volume 27 (2021) p.977-979 DOI: 10.3201/eid2703.202924
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An ancestral 10-bp repeat expansion in VWA1 causes recessive hereditary motor neuropathy.
Pagnamenta AT, Kaiyrzhanov R, Zou Y, Da'as SI, Maroofian R, Donkervoort S, Dominik N, Lauffer M, Ferla MP, Orioli A, Giess A, Tucci A, Beetz C, Sedghi M, Ansari B, Barresi R, Basiri K, Cortese A, Elgar G, Fernandez-Garcia MA, Yip J, Foley AR, Gutowski N, Jungbluth H, Lassche S, Lavin T, Marcelis C, Marks P, Marini-Bettolo C, Medne L, Moslemi AR, Sarkozy A, Reilly MM, Muntoni F, Millan F, Muraresku CC, Need AC, Nemeth AH, Neuhaus SB, Norwood F, O'Donnell M, O'Driscoll M, Rankin J, Yum SW, Zolkipli-Cunningham Z, Brusius I, Wunderlich G, Genomics England Research Consortium, Karakaya M, Wirth B, Fakhro KA, Tajsharghi H, Bönnemann CG, Taylor JC, Houlden H. Brain : a journal of neurology Volume 144 (2021) p.584-600 DOI: 10.1093/brain/awaa420
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, Baumbach J, Beerenwinkel N, Brandt C, Cacciabue M, Chuguransky S, Drechsel O, Finn RD, Fritz A, Fuchs S, Hattab G, Hauschild AC, Heider D, Hoffmann M, Hölzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, Kühnert D, Lasso G, Libin P, List M, Löchel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki EP, O'Toole ÁN, Ontiveros-Palacios N, Petrov AI, Rangel-Pineros G, Redaschi N, Reimering S, Reinert K, Reyes A, Richardson L, Robertson DL, Sadegh S, Singer JB, Theys K, Upton C, Welzel M, Williams L, Marz M. Briefings in bioinformatics Volume 22 (2021) p.642-663 DOI: 10.1093/bib/bbaa232
Publisher Correction: The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors.
Harland LTG, Simon CS, Senft AD, Costello I, Greder L, Imaz-Rosshandler I, Göttgens B, Marioni JC, Bikoff EK, Porcher C, de Bruijn MFTR, Robertson EJ. Nature cell biology Volume 23 (2021) p.293 DOI: 10.1038/s41556-021-00645-6
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An outbreak of multiply antibiotic-resistant ST49:ST128:KL11:OCL8 Acinetobacter baumannii isolates at a Sydney hospital.
Hamidian M, Ambrose SJ, Blackwell GA, Nigro SJ, Hall RM. The Journal of antimicrobial chemotherapy Volume 76 (2021) p.893-900 DOI: 10.1093/jac/dkaa553
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Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.
Niarakis A, Kuiper M, Ostaszewski M, Malik Sheriff RS, Casals-Casas C, Thieffry D, Freeman TC, Thomas P, Touré V, Noël V, Stoll G, Saez-Rodriguez J, Naldi A, Oshurko E, Xenarios I, Soliman S, Chaouiya C, Helikar T, Calzone L. Briefings in bioinformatics Volume 22 (2021) p.1848-1859 DOI: 10.1093/bib/bbaa046
Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE. Science (New York, N.Y.) Volume 372 (2021) DOI: 10.1126/science.abf7117
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A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae
Sim CK, Kashaf SS, Conlan S, Stacy A, Proctor DM, Almeida A, Bouladoux N, Chen M, Finn RD, Belkaid Y, Segre JA, NISC Comparative Sequencing Program. Preprint DOI: 10.1101/2021.02.24.432587
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A missense variant effect prediction and annotation resource for SARS-CoV-2
Dunham A, Jang GM, Muralidharan M, Swaney D, Beltrao P. Preprint DOI: 10.1101/2021.02.24.432721
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An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
MalariaGEN, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare G, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NP, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen T, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo J, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su X, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H. Preprint DOI: 10.12688/wellcomeopenres.16168.1
BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers.
Bai J, Bandla C, Guo J, Vera Alvarez R, Bai M, Vizcaíno JA, Moreno P, Grüning B, Sallou O, Perez-Riverol Y. Journal of proteome research Volume 20 (2021) p.2056-2061 DOI: 10.1021/acs.jproteome.0c00904
Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries.
Gharahkhani P, Jorgenson E, Hysi P, Khawaja AP, Pendergrass S, Han X, Ong JS, Hewitt AW, Segrè AV, Rouhana JM, Hamel AR, Igo RP, Choquet H, Qassim A, Josyula NS, Cooke Bailey JN, Bonnemaijer PWM, Iglesias A, Siggs OM, Young TL, Vitart V, Thiadens AAHJ, Karjalainen J, Uebe S, Melles RB, Nair KS, Luben R, Simcoe M, Amersinghe N, Cree AJ, Hohn R, Poplawski A, Chen LJ, Rong SS, Aung T, Vithana EN, NEIGHBORHOOD consortium, ANZRAG consortium, Biobank Japan project, FinnGen study, UK Biobank Eye and Vision Consortium, GIGA study group, 23 and Me Research Team, Tamiya G, Shiga Y, Yamamoto M, Nakazawa T, Currant H, Birney E, Wang X, Auton A, Lupton MK, Martin NG, Ashaye A, Olawoye O, Williams SE, Akafo S, Ramsay M, Hashimoto K, Kamatani Y, Akiyama M, Momozawa Y, Foster PJ, Khaw PT, Morgan JE, Strouthidis NG, Kraft P, Kang JH, Pang CP, Pasutto F, Mitchell P, Lotery AJ, Palotie A, van Duijn C, Haines JL, Hammond C, Pasquale LR, Klaver CCW, Hauser M, Khor CC, Mackey DA, Kubo M, Cheng CY, Craig JE, MacGregor S, Wiggs JL. Nature communications Volume 12 (2021) p.1258 DOI: 10.1038/s41467-020-20851-4
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.
Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia JM, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, Galazka JM, Gibbons SM, Hays D, Hervey J, Hu B, Hurwitz BL, Jaiswal P, Joachimiak MP, Kinkel L, Ladau J, Martin SL, McCue LA, Miller K, Mouncey N, Mungall C, Pafilis E, Reddy TBK, Richardson L, Roux S, Schriml LM, Shaffer JP, Sundaramurthi JC, Thompson LR, Timme RE, Zheng J, Wood-Charlson EM, Eloe-Fadrosh EA. mSystems Volume 6 (2021) DOI: 10.1128/msystems.01194-20
Reconstructing the Lineage Histories and Differentiation Trajectories of Individual Cancer Cells in Myeloproliferative Neoplasms.
Van Egeren D, Escabi J, Nguyen M, Liu S, Reilly CR, Patel S, Kamaz B, Kalyva M, DeAngelo DJ, Galinsky I, Wadleigh M, Winer ES, Luskin MR, Stone RM, Garcia JS, Hobbs GS, Camargo FD, Michor F, Mullally A, Cortes-Ciriano I, Hormoz S. Cell stem cell Volume 28 (2021) p.514-523.e9 DOI: 10.1016/j.stem.2021.02.001
MAIP: a web service for predicting blood-stage malaria inhibitors.
Bosc N, Felix E, Arcila R, Mendez D, Saunders MR, Green DVS, Ochoada J, Shelat AA, Martin EJ, Iyer P, Engkvist O, Verras A, Duffy J, Burrows J, Gardner JMF, Leach AR. Journal of cheminformatics Volume 13 (2021) p.13 DOI: 10.1186/s13321-021-00487-2
Tumour gene expression signature in primary melanoma predicts long-term outcomes.
Garg M, Couturier DL, Nsengimana J, Fonseca NA, Wongchenko M, Yan Y, Lauss M, Jönsson GB, Newton-Bishop J, Parkinson C, Middleton MR, Bishop DT, McDonald S, Stefanos N, Tadross J, Vergara IA, Lo S, Newell F, Wilmott JS, Thompson JF, Long GV, Scolyer RA, Corrie P, Adams DJ, Brazma A, Rabbie R. Nature communications Volume 12 (2021) p.1137 DOI: 10.1038/s41467-021-21207-2
Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care.
Roberts LW, Forde BM, Hurst T, Ling W, Nimmo GR, Bergh H, George N, Hajkowicz K, McNamara JF, Lipman J, Permana B, Schembri MA, Paterson D, Beatson SA, Harris PNA. Microbial genomics Volume 7 (2021) DOI: 10.1099/mgen.0.000530
LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions.
Roller M, Stamper E, Villar D, Izuogu O, Martin F, Redmond AM, Ramachanderan R, Harewood L, Odom DT, Flicek P. Genome biology Volume 22 (2021) p.62 DOI: 10.1186/s13059-021-02260-y
Toward Understanding the Biochemical Determinants of Protein Degradation Rates.
Correa Marrero M, Barrio-Hernandez I. ACS omega Volume 6 (2021) p.5091-5100 DOI: 10.1021/acsomega.0c05318
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Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in cutaneous T-cell lymphoma.
Jones CL, Degasperi A, Grandi V, Amarante TD, Genomics England Research Consortium, Mitchell TJ, Nik-Zainal S, Whittaker SJ. Scientific reports Volume 11 (2021) p.3962 DOI: 10.1038/s41598-021-83352-4
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes.
Schwartzentruber J, Cooper S, Liu JZ, Barrio-Hernandez I, Bello E, Kumasaka N, Young AMH, Franklin RJM, Johnson T, Estrada K, Gaffney DJ, Beltrao P, Bassett A. Nature genetics Volume 53 (2021) p.392-402 DOI: 10.1038/s41588-020-00776-w
Data Sharing Under the General Data Protection Regulation: Time to Harmonize Law and Research Ethics?
Vlahou A, Hallinan D, Apweiler R, Argiles A, Beige J, Benigni A, Bischoff R, Black PC, Boehm F, Céraline J, Chrousos GP, Delles C, Evenepoel P, Fridolin I, Glorieux G, van Gool AJ, Heidegger I, Ioannidis JPA, Jankowski J, Jankowski V, Jeronimo C, Kamat AM, Masereeuw R, Mayer G, Mischak H, Ortiz A, Remuzzi G, Rossing P, Schanstra JP, Schmitz-Dräger BJ, Spasovski G, Staessen JA, Stamatialis D, Stenvinkel P, Wanner C, Williams SB, Zannad F, Zoccali C, Vanholder R. Hypertension (Dallas, Tex. : 1979) Volume 77 (2021) p.1029-1035 DOI: 10.1161/hypertensionaha.120.16340
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Identification of phenotype-specific networks from paired gene expression-cell shape imaging data
Barker CG, Petsalaki E, Giudice G, Ekpenyong EN, Bakal C, Petsalaki E. Preprint DOI: 10.1101/2021.02.11.430597
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Functional and taxonomic comparison of mouse and human gut microbiotas using extensive culturing and metagenomics
Beresford-Jones BS, Forster SC, Stares MD, Notley G, Viciani E, Browne HP, Kumar N, Vervier K, Almeida A, Lawley TD, Pedicord VA. Preprint DOI: 10.1101/2021.02.11.430759
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gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae
Fennell TG, Blackwell GA, Thomson NR, Dorman MJ. Preprint DOI: 10.1101/2021.02.11.430729
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ELIXIR-EXCELERATE: establishing Europe's data infrastructure for the life science research of the future.
Harrow J, Hancock J, ELIXIR-EXCELERATE Community, Blomberg N. The EMBO journal Volume 40 (2021) p.e107409 DOI: 10.15252/embj.2020107409
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Hepatic deletion of Mboat7 (LPIAT1) causes activation of SREBP-1c and fatty liver.
Xia M, Chandrasekaran P, Rong S, Fu X, Mitsche MA. Journal of lipid research Volume 62 (2021) p.100031 DOI: 10.1194/jlr.ra120000856
Crypt4GH: a file format standard enabling native access to encrypted data.
Senf A, Davies R, Haziza F, Marshall J, Troncoso-Pastoriza J, Hofmann O, Keane TM. Bioinformatics (Oxford, England) (2021) DOI: 10.1093/bioinformatics/btab087
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Using data from the 100,000 Genomes Project to resolve conflicting interpretations of a recurrent TUBB2A mutation.
Ragoussis V, Pagnamenta AT, Haines RL, Giacopuzzi E, McClatchey MA, Sampson JR, Suri M, Gardham A, Cobben JM, Osio D, Fry AE, Genomics England Research Consortium, Taylor JC. Journal of medical genetics (2021) DOI: 10.1136/jmedgenet-2020-107528
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.
Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Herzik MA, Hoh SW, Hou J, Hung LW, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W. Nature methods Volume 18 (2021) p.156-164 DOI: 10.1038/s41592-020-01051-w
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Global spread and evolutionary history of HCV subtype 3a
lin S, De Maio N, Pedergnana V, Wu C, Thézé J, Barnes E, Ansari MA. Preprint DOI: 10.1101/2021.02.03.429581
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Light spectra trigger divergent gene expression in barley cultivars
Monteagudo A, del Río ÁR, Contreras-Moreira B, Kiss T, Mayer M, Karsai I, Igartua E, Casas AM. Preprint DOI: 10.1101/2021.02.03.429565
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MicroPIPE: An end-to-end solution for high-quality complete bacterial genome construction
Murigneux V, Roberts LW, Forde BM, Phan M, Nhu NTK, Irwin AD, Harris PNA, Paterson DL, Schembri MA, Whiley DM, Beatson SA. Preprint DOI: 10.1101/2021.02.02.429319
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Enabling multiscale variation analysis with genome graphs
Letcher B, Hunt M, Iqbal Z. Preprint DOI: 10.1101/2021.02.03.429603
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A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation.
Cazares D, Cazares A, Figueroa W, Guarneros G, Edwards RA, Vinuesa P. mSystems Volume 6 (2021) DOI: 10.1128/msystems.00773-20
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ChIPuana: from raw data to epigenomic dynamics
Daunesse M, Legendre R, Varet H, Pain A, Chica C. Preprint DOI: 10.1101/2021.02.02.429342
Longevity, clonal relationship, and transcriptional program of celiac disease-specific plasma cells.
Lindeman I, Zhou C, Eggesbø LM, Miao Z, Polak J, Lundin KEA, Jahnsen J, Qiao SW, Iversen R, Sollid LM. The Journal of experimental medicine Volume 218 (2021) DOI: 10.1084/jem.20200852
The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment.
De Maio N. Systematic biology Volume 70 (2021) p.236-257 DOI: 10.1093/sysbio/syaa050
Reproducibility in systems biology modelling.
Tiwari K, Kananathan S, Roberts MG, Meyer JP, Sharif Shohan MU, Xavier A, Maire M, Zyoud A, Men J, Ng S, Nguyen TVN, Glont M, Hermjakob H, Malik-Sheriff RS. Molecular systems biology Volume 17 (2021) p.e9982 DOI: 10.15252/msb.20209982
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A comprehensive and high-quality collection of Escherichia coli genomes and their genes.
Horesh G, Blackwell GA, Tonkin-Hill G, Corander J, Heinz E, Thomson NR. Microbial genomics Volume 7 (2021) DOI: 10.1099/mgen.0.000499
Cell type-specific modulation of healthspan by Forkhead family transcription factors in the nervous system.
Bolukbasi E, Woodling NS, Ivanov DK, Adcott J, Foley A, Rajasingam A, Gittings LM, Aleyakpo B, Niccoli T, Thornton JM, Partridge L. Proceedings of the National Academy of Sciences of the United States of America Volume 118 (2021) DOI: 10.1073/pnas.2011491118
Massive expansion of human gut bacteriophage diversity.
Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD. Cell Volume 184 (2021) p.1098-1109.e9 DOI: 10.1016/j.cell.2021.01.029
Twelve years of SAMtools and BCFtools.
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. GigaScience Volume 10 (2021) DOI: 10.1093/gigascience/giab008
HTSlib: C library for reading/writing high-throughput sequencing data.
Bonfield JK, Marshall J, Danecek P, Li H, Ohan V, Whitwham A, Keane T, Davies RM. GigaScience Volume 10 (2021) DOI: 10.1093/gigascience/giab007
SARS-CoV-2 infection remodels the host protein thermal stability landscape.
Selkrig J, Stanifer M, Mateus A, Mitosch K, Barrio-Hernandez I, Rettel M, Kim H, Voogdt CGP, Walch P, Kee C, Kurzawa N, Stein F, Potel C, Jarzab A, Kuster B, Bartenschlager R, Boulant S, Beltrao P, Typas A, Savitski MM. Molecular systems biology Volume 17 (2021) p.e10188 DOI: 10.15252/msb.202010188
Drug Safety Data Curation and Modeling in ChEMBL: Boxed Warnings and Withdrawn Drugs.
Hunter FMI, Bento AP, Bosc N, Gaulton A, Hersey A, Leach AR. Chemical research in toxicology Volume 34 (2021) p.385-395 DOI: 10.1021/acs.chemrestox.0c00296
Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 2: a discussion of chemical and biological data.
Bender A, Cortes-Ciriano I. Drug discovery today Volume 26 (2021) p.1040-1052 DOI: 10.1016/j.drudis.2020.11.037
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The CovR regulatory network drives the evolution of Group B Streptococcus virulence
Mazzuoli M, Daunesse M, Varet H, Rosinski-Chupin I, Legendre R, Sismeiro O, Gominet M, Kaminski P, Glaser P, Chica C, Trieu-Cuot P, Firon A. Preprint DOI: 10.1101/2021.01.25.428120
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Meta-analysis reveals consistent immune response patterns in COVID-19 infected patients at single-cell resolution
Garg M, Li X, Moreno P, Papatheodorou I, Shu Y, Brazma A, Miao Z. Preprint DOI: 10.1101/2021.01.24.427089
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A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases and prostate cancer progression
Magraner-Pardo L, Laskowski RA, Pons T, Thornton JM. Preprint DOI: 10.1101/2021.01.21.427605
Identifying causative mechanisms linking early-life stress to psycho-cardio-metabolic multi-morbidity: The EarlyCause project.
Mariani N, Borsini A, Cecil CAM, Felix JF, Sebert S, Cattaneo A, Walton E, Milaneschi Y, Cochrane G, Amid C, Rajan J, Giacobbe J, Sanz Y, Agustí A, Sorg T, Herault Y, Miettunen J, Parmar P, Cattane N, Jaddoe V, Lötjönen J, Buisan C, González Ballester MA, Piella G, Gelpi JL, Lamers F, Penninx BWJH, Tiemeier H, von Tottleben M, Thiel R, Heil KF, Järvelin MR, Pariante C, Mansuy IM, Lekadir K. PloS one Volume 16 (2021) p.e0245475 DOI: 10.1371/journal.pone.0245475
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Optimising expression quantitative trait locus mapping workflows for single-cell studies
Cuomo AS, Alvari G, Azodi CB, McCarthy DJ, Bonder MJ, single-cell eQTLGen consortium. Preprint DOI: 10.1101/2021.01.20.427401
Correlative multimodal imaging: Building a community.
Walter A, Kleywegt GJ, Verkade P. Methods in cell biology Volume 162 (2021) p.417-430 DOI: 10.1016/bs.mcb.2020.12.010
A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain.
Joglekar A, Prjibelski A, Mahfouz A, Collier P, Lin S, Schlusche AK, Marrocco J, Williams SR, Haase B, Hayes A, Chew JG, Weisenfeld NI, Wong MY, Stein AN, Hardwick SA, Hunt T, Wang Q, Dieterich C, Bent Z, Fedrigo O, Sloan SA, Risso D, Jarvis ED, Flicek P, Luo W, Pitt GS, Frankish A, Smit AB, Ross ME, Tilgner HU. Nature communications Volume 12 (2021) p.463 DOI: 10.1038/s41467-020-20343-5
Sustainable data analysis with Snakemake.
Mölder F, Jablonski KP, Letcher B, Hall MB, Tomkins-Tinch CH, Sochat V, Forster J, Lee S, Twardziok SO, Kanitz A, Wilm A, Holtgrewe M, Rahmann S, Nahnsen S, Köster J. F1000Research Volume 10 (2021) p.33 DOI: 10.12688/f1000research.29032.2
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The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation
Wagner AH, Babb L, Alterovitz G, Baudis M, Brush M, Cameron DL, Cline M, Griffith M, Griffith OL, Hunt S, Kreda D, Lee J, Lopez J, Moyer E, Nelson T, Patel RY, Riehle K, Robinson PN, Rynearson S, Schuilenburg H, Tsukanov K, Walsh B, Konopko M, Rehm H, Yates AD, Freimuth RR, Hart RK. Preprint DOI: 10.1101/2021.01.15.426843
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Structural and dynamical analysis of integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19
Bannerman BP, Julvez J, Oarga A, Moreno P, Blundell TL, Floto RA. Preprint DOI: 10.21203/rs.3.rs-46892/v2
Neocles B. Leontis (1955 - 2020).
Moore PB, Petrov A, Westhof E, Zirbel CL. RNA (New York, N.Y.) (2021) DOI: 10.1261/rna.078673.121
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Validation of lipid-related therapeutic targets for coronary heart disease prevention using human genetics
Gordillo-Maranon M, Zwierzyna M, Charoen P, Drenos F, Chopade S, Shah T, Engmann J, Casas J, Chaturvedi N, Papacosta O, Wannamethee G, Wong A, Sofat R, Kivimaki M, Price J, Hughes A, Gaunt T, Lawlor D, Gaulton A, Hingorani A, Schmidt A, Finan C. Preprint DOI: 10.21203/rs.3.rs-122651/v1
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Mutation rates and selection on synonymous mutations in SARS-CoV-2
De Maio N, Walker CR, Turakhia Y, Lanfear R, Corbett-Detig R, Goldman N. Preprint DOI: 10.1101/2021.01.14.426705
Data-deposition protocols for correlative soft X-ray tomography and super-resolution structured illumination microscopy applications.
Iudin A, Sarkans U, Koronfel MA, Fish T, Dobbie I, Harkiolaki M, Patwardhan A, Kleywegt GJ. STAR protocols Volume 2 (2021) p.100253 DOI: 10.1016/j.xpro.2020.100253
The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors.
Harland LTG, Simon CS, Senft AD, Costello I, Greder L, Imaz-Rosshandler I, Göttgens B, Marioni JC, Bikoff EK, Porcher C, de Bruijn MFTR, Robertson EJ. Nature cell biology Volume 23 (2021) p.61-74 DOI: 10.1038/s41556-020-00611-8
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Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts.
Woo XY, Giordano J, Srivastava A, Zhao ZM, Lloyd MW, de Bruijn R, Suh YS, Patidar R, Chen L, Scherer S, Bailey MH, Yang CH, Cortes-Sanchez E, Xi Y, Wang J, Wickramasinghe J, Kossenkov AV, Rebecca VW, Sun H, Mashl RJ, Davies SR, Jeon R, Frech C, Randjelovic J, Rosains J, Galimi F, Bertotti A, Lafferty A, O'Farrell AC, Modave E, Lambrechts D, Ter Brugge P, Serra V, Marangoni E, El Botty R, Kim H, Kim JI, Yang HK, Lee C, Dean DA, Davis-Dusenbery B, Evrard YA, Doroshow JH, Welm AL, Welm BE, Lewis MT, Fang B, Roth JA, Meric-Bernstam F, Herlyn M, Davies MA, Ding L, Li S, Govindan R, Isella C, Moscow JA, Trusolino L, Byrne AT, Jonkers J, Bult CJ, Medico E, Chuang JH, PDXNET Consortium, EurOPDX Consortium. Nature genetics Volume 53 (2021) p.86-99 DOI: 10.1038/s41588-020-00750-6
Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk.
Kalkauskas A, Perron U, Sun Y, Goldman N, Baele G, Guindon S, De Maio N. PLoS computational biology Volume 17 (2021) p.e1008561 DOI: 10.1371/journal.pcbi.1008561
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Structure-function investigation of a new VUI-202012/01 SARS-CoV-2 variant
Singh J, Ehtesham NZ, Rahman SA, Hasnain SE. Preprint DOI: 10.1101/2021.01.01.425028
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.
Lazar T, Martínez-Pérez E, Quaglia F, Hatos A, Chemes LB, Iserte JA, Méndez NA, Garrone NA, Saldaño TE, Marchetti J, Rueda AJV, Bernadó P, Blackledge M, Cordeiro TN, Fagerberg E, Forman-Kay JD, Fornasari MS, Gibson TJ, Gomes GW, Gradinaru CC, Head-Gordon T, Jensen MR, Lemke EA, Longhi S, Marino-Buslje C, Minervini G, Mittag T, Monzon AM, Pappu RV, Parisi G, Ricard-Blum S, Ruff KM, Salladini E, Skepö M, Svergun D, Vallet SD, Varadi M, Tompa P, Tosatto SCE, Piovesan D. Nucleic acids research Volume 49 (2021) p.D404-D411 DOI: 10.1093/nar/gkaa1021
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. Systematic biology Volume 70 (2021) p.21-32 DOI: 10.1093/sysbio/syaa036
The Protein Data Bank Archive.
Velankar S, Burley SK, Kurisu G, Hoch JC, Markley JL. Methods in molecular biology (Clifton, N.J.) Volume 2305 (2021) p.3-21 DOI: 10.1007/978-1-0716-1406-8_1
High-performance macromolecular data delivery and visualization for the web. Corrigendum.
Sehnal D, Svobodová R, Berka K, Rose AS, Burley SK, Velankar S, Koča J. Acta crystallographica. Section D, Structural biology Volume 77 (2021) p.126 DOI: 10.1107/s205979832001606x
Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses.
Dugourd A, Kuppe C, Sciacovelli M, Gjerga E, Gabor A, Emdal KB, Vieira V, Bekker-Jensen DB, Kranz J, Bindels EMJ, Costa ASH, Sousa A, Beltrao P, Rocha M, Olsen JV, Frezza C, Kramann R, Saez-Rodriguez J. Molecular systems biology Volume 17 (2021) p.e9730 DOI: 10.15252/msb.20209730
From ArrayExpress to BioStudies.
Sarkans U, Füllgrabe A, Ali A, Athar A, Behrangi E, Diaz N, Fexova S, George N, Iqbal H, Kurri S, Munoz J, Rada J, Papatheodorou I, Brazma A. Nucleic acids research Volume 49 (2021) p.D1502-D1506 DOI: 10.1093/nar/gkaa1062
Genenames.org: the HGNC and VGNC resources in 2021.
Tweedie S, Braschi B, Gray K, Jones TEM, Seal RL, Yates B, Bruford EA. Nucleic acids research Volume 49 (2021) p.D939-D946 DOI: 10.1093/nar/gkaa980
Rfam 14: expanded coverage of metagenomic, viral and microRNA families.
Kalvari I, Nawrocki EP, Ontiveros-Palacios N, Argasinska J, Lamkiewicz K, Marz M, Griffiths-Jones S, Toffano-Nioche C, Gautheret D, Weinberg Z, Rivas E, Eddy SR, Finn RD, Bateman A, Petrov AI. Nucleic acids research Volume 49 (2021) p.D192-D200 DOI: 10.1093/nar/gkaa1047
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RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.
RNAcentral Consortium. Nucleic acids research Volume 49 (2021) p.D212-D220 DOI: 10.1093/nar/gkaa921
The InterPro protein families and domains database: 20 years on.
Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD. Nucleic acids research Volume 49 (2021) p.D344-D354 DOI: 10.1093/nar/gkaa977
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.
Tello-Ruiz MK, Naithani S, Gupta P, Olson A, Wei S, Preece J, Jiao Y, Wang B, Chougule K, Garg P, Elser J, Kumari S, Kumar V, Contreras-Moreira B, Naamati G, George N, Cook J, Bolser D, D'Eustachio P, Stein LD, Gupta A, Xu W, Regala J, Papatheodorou I, Kersey PJ, Flicek P, Taylor C, Jaiswal P, Ware D. Nucleic acids research Volume 49 (2021) p.D1452-D1463 DOI: 10.1093/nar/gkaa979
GENCODE 2021.
Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Howe KL, Hunt T, Izuogu OG, Johnson R, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Riera FC, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Wolf MY, Xu J, Yang YT, Yates A, Zerbino D, Zhang Y, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Tress ML, Flicek P. Nucleic acids research Volume 49 (2021) p.D916-D923 DOI: 10.1093/nar/gkaa1087
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UniProt: the universal protein knowledgebase in 2021.
UniProt Consortium. Nucleic acids research Volume 49 (2021) p.D480-D489 DOI: 10.1093/nar/gkaa1100
Europe PMC in 2020.
Ferguson C, Araújo D, Faulk L, Gou Y, Hamelers A, Huang Z, Ide-Smith M, Levchenko M, Marinos N, Nambiar R, Nassar M, Parkin M, Pi X, Rahman F, Rogers F, Roochun Y, Saha S, Selim M, Shafique Z, Sharma S, Stephenson D, Talo' F, Thouvenin A, Tirunagari S, Vartak V, Venkatesan A, Yang X, McEntyre J. Nucleic acids research Volume 49 (2021) p.D1507-D1514 DOI: 10.1093/nar/gkaa994
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The Gene Ontology resource: enriching a GOld mine.
Gene Ontology Consortium. Nucleic acids research Volume 49 (2021) p.D325-D334 DOI: 10.1093/nar/gkaa1113
Pfam: The protein families database in 2021.
Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, Tosatto SCE, Paladin L, Raj S, Richardson LJ, Finn RD, Bateman A. Nucleic acids research Volume 49 (2021) p.D412-D419 DOI: 10.1093/nar/gkaa913
The international nucleotide sequence database collaboration.
Arita M, Karsch-Mizrachi I, Cochrane G. Nucleic acids research Volume 49 (2021) p.D121-D124 DOI: 10.1093/nar/gkaa967
Open Targets Platform: supporting systematic drug-target identification and prioritisation.
Ochoa D, Hercules A, Carmona M, Suveges D, Gonzalez-Uriarte A, Malangone C, Miranda A, Fumis L, Carvalho-Silva D, Spitzer M, Baker J, Ferrer J, Raies A, Razuvayevskaya O, Faulconbridge A, Petsalaki E, Mutowo P, Machlitt-Northen S, Peat G, McAuley E, Ong CK, Mountjoy E, Ghoussaini M, Pierleoni A, Papa E, Pignatelli M, Koscielny G, Karim M, Schwartzentruber J, Hulcoop DG, Dunham I, McDonagh EM. Nucleic acids research Volume 49 (2021) p.D1302-D1310 DOI: 10.1093/nar/gkaa1027
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Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics.
Ghoussaini M, Mountjoy E, Carmona M, Peat G, Schmidt EM, Hercules A, Fumis L, Miranda A, Carvalho-Silva D, Buniello A, Burdett T, Hayhurst J, Baker J, Ferrer J, Gonzalez-Uriarte A, Jupp S, Karim MA, Koscielny G, Machlitt-Northen S, Malangone C, Pendlington ZM, Roncaglia P, Suveges D, Wright D, Vrousgou O, Papa E, Parkinson H, MacArthur JAL, Todd JA, Barrett JC, Schwartzentruber J, Hulcoop DG, Ochoa D, McDonagh EM, Dunham I. Nucleic acids research Volume 49 (2021) p.D1311-D1320 DOI: 10.1093/nar/gkaa840
The Organoid Cell Atlas.
Bock C, Boutros M, Camp JG, Clarke L, Clevers H, Knoblich JA, Liberali P, Regev A, Rios AC, Stegle O, Stunnenberg HG, Teichmann SA, Treutlein B, Vries RGJ, Human Cell Atlas ‘Biological Network’ Organoids. Nature biotechnology Volume 39 (2021) p.13-17 DOI: 10.1038/s41587-020-00762-x
The European Nucleotide Archive in 2020.
Harrison PW, Ahamed A, Aslam R, Alako BTF, Burgin J, Buso N, Courtot M, Fan J, Gupta D, Haseeb M, Holt S, Ibrahim T, Ivanov E, Jayathilaka S, Balavenkataraman Kadhirvelu V, Kumar M, Lopez R, Kay S, Leinonen R, Liu X, O'Cathail C, Pakseresht A, Park Y, Pesant S, Rahman N, Rajan J, Sokolov A, Vijayaraja S, Waheed Z, Zyoud A, Burdett T, Cochrane G. Nucleic acids research Volume 49 (2021) p.D82-D85 DOI: 10.1093/nar/gkaa1028
Ensembl 2021.
Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, El Houdaigui B, Fatima R, Gall A, Garcia Giron C, Grego T, Guijarro-Clarke C, Haggerty L, Hemrom A, Hourlier T, Izuogu OG, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Gonzalez Martinez J, Marugán JC, Maurel T, McMahon AC, Mohanan S, Moore B, Muffato M, Oheh DN, Paraschas D, Parker A, Parton A, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Steed E, Szpak M, Szuba M, Taylor K, Thormann A, Threadgold G, Walts B, Winterbottom A, Chakiachvili M, Chaubal A, De Silva N, Flint B, Frankish A, Hunt SE, IIsley GR, Langridge N, Loveland JE, Martin FJ, Mudge JM, Morales J, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Cunningham F, Yates AD, Zerbino DR, Flicek P. Nucleic acids research Volume 49 (2021) p.D884-D891 DOI: 10.1093/nar/gkaa942
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis.
Cantelli G, Cochrane G, Brooksbank C, McDonagh E, Flicek P, McEntyre J, Birney E, Apweiler R. Nucleic acids research Volume 49 (2021) p.D29-D37 DOI: 10.1093/nar/gkaa1077

2020

OpenStats: A robust and scalable software package for reproducible analysis of high-throughput phenotypic data.
Haselimashhadi H, Mason JC, Mallon AM, Smedley D, Meehan TF, Parkinson H. PloS one Volume 15 (2020) p.e0242933 DOI: 10.1371/journal.pone.0242933
An automated protocol for modelling peptide substrates to proteases.
Ochoa R, Magnitov M, Laskowski RA, Cossio P, Thornton JM. BMC bioinformatics Volume 21 (2020) p.586 DOI: 10.1186/s12859-020-03931-6
Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density.
Swan AL, Schütt C, Rozman J, Del Mar Muñiz Moreno M, Brandmaier S, Simon M, Leuchtenberger S, Griffiths M, Brommage R, Keskivali-Bond P, Grallert H, Werner T, Teperino R, Becker L, Miller G, Moshiri A, Seavitt JR, Cissell DD, Meehan TF, Acar EF, Lelliott CJ, Flenniken AM, Champy MF, Sorg T, Ayadi A, Braun RE, Cater H, Dickinson ME, Flicek P, Gallegos J, Ghirardello EJ, Heaney JD, Jacquot S, Lally C, Logan JG, Teboul L, Mason J, Spielmann N, McKerlie C, Murray SA, Nutter LMJ, Odfalk KF, Parkinson H, Prochazka J, Reynolds CL, Selloum M, Spoutil F, Svenson KL, Vales TS, Wells SE, White JK, Sedlacek R, Wurst W, Lloyd KCK, Croucher PI, Fuchs H, Williams GR, Bassett JHD, Gailus-Durner V, Herault Y, Mallon AM, Brown SDM, Mayer-Kuckuk P, Hrabe de Angelis M, IMPC Consortium. PLoS genetics Volume 16 (2020) p.e1009190 DOI: 10.1371/journal.pgen.1009190
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Influence of HLA class II polymorphism on predicted cellular immunity against SARS-CoV-2 at the population and individual level
Copley HC, Gragert L, Leach AR, Kosmoliaptsis V. Preprint DOI: 10.1101/2020.12.24.424326
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Patterns of within-host genetic diversity in SARS-CoV-2
Tonkin-Hill G, Martincorena I, Amato R, Lawson ARJ, Gerstung M, Johnston I, Jackson DK, Park NR, Lensing SV, Quail MA, Gonçalves S, Ariani C, Chapman MS, Hamilton WL, Meredith LW, Hall G, Jahun AS, Chaudhry Y, Hosmillo M, Pinckert ML, Georgana I, Yakovleva A, Caller LG, Caddy SL, Feltwell T, Khokhar FA, Houldcroft CJ, Curran MD, Parmar S, Alderton A, Nelson R, Harrison E, Sillitoe J, Bentley SD, Barrett JC, Torok ME, Goodfellow IG, Langford C, Kwiatkowski D, The COVID-19 Genomics UK (COG-UK) Consortium, Wellcome Sanger Institute COVID-19 Surveillance Team. Preprint DOI: 10.1101/2020.12.23.424229
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Coordinated Changes in Gene Expression Kinetics Underlie both Mouse and Human Erythroid Maturation
Barile M, Imaz-Rosshandler I, Inzani I, Ghazanfar S, Nichols J, Marioni JC, Guibentif C, Göttgens B. Preprint DOI: 10.1101/2020.12.21.423773
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The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data
De Silva NH, Bhai J, Chakiachvili M, Contreras-Moreira B, Cummins C, Frankish A, Gall A, Genez T, Howe KL, Hunt SE, Martin FJ, Moore B, Ogeh D, Parker A, Parton A, Ruffier M, Sakthivel MP, Sheppard D, Tate J, Thormann A, Thybert D, Trevanion SJ, Winterbottom A, Zerbino DR, Finn RD, Flicek P, Yates AD. Preprint DOI: 10.1101/2020.12.18.422865
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League of Brazilian Bioinformatics: a competition framework to promote scientific training
Carvalho LM, Coimbra NAR, Neves MRC, Fonseca NJ, Costa MA, Horacio ECA, Riyuzo R, Aburjaile FF, Nagamatsu ST. Preprint DOI: 10.1101/2020.12.17.423357
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Bender A, Cortés-Ciriano I. Drug discovery today Volume 26 (2021) p.511-524 DOI: 10.1016/j.drudis.2020.12.009
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HTSlib - C library for reading/writing high-throughput sequencing data
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The Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection
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Deep learning prediction of BRAF-RAS gene expression signature identifies noninvasive follicular thyroid neoplasms with papillary-like nuclear features.
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Universal Spectrum Identifier for mass spectra
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Discovery of Fibrillar Adhesins across Bacterial Species
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Metabolomics - the stethoscope for the 21st century.
Ashrafian H, Sounderajah V, Glen R, Ebbels T, Blaise BJ, Kalra D, Kultima K, Spjuth O, Tenori L, Salek R, Kale N, Haug K, Schober D, Rocca-Serra P, O'Donovan C, Steinbeck C, Cano I, de Atauri P, Cascante M. Medical principles and practice : international journal of the Kuwait University, Health Science Centre (2020) DOI: 10.1159/000513545
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Phylogenetic Novelty Scores: a New Approach for Weighting Genetic Sequences
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Biocuration - mapping resources and needs
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Towards a unified open access dataset of molecular interactions.
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NCKAP1L defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammation.
Castro CN, Rosenzwajg M, Carapito R, Shahrooei M, Konantz M, Khan A, Miao Z, Groß M, Tranchant T, Radosavljevic M, Paul N, Stemmelen T, Pitoiset F, Hirschler A, Nespola B, Molitor A, Rolli V, Pichot A, Faletti LE, Rinaldi B, Friant S, Mednikov M, Karauzum H, Aman MJ, Carapito C, Lengerke C, Ziaee V, Eyaid W, Ehl S, Alroqi F, Parvaneh N, Bahram S. The Journal of experimental medicine Volume 217 (2020) DOI: 10.1084/jem.20192275
Author Correction: A dynamic COVID-19 immune signature includes associations with poor prognosis.
Laing AG, Lorenc A, Del Molino Del Barrio I, Das A, Fish M, Monin L, Muñoz-Ruiz M, McKenzie DR, Hayday TS, Francos-Quijorna I, Kamdar S, Joseph M, Davies D, Davis R, Jennings A, Zlatareva I, Vantourout P, Wu Y, Sofra V, Cano F, Greco M, Theodoridis E, Freedman JD, Gee S, Chan JNE, Ryan S, Bugallo-Blanco E, Peterson P, Kisand K, Haljasmägi L, Chadli L, Moingeon P, Martinez L, Merrick B, Bisnauthsing K, Brooks K, Ibrahim MAA, Mason J, Lopez Gomez F, Babalola K, Abdul-Jawad S, Cason J, Mant C, Seow J, Graham C, Doores KJ, Di Rosa F, Edgeworth J, Shankar-Hari M, Hayday AC. Nature medicine Volume 26 (2020) p.1951 DOI: 10.1038/s41591-020-01186-5
GRaSP: a graph-based residue neighborhood strategy to predict binding sites.
Santana CA, Silveira SA, Moraes JPA, Izidoro SC, de Melo-Minardi RC, Ribeiro AJM, Tyzack JD, Borkakoti N, Thornton JM. Bioinformatics (Oxford, England) Volume 36 (2020) p.i726-i734 DOI: 10.1093/bioinformatics/btaa805
Fine-tuning autophagy maximises lifespan and is associated with changes in mitochondrial gene expression in Drosophila.
Bjedov I, Cochemé HM, Foley A, Wieser D, Woodling NS, Castillo-Quan JI, Norvaisas P, Lujan C, Regan JC, Toivonen JM, Murphy MP, Thornton J, Kinghorn KJ, Neufeld TP, Cabreiro F, Partridge L. PLoS genetics Volume 16 (2020) p.e1009083 DOI: 10.1371/journal.pgen.1009083
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Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L, PCAWG Consortium. Nature communications Volume 11 (2020) p.6232 DOI: 10.1038/s41467-020-20128-w
High-performance macromolecular data delivery and visualization for the web.
Sehnal D, Svobodová R, Berka K, Rose AS, Burley SK, Velankar S, Koča J. Acta crystallographica. Section D, Structural biology Volume 76 (2020) p.1167-1173 DOI: 10.1107/s2059798320014515
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Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis.
Dewan R, Chia R, Ding J, Hickman RA, Stein TD, Abramzon Y, Ahmed S, Sabir MS, Portley MK, Tucci A, Ibáñez K, Shankaracharya FNU, Keagle P, Rossi G, Caroppo P, Tagliavini F, Waldo ML, Johansson PM, Nilsson CF, American Genome Center (TAGC), FALS Sequencing Consortium, Genomics England Research Consortium, International ALS/FTD Genomics Consortium (iAFGC), International FTD Genetics Consortium (IFGC), International LBD Genomics Consortium (iLBDGC), NYGC ALS Consortium, PROSPECT Consortium, Rowe JB, Benussi L, Binetti G, Ghidoni R, Jabbari E, Viollet C, Glass JD, Singleton AB, Silani V, Ross OA, Ryten M, Torkamani A, Tanaka T, Ferrucci L, Resnick SM, Pickering-Brown S, Brady CB, Kowal N, Hardy JA, Van Deerlin V, Vonsattel JP, Harms MB, Morris HR, Ferrari R, Landers JE, Chiò A, Gibbs JR, Dalgard CL, Scholz SW, Traynor BJ. Neuron Volume 109 (2021) p.448-460.e4 DOI: 10.1016/j.neuron.2020.11.005
Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community.
Sala C, Mordhorst H, Grützke J, Brinkmann A, Petersen TN, Poulsen C, Cotter PD, Crispie F, Ellis RJ, Castellani G, Amid C, Hakhverdyan M, Guyader SL, Manfreda G, Mossong J, Nitsche A, Ragimbeau C, Schaeffer J, Schlundt J, Tay MYF, Aarestrup FM, Hendriksen RS, Pamp SJ, De Cesare A. Microorganisms Volume 8 (2020) DOI: 10.3390/microorganisms8121861
Mining a GWAS of Severe Covid-19.
Karim M, Dunham I, Ghoussaini M. The New England journal of medicine Volume 383 (2020) p.2588-2589 DOI: 10.1056/nejmc2025747
From FAANG to fork: application of highly annotated genomes to improve farmed animal production.
Clark EL, Archibald AL, Daetwyler HD, Groenen MAM, Harrison PW, Houston RD, Kühn C, Lien S, Macqueen DJ, Reecy JM, Robledo D, Watson M, Tuggle CK, Giuffra E. Genome biology Volume 21 (2020) p.285 DOI: 10.1186/s13059-020-02197-8
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Milo: differential abundance testing on single-cell data using k-NN graphs
Dann E, Henderson NC, Teichmann SA, Morgan MD, Marioni JC. Preprint DOI: 10.1101/2020.11.23.393769
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Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19
Gaziano L, Giambartolomei C, Pereira AC, Gaulton A, Posner DC, Swanson SA, Ho Y, Iyengar SK, Kosik NM, Vujkovic M, Gagnon DR, Bento AP, Beltrao P, Barrio-Hernandez I, Rönnblom L, Hagberg N, Lundtoft C, Langenberg C, Pietzner M, Valentine D, Allara E, Surendran P, Burgess S, Zhao JH, Peters JE, Prins BP, Danesh J, Devineni P, Shi Y, Lynch KE, DuVall SL, Garcon H, Thomann LO, Zhou JJ, Gorman BR, Huffman JE, O’Donnell CJ, Tsao PS, Beckham JC, Pyarajan S, Muralidhar S, Huang GD, Ramoni R, Hung AM, Chang K, Sun YV, Joseph J, Leach AR, Edwards TL, Cho K, Gaziano JM, Butterworth AS, Casas JP. Preprint DOI: 10.1101/2020.11.19.20234120
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A comprehensive analysis of the global human gut archaeome from a thousand genome catalogue
Chibani CM, Mahnert A, Borrel G, Almeida A, Werner A, Brugere J, Gribaldo S, Finn RD, Schmitz RA, Moissl-Eichinger C. Preprint DOI: 10.1101/2020.11.21.392621
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Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis
Lohoff T, Ghazanfar S, Missarova A, Koulena N, Pierson N, Griffiths J, Bardot E, Eng C, Tyser R, Argelaguet R, Guibentif C, Srinivas S, Briscoe J, Simons B, Hadjantonakis A, Göttgens B, Reik W, Nichols J, Cai L, Marioni J. Preprint DOI: 10.1101/2020.11.20.391896
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SARS-CoV-2 infection remodels the host protein thermal stability landscape
Selkrig J, Stanifer M, Mateus A, Mitosch K, Barrio-Hernandez I, Rettel M, Kim H, Voogdt C, Walch P, Kee C, Kurzawa N, Stein F, Potel C, Jarzab A, Kuster B, Bartenschlager R, Boulant S, Beltrao P, Typas A, Savitski M. Preprint DOI: 10.21203/rs.3.rs-105193/v1
Stability of SARS-CoV-2 phylogenies.
Turakhia Y, De Maio N, Thornlow B, Gozashti L, Lanfear R, Walker CR, Hinrichs AS, Fernandes JD, Borges R, Slodkowicz G, Weilguny L, Haussler D, Goldman N, Corbett-Detig R. PLoS genetics Volume 16 (2020) p.e1009175 DOI: 10.1371/journal.pgen.1009175
Sexual dimorphism in trait variability and its eco-evolutionary and statistical implications.
Zajitschek SR, Zajitschek F, Bonduriansky R, Brooks RC, Cornwell W, Falster DS, Lagisz M, Mason J, Senior AM, Noble DW, Nakagawa S. eLife Volume 9 (2020) DOI: 10.7554/elife.63170
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MegaGO: a fast yet powerful approach to assess functional similarity across meta-omics data sets
Verschaffelt P, Van Den Bossche T, Gabriel W, Burdukiewicz M, Soggiu A, Martens L, Renard BY, Schiebenhoefer H, Mesuere B. Preprint DOI: 10.1101/2020.11.16.384834
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Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics
Kleshchevnikov V, Shmatko A, Dann E, Aivazidis A, King HW, Li T, Lomakin A, Kedlian V, Jain MS, Park JS, Ramona L, Tuck E, Arutyunyan A, Vento-Tormo R, Gerstung M, James L, Stegle O, Bayraktar OA. Preprint DOI: 10.1101/2020.11.15.378125
Cell Surface Mechanics Gate Embryonic Stem Cell Differentiation.
Bergert M, Lembo S, Sharma S, Russo L, Milovanović D, Gretarsson KH, Börmel M, Neveu PA, Hackett JA, Petsalaki E, Diz-Muñoz A. Cell stem cell Volume 28 (2021) p.209-216.e4 DOI: 10.1016/j.stem.2020.10.017
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ISA API: An open platform for interoperable life science experimental metadata
Johnson D, Cochrane K, Davey RP, Etuk A, Gonzalez-Beltran A, Haug K, Izzo M, Larralde M, Lawson TN, Minotto A, Moreno P, Nainala VC, O’Donovan C, Pireddu L, Roger P, Shaw F, Steinbeck C, Weber RJM, Sansone S, Rocca-Serra P. Preprint DOI: 10.1101/2020.11.13.382119
Eco-Evolutionary Effects of Bacterial Cooperation on Phage Therapy: An Unknown Risk?
Cazares A, García-Contreras R, Pérez-Velázquez J. Frontiers in microbiology Volume 11 (2020) p.590294 DOI: 10.3389/fmicb.2020.590294
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Nucleotide-resolution bacterial pan-genomics with reference graphs
Colquhoun RM, Hall MB, Lima L, Roberts LW, Malone KM, Hunt M, Letcher B, Hawkey J, George S, Pankhurst L, Iqbal Z. Preprint DOI: 10.1101/2020.11.12.380378
De Novo VPS4A Mutations Cause Multisystem Disease with Abnormal Neurodevelopment.
Rodger C, Flex E, Allison RJ, Sanchis-Juan A, Hasenahuer MA, Cecchetti S, French CE, Edgar JR, Carpentieri G, Ciolfi A, Pantaleoni F, Bruselles A, Genomics England Research Consortium, Onesimo R, Zampino G, Marcon F, Siniscalchi E, Lees M, Krishnakumar D, McCann E, Yosifova D, Jarvis J, Kruer MC, Marks W, Campbell J, Allen LE, Gustincich S, Raymond FL, Tartaglia M, Reid E. American journal of human genetics Volume 107 (2020) p.1129-1148 DOI: 10.1016/j.ajhg.2020.10.012
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A reference map of potential determinants for the human serum metabolome.
Bar N, Korem T, Weissbrod O, Zeevi D, Rothschild D, Leviatan S, Kosower N, Lotan-Pompan M, Weinberger A, Le Roy CI, Menni C, Visconti A, Falchi M, Spector TD, IMI DIRECT consortium, Adamski J, Franks PW, Pedersen O, Segal E. Nature Volume 588 (2020) p.135-140 DOI: 10.1038/s41586-020-2896-2
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A FGF2-mediated incoherent feedforward loop induces Erk inhibition and promotes naïve pluripotency
Gharibi B, Gonçalves E, Nashun B, Montoya A, Mankalow K, Strohbuecker S, Sheriff RSM, Cicarrelli A, Carvalho J, Nye E, Kramer H, Rosewell I, Hajkova P, Beltrao P, Santos SDM. Preprint DOI: 10.1101/2020.11.11.378869
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Short-range template switching in great ape genomes explored using a pair hidden Markov model
Walker CR, Scally A, De Maio N, Goldman N. Preprint DOI: 10.1101/2020.11.09.374694
Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm.
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Whole genome sequencing for diagnosis of neurological repeat expansion disorders
Ibanez K, Polke J, Hagelstrom T, Dolzhenko E, Pasko D, Thomas E, Daugherty L, Kasperaviciute D, McDonagh EM, Smith KR, Martin AR, Polychronopoulos D, Angus-Leppan H, Bhatia KP, Davison JE, Festenstein R, Fratta P, Giunti P, Howard R, Prasad Korlipara LV, Laurá M, McEntagart M, Menzies L, Morris H, Reilly MM, Robinson R, Rosser E, Faravelli F, Schrag A, Schott JM, Warner TT, Wood NW, Bourn D, Eggleton K, Labrum R, Twiss P, Abbs S, Santos L, Almheiri G, Sheikh I, Vandrovcova J, Patch C, Taylor Tavares AL, Hyder Z, Need A, Brittain H, Baple E, Moutsianas L, Deshpande V, Perry DL, Ajay S, Chawla A, Rajan V, Oprych K, Chinnery PF, Douglas A, Wilson G, Ellard S, Temple K, Mumford A, McMullan D, Naresh K, Flinter F, Taylor JC, Greenhalgh L, Newman W, Brennan P, Sayer JA, Raymond FL, Chitty LS, Deans ZC, Hill S, Fowler T, Scott R, Houlden H, Rendon A, Caulfield MJ, Eberle MA, Taft RJ, Tucci A, Genomics England Research Consortium. Preprint DOI: 10.1101/2020.11.06.371716
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Analysing the Yeast Complexome - The Complex Portal rising to the challenge
Meldal BHM, Pons C, Perfetto L, Del-Toro N, Wong E, Aloy P, Hermjakob H, Orchard S, Porras P. Preprint DOI: 10.1101/2020.11.03.367086
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CoDNaS-RNA: a database of Conformational Diversity in the Native State of RNA
Buitrón MG, Tunque Cahui RR, Ríos EG, Hirsh L, Fornasari MS, Parisi G, Palopoli N. Preprint DOI: 10.1101/2020.10.30.362590
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.
MacDougall A, Volynkin V, Saidi R, Poggioli D, Zellner H, Hatton-Ellis E, Joshi V, O'Donovan C, Orchard S, Auchincloss AH, Baratin D, Bolleman J, Coudert E, de Castro E, Hulo C, Masson P, Pedruzzi I, Rivoire C, Arighi C, Wang Q, Chen C, Huang H, Garavelli J, Vinayaka CR, Yeh LS, Natale DA, Laiho K, Martin MJ, Renaux A, Pichler K, UniProt Consortium. Bioinformatics (Oxford, England) Volume 36 (2020) p.4643-4648 DOI: 10.1093/bioinformatics/btaa485
BioModels Parameters: a treasure trove of parameter values from published systems biology models.
Glont M, Arankalle C, Tiwari K, Nguyen TVN, Hermjakob H, Malik-Sheriff RS. Bioinformatics (Oxford, England) Volume 36 (2020) p.4649-4654 DOI: 10.1093/bioinformatics/btaa560
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UCSC Cell Browser: Visualize Your Single-Cell Data
Speir ML, Bhaduri A, Markov NS, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA, Seninge L, Kent WJ, Haeussler M. Preprint DOI: 10.1101/2020.10.30.361162
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Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny
Zimmermann B, Robb SM, Genikhovich G, Fropf WJ, Weilguny L, He S, Chen S, Lovegrove-Walsh J, Hill EM, Ragkousi K, Praher D, Fredman D, Moran Y, Gibson MC, Technau U. Preprint DOI: 10.1101/2020.10.30.359448
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MAIP: A web service for predicting blood-stage malaria inhibitors
Bosc N, Felix E, Arcila R, Mendez D, Saunders M, Green D, Ochoada J, Shelat A, Martin E, Iyer P, Engkvist O, Verras A, Duffy J, Burrows J, Gardner M, Leach A. Preprint DOI: 10.21203/rs.3.rs-41814/v2
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Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei
Hawkey J, Paranagama K, Baker KS, Bengtsson RJ, Weill F, Thomson NR, Baker S, Cerdeira L, Iqbal Z, Hunt M, Ingle DJ, Dallman TJ, Jenkins C, Williamson DA, Holt KE. Preprint DOI: 10.1101/2020.10.29.360040
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Evaluation of Methods for Protein Representation Learning: A Quantitative Analysis
Unsal S, Ataş H, Albayrak M, Turhan K, Acar AC, Doğan T. Preprint DOI: 10.1101/2020.10.28.359828
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COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
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A GO catalogue of human DNA-binding transcription factors
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The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research
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From FAANG to Fork: Application of Highly Annotated Genomes to Improve Farmed Animal Production
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Global Public Perceptions of Genomic Data Sharing: What Shapes the Willingness to Donate DNA and Health Data?
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Understanding and predicting ciprofloxacin minimum inhibitory concentration in Escherichia coli with machine learning.
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COVID-19 and beyond: a call for action and audacious solidarity to all the citizens and nations, it is humanity’s fight
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Host adaptation in gut Firmicutes is associated with sporulation loss and altered colonisation patterns
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Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison
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Massive expansion of human gut bacteriophage diversity
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Data Forensic Determination of the Accuracy of International COVID-19 Reporting: Using Zipf's Law for Pandemic Investigation
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Genomic and Phenotypic Analyses of Acinetobacter baumannii Isolates From Three Tertiary Care Hospitals in Thailand.
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Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases.
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REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets
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Molecular Analyses of Over Hundred Sixty Clinical Isolates of SARS-CoV-2: Insights on Likely Origin, Evolution and Spread, and Possible Intervention
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A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
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Pitfalls in re-analysis of observational omics studies: a post-mortem of the human pathology atlas
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Modeling protein interactions and complexes in CAPRI: Seventh CAPRI evaluation meeting, April 3-5 EMBL-EBI, Hinxton, UK.
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Efficient and Flexible Integration of Variant Characteristics in Rare Variant Association Studies Using Integrated Nested Laplace Approximation
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Freeman TM, Genomics England Research Consortium, Wang D, Harris J. Genome research Volume 30 (2020) p.415-426 DOI: 10.1101/gr.255349.119
Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections.
Filippi CV, Merino GA, Montecchia JF, Aguirre NC, Rivarola M, Naamati G, Fass MI, Álvarez D, Di Rienzo J, Heinz RA, Contreras Moreira B, Lia VV, Paniego NB. Genes Volume 11 (2020) DOI: 10.3390/genes11030283
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Motif analysis in co-expression networks reveals regulatory elements in plants: The peach as a model
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Enzyme annotation in UniProtKB using Rhea.
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Kramarz B, Huntley RP, Rodríguez-López M, Roncaglia P, Saverimuttu SCC, Parkinson H, Bandopadhyay R, Martin MJ, Orchard S, Hooper NM, Brough D, Lovering RC. Journal of Alzheimer's disease : JAD Volume 75 (2020) p.1417-1435 DOI: 10.3233/jad-200207
IPD-IMGT/HLA Database.
Robinson J, Barker DJ, Georgiou X, Cooper MA, Flicek P, Marsh SGE. Nucleic acids research Volume 48 (2020) p.D948-D955 DOI: 10.1093/nar/gkz950
The International Genome Sample Resource (IGSR) collection of open human genomic variation resources.
Fairley S, Lowy-Gallego E, Perry E, Flicek P. Nucleic acids research Volume 48 (2020) p.D941-D947 DOI: 10.1093/nar/gkz836
Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics.
Walzer M, Vizcaíno JA. Methods in molecular biology (Clifton, N.J.) Volume 2051 (2020) p.345-371 DOI: 10.1007/978-1-4939-9744-2_15
The European Nucleotide Archive in 2019.
Amid C, Alako BTF, Balavenkataraman Kadhirvelu V, Burdett T, Burgin J, Fan J, Harrison PW, Holt S, Hussein A, Ivanov E, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martinez-Villacorta J, Milano A, Pakseresht A, Rahman N, Rajan J, Reddy K, Richards E, Smirnov D, Sokolov A, Vijayaraja S, Cochrane G. Nucleic acids research Volume 48 (2020) p.D70-D76 DOI: 10.1093/nar/gkz1063
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences.
Cook CE, Stroe O, Cochrane G, Birney E, Apweiler R. Nucleic acids research Volume 48 (2020) p.D17-D23 DOI: 10.1093/nar/gkz1033
GlyGen: Computational and Informatics Resources for Glycoscience.
York WS, Mazumder R, Ranzinger R, Edwards N, Kahsay R, Aoki-Kinoshita KF, Campbell MP, Cummings RD, Feizi T, Martin M, Natale DA, Packer NH, Woods RJ, Agarwal G, Arpinar S, Bhat S, Blake J, Castro LJG, Fochtman B, Gildersleeve J, Goldman R, Holmes X, Jain V, Kulkarni S, Mahadik R, Mehta A, Mousavi R, Nakarakommula S, Navelkar R, Pattabiraman N, Pierce MJ, Ross K, Vasudev P, Vora J, Williamson T, Zhang W. Glycobiology Volume 30 (2020) p.72-73 DOI: 10.1093/glycob/cwz080
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Amyloid Beta Hypothesis in Alzheimer's Disease: Major Culprits and Recent Therapeutic Strategies.
Vijayan D, Chandra R. Current drug targets Volume 21 (2020) p.148-166 DOI: 10.2174/1389450120666190806153206
Plant Reactome: a knowledgebase and resource for comparative pathway analysis.
Naithani S, Gupta P, Preece J, D'Eustachio P, Elser JL, Garg P, Dikeman DA, Kiff J, Cook J, Olson A, Wei S, Tello-Ruiz MK, Mundo AF, Munoz-Pomer A, Mohammed S, Cheng T, Bolton E, Papatheodorou I, Stein L, Ware D, Jaiswal P. Nucleic acids research Volume 48 (2020) p.D1093-D1103 DOI: 10.1093/nar/gkz996
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Urban M, Cuzick A, Seager J, Wood V, Rutherford K, Venkatesh SY, De Silva N, Martinez MC, Pedro H, Yates AD, Hassani-Pak K, Hammond-Kosack KE. Nucleic acids research Volume 48 (2020) p.D613-D620 DOI: 10.1093/nar/gkz904
Ensembl Genomes 2020-enabling non-vertebrate genomic research.
Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W, Allen J, Alvarez-Jarreta J, Barba M, Bolser DM, Cambell L, Carbajo M, Chakiachvili M, Christensen M, Cummins C, Cuzick A, Davis P, Fexova S, Gall A, George N, Gil L, Gupta P, Hammond-Kosack KE, Haskell E, Hunt SE, Jaiswal P, Janacek SH, Kersey PJ, Langridge N, Maheswari U, Maurel T, McDowall MD, Moore B, Muffato M, Naamati G, Naithani S, Olson A, Papatheodorou I, Patricio M, Paulini M, Pedro H, Perry E, Preece J, Rosello M, Russell M, Sitnik V, Staines DM, Stein J, Tello-Ruiz MK, Trevanion SJ, Urban M, Wei S, Ware D, Williams G, Yates AD, Flicek P. Nucleic acids research Volume 48 (2020) p.D689-D695 DOI: 10.1093/nar/gkz890
Ensembl 2020.
Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Marugán JC, Cummins C, Davidson C, Dodiya K, Fatima R, Gall A, Giron CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Lavidas I, Le T, Lemos D, Martinez JG, Maurel T, McDowall M, McMahon A, Mohanan S, Moore B, Nuhn M, Oheh DN, Parker A, Parton A, Patricio M, Sakthivel MP, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sycheva M, Szuba M, Taylor K, Thormann A, Threadgold G, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Flint B, Frankish A, Hunt SE, IIsley G, Kostadima M, Langridge N, Loveland JE, Martin FJ, Morales J, Mudge JM, Muffato M, Perry E, Ruffier M, Trevanion SJ, Cunningham F, Howe KL, Zerbino DR, Flicek P. Nucleic acids research Volume 48 (2020) p.D682-D688 DOI: 10.1093/nar/gkz966
MGnify: the microbiome analysis resource in 2020.
Mitchell AL, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G, Crusoe MR, Kale V, Potter SC, Richardson LJ, Sakharova E, Scheremetjew M, Korobeynikov A, Shlemov A, Kunyavskaya O, Lapidus A, Finn RD. Nucleic acids research Volume 48 (2020) p.D570-D578 DOI: 10.1093/nar/gkz1035
A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets.
Breuza L, Arighi CN, Argoud-Puy G, Casals-Casas C, Estreicher A, Famiglietti ML, Georghiou G, Gos A, Gruaz-Gumowski N, Hinz U, Hyka-Nouspikel N, Kramarz B, Lovering RC, Lussi Y, Magrane M, Masson P, Perfetto L, Poux S, Rodriguez-Lopez M, Stoeckert C, Sundaram S, Wang LS, Wu E, Orchard S, IMEx Consortium, UniProt Consortium. Journal of Alzheimer's disease : JAD Volume 77 (2020) p.257-273 DOI: 10.3233/jad-200206
PDBe: improved findability of macromolecular structure data in the PDB.
Armstrong DR, Berrisford JM, Conroy MJ, Gutmanas A, Anyango S, Choudhary P, Clark AR, Dana JM, Deshpande M, Dunlop R, Gane P, Gáborová R, Gupta D, Haslam P, Koča J, Mak L, Mir S, Mukhopadhyay A, Nadzirin N, Nair S, Paysan-Lafosse T, Pravda L, Sehnal D, Salih O, Smart O, Tolchard J, Varadi M, Svobodova-Vařeková R, Zaki H, Kleywegt GJ, Velankar S. Nucleic acids research Volume 48 (2020) p.D335-D343 DOI: 10.1093/nar/gkz990
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Revenant: a database of resurrected proteins.
Carletti MS, Monzon AM, Garcia-Rios E, Benitez G, Hirsh L, Fornasari MS, Parisi G. Database : the journal of biological databases and curation Volume 2020 (2020) DOI: 10.1093/database/baaa031
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.
Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, Hermjakob H, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA. Nucleic acids research Volume 48 (2020) p.D1145-D1152 DOI: 10.1093/nar/gkz984
PhaSepDB: a database of liquid-liquid phase separation related proteins.
You K, Huang Q, Yu C, Shen B, Sevilla C, Shi M, Hermjakob H, Chen Y, Li T. Nucleic acids research Volume 48 (2020) p.D354-D359 DOI: 10.1093/nar/gkz847
The reactome pathway knowledgebase.
Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. Nucleic acids research Volume 48 (2020) p.D498-D503 DOI: 10.1093/nar/gkz1031
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Investigating Sex Related Phenotype Changes in Knockout Mice by Applying Deep Learning to X-Ray Images
Babalola K, Mashhadi HH, Muñoz-Fuentes V, Mason J, Meehan T. Communications in Computer and Information Science Volume 1248 (2020) p.359-369 DOI: 10.1007/978-3-030-52791-4_28
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Alliance of Genome Resources Portal: unified model organism research platform.
Alliance of Genome Resources Consortium. Nucleic acids research Volume 48 (2020) p.D650-D658 DOI: 10.1093/nar/gkz813
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation.
Sillitoe I, Andreeva A, Blundell TL, Buchan DWA, Finn RD, Gough J, Jones D, Kelley LA, Paysan-Lafosse T, Lam SD, Murzin AG, Pandurangan AP, Salazar GA, Skwark MJ, Sternberg MJE, Velankar S, Orengo C. Nucleic acids research Volume 48 (2020) p.D314-D319 DOI: 10.1093/nar/gkz967
WormBase: a modern Model Organism Information Resource.
Harris TW, Arnaboldi V, Cain S, Chan J, Chen WJ, Cho J, Davis P, Gao S, Grove CA, Kishore R, Lee RYN, Muller HM, Nakamura C, Nuin P, Paulini M, Raciti D, Rodgers FH, Russell M, Schindelman G, Auken KV, Wang Q, Williams G, Wright AJ, Yook K, Howe KL, Schedl T, Stein L, Sternberg PW. Nucleic acids research Volume 48 (2020) p.D762-D767 DOI: 10.1093/nar/gkz920
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Della Rocca M, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. Nucleic acids research Volume 48 (2020) p.D704-D715 DOI: 10.1093/nar/gkz997
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PDBe-KB: a community-driven resource for structural and functional annotations.
PDBe-KB consortium. Nucleic acids research Volume 48 (2020) p.D344-D353 DOI: 10.1093/nar/gkz853
Expression Atlas update: from tissues to single cells.
Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N, Fexova S, Fonseca NA, Füllgrabe A, Green M, Huang N, Huerta L, Iqbal H, Jianu M, Mohammed S, Zhao L, Jarnuczak AF, Jupp S, Marioni J, Meyer K, Petryszak R, Prada Medina CA, Talavera-López C, Teichmann S, Vizcaino JA, Brazma A. Nucleic acids research Volume 48 (2020) p.D77-D83 DOI: 10.1093/nar/gkz947
BioModels-15 years of sharing computational models in life science.
Malik-Sheriff RS, Glont M, Nguyen TVN, Tiwari K, Roberts MG, Xavier A, Vu MT, Men J, Maire M, Kananathan S, Fairbanks EL, Meyer JP, Arankalle C, Varusai TM, Knight-Schrijver V, Li L, Dueñas-Roca C, Dass G, Keating SM, Park YM, Buso N, Rodriguez N, Hucka M, Hermjakob H. Nucleic acids research Volume 48 (2020) p.D407-D415 DOI: 10.1093/nar/gkz1055

2019

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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
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
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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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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Integrative analysis of the plasma proteome and polygenic risk of cardiometabolic diseases
Ritchie SC, Lambert SA, Arnold M, Teo SM, Lim S, Scepanovic P, Marten J, Zahid S, Chaffin M, Liu Y, Abraham G, Ouwehand WH, Roberts DJ, Watkins NA, Drew BG, Calkin AC, Di Angelantonio E, Soranzo N, Burgess S, Chapman M, Kathiresan S, Khera AV, Danesh J, Butterworth AS, Inouye M. Preprint DOI: 10.1101/2019.12.14.876474
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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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
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
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
PDBe-KB Aggregated Views: Presenting PDB data in a different context
Pravda L, Varadi M. DOI: 10.6019/tol.pdbe-kb-w.2019.00001.1
Explore the known protein space through UniProt Archive and Clusters
Zellner H, Burstei B. DOI: 10.6019/tol.uniparc-w.2019.00001.1
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
A guide to UniProt for students
Bye-A-Jee H, Pundir S. DOI: 10.6019/tol.uniprotguide-w.2019.00001.1
Ensembl gene annotation for clinical genomics
Perry E, Morales J. DOI: 10.6019/tol.ensembl_clingen-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
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
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
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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
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
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
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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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
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
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
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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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Transposable element landscape in Drosophila populations selected for longevity
Fabian DK, Dönertaş HM, Fuentealba M, Partridge L, Thornton JM. Preprint DOI: 10.1101/867838
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
Identifying pseudoenzymes using functional annotation: pitfalls of common practice.
Ribeiro AJM, Tyzack JD, Borkakoti N, Thornton JM. The FEBS journal Volume 287 (2020) p.4128-4140 DOI: 10.1111/febs.15142
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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
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
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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
Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A.
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Cohesin-dependent regulation of gene expression during differentiation is lost in cohesin-mutated myeloid malignancies.
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Rood JE, Stuart T, Ghazanfar S, Biancalani T, Fisher E, Butler A, Hupalowska A, Gaffney L, Mauck W, Eraslan G, Marioni JC, Regev A, Satija R. Cell Volume 179 (2019) p.1455-1467 DOI: 10.1016/j.cell.2019.11.019
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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
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Jenner RA, von Reumont BM, Campbell LI, Undheim EAB. Molecular biology and evolution Volume 36 (2019) p.2748-2763 DOI: 10.1093/molbev/msz181
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The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases.
Alliance of Genome Resources Consortium. Genetics Volume 213 (2019) p.1189-1196 DOI: 10.1534/genetics.119.302523
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
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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
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Intensive infection control responses and whole genome sequencing to interrupt and resolve widespread transmission of OXA-181 Escherichia coli in a hospital setting
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Brain DNA Methylation Patterns in CLDN5 Associated With Cognitive Decline
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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
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Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry.
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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
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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
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BlobToolKit – Interactive quality assessment of genome assemblies
Challis R, Richards E, Rajan J, Cochrane G, Blaxter M. Preprint DOI: 10.1101/844852
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Lilue J, Shivalikanjli A, Adams DJ, Keane TM. PLoS genetics Volume 15 (2019) p.e1008446 DOI: 10.1371/journal.pgen.1008446
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Investigating higher order interactions in single cell data with scHOT
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Pedro H, Yates AD, Kersey PJ, De Silva NH. Frontiers in microbiology Volume 10 (2019) p.2477 DOI: 10.3389/fmicb.2019.02477
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Bosc N, Atkinson F, Félix E, Gaulton A, Hersey A, Leach AR. Journal of cheminformatics Volume 11 (2019) p.64 DOI: 10.1186/s13321-019-0388-x
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Dynamical Rearrangement of Human Epidermal Growth Factor Receptor 2 upon Antibody Binding: Effects on the Dimerization.
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Exploring Chemical Biosynthetic Design Space with Transform-MinER.
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Global Trends in Marine Plankton Diversity across Kingdoms of Life.
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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
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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
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
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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
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Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis
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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
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
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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
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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
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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
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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
Novel functional proteins coded by the human genome discovered in metastases of melanoma patients.
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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
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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
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Metabolic dysregulation of the lysophospholipid/autotaxin axis in the chromosome 9p21 gene SNP rs10757274
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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
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
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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
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
Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems.
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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
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Expert Curation of the Human and Mouse Olfactory Receptor Gene Repertoires Identifies Conserved Coding Regions Split Across Two Exons
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Understanding life sciences data curation practices via user research
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12 Grand Challenges in Single-Cell Data Science
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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
Comparison of Associations with Different Macular Inner Retinal Thickness Parameters in a Large Cohort: The UK Biobank.
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Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma
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Hardwick SA, Joglekar A, Flicek P, Frankish A, Tilgner HU. Frontiers in genetics Volume 10 (2019) p.709 DOI: 10.3389/fgene.2019.00709
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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.
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Emerging concepts in pseudoenzyme classification, evolution, and signaling.
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Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
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Rawlings ND, Bateman A. Biochimie Volume 166 (2019) p.4-18 DOI: 10.1016/j.biochi.2019.07.026
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Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation
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Genome-wide screening of mouse knockouts reveals novel genes required for normal integumentary and oculocutaneous structure and function.
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Huang R, Huang Y, Guo Y, Ji S, Lu M, Li T. Bioinformatics (Oxford, England) Volume 35 (2019) p.2626-2633 DOI: 10.1093/bioinformatics/bty1033
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Genomic properties of structural variants and short tandem repeats that impact gene expression and complex traits in humans
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Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits.
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Rora regulates activated T helper cells during inflammation
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A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division
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A simple approach for accurate peptide quantification in MS-based proteomics
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Detection of simple and complex de novo mutations without, with, or with multiple reference sequences
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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
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Mutational signatures are jointly shaped by DNA damage and repair
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From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training.
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Analyzing the heterogeneity of rule-based EHR phenotyping algorithms in CALIBER and the UK Biobank
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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
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The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples
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Best Practices to Maximize the Use and Reuse of Quantitative and Systems Pharmacology Models: Recommendations From the United Kingdom Quantitative and Systems Pharmacology Network.
Cucurull-Sanchez L, Chappell MJ, Chelliah V, Amy Cheung SY, Derks G, Penney M, Phipps A, Malik-Sheriff RS, Timmis J, Tindall MJ, van der Graaf PH, Vicini P, Yates JWT. CPT: pharmacometrics & systems pharmacology Volume 8 (2019) p.259-272 DOI: 10.1002/psp4.12381
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Recommendations for the packaging and containerizing of bioinformatics software
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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
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage.
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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
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
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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
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
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
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SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex.
Lipworth S, Jajou R, de Neeling A, Bradley P, van der Hoek W, Maphalala G, Bonnet M, Sanchez-Padilla E, Diel R, Niemann S, Iqbal Z, Smith G, Peto T, Crook D, Walker T, van Soolingen D. Emerging infectious diseases Volume 25 (2019) p.482-488 DOI: 10.3201/eid2503.180894
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
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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
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
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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
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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
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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
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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
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
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
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
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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
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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
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Sequence analysis allows functional annotation of tyrosine recombinases in prokaryotic genomes
Smyshlyaev G, Barabas O, Bateman A. Preprint DOI: 10.1101/542381
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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
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
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
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
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
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
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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
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
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
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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
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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
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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
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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
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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
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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
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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
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Genomics of 1 million parent lifespans implicates novel pathways and common diseases and distinguishes survival chances.
Timmers PR, Mounier N, Lall K, Fischer K, Ning Z, Feng X, Bretherick AD, Clark DW, eQTLGen Consortium, Shen X, Esko T, Kutalik Z, Wilson JF, Joshi PK. eLife Volume 8 (2019) DOI: 10.7554/elife.39856
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Fine-mapping of 150 breast cancer risk regions identifies 178 high confidence target genes
Fachal L, Aschard H, Beesley J, Barnes DR, Allen J, Kar S, Pooley KA, Dennis J, Michailidou K, Turman C, Soucy P, Lemaçon A, Lush M, Tyrer JP, Ghoussaini M, Marjaneh MM, Jiang X, Agata S, Aittomäki K, Alonso MR, Andrulis IL, Anton-Culver H, Antonenkova NN, Arason A, Arndt V, Aronson KJ, Arun BK, Auber B, Auer PL, Azzollini J, Balmaña J, Barkardottir RB, Barrowdale D, Beeghly-Fadiel A, Benitez J, Bermisheva M, Bialkowska K, Blanco AM, Blomqvist C, Blot W, Bogdanova NV, Bojesen SE, Bolla MK, Bonanni B, Borg A, Bosse K, Brauch H, Brenner H, Briceno I, Brock IW, Brooks-Wilson A, Brüning T, Burwinkel B, Buys SS, Cai Q, Caldés T, Caligo MA, Camp NJ, Campbell I, Canzian F, Carroll JS, Carter BD, Castelao JE, Chiquette J, Christiansen H, Chung WK, Claes KB, Clarke CL, Collaborators GS, Collaborators E, Collée JM, Cornelissen S, Couch FJ, Cox A, Cross SS, Cybulski C, Czene K, Daly MB, la Hoya Md, Devilee P, Diez O, Ding YC, Dite GS, Domchek SM, Dörk T, dos-Santos-Silva I, Droit A, Dubois S, Dumont M, Duran M, Durcan L, Dwek M, Eccles DM, Engel C, Eriksson M, Evans DG, Fasching PA, Fletcher O, Floris G, Flyger H, Foretova L, Foulkes WD, Friedman E, Fritschi L, Frost D, Gabrielson M, Gago-Dominguez M, Gambino G, Ganz PA, Gapstur SM, Garber J, García-Sáenz JA, Gaudet MM, Georgoulias V, Giles GG, Glendon G, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Greene MH, Grip M, Gronwald J, Grundy A, Guénel P, Hahnen E, Haiman CA, Håkansson N, Hall P, Hamann U, Harrington PA, Hartikainen JM, Hartman M, He W, Healey CS, Heemskerk-Gerritsen BA, Heyworth J, Hillemanns P, Hogervorst FB, Hollestelle A, Hooning MJ, Hopper JL, Howell A, Huang G, Hulick PJ, Imyanitov EN, Isaacs C, Iwasaki M, Jager A, Jakimovska M, Jakubowska A, James P, Janavicius R, Jankowitz RC, John EM, Johnson N, Jones ME, Jukkola-Vuorinen A, Jung A, Kaaks R, Kang D, Karlan BY, Keeman R, Kerin MJ, Khusnutdinova E, Kiiski JI, Kirk J, Kitahara CM, 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 JT, Lubinski J, MacInnis RJ, 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, Muñoz-Garzon VM, Muranen TA, Narod SA, Nassir R, Nathanson KL, Neuhausen SL, Nevanlinna H, Neven P, Nielsen FC, Nikitina-Zake L, Norman A, Offit K, Olah E, Olopade OI, Olsson H, Orr N, Osorio A, Pankratz VS, Papp J, Park SK, Park-Simon T, Parsons MT, Paul J, Pedersen IS, Pe B. Preprint DOI: 10.1101/521054
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Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences.
Karlsson Linnér R, Biroli P, Kong E, Meddens SFW, Wedow R, Fontana MA, Lebreton M, Tino SP, Abdellaoui A, Hammerschlag AR, Nivard MG, Okbay A, Rietveld CA, Timshel PN, Trzaskowski M, Vlaming R, Zünd CL, Bao Y, Buzdugan L, Caplin AH, Chen CY, Eibich P, Fontanillas P, Gonzalez JR, Joshi PK, Karhunen V, Kleinman A, Levin RZ, Lill CM, Meddens GA, Muntané G, Sanchez-Roige S, Rooij FJV, Taskesen E, Wu Y, Zhang F, 23and Me Research Team, eQTLgen Consortium, International Cannabis Consortium, Social Science Genetic Association Consortium, Auton A, Boardman JD, Clark DW, Conlin A, Dolan CC, Fischbacher U, Groenen PJF, Harris KM, Hasler G, Hofman A, Ikram MA, Jain S, Karlsson R, Kessler RC, Kooyman M, MacKillop J, Männikkö M, Morcillo-Suarez C, McQueen MB, Schmidt KM, Smart MC, Sutter M, Thurik AR, Uitterlinden AG, White J, Wit H, Yang J, Bertram L, Boomsma DI, Esko T, Fehr E, Hinds DA, Johannesson M, Kumari M, Laibson D, Magnusson PKE, Meyer MN, Navarro A, Palmer AA, Pers TH, Posthuma D, Schunk D, Stein MB, Svento R, Tiemeier H, Timmers PRHJ, Turley P, Ursano RJ, Wagner GG, Wilson JF, Gratten J, Lee JJ, Cesarini D, Benjamin DJ, Koellinger PD, Beauchamp JP. Nature genetics Volume 51 (2019) p.245-257 DOI: 10.1038/s41588-018-0309-3
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
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Copy number aberrations drive kinase re-wiring leading to genetic vulnerabilities in cancer
Memon D, Gill MB, 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
West-Life: A Virtual Research Environment for structural biology.
Morris C, Andreetto P, Banci L, Bonvin AMJJ, Chojnowski G, Cano LD, Carazo JM, Conesa P, Daenke S, Damaskos G, Giachetti A, Haley NEC, Hekkelman ML, Heuser P, Joosten RP, Kouřil D, Křenek A, Kulhánek T, Lamzin VS, Nadzirin N, Perrakis A, Rosato A, Sanderson F, Segura J, Schaarschmidt J, Sobolev E, Traldi S, Trellet ME, Velankar S, Verlato M, Winn M. Journal of structural biology: X Volume 1 (2019) p.100006 DOI: 10.1016/j.yjsbx.2019.100006
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
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
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
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
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
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
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The Gene Ontology Resource: 20 years and still GOing strong.
The Gene Ontology Consortium. Nucleic acids research Volume 47 (2019) p.D330-D338 DOI: 10.1093/nar/gky1055
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
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
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
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
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
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
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
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
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
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
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
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
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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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UniProt: a worldwide hub of protein knowledge.
UniProt Consortium. Nucleic acids research Volume 47 (2019) p.D506-D515 DOI: 10.1093/nar/gky1049
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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An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.
Famiglietti ML, Estreicher A, Breuza L, Poux S, Redaschi N, Xenarios I, Bridge A, UniProt Consortium. Database : the journal of biological databases and curation Volume 2019 (2019) DOI: 10.1093/database/baz040
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 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
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
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
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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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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

2018

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Rapid identification of novel protein families using similarity searches
Jeffryes M, Bateman A. Preprint DOI: 10.12688/f1000research.17315.1
Rapid identification of novel protein families using similarity searches.
Jeffryes M, Bateman A. F1000Research Volume 7 (2018) DOI: 10.12688/f1000research.17315.1
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, Lloyd KCK, Murphy CJ, Moshiri A. Communications biology Volume 1 (2018) p.236 DOI: 10.1038/s42003-018-0226-0
A resource of variant effect predictions of single nucleotide variants in model organisms.
Wagih O, Galardini M, Busby BP, Memon D, Typas A, Beltrao P. Molecular systems biology Volume 14 (2018) p.e8430 DOI: 10.15252/msb.20188430
Identifying Potential Ageing-Modulating Drugs In Silico.
Dönertaş HM, Fuentealba M, Partridge L, Thornton JM. Trends in endocrinology and metabolism: TEM Volume 30 (2019) p.118-131 DOI: 10.1016/j.tem.2018.11.005
Minimum Information about an Uncultivated Virus Genome (MIUViG).
Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA. Nature biotechnology Volume 37 (2019) p.29-37 DOI: 10.1038/nbt.4306
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Skewed X-inactivation is common in the general female population.
Shvetsova E, Sofronova A, Monajemi R, Gagalova K, Draisma HHM, White SJ, Santen GWE, Chuva de Sousa Lopes SM, Heijmans BT, van Meurs J, Jansen R, Franke L, Kiełbasa SM, den Dunnen JT, 't Hoen PAC, BIOS consortium, GoNL consortium. European journal of human genetics : EJHG Volume 27 (2019) p.455-465 DOI: 10.1038/s41431-018-0291-3
Eleven quick tips to build a usable REST API for life sciences.
Tarkowska A, Carvalho-Silva D, Cook CE, Turner E, Finn RD, Yates AD. PLoS computational biology Volume 14 (2018) p.e1006542 DOI: 10.1371/journal.pcbi.1006542
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DEEPScreen: High Performance Drug-Target Interaction Prediction with Convolutional Neural Networks Using 2-D Structural Compound Representations
Rifaioglu AS, Atalay V, Martin MJ, Cetin-Atalay R, Dogan T. Preprint DOI: 10.1101/491365
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Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud
Moreno P, Pireddu L, Roger P, Goonasekera N, Afgan E, van den Beek M, He S, Larsson A, Schober D, Ruttkies C, Johnson D, Rocca-Serra P, Weber RJ, Gruening B, Salek RM, Kale N, Perez-Riverol Y, Papatheodorou I, Spjuth O, Neumann S. Preprint DOI: 10.1101/488643
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The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies
Angers-Loustau A, Petrillo M, Bengtsson-Palme J, Berendonk T, Blais B, Chan K, Coque TM, Hammer P, Heß S, Kagkli DM, Krumbiegel C, Lanza VF, Madec J, Naas T, O'Grady J, Paracchini V, Rossen JW, Ruppé E, Vamathevan J, Venturi V, Van den Eede G. Preprint DOI: 10.12688/f1000research.14509.2
The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest.
Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze MW, Krijgsveld J. Cell Volume 176 (2019) p.391-403.e19 DOI: 10.1016/j.cell.2018.11.004
Protein Inference Using PIA Workflows and PSI Standard File Formats.
Uszkoreit J, Perez-Riverol Y, Eggers B, Marcus K, Eisenacher M. Journal of proteome research Volume 18 (2019) p.741-747 DOI: 10.1021/acs.jproteome.8b00723
Efficiently Mining Recurrent Substructures from Protein Three-Dimensional Structure Graphs.
Saidi R, Dhifli W, Maddouri M, Mephu Nguifo E. Journal of computational biology : a journal of computational molecular cell biology Volume 26 (2019) p.561-571 DOI: 10.1089/cmb.2018.0171
Neutral tumor evolution?
Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz F, PCAWG Evolution and Heterogeneity Working Group, Spellman PT, Morris QD, Lingjærde OC, Wedge DC, Van Loo P. Nature genetics Volume 50 (2018) p.1630-1633 DOI: 10.1038/s41588-018-0258-x
Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data.
Kramarz B, Roncaglia P, Meldal BHM, Huntley RP, Martin MJ, Orchard S, Parkinson H, Brough D, Bandopadhyay R, Hooper NM, Lovering RC. Genes Volume 9 (2018) DOI: 10.3390/genes9120593
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Altered composition of the γδ T cell pool in lymph nodes during ageing enhances tumour growth
Chen H, Eling N, Martinez-Jimenez CP, O’Brien LM, Marioni JC, Odom DT, la Roche Md. Preprint DOI: 10.1101/480327
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A linear mixed-model approach to study multivariate gene-environment interactions.
Moore R, Casale FP, Jan Bonder M, Horta D, BIOS Consortium, Franke L, Barroso I, Stegle O. Nature genetics Volume 51 (2019) p.180-186 DOI: 10.1038/s41588-018-0271-0
Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores.
Ben-David M, Huang H, Sun MGF, Corbi-Verge C, Petsalaki E, Liu K, Gfeller D, Garg P, Tempel W, Sochirca I, Shifman JM, Davidson A, Min J, Kim PM, Sidhu SS. Journal of molecular biology Volume 431 (2019) p.336-350 DOI: 10.1016/j.jmb.2018.11.018
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A well-ordered nanoflow LC-MS/MS approach for proteome profiling using 200 cm long micro pillar array columns
De Beeck JO, Pauwels J, Van Landuyt N, Jacobs P, De Malsche W, Desmet G, Argentini A, Staes A, Martens L, Impens F, Gevaert K. Preprint DOI: 10.1101/472134
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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, Maio ND, Matschiner M, Mendes FK, Müller NF, Ogilvie H, Plessis Ld, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu C, Xie D, Zhang C, Stadler T, Drummond AJ. Preprint DOI: 10.1101/474296
Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars.
Carvalho-Silva D, Garcia L, Morgan SL, Brooksbank C, Dunham I. PLoS computational biology Volume 14 (2018) p.e1006419 DOI: 10.1371/journal.pcbi.1006419
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Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap.
Giuffra E, Tuggle CK, FAANG Consortium. Annual review of animal biosciences Volume 7 (2019) p.65-88 DOI: 10.1146/annurev-animal-020518-114913
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Novel autoregulatory cases of alternative splicing coupled with nonsense-mediated mRNA decay
Pervouchine D, Popov Y, Berry A, Borsari B, Frankish A, Guigó R. Preprint DOI: 10.1101/464404
The pervasive effects of recombinant Fasciola gigantica Ras-related protein Rab10 on the functions of goat peripheral blood mononuclear cells.
Tian AL, Lu M, Zhang FK, Calderón-Mantilla G, Petsalaki E, Tian X, Wang W, Huang SY, Li X, Elsheikha HM, Zhu XQ. Parasites & vectors Volume 11 (2018) p.579 DOI: 10.1186/s13071-018-3148-2
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 12 (2018) p.625-629 DOI: 10.1007/s12079-018-0491-1
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Comparative genomics of the major parasitic worms.
International Helminth Genomes Consortium. Nature genetics Volume 51 (2019) p.163-174 DOI: 10.1038/s41588-018-0262-1
Publisher Correction: Image Data Resource: a bioimage data integration and publication platform.
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Carazo Salas RE, Swedlow JR. Nature methods Volume 15 (2018) p.984 DOI: 10.1038/s41592-018-0169-x
A call for public archives for biological image data.
Ellenberg J, Swedlow JR, Barlow M, Cook CE, Sarkans U, Patwardhan A, Brazma A, Birney E. Nature methods Volume 15 (2018) p.849-854 DOI: 10.1038/s41592-018-0195-8
ClinGen advancing genomic data-sharing standards as a GA4GH driver project.
Dolman L, Page A, Babb L, Freimuth RR, Arachchi H, Bizon C, Brush M, Fiume M, Haendel M, Hansen DP, Milosavljevic A, Patel RY, Pawliczek P, Yates AD, Rehm HL. Human mutation Volume 39 (2018) p.1686-1689 DOI: 10.1002/humu.23625
Parents in science.
Perry E, Tessmar-Raible K, Raible F. Genome biology Volume 19 (2018) p.180 DOI: 10.1186/s13059-018-1549-3
Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data.
Invergo BM, Beltrao P. Essays in biochemistry Volume 62 (2018) p.525-534 DOI: 10.1042/ebc20180019
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Bacterial contribution to genesis of the novel germ line determinant oskar
Blondel L, Jones TEM, Extavour CG. Preprint DOI: 10.1101/453514
Gene expression variability across cells and species shapes innate immunity.
Hagai T, Chen X, Miragaia RJ, Rostom R, Gomes T, Kunowska N, Henriksson J, Park JE, Proserpio V, Donati G, Bossini-Castillo L, Vieira Braga FA, Naamati G, Fletcher J, Stephenson E, Vegh P, Trynka G, Kondova I, Dennis M, Haniffa M, Nourmohammad A, Lässig M, Teichmann SA. Nature Volume 563 (2018) p.197-202 DOI: 10.1038/s41586-018-0657-2
A large-scale dataset of in vivo pharmacology assay results.
Hunter FMI, L Atkinson F, Bento AP, Bosc N, Gaulton A, Hersey A, Leach AR. Scientific data Volume 5 (2018) p.180230 DOI: 10.1038/sdata.2018.230
Chromosome assembly of large and complex genomes using multiple references.
Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S. Genome research Volume 28 (2018) p.1720-1732 DOI: 10.1101/gr.236273.118
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Unraveling the polygenic architecture of complex traits using blood eQTL metaanalysis
Võsa U, Claringbould A, Westra H, Bonder MJ, Deelen P, Zeng B, Kirsten H, Saha A, Kreuzhuber R, Kasela S, Pervjakova N, Alvaes I, Fave M, Agbessi M, Christiansen M, Jansen R, Seppälä I, Tong L, Teumer A, Schramm K, Hemani G, Verlouw J, Yaghootkar H, Sönmez R, Brown A, Kukushkina V, Kalnapenkis A, Rüeger S, Porcu E, Kronberg-Guzman J, Kettunen J, Powell J, Lee B, Zhang F, Arindrarto W, Beutner F, Brugge H, Dmitreva J, Elansary M, Fairfax BP, Georges M, Heijmans BT, Kähönen M, Kim Y, Knight JC, Kovacs P, Krohn K, Li S, Loeffler M, Marigorta UM, Mei H, Momozawa Y, Müller-Nurasyid M, Nauck M, Nivard M, Penninx B, Pritchard J, Raitakari O, Rotzchke O, Slagboom EP, Stehouwer CD, Stumvoll M, Sullivan P, Hoen PA‘, Thiery J, Tönjes A, van Dongen J, van Iterson M, Veldink J, Völker U, Wijmenga C, Swertz M, Andiappan A, Montgomery GW, Ripatti S, Perola M, Kutalik Z, Dermitzakis E, Bergmann S, Frayling T, van Meurs J, Prokisch H, Ahsan H, Pierce B, Lehtimäki T, Boomsma D, Psaty BM, Gharib SA, Awadalla P, Milani L, Ouwehand W, Downes K, Stegle O, Battle A, Yang J, Visscher PM, Scholz M, Gibson G, Esko T, Franke L, BIOS Consortium, i2QTL Consortium. Preprint DOI: 10.1101/447367
Publishing peer review materials.
Beck J, Funk K, Harrison M, McEntyre J, Breen J, Collings A, Donohoe P, Evans M, Flintoft L, Hamelers A, Hurst P, Lemberger T, Lin J, O'Connor N, Parkin M, Parker S, Rodgers P, Skipper M, Stoner M. F1000Research Volume 7 (2018) p.1655 DOI: 10.12688/f1000research.16460.1
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Publishing peer review materials
Beck J, Funk K, Harrison M, McEntyre J, Breen J, Collings A, Donohoe P, Evans M, Flintoft L, Hamelers A, Hurst P, Lemberger T, Lin J, O'Connor N, Parkin M, Parker S, Rodgers P, Skipper M, Stoner M. Preprint DOI: 10.12688/f1000research.16460.1
FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community.
Harrison PW, Fan J, Richardson D, Clarke L, Zerbino D, Cochrane G, Archibald AL, Schmidt CJ, Flicek P. Animal genetics Volume 49 (2018) p.520-526 DOI: 10.1111/age.12736
Expanding the Use of Spectral Libraries in Proteomics.
Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H. Journal of proteome research Volume 17 (2018) p.4051-4060 DOI: 10.1021/acs.jproteome.8b00485
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Population-scale proteome variation in human induced pluripotent stem cells
Mirauta BA, Seaton DD, Bensaddek D, Brenes A, Bonder MJ, Kilpinen H, Stegle O, Lamond AI, HipSci Consortium. Preprint DOI: 10.1101/439216
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Using the drug-protein interactome to identify anti-ageing compounds for humans
Fuentealba Valenzuela M, Melike Dönertaş H, Williams R, Labbadia J, Thornton J, Partridge L. Preprint DOI: 10.1101/438234
Haplosaurus computes protein haplotypes for use in precision drug design.
Spooner W, McLaren W, Slidel T, Finch DK, Butler R, Campbell J, Eghobamien L, Rider D, Kiefer CM, Robinson MJ, Hardman C, Cunningham F, Vaughan T, Flicek P, Huntington CC. Nature communications Volume 9 (2018) p.4128 DOI: 10.1038/s41467-018-06542-1
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Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
Waterhouse RM, Aganezov S, Anselmetti Y, Lee J, Ruzzante L, Reijnders MJ, Feron R, Bérard S, George P, Hahn MW, Howell PI, Kamali M, Koren S, Lawson D, Maslen G, Peery A, Phillippy AM, Sharakhova MV, Tannier E, Unger MF, Zhang SV, Alekseyev MA, Besansky NJ, Chauve C, Emrich SJ, Sharakhov IV. Preprint DOI: 10.1101/434670
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Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions
C. Silva AS, Martens L, Degroeve S. Preprint DOI: 10.1101/428805
Classification and Personalized Prognosis in Myeloproliferative Neoplasms.
Grinfeld J, Nangalia J, Baxter EJ, Wedge DC, Angelopoulos N, Cantrill R, Godfrey AL, Papaemmanuil E, Gundem G, MacLean C, Cook J, O'Neil L, O'Meara S, Teague JW, Butler AP, Massie CE, Williams N, Nice FL, Andersen CL, Hasselbalch HC, Guglielmelli P, McMullin MF, Vannucchi AM, Harrison CN, Gerstung M, Green AR, Campbell PJ. The New England journal of medicine Volume 379 (2018) p.1416-1430 DOI: 10.1056/nejmoa1716614
Transform-MinER: transforming molecules in enzyme reactions.
Tyzack JD, Ribeiro AJM, Borkakoti N, Thornton JM. Bioinformatics (Oxford, England) Volume 34 (2018) p.3597-3599 DOI: 10.1093/bioinformatics/bty394
Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.
Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM. Nature genetics Volume 50 (2018) p.1574-1583 DOI: 10.1038/s41588-018-0223-8
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Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.
CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B. The New England journal of medicine Volume 379 (2018) p.1403-1415 DOI: 10.1056/nejmoa1800474
Human genes: Time to follow the roads less traveled?
Dunham I. PLoS biology Volume 16 (2018) p.e3000034 DOI: 10.1371/journal.pbio.3000034
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Process-specific somatic mutation distributions vary with three-dimensional genome structure
Akdemir KC, Le VT, Killcoyne S, King DA, Li Y, Tian Y, Inoue A, Amin S, Robinson FS, Herrera RE, Lynn EJ, Chan K, Seth S, Klimczak LJ, Gerstung M, Gordenin DA, O’Brien J, Li L, Verhaak RG, Campbell P, Fitzgerald R, Morrison AJ, Dixon JR, Andrew Futreal P. Preprint DOI: 10.1101/426080
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Protein inference using PIA workflows and PSI standard file formats
Uszkoreit J, Perez-Riverol Y, Eggers B, Marcus K, Eisenacher M. Preprint DOI: 10.1101/424473
ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature.
Dalkiran A, Rifaioglu AS, Martin MJ, Cetin-Atalay R, Atalay V, Doğan T. BMC bioinformatics Volume 19 (2018) p.334 DOI: 10.1186/s12859-018-2368-y
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Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation.
Luijk R, Wu H, Ward-Caviness CK, Hannon E, Carnero-Montoro E, Min JL, Mandaviya P, Müller-Nurasyid M, Mei H, van der Maarel SM, BIOS Consortium, Relton C, Mill J, Waldenberger M, Bell JT, Jansen R, Zhernakova A, Franke L, 't Hoen PAC, Boomsma DI, van Duijn CM, van Greevenbroek MMJ, Veldink JH, Wijmenga C, van Meurs J, Daxinger L, Slagboom PE, van Zwet EW, Heijmans BT. Nature communications Volume 9 (2018) p.3738 DOI: 10.1038/s41467-018-05714-3
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.837-849 DOI: 10.1038/s41436-018-0268-1
An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures.
Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Young MD, Berna J, Tubio JMC, McMurran CE, Young AMH, Sanders M, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson MD, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott MW, Kirollos RW, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U. Scientific reports Volume 8 (2018) p.13537 DOI: 10.1038/s41598-018-31659-0
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Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants
McCarthy DJ, Rostom R, Huang Y, Kunz DJ, Danecek P, Bonder MJ, Hagai T, Wang W, Gaffney DJ, Simons BD, Stegle O, Teichmann SA, HipSci Consortium. Preprint DOI: 10.1101/413047
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HLA-DQA1*05 is associated with the development of antibodies to anti-TNF therapy
Sazonovs A, Kennedy N, Moutsianas L, Heap GA, Rice DL, Reppell M, Bewshea C, Walker G, Perry MH, McDonald TJ, Lees C, Cummings F, Parkes M, Mansfield J, Barrett JC, McGovern D, Goodhand J, Anderson CA, Ahmad T, PANTS consortium. Preprint DOI: 10.1101/410035
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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, Guenther U, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Khonsari PE, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O’Donovan C, Pearce JT, Peluso A, Pireddu L, Piras ME, Reed MA, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone S, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C. Preprint DOI: 10.1101/409151
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Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.
Farmery JHR, Smith ML, NIHR BioResource - Rare Diseases, Lynch AG. Scientific reports Volume 8 (2018) p.13376 DOI: 10.1038/s41598-018-31524-0
PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships.
Meyer HV, Birney E. Bioinformatics (Oxford, England) Volume 34 (2018) p.2951-2956 DOI: 10.1093/bioinformatics/bty197
Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils.
Grassi L, Pourfarzad F, Ullrich S, Merkel A, Were F, Carrillo-de-Santa-Pau E, Yi G, Hiemstra IH, Tool ATJ, Mul E, Perner J, Janssen-Megens E, Berentsen K, Kerstens H, Habibi E, Gut M, Yaspo ML, Linser M, Lowy E, Datta A, Clarke L, Flicek P, Vingron M, Roos D, van den Berg TK, Heath S, Rico D, Frontini M, Kostadima M, Gut I, Valencia A, Ouwehand WH, Stunnenberg HG, Martens JHA, Kuijpers TW. Cell reports Volume 24 (2018) p.2784-2794 DOI: 10.1016/j.celrep.2018.08.018
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 7 (2018) p.284-294.e12 DOI: 10.1016/j.cels.2018.06.011
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Validating a 14-Drug Microtiter Plate Containing Bedaquiline and Delamanid for Large-Scale Research Susceptibility Testing of Mycobacterium tuberculosis.
Rancoita PMV, Cugnata F, Gibertoni Cruz AL, Borroni E, Hoosdally SJ, Walker TM, Grazian C, Davies TJ, Peto TEA, Crook DW, Fowler PW, Cirillo DM, CRyPTIC Consortiumfor the CRyPTIC Consortiumfor the CRyPTIC Consortium. Antimicrobial agents and chemotherapy Volume 62 (2018) DOI: 10.1128/aac.00344-18
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Approaches for containerized scientific workflows in cloud environments with applications in life science
Spjuth O, Capuccini M, Carone M, Larsson A, Schaal W, Novella J, Di Tommaso P, Notredame C, Moreno P, Khoonsari PE, Herman S, Kultima K, Lampa S. Preprint DOI: 10.7287/peerj.preprints.27141v1
Mass spectrometry evaluation of a neuroblastoma SH-SY5Y cell culture protocol.
Murillo JR, Pla I, Goto-Silva L, Nogueira FCS, Domont GB, Perez-Riverol Y, Sánchez A, Junqueira M. Analytical biochemistry Volume 559 (2018) p.51-54 DOI: 10.1016/j.ab.2018.08.013
The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for bluetongue virus.
Morales-Hojas R, Hinsley M, Armean IM, Silk R, Harrup LE, Gonzalez-Uriarte A, Veronesi E, Campbell L, Nayduch D, Saski C, Tabachnick WJ, Kersey P, Carpenter S, Fife M. BMC genomics Volume 19 (2018) p.624 DOI: 10.1186/s12864-018-5014-1
Scaling up data curation using deep learning: An application to literature triage in genomic variation resources.
Lee K, Famiglietti ML, McMahon A, Wei CH, MacArthur JAL, Poux S, Breuza L, Bridge A, Cunningham F, Xenarios I, Lu Z. PLoS computational biology Volume 14 (2018) p.e1006390 DOI: 10.1371/journal.pcbi.1006390
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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. Preprint DOI: 10.1101/391185
The first single particle analysis Map Challenge: A summary of the assessments.
Heymann JB, Marabini R, Kazemi M, Sorzano COS, Holmdahl M, Mendez JH, Stagg SM, Jonic S, Palovcak E, Armache JP, Zhao J, Cheng Y, Pintilie G, Chiu W, Patwardhan A, Carazo JM. Journal of structural biology Volume 204 (2018) p.291-300 DOI: 10.1016/j.jsb.2018.08.010
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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, 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. Preprint DOI: 10.1101/388611
Gene expression-based drug repurposing to target aging.
Dönertaş HM, Fuentealba Valenzuela M, Partridge L, Thornton JM. Aging cell Volume 17 (2018) p.e12819 DOI: 10.1111/acel.12819
CTCF maintains regulatory homeostasis of cancer pathways.
Aitken SJ, Ibarra-Soria X, Kentepozidou E, Flicek P, Feig C, Marioni JC, Odom DT. Genome biology Volume 19 (2018) p.106 DOI: 10.1186/s13059-018-1484-3
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Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history
Sisu C, Muir P, Frankish A, Fiddes I, Diekhans M, Thybert D, Odom DT, Flicek P, Keane T, Hubbard T, Harrow J, Gerstein M. Preprint DOI: 10.1101/386656
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Genome-wide identification of directed gene networks using large-scale population genomics data.
Luijk R, Dekkers KF, van Iterson M, Arindrarto W, Claringbould A, Hop P, Boomsma DI, van Duijn CM, van Greevenbroek MMJ, Veldink JH, Wijmenga C, Franke L, 't Hoen PAC, Jansen R, van Meurs J, Mei H, Slagboom PE, Heijmans BT, van Zwet EW, BIOS (Biobank-based Integrative Omics Study) Consortium. Nature communications Volume 9 (2018) p.3097 DOI: 10.1038/s41467-018-05452-6
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CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination
Perfetto L, Acencio M, Bradley G, Cesareni G, Toro N, Fazekas D, Hermjakob H, Korcsmaros T, Kuiper M, Lægreid A, Surdo PL, Lovering R, Orchard S, Porras P, Thomas P, Touré V, Zobolas J, Licata L. Preprint DOI: 10.1101/385773
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Common ELIXIR Service for Researcher Authentication and Authorisation
Linden M, Prochazka M, Lappalainen I, Bucik D, Vyskocil P, Kuba M, Silén S, Belmann P, Sczyrba A, Newhouse S, Matyska L, Nyrönen T. Preprint DOI: 10.12688/f1000research.15161.1
Registered access: authorizing data access.
Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, Flicek P. European journal of human genetics : EJHG Volume 26 (2018) p.1721-1731 DOI: 10.1038/s41431-018-0219-y
A roadmap for restoring trust in Big Data.
Lawler M, Morris AD, Sullivan R, Birney E, Middleton A, Makaroff L, Knoppers BM, Horgan D, Eggermont A. The Lancet. Oncology Volume 19 (2018) p.1014-1015 DOI: 10.1016/s1470-2045(18)30425-x
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A locus at 7p14.3 predisposes to refractory celiac disease progression from celiac disease.
Hrdlickova B, Mulder CJ, Malamut G, Meresse B, Platteel M, Kamatani Y, Ricaño-Ponce I, van Wanrooij RLJ, Zorro MM, Jan Bonder M, Gutierrez-Achury J, Cellier C, Zhernakova A, Nijeboer P, Galan P, Withoff S, Lathrop M, Bouma G, Xavier RJ, Jabri B, Bensussan NC, Wijmenga C, Kumar V. European journal of gastroenterology & hepatology Volume 30 (2018) p.828-837 DOI: 10.1097/meg.0000000000001168
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The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform
Matthews TC, Bristow FR, Griffiths EJ, Petkau A, Adam J, Dooley D, Kruczkiewicz P, Curatcha J, Cabral J, Fornika D, Winsor GL, Courtot M, Bertelli C, Roudgar A, Feijao P, Mabon P, Enns E, Thiessen J, Keddy A, Isaac-Renton J, Gardy JL, Tang P, The IRIDA Consortium João A Carriço, Chindelevitch L, Chauve C, Graham MR, McArthur AG, Taboada EN, Beiko RG, Brinkman FS, Hsiao WW, Domselaar GV. Preprint DOI: 10.1101/381830
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HPO2GO: prediction of human phenotype ontology term associations using cross ontology annotation co-occurrences
Doğan T. Preprint DOI: 10.7287/peerj.preprints.26663v2
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Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes.
Xue A, Wu Y, Zhu Z, Zhang F, Kemper KE, Zheng Z, Yengo L, Lloyd-Jones LR, Sidorenko J, Wu Y, eQTLGen Consortium, McRae AF, Visscher PM, Zeng J, Yang J. Nature communications Volume 9 (2018) p.2941 DOI: 10.1038/s41467-018-04951-w
NonA and CPX Link the Circadian Clockwork to Locomotor Activity in Drosophila.
Luo W, Guo F, McMahon A, Couvertier S, Jin H, Diaz M, Fieldsend A, Weerapana E, Rosbash M. Neuron Volume 99 (2018) p.768-780.e3 DOI: 10.1016/j.neuron.2018.07.001
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PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping
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Ndila CM, Uyoga S, Macharia AW, Nyutu G, Peshu N, Ojal J, Shebe M, Awuondo KO, Mturi N, Tsofa B, Sepúlveda N, Clark TG, Band G, Clarke G, Rowlands K, Hubbart C, Jeffreys A, Kariuki S, Marsh K, Mackinnon M, Maitland K, Kwiatkowski DP, Rockett KA, Williams TN, MalariaGEN Consortium. The Lancet. Haematology Volume 5 (2018) p.e333-e345 DOI: 10.1016/s2352-3026(18)30107-8
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Nearly all new protein-coding predictions in the CHESS database are not protein-coding
Jungreis I, Tress ML, Mudge J, Sisu C, Hunt T, Johnson R, Uszczynska-Ratajczak B, Lagarde J, Wright J, Muir P, Gerstein M, Guigo R, Kellis M, Frankish A, Flicek P, The GENCODE Consortium. Preprint DOI: 10.1101/360602
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Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J, Bioconda Team. Nature methods Volume 15 (2018) p.475-476 DOI: 10.1038/s41592-018-0046-7
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Vialle RA, Tamuri AU, Goldman N. Molecular biology and evolution Volume 35 (2018) p.1783-1797 DOI: 10.1093/molbev/msy055
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Zhao L, Hansard M, Cavallaro A. IEEE transactions on visualization and computer graphics Volume 24 (2018) p.2167-2179 DOI: 10.1109/tvcg.2017.2708108
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De Novo Truncating Mutations in WASF1 Cause Intellectual Disability with Seizures.
Ito Y, Carss KJ, Duarte ST, Hartley T, Keren B, Kurian MA, Marey I, Charles P, Mendonça C, Nava C, Pfundt R, Sanchis-Juan A, van Bokhoven H, van Essen A, van Ravenswaaij-Arts C, NIHR BioResource, Care4Rare Canada Consortium, Boycott KM, Kernohan KD, Dyack S, Raymond FL. American journal of human genetics Volume 103 (2018) p.144-153 DOI: 10.1016/j.ajhg.2018.06.001
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Melamed A, Yaguchi H, Miura M, Witkover A, Fitzgerald TW, Birney E, Bangham CR. eLife Volume 7 (2018) DOI: 10.7554/elife.36245
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Müller PM, Rademacher J, Bagshaw RD, Alp KM, Giudice G, Heinrich LE, Barth C, Eccles RL, Sanchez-Castro M, Brandenburg L, Mbamalu G, Tucholska M, Spatt L, Wortmann C, Czajkowski MT, Welke R, Zhang S, Nguyen V, Rrustemi T, Trnka P, Freitag K, Larsen B, Popp O, Mertins P, Bakal C, Gingras A, Pertz O, Roth FP, Colwill K, Pawson T, Petsalaki E, Rocks O. Preprint DOI: 10.1101/354316
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Lee JY, Choi H, Colangelo CM, Davis D, Hoopmann MR, Käll L, Lam H, Payne SH, Perez-Riverol Y, The M, Wilson R, Weintraub ST, Palmblad M. Journal of biomolecular techniques : JBT Volume 29 (2018) p.39-45 DOI: 10.7171/jbt.18-2902-003
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Memote: A community driven effort towards a standardized genome-scale metabolic model test suite
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist A, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kim HU, King Z, Koehorst JJ, Klamt S, Klipp E, Lakshmanan M, Le Novère N, Lee D, Lee SY, Lee S, Lewis NE, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Resendis-Antonio O, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Richelle A, Rocha I, Sanchez BJ, Schaap PJ, Malik Sheriff RS, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JA, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. Preprint DOI: 10.1101/350991
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Argelaguet R, Velten B, Arnol D, Dietrich S, Zenz T, Marioni JC, Buettner F, Huber W, Stegle O. Molecular systems biology Volume 14 (2018) p.e8124 DOI: 10.15252/msb.20178124
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Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis
Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC, Odom DT. Preprint DOI: 10.1101/350868
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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, BioContainers Community, Perez-Riverol Y. F1000Research Volume 7 (2018) DOI: 10.12688/f1000research.15140.2
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Comprehensive Cancer-Predisposition Gene Testing in an Adult Multiple Primary Tumor Series Shows a Broad Range of Deleterious Variants and Atypical Tumor Phenotypes.
Whitworth J, Smith PS, Martin JE, West H, Luchetti A, Rodger F, Clark G, Carss K, Stephens J, Stirrups K, Penkett C, Mapeta R, Ashford S, Megy K, Shakeel H, Ahmed M, Adlard J, Barwell J, Brewer C, Casey RT, Armstrong R, Cole T, Evans DG, Fostira F, Greenhalgh L, Hanson H, Henderson A, Hoffman J, Izatt L, Kumar A, Kwong A, Lalloo F, Ong KR, Paterson J, Park SM, Chen-Shtoyerman R, Searle C, Side L, Skytte AB, Snape K, Woodward ER, NIHR BioResource Rare Diseases Consortium, Tischkowitz MD, Maher ER. American journal of human genetics Volume 103 (2018) p.3-18 DOI: 10.1016/j.ajhg.2018.04.013
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Capturing variation impact on molecular interactions: the IMEx Consortium mutations data set
The IMEx Consortium Curators, del Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong L, Jurisica I, Hermjakob H, Orchard S, Porras P. Preprint DOI: 10.1101/346833
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Understanding trivial challenges of microbial genomics: An assembly example
Lariviere D, Mei H, Freeberg M, Taylor J, Nekrutenko A. Preprint DOI: 10.1101/347625
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Qi T, Wu Y, Zeng J, Zhang F, Xue A, Jiang L, Zhu Z, Kemper K, Yengo L, Zheng Z, eQTLGen Consortium, Marioni RE, Montgomery GW, Deary IJ, Wray NR, Visscher PM, McRae AF, Yang J. Nature communications Volume 9 (2018) p.2282 DOI: 10.1038/s41467-018-04558-1
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Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B. Genome research Volume 28 (2018) p.1029-1038 DOI: 10.1101/gr.233460.117
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Kalvari I, Nawrocki EP, Argasinska J, Quinones-Olvera N, Finn RD, Bateman A, Petrov AI. Current protocols in bioinformatics Volume 62 (2018) p.e51 DOI: 10.1002/cpbi.51
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Best practice data life cycle approaches for the life sciences
Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WW, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. Preprint DOI: 10.12688/f1000research.12344.2
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Universal Patterns of Selection in Cancer and Somatic Tissues.
Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K, Van Loo P, Davies H, Stratton MR, Campbell PJ. Cell Volume 173 (2018) p.1823 DOI: 10.1016/j.cell.2018.06.001
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Lill JR, van Veelen PA, Tenzer S, Admon A, Caron E, Elias JE, Heck AJR, Marcilla M, Marino F, Müller M, Peters B, Purcell A, Sette A, Sturm T, Ternette N, Vizcaíno JA, Bassani-Sternberg M. Proteomics Volume 18 (2018) p.e1800110 DOI: 10.1002/pmic.201800110
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The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest
Trendel J, Schwarzl T, Prakash A, Bateman A, Hentze MW, Krijgsveld J. Preprint DOI: 10.1101/329995
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Kleywegt GJ, Velankar S, Patwardhan A. FEBS letters Volume 592 (2018) p.2153-2167 DOI: 10.1002/1873-3468.13086
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Pichler K, Warner K, Magrane M, UniProt Consortium. Current protocols in bioinformatics Volume 62 (2018) p.e52 DOI: 10.1002/cpbi.52
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Petraglia F, Singh AA, Carafa V, Nebbioso A, Conte M, Scisciola L, Valente S, Baldi A, Mandoli A, Petrizzi VB, Ingenito C, De Falco S, Cicatiello V, Apicella I, Janssen-Megens EM, Kim B, Yi G, Logie C, Heath S, Ruvo M, Wierenga ATJ, Flicek P, Yaspo ML, Della Valle V, Bernard O, Tomassi S, Novellino E, Feoli A, Sbardella G, Gut I, Vellenga E, Stunnenberg HG, Mai A, Martens JHA, Altucci L. Oncotarget Volume 9 (2018) p.25630-25646 DOI: 10.18632/oncotarget.25428
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Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity
Linker SM, Urban L, Clark S, Chhatriwala M, Amatya S, McCarthy DJ, Ebersberger I, Vallier L, Reik W, Stegle O, Bonder MJ. Preprint DOI: 10.1101/328138
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Analysis of the genomic landscape of multiple myeloma highlights novel prognostic markers and disease subgroups.
Bolli N, Biancon G, Moarii M, Gimondi S, Li Y, de Philippis C, Maura F, Sathiaseelan V, Tai YT, Mudie L, O'Meara S, Raine K, Teague JW, Butler AP, Carniti C, Gerstung M, Bagratuni T, Kastritis E, Dimopoulos M, Corradini P, Anderson KC, Moreau P, Minvielle S, Campbell PJ, Papaemmanuil E, Avet-Loiseau H, Munshi NC. Leukemia Volume 32 (2018) p.2604-2616 DOI: 10.1038/s41375-018-0037-9
The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia.
Beekman R, Chapaprieta V, Russiñol N, Vilarrasa-Blasi R, Verdaguer-Dot N, Martens JHA, Duran-Ferrer M, Kulis M, Serra F, Javierre BM, Wingett SW, Clot G, Queirós AC, Castellano G, Blanc J, Gut M, Merkel A, Heath S, Vlasova A, Ullrich S, Palumbo E, Enjuanes A, Martín-García D, Beà S, Pinyol M, Aymerich M, Royo R, Puiggros M, Torrents D, Datta A, Lowy E, Kostadima M, Roller M, Clarke L, Flicek P, Agirre X, Prosper F, Baumann T, Delgado J, López-Guillermo A, Fraser P, Yaspo ML, Guigó R, Siebert R, Martí-Renom MA, Puente XS, López-Otín C, Gut I, Stunnenberg HG, Campo E, Martin-Subero JI. Nature medicine Volume 24 (2018) p.868-880 DOI: 10.1038/s41591-018-0028-4
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, Brown SDM, Flenniken AM, Flicek P, Galli A, Mashhadi HH, 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, IMPC consortium. Conservation genetics (Print) Volume 19 (2018) p.995-1005 DOI: 10.1007/s10592-018-1072-9
Aberration hubs in protein interaction networks highlight actionable targets in cancer.
Karimzadeh M, Jandaghi P, Papadakis AI, Trainor S, Rung J, Gonzàlez-Porta M, Scelo G, Vasudev NS, Brazma A, Huang S, Banks RE, Lathrop M, Najafabadi HS, Riazalhosseini Y. Oncotarget Volume 9 (2018) p.25166-25180 DOI: 10.18632/oncotarget.25382
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Agronomic Linked Data (AgroLD): a Knowledge-based System to Enable Integrative Biology in Agronomy
Venkatesan A, Tagny G, El Hassouni N, Chentli I, Guignon V, Jonquet C, Ruiz M, Larmande P. Preprint DOI: 10.1101/325423
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Ensembl - Analysing Linkage Disequilibrium: webinar
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InterPro: A case study of 3 protein family building methodologies
Richardson L, Brown S, Thomas P, Haft D. DOI: 10.6019/tol.interprofam-t.2018.00001.1
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Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T. Scientific data Volume 5 (2018) p.180029 DOI: 10.1038/sdata.2018.29
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Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher S, Fan Y, Fittall M, Drews RM, Yao X, Lee J, Schlesner M, Zhu H, Adams DJ, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P, on behalf of the PCAWG Evolution and Heterogeneity Working Groupthe PCAWG consortium, the PCAWG consortium. Preprint DOI: 10.1101/312041
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Comprehensive variant effect predictions of single nucleotide variants in model organisms
Wagih O, Busby B, Galardini M, Memon D, Typas A, Beltrao P. Preprint DOI: 10.1101/313031
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Proteomic Analysis of Cancer-Associated Fibroblasts Reveals a Paracrine Role for MFAP5 in Human Oral Tongue Squamous Cell Carcinoma.
Principe S, Mejia-Guerrero S, Ignatchenko V, Sinha A, Ignatchenko A, Shi W, Pereira K, Su S, Huang SH, O'Sullivan B, Xu W, Goldstein DP, Weinreb I, Ailles L, Liu FF, Kislinger T. Journal of proteome research Volume 17 (2018) p.2045-2059 DOI: 10.1021/acs.jproteome.7b00925
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Resequencing theVrs1 gene in Spanish barley landraces revealed reversion of six-rowed to two-rowed spike
Casas A, Bruno Contreras-Moreira, Carlos P. Cantalapiedra, Shun Sakuma, María Pilar Gracia, Marian Moralejo, José Luis Molina-Cano, Takao Komatsuda, Ernesto Igartua. Molecular breeding : new strategies in plant improvement Volume 38 (2018) p.51 DOI: 10.1007/s11032-018-0816-z
Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments.
Almeida A, Mitchell AL, Tarkowska A, Finn RD. GigaScience Volume 7 (2018) DOI: 10.1093/gigascience/giy054
Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body.
Achim K, Eling N, Vergara HM, Bertucci PY, Musser J, Vopalensky P, Brunet T, Collier P, Benes V, Marioni JC, Arendt D. Molecular biology and evolution Volume 35 (2018) p.1047-1062 DOI: 10.1093/molbev/msx336
A General Framework for Interrogation of mRNA Stability Programs Identifies RNA-Binding Proteins that Govern Cancer Transcriptomes.
Perron G, Jandaghi P, Solanki S, Safisamghabadi M, Storoz C, Karimzadeh M, Papadakis AI, Arseneault M, Scelo G, Banks RE, Tost J, Lathrop M, Tanguay S, Brazma A, Huang S, Brimo F, Najafabadi HS, Riazalhosseini Y. Cell reports Volume 23 (2018) p.1639-1650 DOI: 10.1016/j.celrep.2018.04.031
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Unlocking biodiversity data: Prioritization and filling the gaps in biodiversity observation data in Europe
Wetzel FT, Christoph L. Häuser, Corinne S. Martin, Dirk S. Schmeller, Hannu Saarenmaa, Heather C. Bingham, Jonathan D. Tonkin, Lyubomir Penev, Michael Kuhlmann, Peter Haase, Quentin Groom, Stefan Stoll, Tim Robertson, Urmas Kõljalg. Biological conservation Volume 221 (2018) p.78-85 DOI: 10.1016/j.biocon.2017.12.024
Cell type discovery using single-cell transcriptomics: implications for ontological representation.
Aevermann BD, Novotny M, Bakken T, Miller JA, Diehl AD, Osumi-Sutherland D, Lasken RS, Lein ES, Scheuermann RH. Human molecular genetics Volume 27 (2018) p.R40-R47 DOI: 10.1093/hmg/ddy100
Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.
Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TMF, Bacanu SA, Bækvad-Hansen M, Beekman AFT, Bigdeli TB, Binder EB, Blackwood DRH, Bryois J, Buttenschøn HN, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen JH, Clarke TK, Coleman JIR, Colodro-Conde L, Couvy-Duchesne B, Craddock N, Crawford GE, Crowley CA, Dashti HS, Davies G, Deary IJ, Degenhardt F, Derks EM, Direk N, Dolan CV, Dunn EC, Eley TC, Eriksson N, Escott-Price V, Kiadeh FHF, Finucane HK, Forstner AJ, Frank J, Gaspar HA, Gill M, Giusti-Rodríguez P, Goes FS, Gordon SD, Grove J, Hall LS, Hannon E, Hansen CS, Hansen TF, Herms S, Hickie IB, Hoffmann P, Homuth G, Horn C, Hottenga JJ, Hougaard DM, Hu M, Hyde CL, Ising M, Jansen R, Jansen R, Jin F, Jorgenson E, Knowles JA, Kohane IS, Kraft J, Kretzschmar WW, Krogh J, Kutalik Z, Lane JM, Li Y, Li Y, Lind PA, Liu X, Lu L, MacIntyre DJ, MacKinnon DF, Maier RM, Maier W, Marchini J, Mbarek H, McGrath P, McGuffin P, Medland SE, Mehta D, Middeldorp CM, Mihailov E, Milaneschi Y, Milani L, Mill J, Mondimore FM, Montgomery GW, Mostafavi S, Mullins N, Nauck M, Ng B, Nivard MG, Nyholt DR, O'Reilly PF, Oskarsson H, Owen MJ, Painter JN, Pedersen CB, Pedersen MG, Peterson RE, Pettersson E, Peyrot WJ, Pistis G, Posthuma D, Purcell SM, Quiroz JA, Qvist P, Rice JP, Riley BP, Rivera M, Saeed Mirza S, Saxena R, Schoevers R, Schulte EC, Shen L, Shi J, Shyn SI, Sigurdsson E, Sinnamon GBC, Smit JH, Smith DJ, Stefansson H, Steinberg S, Stockmeier CA, Streit F, Strohmaier J, Tansey KE, Teismann H, Teumer A, Thompson W, Thomson PA, Thorgeirsson TE, Tian C, Traylor M, Treutlein J, Trubetskoy V, Uitterlinden AG, Umbricht D, Van der Auwera S, van Hemert AM, Viktorin A, Visscher PM, Wang Y, Webb BT, Weinsheimer SM, Wellmann J, Willemsen G, Witt SH, Wu Y, Xi HS, Yang J, Zhang F, eQTLGen, 23andMe, Arolt V, Baune BT, Berger K, Boomsma DI, Cichon S, Dannlowski U, de Geus ECJ, DePaulo JR, Domenici E, Domschke K, Esko T, Grabe HJ, Hamilton SP, Hayward C, Heath AC, Hinds DA, Kendler KS, Kloiber S, Lewis G, Li QS, Lucae S, Madden PFA, Magnusson PK, Martin NG, McIntosh AM, Metspalu A, Mors O, Mortensen PB, Müller-Myhsok B, Nordentoft M, Nöthen MM, O'Donovan MC, Paciga SA, Pedersen NL, Penninx BWJH, Perlis RH, Porteous DJ, Potash JB, Preisig M, Rietschel M, Schaefer C, Schulze TG, Smoller JW, Stefansson K, Tiemeier H, Uher R, Völzke H, Weissman MM, Werge T, Winslow AR, Lewis CM, Levinson DF, Breen G, Børglum AD, Sullivan PF, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium. Nature genetics Volume 50 (2018) p.668-681 DOI: 10.1038/s41588-018-0090-3
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Griss J, Perez-Riverol Y, The M, Käll L, Vizcaíno JA. Journal of proteome research Volume 17 (2018) p.1993-1996 DOI: 10.1021/acs.jproteome.7b00824
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A novel panel of short mononucleotide repeats linked to informative polymorphisms enabling effective high volume low cost discrimination between mismatch repair deficient and proficient tumours
Redford L, Alhilal G, Needham S, O’Brien O, Coaker J, Tyson J, Amorim LM, Middleton I, Sheth H, Izuogu O, Arends M, Oniscu A, Alonso ÁM, Laguna SM, Santibanez-Koref M, Jackson MS, Burn J. Preprint DOI: 10.1101/305383
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Comprehensive and empirical evaluation of machine learning algorithms for LC retention time prediction
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Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response.
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Garcia A, Lopez F, Garcia L, Giraldo O, Bucheli V, Dumontier M. PeerJ Volume 6 (2018) p.e4201 DOI: 10.7717/peerj.4201
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.
Young JY, Westbrook JD, Feng Z, Peisach E, Persikova I, Sala R, Sen S, Berrisford JM, Swaminathan GJ, Oldfield TJ, Gutmanas A, Igarashi R, Armstrong DR, Baskaran K, Chen L, Chen M, Clark AR, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Ikegawa Y, Kengaku Y, Lawson CL, Liang Y, Mak L, Mukhopadhyay A, Narayanan B, Nishiyama K, Patwardhan A, Sahni G, Sanz-García E, Sato J, Sekharan MR, Shao C, Smart OS, Tan L, van Ginkel G, Yang H, Zhuravleva MA, Markley JL, Nakamura H, Kurisu G, Kleywegt GJ, Velankar S, Berman HM, Burley SK. Database : the journal of biological databases and curation Volume 2018 (2018) DOI: 10.1093/database/bay002
Metabolomics data analysis in the Cloud: live online training series
Moreno P, Cochrane K, Neumann S, Rocca-Serra P, Sadawi N, Thévenot E. DOI: 10.6019/tol.met_cloud_online-w.2018.00001.1
PhenoMeNal: Metabolomics data analysis in the cloud
Pireddu L, Moreno P. DOI: 10.6019/tol.phenomenal-w.2017.00001.1
ProteomeXchange submissions via PRIDE
Vizcaino JA, Ternent T, Sehra M, Csordas A. DOI: 10.6019/tol.pxd-t.2014.00001.1
AmyPro: a database of proteins with validated amyloidogenic regions.
Varadi M, De Baets G, Vranken WF, Tompa P, Pancsa R. Nucleic acids research Volume 46 (2018) p.D387-D392 DOI: 10.1093/nar/gkx950
Europe PMC in 2017.
Levchenko M, Gou Y, Graef F, Hamelers A, Huang Z, Ide-Smith M, Iyer A, Kilian O, Katuri J, Kim JH, Marinos N, Nambiar R, Parkin M, Pi X, Rogers F, Talo F, Vartak V, Venkatesan A, McEntyre J. Nucleic acids research Volume 46 (2018) p.D1254-D1260 DOI: 10.1093/nar/gkx1005
Genome Properties: Tutorial
Richardson L. DOI: 10.6019/tol.genprop-t.2018.00001.1
Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.
Pujar S, O'Leary NA, Farrell CM, Loveland JE, Mudge JM, Wallin C, Girón CG, Diekhans M, Barnes I, Bennett R, Berry AE, Cox E, Davidson C, Goldfarb T, Gonzalez JM, Hunt T, Jackson J, Joardar V, Kay MP, Kodali VK, Martin FJ, McAndrews M, McGarvey KM, Murphy M, Rajput B, Rangwala SH, Riddick LD, Seal RL, Suner MM, Webb D, Zhu S, Aken BL, Bruford EA, Bult CJ, Frankish A, Murphy T, Pruitt KD. Nucleic acids research Volume 46 (2018) p.D221-D228 DOI: 10.1093/nar/gkx1031
Preprint discovery 101: Tips & tricks for authors and readers
Levchenko M. DOI: 10.6019/tol.preprint-w.2018.00001.1
The BioStudies database-one stop shop for all data supporting a life sciences study.
Sarkans U, Gostev M, Athar A, Behrangi E, Melnichuk O, Ali A, Minguet J, Rada JC, Snow C, Tikhonov A, Brazma A, McEntyre J. Nucleic acids research Volume 46 (2018) p.D1266-D1270 DOI: 10.1093/nar/gkx965
The Reactome Pathway Knowledgebase.
Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B, Milacic M, Roca CD, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Viteri G, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. Nucleic acids research Volume 46 (2018) p.D649-D655 DOI: 10.1093/nar/gkx1132
Data visualisation 101: A practical introduction to designing scientific Figures
Karamanis N. DOI: 10.6019/tol.datavis-w.2018.00001.1
Effective Literature Research with Europe PMC
Levchenko M. DOI: 10.6019/tol.europepmc-w.2018.00001.1
Gramene 2018: unifying comparative genomics and pathway resources for plant research.
Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D'Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D. Nucleic acids research Volume 46 (2018) p.D1181-D1189 DOI: 10.1093/nar/gkx1111
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
Kersey PJ, Allen JE, Allot A, Barba M, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Grabmueller C, Kumar N, Liu Z, Maurel T, Moore B, McDowall MD, Maheswari U, Naamati G, Newman V, Ong CK, Paulini M, Pedro H, Perry E, Russell M, Sparrow H, Tapanari E, Taylor K, Vullo A, Williams G, Zadissia A, Olson A, Stein J, Wei S, Tello-Ruiz M, Ware D, Luciani A, Potter S, Finn RD, Urban M, Hammond-Kosack KE, Bolser DM, De Silva N, Howe KL, Langridge N, Maslen G, Staines DM, Yates A. Nucleic acids research Volume 46 (2018) p.D802-D808 DOI: 10.1093/nar/gkx1011
Extracting gene-disease evidence from literature, genetics, genomics and more
Carvalho-Silva D, Levchenko M. DOI: 10.6019/tol.gene-disease-w.2018.00001.1
The Ensembl Genome Browser: Strategies for Accessing Eukaryotic Genome Data.
Newman V, Moore B, Sparrow H, Perry E. Methods in molecular biology (Clifton, N.J.) Volume 1757 (2018) p.115-139 DOI: 10.1007/978-1-4939-7737-6_6
Ensembl variation resources.
Hunt SE, McLaren W, Gil L, Thormann A, Schuilenburg H, Sheppard D, Parton A, Armean IM, Trevanion SJ, Flicek P, Cunningham F. Database : the journal of biological databases and curation Volume 2018 (2018) DOI: 10.1093/database/bay119
Repeats in Pfam
El-Gebali S, Richardson L, Finn R. DOI: 10.6019/tol.pfam_repeats-t.2018.00001.1
EMBL-EBI resources: An introduction
Gopalasingam P. DOI: 10.6019/tol.intr-ebi-res-w.2015.00001.1
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.
Ribeiro AJM, Holliday GL, Furnham N, Tyzack JD, Ferris K, Thornton JM. Nucleic acids research Volume 46 (2018) p.D618-D623 DOI: 10.1093/nar/gkx1012
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.
Mir S, Alhroub Y, Anyango S, Armstrong DR, Berrisford JM, Clark AR, Conroy MJ, Dana JM, Deshpande M, Gupta D, Gutmanas A, Haslam P, Mak L, Mukhopadhyay A, Nadzirin N, Paysan-Lafosse T, Sehnal D, Sen S, Smart OS, Varadi M, Kleywegt GJ, Velankar S. Nucleic acids research Volume 46 (2018) p.D486-D492 DOI: 10.1093/nar/gkx1070
Exploring protein function and sequences using UniProt - 2018
Bye-A-Jee H. DOI: 10.6019/tol.uniprot_funseq-w.2018.00001.1
The European Bioinformatics Institute in 2017: data coordination and integration.
Cook CE, Bergman MT, Cochrane G, Apweiler R, Birney E. Nucleic acids research Volume 46 (2018) p.D21-D29 DOI: 10.1093/nar/gkx1154
Bioinformatics Sequence Analysis Web Services with Job Dispatcher
Madeira F. DOI: 10.6019/tol.bio_seq-w.2018.00001.1
A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.
Kurtz A, Seltmann S, Bairoch A, Bittner MS, Bruce K, Capes-Davis A, Clarke L, Crook JM, Daheron L, Dewender J, Faulconbridge A, Fujibuchi W, Gutteridge A, Hei DJ, Kim YO, Kim JH, Kokocinski AK, Lekschas F, Lomax GP, Loring JF, Ludwig T, Mah N, Matsui T, Müller R, Parkinson H, Sheldon M, Smith K, Stachelscheid H, Stacey G, Streeter I, Veiga A, Xu RH. Stem cell reports Volume 10 (2018) p.1-6 DOI: 10.1016/j.stemcr.2017.12.002
Pfam Database: Creating Protein Families
El-Gebali S, Richardson L, Finn R. DOI: 10.6019/tol.pfam_fams-t.2018.00001.1
Ensembl 2018.
Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Girón CG, Gil L, Gordon L, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, To JK, Laird MR, Lavidas I, Liu Z, Loveland JE, Maurel T, McLaren W, Moore B, Mudge J, Murphy DN, Newman V, Nuhn M, Ogeh D, Ong CK, Parker A, Patricio M, Riat HS, Schuilenburg H, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Zadissa A, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Cunningham F, Yates A, Flicek P. Nucleic acids research Volume 46 (2018) p.D754-D761 DOI: 10.1093/nar/gkx1098
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.
Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI. Nucleic acids research Volume 46 (2018) p.D335-D342 DOI: 10.1093/nar/gkx1038
HMMER: Fast and sensitive sequence similarity searches
Finn R. DOI: 10.6019/tol.hmmer-w.2018.00001.1
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.
Mitchell AL, Scheremetjew M, Denise H, Potter S, Tarkowska A, Qureshi M, Salazar GA, Pesseat S, Boland MA, Hunter FMI, Ten Hoopen P, Alako B, Amid C, Wilkinson DJ, Curtis TP, Cochrane G, Finn RD. Nucleic acids research Volume 46 (2018) p.D726-D735 DOI: 10.1093/nar/gkx967
Using WormBase ParaSite: An Integrated Platform for Exploring Helminth Genomic Data.
Bolt BJ, Rodgers FH, Shafie M, Kersey PJ, Berriman M, Howe KL. Methods in molecular biology (Clifton, N.J.) Volume 1757 (2018) p.471-491 DOI: 10.1007/978-1-4939-7737-6_15
Ensembl REST API
Perry E. DOI: 10.6019/tol.ensembl_api-t.2018.00001.1
The international nucleotide sequence database collaboration.
Karsch-Mizrachi I, Takagi T, Cochrane G, International Nucleotide Sequence Database Collaboration. Nucleic acids research Volume 46 (2018) p.D48-D51 DOI: 10.1093/nar/gkx1097
Bringing data to life: data management for the biomolecular sciences
Teperek M, Türkyilmaz-van der Velden Y, Birney E, Busch-Nentwich E, George N, Cochrane K, Levchenko M, Sarntivijai S, Jones S, Hooft R, Morgan S, Burke M. DOI: 10.6019/tol.data_management-w.2018.00001.1
BioModels: expanding horizons to include more modelling approaches and formats.
Glont M, Nguyen TVN, Graesslin M, Hälke R, Ali R, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat MJ, Eils J, Eils R, Laibe C, Malik-Sheriff RS, Chelliah V, Le Novère N, Hermjakob H. Nucleic acids research Volume 46 (2018) p.D1248-D1253 DOI: 10.1093/nar/gkx1023
Migration-Selection Balance Drives Genetic Differentiation in Genes Associated with High-Altitude Function in the Speckled Teal (Anas flavirostris) in the Andes.
Graham AM, Lavretsky P, Muñoz-Fuentes V, Green AJ, Wilson RE, McCracken KG. Genome biology and evolution Volume 10 (2018) p.14-32 DOI: 10.1093/gbe/evx253
Gearing up to handle the mosaic nature of life in the quest for orthologs.
Forslund K, Pereira C, Capella-Gutierrez S, da Silva AS, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT, Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S, Quest for Orthologs Consortium . Bioinformatics (Oxford, England) Volume 34 (2018) p.323-329 DOI: 10.1093/bioinformatics/btx542
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.
Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD. Nucleic acids research Volume 46 (2018) p.D624-D632 DOI: 10.1093/nar/gkx1134
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes.
Grove C, Cain S, Chen WJ, Davis P, Harris T, Howe KL, Kishore R, Lee R, Paulini M, Raciti D, Tuli MA, Van Auken K, Williams G, WormBase Consortium. Methods in molecular biology (Clifton, N.J.) Volume 1757 (2018) p.399-470 DOI: 10.1007/978-1-4939-7737-6_14
Searching and Extracting Data from the EMBL-EBI Complex Portal.
Meldal BHM, Orchard S. Methods in molecular biology (Clifton, N.J.) Volume 1764 (2018) p.377-390 DOI: 10.1007/978-1-4939-7759-8_24
Complex Portal: Quick tour
Meldal B. DOI: 10.6019/tol.comport-w.2015.00001.1
Mouse strains in Ensembl
Haskell E. DOI: 10.6019/tol.ensembl_mouse-w.2018.00001.1
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Proteomic Profiling of Secreted Proteins, Exosomes, and Microvesicles in Cell Culture Conditioned Media.
Sinha A, Principe S, Alfaro J, Ignatchenko A, Ignatchenko V, Kislinger T. Methods in molecular biology (Clifton, N.J.) Volume 1722 (2018) p.91-102 DOI: 10.1007/978-1-4939-7553-2_6
The European Nucleotide Archive in 2017.
Silvester N, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Harrison PW, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Menchi M, Reddy K, Pakseresht N, Rajan J, Rossello M, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Nucleic acids research Volume 46 (2018) p.D36-D40 DOI: 10.1093/nar/gkx1125
WormBase 2017: molting into a new stage.
Lee RYN, Howe KL, Harris TW, Arnaboldi V, Cain S, Chan J, Chen WJ, Davis P, Gao S, Grove C, Kishore R, Muller HM, Nakamura C, Nuin P, Paulini M, Raciti D, Rodgers F, Russell M, Schindelman G, Tuli MA, Van Auken K, Wang Q, Williams G, Wright A, Yook K, Berriman M, Kersey P, Schedl T, Stein L, Sternberg PW. Nucleic acids research Volume 46 (2018) p.D869-D874 DOI: 10.1093/nar/gkx998
The SysteMHC Atlas project.
Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E. Nucleic acids research Volume 46 (2018) p.D1237-D1247 DOI: 10.1093/nar/gkx664
Expression Atlas: gene and protein expression across multiple studies and organisms.
Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AM, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R. Nucleic acids research Volume 46 (2018) p.D246-D251 DOI: 10.1093/nar/gkx1158
Hands-on on Protein Function Prediction with Machine Learning and Interactive Analytics
Saidi R. DOI: 10.6019/tol.unip_machine-w.2018.00001.1

2017

Phenotype inference in an Escherichia coli strain panel.
Galardini M, Koumoutsi A, Herrera-Dominguez L, Cordero Varela JA, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P. eLife Volume 6 (2017) DOI: 10.7554/elife.31035
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Comparative analysis of neutrophil and monocyte epigenomes
Rico D, Martens JH, Downes K, Carrillo-de-Santa-Pau E, Pancaldi V, Breschi A, Richardson D, Heath S, Saeed S, Frontini M, Chen L, Watt S, Müller F, Clarke L, Kerstens HH, Wilder SP, Palumbo E, Djebali S, Raineri E, Merkel A, Esteve-Codina A, Sultan M, van Bommel A, Gut M, Yaspo M, Rubio M, Fernandez JM, Attwood A, de la Torre V, Royo R, Fragkogianni S, Gelpí JL, Torrents D, Iotchkova V, Logie C, Aghajanirefah A, Singh AA, Janssen-Megens EM, Berentsen K, Erber W, Rendon A, Kostadima M, Loos R, van der Ent MA, Kaan A, Sharifi N, Paul DS, Ifrim DC, Quintin J, Love MI, Pisano DG, Burden F, Foad N, Farrow S, Zerbino DR, Dunham I, Kuijpers T, Lehrach H, Lengauer T, Bertone P, Netea MG, Vingron M, Beck S, Flicek P, Gut I, Ouwehand WH, Bock C, Soranzo N, Guigo R, Valencia A, Stunnenberg HG. Preprint DOI: 10.1101/237784
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat.
Martín-Gálvez D, Dunoyer de Segonzac D, Ma MCJ, Kwitek AE, Thybert D, Flicek P. BMC genomics Volume 18 (2017) p.986 DOI: 10.1186/s12864-017-4351-9
Usage of cell nomenclature in biomedical literature.
Kafkas Ş, Sarntivijai S, Hoehndorf R. BMC bioinformatics Volume 18 (2017) p.561 DOI: 10.1186/s12859-017-1978-0
Comparison, alignment, and synchronization of cell line information between CLO and EFO.
Ong E, Sarntivijai S, Jupp S, Parkinson H, He Y. BMC bioinformatics Volume 18 (2017) p.557 DOI: 10.1186/s12859-017-1979-z
Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge.
Sarntivijai S, Diehl AD, He Y. BMC bioinformatics Volume 18 (2017) p.560 DOI: 10.1186/s12859-017-1976-2
Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions.
Tang J, Tanoli ZU, Ravikumar B, Alam Z, Rebane A, Vähä-Koskela M, Peddinti G, van Adrichem AJ, Wakkinen J, Jaiswal A, Karjalainen E, Gautam P, He L, Parri E, Khan S, Gupta A, Ali M, Yetukuri L, Gustavsson AL, Seashore-Ludlow B, Hersey A, Leach AR, Overington JP, Repasky G, Wennerberg K, Aittokallio T. Cell chemical biology Volume 25 (2018) p.224-229.e2 DOI: 10.1016/j.chembiol.2017.11.009
Cell ontology in an age of data-driven cell classification.
Osumi-Sutherland D. BMC bioinformatics Volume 18 (2017) p.558 DOI: 10.1186/s12859-017-1980-6
Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses.
Ong E, Xie J, Ni Z, Liu Q, Sarntivijai S, Lin Y, Cooper D, Terryn R, Stathias V, Chung C, Schürer S, He Y. BMC bioinformatics Volume 18 (2017) p.556 DOI: 10.1186/s12859-017-1981-5
Accurate and fast feature selection workflow for high-dimensional omics data.
Perez-Riverol Y, Kuhn M, Vizcaíno JA, Hitz MP, Audain E. PloS one Volume 12 (2017) p.e0189875 DOI: 10.1371/journal.pone.0189875
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A protein standard that emulates homology for the characterization of protein inference algorithms
The M, Edfors F, Perez-Riverol Y, Payne SH, Hoopmann MR, Palmblad M, Forsström B, Käll L. Preprint DOI: 10.1101/236471
Navigating the data-rich literature: finding evidence in biomedical publications
Levchenko M. DOI: 10.6019/tol.epmc_oct-w.2017.00001.1
Enzymes in UniProt
Zaru R. DOI: 10.6019/tol.unip-enzymes-w.2017.00001.1
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Real-time search of all bacterial and viral genomic data
Bradley P, Den Bakker HC, Rocha EPC, McVean G, Iqbal Z. Preprint DOI: 10.1101/234955
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Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis
Stojic L, Lun A, Mangei J, Mascalchi P, Quarantotti V, Barr AR, Bakal C, Marioni JC, Gergely F, Odom DT. Preprint DOI: 10.1101/234930
Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.
Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Peat G, Pignatelli M, Falcone F, Benes CH, Dunham I, Bignell G, McDade SS, Garnett MJ, Saez-Rodriguez J. Cancer research Volume 78 (2018) p.769-780 DOI: 10.1158/0008-5472.can-17-1679
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Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation
Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B. Preprint DOI: 10.1101/231118
The HMMER Web Server for Protein Sequence Similarity Search.
Prakash A, Jeffryes M, Bateman A, Finn RD. Current protocols in bioinformatics Volume 60 (2017) p.3.15.1-3.15.23 DOI: 10.1002/cpbi.40
Immuno-oncology from the perspective of somatic evolution.
González S, Volkova N, Beer P, Gerstung M. Seminars in cancer biology Volume 52 (2018) p.75-85 DOI: 10.1016/j.semcancer.2017.12.001
Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the "Gene-Battery" Model.
Sundaram V, Wang T. BioEssays : news and reviews in molecular, cellular and developmental biology Volume 40 (2018) DOI: 10.1002/bies.201700155
The Human Cell Atlas.
Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N, Human Cell Atlas Meeting Participants. eLife Volume 6 (2017) DOI: 10.7554/elife.27041
Editorial overview: Catalysis and regulation.
Thornton J, Orengo C. Current opinion in structural biology Volume 47 (2017) p.vi-viii DOI: 10.1016/j.sbi.2017.11.005
clustComp, a bioconductor package for the comparison of clustering results.
Torrente A, Brazma A. Bioinformatics (Oxford, England) Volume 33 (2017) p.4001-4003 DOI: 10.1093/bioinformatics/btx532
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DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation.
Richard MA, Huan T, Ligthart S, Gondalia R, Jhun MA, Brody JA, Irvin MR, Marioni R, Shen J, Tsai PC, Montasser ME, Jia Y, Syme C, Salfati EL, Boerwinkle E, Guan W, Mosley TH, Bressler J, Morrison AC, Liu C, Mendelson MM, Uitterlinden AG, van Meurs JB, BIOS Consortium, Franco OH, Zhang G, Li Y, Stewart JD, Bis JC, Psaty BM, Chen YI, Kardia SLR, Zhao W, Turner ST, Absher D, Aslibekyan S, Starr JM, McRae AF, Hou L, Just AC, Schwartz JD, Vokonas PS, Menni C, Spector TD, Shuldiner A, Damcott CM, Rotter JI, Palmas W, Liu Y, Paus T, Horvath S, O'Connell JR, Guo X, Pausova Z, Assimes TL, Sotoodehnia N, Smith JA, Arnett DK, Deary IJ, Baccarelli AA, Bell JT, Whitsel E, Dehghan A, Levy D, Fornage M. American journal of human genetics Volume 101 (2017) p.888-902 DOI: 10.1016/j.ajhg.2017.09.028
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Genetic diversity of the African malaria vector Anopheles gambiae.
Anopheles gambiae 1000 Genomes Consortium, Data analysis group, Partner working group, Sample collections—Angola:, Burkina Faso:, Cameroon:, Gabon:, Guinea:, Guinea-Bissau:, Kenya:, Uganda:, Crosses:, Sequencing and data production, Web application development, Project coordination. Nature Volume 552 (2017) p.96-100 DOI: 10.1038/nature24995
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Community-driven data analysis training for biology
Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz H, Houwaart T, Jagtap P, Larivière D, Corguillé GL, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D, Network GT, Backofen R, Taylor J, Nekrutenko A, Grüning B. Preprint DOI: 10.1101/225680
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Assessing the Gene Regulatory Landscape in 1,188 Human Tumors
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NCBI will no longer make taxonomy identifiers for individual influenza strains on January 15, 2018
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A novel multi SNP based method for the identification of subspecies and associated lineages and sub-lineages of theMycobacterium tuberculosiscomplex by whole genome sequencing
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Genomic Research Data Generation, Analysis and Sharing - Challenges in the African Setting
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Genomics in healthcare: GA4GH looks to 2022
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Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
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Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis.
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Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.
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Multi-platform discovery of haplotype-resolved structural variation in human genomes
Chaisson MJ, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez O, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie A, Antaki D, Audano P, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin C, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin D, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lee JE, Lee J, Lee W, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro F, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang A, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DC, 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 P, Lansdorp PM, Marth G, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski M, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Preprint DOI: 10.1101/193144
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UniProt Genomic Mapping for Deciphering Functional Effects of Missense Variants
McGarvey PB, Nightingale A, Luo J, Huang H, Martin MJ, Wu C, the UniProt Consortium. Preprint DOI: 10.1101/192914
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C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis.
Lepik K, Annilo T, Kukuškina V, eQTLGen Consortium, Kisand K, Kutalik Z, Peterson P, Peterson H. PLoS computational biology Volume 13 (2017) p.e1005766 DOI: 10.1371/journal.pcbi.1005766
Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles.
Collins C, Hurley R, Almutlaqah N, O'Keeffe G, Keane TM, Fitzpatrick DA, Owens RA. Microorganisms Volume 5 (2017) DOI: 10.3390/microorganisms5030060
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.
Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR. Journal of proteome research Volume 16 (2017) p.4288-4298 DOI: 10.1021/acs.jproteome.7b00370
Uncovering novel repositioning opportunities using the Open Targets platform.
Khaladkar M, Koscielny G, Hasan S, Agarwal P, Dunham I, Rajpal D, Sanseau P. Drug discovery today Volume 22 (2017) p.1800-1807 DOI: 10.1016/j.drudis.2017.09.007
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clusterSeq: methods for identifying co-expression in high-throughput sequencing data
Hardcastle TJ, Papatheodorou I. Preprint DOI: 10.1101/188581
Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets.
Jarnuczak AF, Vizcaíno JA. Current protocols in bioinformatics Volume 59 (2017) p.13.31.1-13.31.12 DOI: 10.1002/cpbi.30
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Avoiding ascertainment bias in the maximum likelihood inference of phylogenies based on truncated data
Tamuri A, Goldman N. Preprint DOI: 10.1101/186478
Understanding enzyme function evolution from a computational perspective.
Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM. Current opinion in structural biology Volume 47 (2017) p.131-139 DOI: 10.1016/j.sbi.2017.08.003
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Biased numerical cognition impairs economic decision-making in Parkinson's disease.
Arshad Q, Bonsu A, Lobo R, Fluri AS, Sheriff R, Bain P, Pavese N, Bronstein AM. Annals of clinical and translational neurology Volume 4 (2017) p.739-748 DOI: 10.1002/acn3.449
The future of metabolomics in ELIXIR.
van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Le Corguillé G, Moreno P, Moschonas NK, Neumann S, O'Donovan C, Reczko M, Rocca-Serra P, Rosato A, Salek RM, Sansone SA, Satagopam V, Schober D, Shimmo R, Spicer RA, Spjuth O, Thévenot EA, Viant MR, Weber RJM, Willighagen EL, Zanetti G, Steinbeck C. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.12342.2
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Societal challenges of precision medicine: Bringing order to chaos.
Salgado R, Moore H, Martens JWM, Lively T, Malik S, McDermott U, Michiels S, Moscow JA, Tejpar S, McKee T, Lacombe D, IBCD-Faculty. European journal of cancer (Oxford, England : 1990) Volume 84 (2017) p.325-334 DOI: 10.1016/j.ejca.2017.07.028
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Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Fonseca NA, He Y, Kahles A, Lehmann K, Liu F, Shiraishi Y, Soulette CM, Urban L, Demircioğlu D, Greger L, Li S, Liu D, Perry MD, Xiang L, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, PCAWG Transcriptome Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/183889
More on the Best Evolutionary Rate for Phylogenetic Analysis.
Klopfstein S, Massingham T, Goldman N. Systematic biology Volume 66 (2017) p.769-785 DOI: 10.1093/sysbio/syx051
PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models.
Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J. Structure (London, England : 1993) Volume 25 (2017) p.1317-1318 DOI: 10.1016/j.str.2017.08.001
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Hoskins RA, Repo S, Barsky D, Andreoletti G, Moult J, Brenner SE. Human mutation Volume 38 (2017) p.1039-1041 DOI: 10.1002/humu.23290
Best practice data life cycle approaches for the life sciences.
Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. F1000Research Volume 6 (2017) p.1618 DOI: 10.12688/f1000research.12344.2
In silico prediction of novel therapeutic targets using gene-disease association data.
Ferrero E, Dunham I, Sanseau P. Journal of translational medicine Volume 15 (2017) p.182 DOI: 10.1186/s12967-017-1285-6
A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity.
Kuepfer L, Clayton O, Thiel C, Cordes H, Nudischer R, Blank LM, Baier V, Heymans S, Caiment F, Roth A, Fluri DA, Kelm JM, Castell J, Selevsek N, Schlapbach R, Keun H, Hynes J, Sarkans U, Gmuender H, Herwig R, Niederer S, Schuchhardt J, Segall M, Kleinjans J. Archives of toxicology Volume 92 (2018) p.553-555 DOI: 10.1007/s00204-017-2041-7
The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training.
Morgan SL, Palagi PM, Fernandes PL, Koperlainen E, Dimec J, Marek D, Larcombe L, Rustici G, Attwood TK, Via A. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.12332.1
The application of project-based learning in bioinformatics training.
Emery LR, Morgan SL. PLoS computational biology Volume 13 (2017) p.e1005620 DOI: 10.1371/journal.pcbi.1005620
User experience design for more user-friendly applications
Ide-Smith M, Karamanis N. DOI: 10.6019/tol.uxapp-w.2017.00001.1
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Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data.
Zhang C, Bijlard J, Staiger C, Scollen S, van Enckevort D, Hoogstrate Y, Senf A, Hiltemann S, Repo S, Pipping W, Bierkens M, Payralbe S, Stringer B, Heringa J, Stubbs A, Bonino Da Silva Santos LO, Belien J, Weistra W, Azevedo R, van Bochove K, Meijer G, Boiten JW, Rambla J, Fijneman R, Spalding JD, Abeln S. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.12168.1
Europe PMC: Quick tour
Parkin M. DOI: 10.6019/tol.epmc-qt.2017.00001.2
Ensembl tools: webinar
Perry E. DOI: 10.6019/tol.ens-too-w.2017.00001.2
Europe PMC: get the most from literature searches
Parkin M. DOI: 10.6019/tol.epmcsearch-w.2017.00001.1
Human genetic variation (II): exploring publicly available data
Armstrong D, Burke M, Emery L, MacArthur J, Nightingale A, Perry E, Pundir S, Saunders G. DOI: 10.6019/tol.hugenvar_2-t.2017.00001.1
Human genetic variation (I): an introduction
Armstrong D, Burke M, Emery L, MacArthur J, Nightingale A, Perry E, Pundir S, Saunders G. DOI: 10.6019/tol.hugenvar_1-t.2017.00001.1
How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.
Marioni JC, Arendt D. Annual review of cell and developmental biology Volume 33 (2017) p.537-553 DOI: 10.1146/annurev-cellbio-100616-060818
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Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data
Zhang C, Bijlard J, Staiger C, Scollen S, van Enckevort D, Hoogstrate Y, Senf A, Hiltemann S, Repo S, Pipping W, Bierkens M, Payralbe S, Stringer B, Heringa J, Stubbs A, Bonino Da Silva Santos LO, Belien J, Weistra W, Azevedo R, van Bochove K, Meijer G, Boiten J, Rambla J, Fijneman R, Spalding JD, Abeln S. Preprint DOI: 10.12688/f1000research.12168.1
10th Anniversary Treasure Hunt
Armstrong D, Burke M, Huerta L, Levchenko M, Mitchell A, Morgan S, Mugumbate G, Mutowo P, Orchard S, Perry E, Pundir S, Richardson L, Tang A. DOI: 10.6019/tol.treasure-t.2017.00001.1
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Detection and removal of barcode swapping in single-cell RNA-seq data
Griffiths JA, Richard AC, Bach K, Lun AT, Marioni JC. Preprint DOI: 10.1101/177048
EMBL-EBI, programmatically: take a REST from manual searches
Burke M, Armstrong D, Carvalho-Silva D, Castro L, Cowley A, Finn R, Foix A, Katuri J, Laird M, Lee J, Levchenko M, Lopez R, Nightingale A, Nightingale A, Nowotka M, Perry E, Pichler K, Pundir S, Morgan S, Saunders G, Garcia P, Squizzato S. DOI: 10.6019/tol.ebiprogrammatically-w.2017.00001.1
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A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters
Demircioğlu D, Kindermans M, Nandi T, Cukuroglu E, Calabrese C, Fonseca NA, Kahles A, Lehmann K, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J, on behalf of the PCAWG Transcriptome Working Group, and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/176487
Navigating freely-available software tools for metabolomics analysis.
Spicer R, Salek RM, Moreno P, Cañueto D, Steinbeck C. Metabolomics : Official journal of the Metabolomic Society Volume 13 (2017) p.106 DOI: 10.1007/s11306-017-1242-7
Impact of Alternative Splicing on the Human Proteome.
Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. Cell reports Volume 20 (2017) p.1229-1241 DOI: 10.1016/j.celrep.2017.07.025
Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient.
Jiménez-Sánchez A, Memon D, Pourpe S, Veeraraghavan H, Li Y, Vargas HA, Gill MB, Park KJ, Zivanovic O, Konner J, Ricca J, Zamarin D, Walther T, Aghajanian C, Wolchok JD, Sala E, Merghoub T, Snyder A, Miller ML. Cell Volume 170 (2017) p.927-938.e20 DOI: 10.1016/j.cell.2017.07.025
Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS. Cell reports Volume 20 (2017) p.2201-2214 DOI: 10.1016/j.celrep.2017.08.010
Genomic Evolution of Breast Cancer Metastasis and Relapse.
Yates LR, Knappskog S, Wedge D, Farmery JHR, Gonzalez S, Martincorena I, Alexandrov LB, Van Loo P, Haugland HK, Lilleng PK, Gundem G, Gerstung M, Pappaemmanuil E, Gazinska P, Bhosle SG, Jones D, Raine K, Mudie L, Latimer C, Sawyer E, Desmedt C, Sotiriou C, Stratton MR, Sieuwerts AM, Lynch AG, Martens JW, Richardson AL, Tutt A, Lønning PE, Campbell PJ. Cancer cell Volume 32 (2017) p.169-184.e7 DOI: 10.1016/j.ccell.2017.07.005
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A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine.
Vamathevan J, Birney E. Yearbook of medical informatics Volume 26 (2017) p.178-187 DOI: 10.15265/iy-2017-017
BioContainers: an open-source and community-driven framework for software standardization.
da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y. Bioinformatics (Oxford, England) Volume 33 (2017) p.2580-2582 DOI: 10.1093/bioinformatics/btx192
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Genoscope Technical Team, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Tara Oceans Consortium Coordinators, Pesant S, Karsenti E, Wincker P. Scientific data Volume 4 (2017) p.170093 DOI: 10.1038/sdata.2017.93
Automated assembly of species metabolomes through data submission into a public repository.
Salek RM, Conesa P, Cochrane K, Haug K, Williams M, Kale N, Moreno P, Jayaseelan KV, Macias JR, Nainala VC, Hall RD, Reed LK, Viant MR, O'Donovan C, Steinbeck C. GigaScience Volume 6 (2017) p.1-4 DOI: 10.1093/gigascience/gix062
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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Nature biotechnology Volume 35 (2017) p.725-731 DOI: 10.1038/nbt.3893
The metagenomic data life-cycle: standards and best practices.
Ten Hoopen P, Finn RD, Bongo LA, Corre E, Fosso B, Meyer F, Mitchell A, Pelletier E, Pesole G, Santamaria M, Willassen NP, Cochrane G. GigaScience Volume 6 (2017) p.1-11 DOI: 10.1093/gigascience/gix047
mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.
Larralde M, Lawson TN, Weber RJM, Moreno P, Haug K, Rocca-Serra P, Viant MR, Steinbeck C, Salek RM. Bioinformatics (Oxford, England) Volume 33 (2017) p.2598-2600 DOI: 10.1093/bioinformatics/btx169
Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.
Mohammed H, Hernando-Herraez I, Savino A, Scialdone A, Macaulay I, Mulas C, Chandra T, Voet T, Dean W, Nichols J, Marioni JC, Reik W. Cell reports Volume 20 (2017) p.1215-1228 DOI: 10.1016/j.celrep.2017.07.009
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Designing an intuitive web application for drug discovery scientists
Karamanis N, Carvalho-Silva D, Cham JA, Fumis L, Hasan S, Hulcoop D, Koscielny G, Maguire M, Newell W, Ong C, Papa E, Pierleoni A, Pignatelli M, Pundir S, Rowland F, Vamathevan J, Watkins X, Barrett JC, Dunham I. Preprint DOI: 10.1101/169193
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Best Practice Data Life Cycle Approaches for the Life Sciences
Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. Preprint DOI: 10.1101/167619
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Whole-body single-cell sequencing of the Platynereis larva reveals a subdivision into apical versus non-apical tissues
Achim K, Eling N, Martinez Vergara H, Bertucci PY, Brunet T, Collier P, Benes V, Marioni JC, Arendt D. Preprint DOI: 10.1101/167742
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Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines.
Alfaro JA, Ignatchenko A, Ignatchenko V, Sinha A, Boutros PC, Kislinger T. Genome medicine Volume 9 (2017) p.62 DOI: 10.1186/s13073-017-0454-9
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Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours
Haghverdi L, Lun ATL, Morgan MD, Marioni JC. Preprint DOI: 10.1101/165118
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A user’s guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)
Goldman M, Zhang J, Fonseca NA, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, O’Connor BD, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, Haussler D, Weinstein JN, Huber W, Valencia A, Park PJ, Papatheodorou I, Zhu J, Ferretti V, Vazquez M, on behalf of the PCAWG Portals and Visualization Working Group, the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/163907
Platelet function is modified by common sequence variation in megakaryocyte super enhancers.
Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts AS, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide ME, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M, Ouwehand WH, Astle WJ, Downes K, Kostadima M, Frontini M. Nature communications Volume 8 (2017) p.16058 DOI: 10.1038/ncomms16058
The yeast noncoding RNA interaction network.
Panni S, Prakash A, Bateman A, Orchard S. RNA (New York, N.Y.) Volume 23 (2017) p.1479-1492 DOI: 10.1261/rna.060996.117
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General guidelines for biomedical software development
Silva LB, Jimenez RC, Blomberg N, Luis Oliveira J. Preprint DOI: 10.12688/f1000research.10750.2
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The evolutionary history of 2,658 cancers
Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Loo PV, on behalf of the PCAWG Evolution and Heterogeneity Working Group, the PCAWG network. Preprint DOI: 10.1101/161562
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Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments
Yung CK, O’Connor BD, Yakneen S, Zhang J, Ellrott K, Kleinheinz K, Miyoshi N, Raine KM, Royo R, Saksena GB, Schlesner M, Shorser SI, Vazquez M, Weischenfeldt J, Yuen D, Butler AP, Davis-Dusenbery BN, Eils R, Ferretti V, Grossman RL, Harismendy O, Kim Y, Nakagawa H, Newhouse SJ, Torrents D, Stein LD, Rodriguez JB, Boroevich KA, Boyce R, Brooks AN, Buchanan A, Buchhalter I, Byrne NJ, Cafferkey A, Campbell PJ, Chen Z, Cho S, Choi W, Clapham P, De La Vega FM, Demeulemeester J, Dow MT, Dursi LJ, Eils J, Farcas C, Favero F, Fayzullaev N, Flicek P, Fonseca NA, Gelpi JL, Getz G, Gibson B, Heinold MC, Hess JM, Hofmann O, Hong JH, Hudson TJ, Huebschmann D, Hutter B, Hutter CM, Imoto S, Ivkovic S, Jeon S, Jiao W, Jung J, Kabbe R, Kahles A, Kerssemakers J, Kim H, Kim H, Kim J, Korbel JO, Koscher M, Koures A, Kovacevic M, Lawerenz C, Leshchiner I, Livitz DG, Mihaiescu GL, Mijalkovic S, Lazic AM, Miyano S, Nahal HK, Nastic M, Nicholson J, Ocana D, Ohi K, Ohno-Machado L, Omberg L, Francis Ouellette B, Paramasivam N, Perry MD, Pihl TD, Prinz M, Puiggròs M, Radovic P, Rheinbay E, Rosenberg MW, Short C, Sofia HJ, Spring J, Struck AJ, Tiao G, Tijanic N, Loo PV, Vicente D, Wala JA, Wang Z, Werner J, Williams A, Woo Y, Wright AJ, Xiang Q, on behalf of the PCAWG Technical Working Group, the PCAWG Network. Preprint DOI: 10.1101/161638
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Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.
Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat RR, Li X, Pal LR, Kundu K, Yin Y, Moult J, Jiang Y, Pejaver V, Pagel KA, Li B, Mooney SD, Radivojac P, Shah S, Carraro M, Gasparini A, Leonardi E, Giollo M, Ferrari C, Tosatto SCE, Bachar E, Azaria JR, Ofran Y, Unger R, Niroula A, Vihinen M, Chang B, Wang MH, Franke A, Petersen BS, Pirooznia M, Zandi P, McCombie R, Potash JB, Altman RB, Klein TE, Hoskins RA, Repo S, Brenner SE, Morgan AA. Human mutation Volume 38 (2017) p.1182-1192 DOI: 10.1002/humu.23280
Building bridges between cellular and molecular structural biology.
Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M, Kleywegt GJ. eLife Volume 6 (2017) DOI: 10.7554/elife.25835
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Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
Thybert D, Roller M, Navarro FC, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin A, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Quail MA, Sisu C, Stanke M, Stefflova K, Oosterhout CV, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams D, Brazma A, Gerstein M, Paten B, Pham S, Keane T, Odom DT, Flicek P. Preprint DOI: 10.1101/158659
The EBI search engine: EBI search as a service-making biological data accessible for all.
Park YM, Squizzato S, Buso N, Gur T, Lopez R. Nucleic acids research Volume 45 (2017) p.W545-W549 DOI: 10.1093/nar/gkx359
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Petryszak R, Fonseca NA, Füllgrabe A, Huerta L, Keays M, Tang YA, Brazma A. Bioinformatics (Oxford, England) Volume 33 (2017) p.2218-2220 DOI: 10.1093/bioinformatics/btx143
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ANOS1: a unified nomenclature for Kallmann syndrome 1 gene (KAL1) and anosmin-1.
de Castro F, Seal R, Maggi R, Group of HGNC consultants for KAL1 nomenclature. Briefings in functional genomics Volume 16 (2017) p.205-210 DOI: 10.1093/bfgp/elw037
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Zheng-Bradley X, Streeter I, Fairley S, Richardson D, Clarke L, Flicek P, 1000 Genomes Project Consortium. GigaScience Volume 6 (2017) p.1-8 DOI: 10.1093/gigascience/gix038
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Chojnacki S, Cowley A, Lee J, Foix A, Lopez R. Nucleic acids research Volume 45 (2017) p.W550-W553 DOI: 10.1093/nar/gkx273
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Nightingale A, Antunes R, Alpi E, Bursteinas B, Gonzales L, Liu W, Luo J, Qi G, Turner E, Martin M. Nucleic acids research Volume 45 (2017) p.W539-W544 DOI: 10.1093/nar/gkx237
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Watkins X, Garcia LJ, Pundir S, Martin MJ, UniProt Consortium. Bioinformatics (Oxford, England) Volume 33 (2017) p.2040-2041 DOI: 10.1093/bioinformatics/btx120
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Raisaro JL, Tramèr F, Ji Z, Bu D, Zhao Y, Carey K, Lloyd D, Sofia H, Baker D, Flicek P, Shringarpure S, Bustamante C, Wang S, Jiang X, Ohno-Machado L, Tang H, Wang X, Hubaux JP. Journal of the American Medical Informatics Association : JAMIA Volume 24 (2017) p.799-805 DOI: 10.1093/jamia/ocw167
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McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H. PLoS biology Volume 15 (2017) p.e2001414 DOI: 10.1371/journal.pbio.2001414
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Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity.
Hendricks AE, Bochukova EG, Marenne G, Keogh JM, Atanassova N, Bounds R, Wheeler E, Mistry V, Henning E, Körner A, Muddyman D, McCarthy S, Hinney A, Hebebrand J, Scott RA, Langenberg C, Wareham NJ, Surendran P, Howson JM, Butterworth AS, Danesh J, Nordestgaard BG, Nielsen SF, Afzal S, Papadia S, Ashford S, Garg S, Millhauser GL, Palomino RI, Kwasniewska A, Tachmazidou I, O'Rahilly S, Zeggini E, Barroso I, Farooqi IS, Understanding Society Scientific Group, EPIC-CVD Consortium, UK10K Consortium. Scientific reports Volume 7 (2017) p.4394 DOI: 10.1038/s41598-017-03054-8
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Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture.
Macqueen DJ, Primmer CR, Houston RD, Nowak BF, Bernatchez L, Bergseth S, Davidson WS, Gallardo-Escárate C, Goldammer T, Guiguen Y, Iturra P, Kijas JW, Koop BF, Lien S, Maass A, Martin SAM, McGinnity P, Montecino M, Naish KA, Nichols KM, Ólafsson K, Omholt SW, Palti Y, Plastow GS, Rexroad CE, Rise ML, Ritchie RJ, Sandve SR, Schulte PM, Tello A, Vidal R, Vik JO, Wargelius A, Yáñez JM, FAASG Consortium. BMC genomics Volume 18 (2017) p.484 DOI: 10.1186/s12864-017-3862-8
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Karp NA, Mason J, Beaudet AL, Benjamini Y, Bower L, Braun RE, Brown SDM, Chesler EJ, Dickinson ME, Flenniken AM, Fuchs H, Angelis MH, Gao X, Guo S, Greenaway S, Heller R, Herault Y, Justice MJ, Kurbatova N, Lelliott CJ, Lloyd KCK, Mallon AM, Mank JE, Masuya H, McKerlie C, Meehan TF, Mott RF, Murray SA, Parkinson H, Ramirez-Solis R, Santos L, Seavitt JR, Smedley D, Sorg T, Speak AO, Steel KP, Svenson KL, International Mouse Phenotyping Consortium, Wakana S, West D, Wells S, Westerberg H, Yaacoby S, White JK. Nature communications Volume 8 (2017) p.15475 DOI: 10.1038/ncomms15475
Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1.
Suri M, Evers JMG, Laskowski RA, O'Brien S, Baker K, Clayton-Smith J, Dabir T, Josifova D, Joss S, Kerr B, Kraus A, McEntagart M, Morton J, Smith A, Splitt M, Thornton JM, DDD Study, Wright CF. Molecular genetics & genomic medicine Volume 5 (2017) p.495-507 DOI: 10.1002/mgg3.304
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Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.
Cai B, Li B, Kiga N, Thusberg J, Bergquist T, Chen YC, Niknafs N, Carter H, Tokheim C, Beleva-Guthrie V, Douville C, Bhattacharya R, Yeo HTG, Fan J, Sengupta S, Kim D, Cline M, Turner T, Diekhans M, Zaucha J, Pal LR, Cao C, Yu CH, Yin Y, Carraro M, Giollo M, Ferrari C, Leonardi E, Tosatto SCE, Bobe J, Ball M, Hoskins RA, Repo S, Church G, Brenner SE, Moult J, Gough J, Stanke M, Karchin R, Mooney SD. Human mutation Volume 38 (2017) p.1266-1276 DOI: 10.1002/humu.23265
The Image Data Resource: A Bioimage Data Integration and Publication Platform.
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR. Nature methods Volume 14 (2017) p.775-781 DOI: 10.1038/nmeth.4326
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Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Nature Volume 546 (2017) p.686 DOI: 10.1038/nature23012
Four simple recommendations to encourage best practices in research software.
Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.11407.1
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A community proposal to integrate proteomics activities in ELIXIR
Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJ, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O. Preprint DOI: 10.12688/f1000research.11751.1
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Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.11751.1
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Nowotka MM, Gaulton A, Mendez D, Bento AP, Hersey A, Leach A. Expert opinion on drug discovery Volume 12 (2017) p.757-767 DOI: 10.1080/17460441.2017.1339032
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Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer
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Integrating long-range connectivity information into de Bruijn graphs
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An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures
Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Berna J, Tubio JM, McMurran CE, Young AM, Young MD, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson MD, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott MW, Kirollos RW, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U. Preprint DOI: 10.1101/146811
Literature evidence in open targets - a target validation platform.
Kafkas Ş, Dunham I, McEntyre J. Journal of biomedical semantics Volume 8 (2017) p.20 DOI: 10.1186/s13326-017-0131-3
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Accurate and Fast feature selection workflow for high-dimensional omics data
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PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance.
Nadon C, Van Walle I, Gerner-Smidt P, Campos J, Chinen I, Concepcion-Acevedo J, Gilpin B, Smith AM, Man Kam K, Perez E, Trees E, Kubota K, Takkinen J, Nielsen EM, Carleton H, FWD-NEXT Expert Panel. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin Volume 22 (2017) DOI: 10.2807/1560-7917.es.2017.22.23.30544
Structural Variation Shapes the Landscape of Recombination in Mouse.
Morgan AP, Gatti DM, Najarian ML, Keane TM, Galante RJ, Pack AI, Mott R, Churchill GA, de Villena FP. Genetics Volume 206 (2017) p.603-619 DOI: 10.1534/genetics.116.197988
MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry.
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MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry
Jain M, Tyson JR, Loose M, Ip CL, Eccles DA, O'Grady J, Malla S, Leggett RM, Wallerman O, Jansen HJ, Zalunin V, Birney E, Brown BL, Snutch TP, Olsen HE, MinION Analysis and Reference Consortium. Preprint DOI: 10.12688/f1000research.11354.1
OpenMS - A platform for reproducible analysis of mass spectrometry data.
Pfeuffer J, Sachsenberg T, Alka O, Walzer M, Fillbrunn A, Nilse L, Schilling O, Reinert K, Kohlbacher O. Journal of biotechnology Volume 261 (2017) p.142-148 DOI: 10.1016/j.jbiotec.2017.05.016
Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.
Joseph AP, Lagerstedt I, Patwardhan A, Topf M, Winn M. Journal of structural biology Volume 199 (2017) p.12-26 DOI: 10.1016/j.jsb.2017.05.007
Bacterial Virus Ontology; Coordinating across Databases.
Hulo C, Masson P, Toussaint A, Osumi-Sutherland D, de Castro E, Auchincloss AH, Poux S, Bougueleret L, Xenarios I, Le Mercier P. Viruses Volume 9 (2017) DOI: 10.3390/v9060126
The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.
Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR. Molecular & cellular proteomics : MCP Volume 16 (2017) p.1275-1285 DOI: 10.1074/mcp.m117.068429
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Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.
Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, Gough J, Katsonis P, Leonardi E, Lichtarge O, Menin C, Martelli PL, Niroula A, Pal LR, Repo S, Scaini MC, Vihinen M, Wei Q, Xu Q, Yang Y, Yin Y, Zaucha J, Zhao H, Zhou Y, Brenner SE, Moult J, Tosatto SCE. Human mutation Volume 38 (2017) p.1042-1050 DOI: 10.1002/humu.23235
Normalizing single-cell RNA sequencing data: challenges and opportunities.
Vallejos CA, Risso D, Scialdone A, Dudoit S, Marioni JC. Nature methods Volume 14 (2017) p.565-571 DOI: 10.1038/nmeth.4292
Common genetic variation drives molecular heterogeneity in human iPSCs.
Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Nature Volume 546 (2017) p.370-375 DOI: 10.1038/nature22403
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The Human Cell Atlas
Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe’er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N, the Human Cell Atlas Meeting Participants. Preprint DOI: 10.1101/121202
Anna Tramontano 1957-2017.
Thornton JM, Valencia A, Schwede T. Nature structural & molecular biology Volume 24 (2017) p.431-432 DOI: 10.1038/nsmb.3410
An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.
Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu FH, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser DM, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Palma FD, Phillips AL, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD. Genome research Volume 27 (2017) p.885-896 DOI: 10.1101/gr.217117.116
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Applications of the 1000 Genomes Project resources.
Zheng-Bradley X, Flicek P. Briefings in functional genomics Volume 16 (2017) p.163-170 DOI: 10.1093/bfgp/elw027
Discovering and linking public omics data sets using the Omics Discovery Index.
Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H. Nature biotechnology Volume 35 (2017) p.406-409 DOI: 10.1038/nbt.3790
UniEuk: Time to Speak a Common Language in Protistology!
Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C. The Journal of eukaryotic microbiology Volume 64 (2017) p.407-411 DOI: 10.1111/jeu.12414
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A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog
Morales J, Bowler EH, Buniello A, Cerezo M, Hall P, Harris LW, Hastings E, Junkins HA, Malangone C, McMahon AC, Milano A, Welter D, Burdett T, Cunningham F, Flicek P, Parkinson H, Hindorff LA, MacArthur JAL. Preprint DOI: 10.1101/129395
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Patwardhan A. Acta crystallographica. Section D, Structural biology Volume 73 (2017) p.503-508 DOI: 10.1107/s2059798317004181
Multi-tissue DNA methylation age predictor in mouse.
Stubbs TM, Bonder MJ, Stark AK, Krueger F, BI Ageing Clock Team, von Meyenn F, Stegle O, Reik W. Genome biology Volume 18 (2017) p.68 DOI: 10.1186/s13059-017-1203-5
Visualising protein structures online
Armstrong A. DOI: 10.6019/tol.pdbe-litemol-w.2017.00001.1
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM. Genome research Volume 27 (2017) p.849-864 DOI: 10.1101/gr.213611.116
EMPIAR: Quick tour
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PhenoMeNal: accessing metabolomics workflows in Galaxy
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Decoding the functional Fes kinase signaling network topology in a lymphocyte model
Helbig AO, Kofler M, Gish G, Sriraja L, Lorenzen K, Tucholska M, Zhang C, Roth FP, Pawson T, Colwill K, Petsalaki E. Preprint DOI: 10.1101/125088
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Literature Evidence in Open Targets – a target validation platform
Kafkas Ş, Dunham I, McEntyre J. Preprint DOI: 10.1101/124719
Short template switch events explain mutation clusters in the human genome.
Löytynoja A, Goldman N. Genome research Volume 27 (2017) p.1039-1049 DOI: 10.1101/gr.214973.116
Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold.
Pearson WR, Li W, Lopez R. Nucleic acids research Volume 45 (2017) p.e46 DOI: 10.1093/nar/gkw1207
Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity.
Thomas DC, Clare S, Sowerby JM, Pardo M, Juss JK, Goulding DA, van der Weyden L, Storisteanu D, Prakash A, Espéli M, Flint S, Lee JC, Hoenderdos K, Kane L, Harcourt K, Mukhopadhyay S, Umrania Y, Antrobus R, Nathan JA, Adams DJ, Bateman A, Choudhary JS, Lyons PA, Condliffe AM, Chilvers ER, Dougan G, Smith KG. The Journal of experimental medicine Volume 214 (2017) p.1111-1128 DOI: 10.1084/jem.20161382
Microbiology Managers: Managerial Training in the RItrain Project.
Paterson RRM, Lima N, Brooksbank C, Guarini E, Pasterk M, Lavitrano M, RItrain project consortium. Trends in microbiology Volume 25 (2017) p.425-428 DOI: 10.1016/j.tim.2017.03.002
Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma.
Arseneault M, Monlong J, Vasudev NS, Laskar RS, Safisamghabadi M, Harnden P, Egevad L, Nourbehesht N, Panichnantakul P, Holcatova I, Brisuda A, Janout V, Kollarova H, Foretova L, Navratilova M, Mates D, Jinga V, Zaridze D, Mukeria A, Jandaghi P, Brennan P, Brazma A, Tost J, Scelo G, Banks RE, Lathrop M, Bourque G, Riazalhosseini Y. Scientific reports Volume 7 (2017) p.44876 DOI: 10.1038/srep44876
Orchestrating differential data access for translational research: a pilot implementation.
Brandizi M, Melnichuk O, Bild R, Kohlmayer F, Rodriguez-Castro B, Spengler H, Kuhn KA, Kuchinke W, Ohmann C, Mustonen T, Linden M, Nyrönen T, Lappalainen I, Brazma A, Sarkans U. BMC medical informatics and decision making Volume 17 (2017) p.30 DOI: 10.1186/s12911-017-0424-6
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Multi-tissue DNA methylation age predictor in mouse
Stubbs TM, Bonder MJ, Stark A, Krueger F, von Meyenn F, Stegle O, Reik W, Clock Team BI Ageing. Preprint DOI: 10.1101/119206
Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.
Huang Y, Kim JK, Do DV, Lee C, Penfold CA, Zylicz JJ, Marioni JC, Hackett JA, Surani MA. eLife Volume 6 (2017) DOI: 10.7554/elife.22345
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Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
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HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
Davies H, Glodzik D, Morganella S, Yates LR, Staaf J, Zou X, Ramakrishna M, Martin S, Boyault S, Sieuwerts AM, Simpson PT, King TA, Raine K, Eyfjord JE, Kong G, Borg Å, Birney E, Stunnenberg HG, van de Vijver MJ, Børresen-Dale AL, Martens JW, Span PN, Lakhani SR, Vincent-Salomon A, Sotiriou C, Tutt A, Thompson AM, Van Laere S, Richardson AL, Viari A, Campbell PJ, Stratton MR, Nik-Zainal S. Nature medicine Volume 23 (2017) p.517-525 DOI: 10.1038/nm.4292
Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.
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ChromoTrace: Computational Reconstruction of 3D Chromosome Configurations for Super-Resolution Microscopy
Barton C, Morganella S, Ødegård-Fougner Ø, Alexander S, Ries J, Fitzgerald T, Ellenberg J, Ellenberg J, Birney E. Preprint DOI: 10.1101/115436
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A global perspective on bioinformatics training needs
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Towards Coordinated International Support of Core Data Resources for the Life Sciences
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Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration.
Arno G, Carss KJ, Hull S, Zihni C, Robson AG, Fiorentino A, UK Inherited Retinal Disease Consortium, Hardcastle AJ, Holder GE, Cheetham ME, Plagnol V, NIHR Bioresource - Rare Diseases Consortium, Moore AT, Raymond FL, Matter K, Balda MS, Webster AR. American journal of human genetics Volume 100 (2017) p.334-342 DOI: 10.1016/j.ajhg.2016.12.014
A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.
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ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services.
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A Golden Age for Working with Public Proteomics Data.
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Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, Creighton CJ, on behalf of the PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/099861
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.
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The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying Neurodegeneration: Evolving Dimensions and Future Directions.
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Molecular and functional variation in iPSC-derived sensory neurons
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Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149.
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A Data Citation Roadmap for Scholarly Data Repositories
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Pharos: Collating protein information to shed light on the druggable genome.
Nguyen DT, Mathias S, Bologa C, Brunak S, Fernandez N, Gaulton A, Hersey A, Holmes J, Jensen LJ, Karlsson A, Liu G, Ma'ayan A, Mandava G, Mani S, Mehta S, Overington J, Patel J, Rouillard AD, Schürer S, Sheils T, Simeonov A, Sklar LA, Southall N, Ursu O, Vidovic D, Waller A, Yang J, Jadhav A, Oprea TI, Guha R. Nucleic acids research Volume 45 (2017) p.D995-D1002 DOI: 10.1093/nar/gkw1072
InterPro in 2017-beyond protein family and domain annotations.
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. Nucleic acids research Volume 45 (2017) p.D190-D199 DOI: 10.1093/nar/gkw1107
Open Targets: a platform for therapeutic target identification and validation.
Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I. Nucleic acids research Volume 45 (2017) p.D985-D994 DOI: 10.1093/nar/gkw1055
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog).
MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H. Nucleic acids research Volume 45 (2017) p.D896-D901 DOI: 10.1093/nar/gkw1133
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UniProt: the universal protein knowledgebase.
The UniProt Consortium. Nucleic acids research Volume 45 (2017) p.D158-D169 DOI: 10.1093/nar/gkw1099
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Expansion of the Gene Ontology knowledgebase and resources.
The Gene Ontology Consortium. Nucleic acids research Volume 45 (2017) p.D331-D338 DOI: 10.1093/nar/gkw1108
Increased DNA methylation variability in type 1 diabetes across three immune effector cell types.
Paul DS, Teschendorff AE, Dang MA, Lowe R, Hawa MI, Ecker S, Beyan H, Cunningham S, Fouts AR, Ramelius A, Burden F, Farrow S, Rowlston S, Rehnstrom K, Frontini M, Downes K, Busche S, Cheung WA, Ge B, Simon MM, Bujold D, Kwan T, Bourque G, Datta A, Lowy E, Clarke L, Flicek P, Libertini E, Heath S, Gut M, Gut IG, Ouwehand WH, Pastinen T, Soranzo N, Hofer SE, Karges B, Meissner T, Boehm BO, Cilio C, Elding Larsson H, Lernmark Å, Steck AK, Rakyan VK, Beck S, Leslie RD. Nature communications Volume 7 (2016) p.13555 DOI: 10.1038/ncomms13555
European Nucleotide Archive in 2016.
Toribio AL, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Fairley S, Gibson R, Goodgame N, Ten Hoopen P, Jayathilaka S, Kay S, Leinonen R, Liu X, Martínez-Villacorta J, Pakseresht N, Rajan J, Reddy K, Rosello M, Silvester N, Smirnov D, Vaughan D, Zalunin V, Cochrane G. Nucleic acids research Volume 45 (2017) p.D32-D36 DOI: 10.1093/nar/gkw1106
Uniclust databases of clustered and deeply annotated protein sequences and alignments.
Mirdita M, von den Driesch L, Galiez C, Martin MJ, Söding J, Steinegger M. Nucleic acids research Volume 45 (2017) p.D170-D176 DOI: 10.1093/nar/gkw1081
The ChEMBL database in 2017.
Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibrián-Uhalte E, Davies M, Dedman N, Karlsson A, Magariños MP, Overington JP, Papadatos G, Smit I, Leach AR. Nucleic acids research Volume 45 (2017) p.D945-D954 DOI: 10.1093/nar/gkw1074
Ensembl 2017.
Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Juettemann T, Keenan S, Laird MR, Lavidas I, Maurel T, McLaren W, Moore B, Murphy DN, Nag R, Newman V, Nuhn M, Ong CK, Parker A, Patricio M, Riat HS, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Wilder SP, Zadissa A, Kostadima M, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Cunningham F, Yates A, Zerbino DR, Flicek P. Nucleic acids research Volume 45 (2017) p.D635-D642 DOI: 10.1093/nar/gkw1104
IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex.
Maccari G, Robinson J, Ballingall K, Guethlein LA, Grimholt U, Kaufman J, Ho CS, de Groot NG, Flicek P, Bontrop RE, Hammond JA, Marsh SG. Nucleic acids research Volume 45 (2017) p.D860-D864 DOI: 10.1093/nar/gkw1050
WormBase ParaSite - a comprehensive resource for helminth genomics.
Howe KL, Bolt BJ, Shafie M, Kersey P, Berriman M. Molecular and biochemical parasitology Volume 215 (2017) p.2-10 DOI: 10.1016/j.molbiopara.2016.11.005
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The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Dissemination
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Carazo Salas RE, Swedlow JR. Preprint DOI: 10.1101/089359
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Chromosome assembly of large and complex genomes using multiple references
Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane T, Thybert D, Paten B, Pham S. Preprint DOI: 10.1101/088435
The BLUEPRINT Data Analysis Portal.
Fernández JM, de la Torre V, Richardson D, Royo R, Puiggròs M, Moncunill V, Fragkogianni S, Clarke L, BLUEPRINT Consortium, Flicek P, Rico D, Torrents D, Carrillo de Santa Pau E, Valencia A. Cell systems Volume 3 (2016) p.491-495.e5 DOI: 10.1016/j.cels.2016.10.021
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Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation
Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird MR, Longden I, Proctor G, Steve S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P. Preprint DOI: 10.1101/087239
Erratum to: Making sense of big data in health research: towards an EU action plan.
Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G. Genome medicine Volume 8 (2016) p.118 DOI: 10.1186/s13073-016-0376-y
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GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
Iotchkova V, Ritchie GR, Geihs M, Morganella S, Min JL, Walter K, Timpson N, Dunham I, Birney E, Soranzo N, UK10K Consortium. Preprint DOI: 10.1101/085738
The Mighty Fruit Fly Moves into Outbred Genetics.
Birney E. PLoS genetics Volume 12 (2016) p.e1006388 DOI: 10.1371/journal.pgen.1006388
eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data.
Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JHA, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S. Cell reports Volume 17 (2016) p.2137-2150 DOI: 10.1016/j.celrep.2016.10.059
β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance.
Novakovic B, Habibi E, Wang SY, Arts RJW, Davar R, Megchelenbrink W, Kim B, Kuznetsova T, Kox M, Zwaag J, Matarese F, van Heeringen SJ, Janssen-Megens EM, Sharifi N, Wang C, Keramati F, Schoonenberg V, Flicek P, Clarke L, Pickkers P, Heath S, Gut I, Netea MG, Martens JHA, Logie C, Stunnenberg HG. Cell Volume 167 (2016) p.1354-1368.e14 DOI: 10.1016/j.cell.2016.09.034
Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium.
Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP, Moreno P, Verma D, Hill E, Drijkoningen J, Gilligan P, Esther CR, Noone PG, Giddings O, Bell SC, Thomson R, Wainwright CE, Coulter C, Pandey S, Wood ME, Stockwell RE, Ramsay KA, Sherrard LJ, Kidd TJ, Jabbour N, Johnson GR, Knibbs LD, Morawska L, Sly PD, Jones A, Bilton D, Laurenson I, Ruddy M, Bourke S, Bowler IC, Chapman SJ, Clayton A, Cullen M, Daniels T, Dempsey O, Denton M, Desai M, Drew RJ, Edenborough F, Evans J, Folb J, Humphrey H, Isalska B, Jensen-Fangel S, Jönsson B, Jones AM, Katzenstein TL, Lillebaek T, MacGregor G, Mayell S, Millar M, Modha D, Nash EF, O'Brien C, O'Brien D, Ohri C, Pao CS, Peckham D, Perrin F, Perry A, Pressler T, Prtak L, Qvist T, Robb A, Rodgers H, Schaffer K, Shafi N, van Ingen J, Walshaw M, Watson D, West N, Whitehouse J, Haworth CS, Harris SR, Ordway D, Parkhill J, Floto RA. Science (New York, N.Y.) Volume 354 (2016) p.751-757 DOI: 10.1126/science.aaf8156
Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage.
Queirós AC, Beekman R, Vilarrasa-Blasi R, Duran-Ferrer M, Clot G, Merkel A, Raineri E, Russiñol N, Castellano G, Beà S, Navarro A, Kulis M, Verdaguer-Dot N, Jares P, Enjuanes A, Calasanz MJ, Bergmann A, Vater I, Salaverría I, van de Werken HJG, Wilson WH, Datta A, Flicek P, Royo R, Martens J, Giné E, Lopez-Guillermo A, Stunnenberg HG, Klapper W, Pott C, Heath S, Gut IG, Siebert R, Campo E, Martín-Subero JI. Cancer cell Volume 30 (2016) p.806-821 DOI: 10.1016/j.ccell.2016.09.014
Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems.
Schuyler RP, Merkel A, Raineri E, Altucci L, Vellenga E, Martens JHA, Pourfarzad F, Kuijpers TW, Burden F, Farrow S, Downes K, Ouwehand WH, Clarke L, Datta A, Lowy E, Flicek P, Frontini M, Stunnenberg HG, Martín-Subero JI, Gut I, Heath S. Cell reports Volume 17 (2016) p.2101-2111 DOI: 10.1016/j.celrep.2016.10.054
Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.
Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F, BLUEPRINT Consortium, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P. Cell Volume 167 (2016) p.1369-1384.e19 DOI: 10.1016/j.cell.2016.09.037
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The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.
Stunnenberg HG, International Human Epigenome Consortium, Hirst M. Cell Volume 167 (2016) p.1145-1149 DOI: 10.1016/j.cell.2016.11.007
Gramene Database: Navigating Plant Comparative Genomics Resources.
Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P. Current plant biology Volume 7-8 (2016) p.10-15 DOI: 10.1016/j.cpb.2016.12.005
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.
Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N. Cell Volume 167 (2016) p.1398-1414.e24 DOI: 10.1016/j.cell.2016.10.026
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RUNX1 mutations in acute myeloid leukemia are associated with distinct clinico-pathologic and genetic features.
Gaidzik VI, Teleanu V, Papaemmanuil E, Weber D, Paschka P, Hahn J, Wallrabenstein T, Kolbinger B, Köhne CH, Horst HA, Brossart P, Held G, Kündgen A, Ringhoffer M, Götze K, Rummel M, Gerstung M, Campbell P, Kraus JM, Kestler HA, Thol F, Heuser M, Schlegelberger B, Ganser A, Bullinger L, Schlenk RF, Döhner K, Döhner H. Leukemia Volume 30 (2016) p.2282 DOI: 10.1038/leu.2016.207
Plant Reactome: a resource for plant pathways and comparative analysis.
Naithani S, Preece J, D'Eustachio P, Gupta P, Amarasinghe V, Dharmawardhana PD, Wu G, Fabregat A, Elser JL, Weiser J, Keays M, Fuentes AM, Petryszak R, Stein LD, Ware D, Jaiswal P. Nucleic acids research Volume 45 (2017) p.D1029-D1039 DOI: 10.1093/nar/gkw932
Genenames.org: the HGNC and VGNC resources in 2017.
Yates B, Braschi B, Gray KA, Seal RL, Tweedie S, Bruford EA. Nucleic acids research Volume 45 (2017) p.D619-D625 DOI: 10.1093/nar/gkw1033
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RNAcentral: a comprehensive database of non-coding RNA sequences.
The RNAcentral Consortium, Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, Lau BY, Williams KP, Chan PP, Lowe TM, Cannone JJ, Gutell R, Machnicka MA, Bujnicki JM, Yoshihama M, Kenmochi N, Chai B, Cole JR, Szymanski M, Karlowski WM, Wood V, Huala E, Berardini TZ, Zhao Y, Chen R, Zhu W, Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG, Ma L, Zhang Z, Puetz J, Stadler PF, McDonald D, Basu S, Fey P, Engel SR, Cherry JM, Volders PJ, Mestdagh P, Wower J, Clark MB, Quek XC, Dinger ME. Nucleic acids research Volume 45 (2017) p.D128-D134 DOI: 10.1093/nar/gkw1008
Resolution of ab initio shapes determined from small-angle scattering.
Tuukkanen AT, Kleywegt GJ, Svergun DI. IUCrJ Volume 3 (2016) p.440-447 DOI: 10.1107/s2052252516016018
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.
Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA. Nucleic acids research Volume 45 (2017) p.D1100-D1106 DOI: 10.1093/nar/gkw936
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An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu F, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser D, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Di Palma F, Phillips A, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD. Preprint DOI: 10.1101/080796
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.
Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y. Nucleic acids research Volume 45 (2017) p.D347-D352 DOI: 10.1093/nar/gkw918
The human-induced pluripotent stem cell initiative-data resources for cellular genetics.
Streeter I, Harrison PW, Faulconbridge A, The HipSci Consortium, Flicek P, Parkinson H, Clarke L. Nucleic acids research Volume 45 (2017) p.D691-D697 DOI: 10.1093/nar/gkw928
A multicenter study benchmarks software tools for label-free proteome quantification.
Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S. Nature biotechnology Volume 34 (2016) p.1130-1136 DOI: 10.1038/nbt.3685
ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions.
Marenco L, Wang R, McDougal R, Olender T, Twik M, Bruford E, Liu X, Zhang J, Lancet D, Shepherd G, Crasto C. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw132
Evolution of protein phosphorylation across 18 fungal species.
Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Viéitez C, Solé C, Swaney DL, Stanford LB, Liachko I, Böttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villén J. Science (New York, N.Y.) Volume 354 (2016) p.229-232 DOI: 10.1126/science.aaf2144
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Positive Feedback Keeps Duration of Mitosis Temporally Insulated from Upstream Cell-Cycle Events.
Araujo AR, Gelens L, Sheriff RS, Santos SD. Molecular cell Volume 64 (2016) p.362-375 DOI: 10.1016/j.molcel.2016.09.018
Identifying ELIXIR Core Data Resources.
Durinx C, McEntyre J, Appel R, Apweiler R, Barlow M, Blomberg N, Cook C, Gasteiger E, Kim JH, Lopez R, Redaschi N, Stockinger H, Teixeira D, Valencia A. F1000Research Volume 5 (2016) DOI: 10.12688/f1000research.9656.2
Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs.
Zerbino DR, Ballinger T, Paten B, Hickey G, Haussler D. BMC bioinformatics Volume 17 (2016) p.400 DOI: 10.1186/s12859-016-1258-4
2016 update of the PRIDE database and its related tools.
Vizcaíno JA, Csordas A, Del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H. Nucleic acids research Volume 44 (2016) p.11033 DOI: 10.1093/nar/gkw880
A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL.
Mutowo P, Bento AP, Dedman N, Gaulton A, Hersey A, Lomax J, Overington JP. Journal of biomedical semantics Volume 7 (2016) p.59 DOI: 10.1186/s13326-016-0102-0
Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.
Smid M, Rodríguez-González FG, Sieuwerts AM, Salgado R, Prager-Van der Smissen WJ, Vlugt-Daane MV, van Galen A, Nik-Zainal S, Staaf J, Brinkman AB, van de Vijver MJ, Richardson AL, Fatima A, Berentsen K, Butler A, Martin S, Davies HR, Debets R, Gelder ME, van Deurzen CH, MacGrogan G, Van den Eynden GG, Purdie C, Thompson AM, Caldas C, Span PN, Simpson PT, Lakhani SR, Van Laere S, Desmedt C, Ringnér M, Tommasi S, Eyford J, Broeks A, Vincent-Salomon A, Futreal PA, Knappskog S, King T, Thomas G, Viari A, Langerød A, Børresen-Dale AL, Birney E, Stunnenberg HG, Stratton M, Foekens JA, Martens JW. Nature communications Volume 7 (2016) p.12910 DOI: 10.1038/ncomms12910
Selenoprotein Gene Nomenclature.
Gladyshev VN, Arnér ES, Berry MJ, Brigelius-Flohé R, Bruford EA, Burk RF, Carlson BA, Castellano S, Chavatte L, Conrad M, Copeland PR, Diamond AM, Driscoll DM, Ferreiro A, Flohé L, Green FR, Guigó R, Handy DE, Hatfield DL, Hesketh J, Hoffmann PR, Holmgren A, Hondal RJ, Howard MT, Huang K, Kim HY, Kim IY, Köhrle J, Krol A, Kryukov GV, Lee BJ, Lee BC, Lei XG, Liu Q, Lescure A, Lobanov AV, Loscalzo J, Maiorino M, Mariotti M, Sandeep Prabhu K, Rayman MP, Rozovsky S, Salinas G, Schmidt EE, Schomburg L, Schweizer U, Simonović M, Sunde RA, Tsuji PA, Tweedie S, Ursini F, Whanger PD, Zhang Y. The Journal of biological chemistry Volume 291 (2016) p.24036-24040 DOI: 10.1074/jbc.m116.756155
The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.
Clarke L, Fairley S, Zheng-Bradley X, Streeter I, Perry E, Lowy E, Tassé AM, Flicek P. Nucleic acids research Volume 45 (2017) p.D854-D859 DOI: 10.1093/nar/gkw829
Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence.
Garin-Muga A, Odriozola L, Martínez-Val A, Del Toro N, Martínez R, Molina M, Cantero L, Rivera R, Garrido N, Dominguez F, Sanchez Del Pino MM, Vizcaíno JA, Corrales FJ, Segura V. Journal of proteome research Volume 15 (2016) p.4101-4115 DOI: 10.1021/acs.jproteome.6b00437
High-throughput discovery of novel developmental phenotypes.
Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie SM, Fuchs H, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Newbigging S, Nutter LM, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, International Mouse Phenotyping Consortium, Jackson Laboratory, Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS), Charles River Laboratories, MRC Harwell, Toronto Centre for Phenogenomics, Wellcome Trust Sanger Institute, RIKEN BioResource Center, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SD, Adams DJ, Lloyd KC, McKerlie C, Beaudet AL, Bućan M, Murray SA. Nature Volume 537 (2016) p.508-514 DOI: 10.1038/nature19356
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Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.
Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A, GEUVADIS Consortium, Rosenstiel P, Strom TM, Lappalainen T, Guigó R, Sammeth M. Scientific reports Volume 6 (2016) p.32406 DOI: 10.1038/srep32406
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Speranzini V, Rotili D, Ciossani G, Pilotto S, Marrocco B, Forgione M, Lucidi A, Forneris F, Mehdipour P, Velankar S, Mai A, Mattevi A. Science advances Volume 2 (2016) p.e1601017 DOI: 10.1126/sciadv.1601017
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Lun ATL, Marioni JC. Preprint DOI: 10.1101/073973
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Overview of the interactive task in BioCreative V.
Wang Q, S Abdul S, Almeida L, Ananiadou S, Balderas-Martínez YI, Batista-Navarro R, Campos D, Chilton L, Chou HJ, Contreras G, Cooper L, Dai HJ, Ferrell B, Fluck J, Gama-Castro S, George N, Gkoutos G, Irin AK, Jensen LJ, Jimenez S, Jue TR, Keseler I, Madan S, Matos S, McQuilton P, Milacic M, Mort M, Natarajan J, Pafilis E, Pereira E, Rao S, Rinaldi F, Rothfels K, Salgado D, Silva RM, Singh O, Stefancsik R, Su CH, Subramani S, Tadepally HD, Tsaprouni L, Vasilevsky N, Wang X, Chatr-Aryamontri A, Laulederkind SJ, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Wu CH, Hirschman L, Arighi CN. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw119
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Lun AT, McCarthy DJ, Marioni JC. F1000Research Volume 5 (2016) p.2122 DOI: 10.12688/f1000research.9501.2
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Muetze T, Goenawan IH, Wiencko HL, Bernal-Llinares M, Bryan K, Lynn DJ. Preprint DOI: 10.12688/f1000research.9118.2
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Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen H, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood J, Clarke L, Koren S, Boitano M, Li H, Chin C, Phillippy AM, Durbin R, Wilson RK, Flicek P, Church DM. Preprint DOI: 10.1101/072116
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.
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The health care and life sciences community profile for dataset descriptions.
Dumontier M, Gray AJG, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall CJ, Rietveld L, Wimalaratne SM, Yamaguchi A. PeerJ Volume 4 (2016) p.e2331 DOI: 10.7717/peerj.2331
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Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification
Oyola SO, Ariani CV, Hamilton WL, Kekre M, Amenga-Etego LN, Ghansah A, Rutledge GG, Redmond S, Manske M, Jyothi D, Jacob CG, Otto TD, Rockett K, Newbold CI, Berriman M, Kwiatkowski DP. Preprint DOI: 10.1101/067546
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GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes.
Tuggle CK, Giuffra E, White SN, Clarke L, Zhou H, Ross PJ, Acloque H, Reecy JM, Archibald A, Bellone RR, Boichard M, Chamberlain A, Cheng H, Crooijmans RP, Delany ME, Finno CJ, Groenen MA, Hayes B, Lunney JK, Petersen JL, Plastow GS, Schmidt CJ, Song J, Watson M. Animal genetics Volume 47 (2016) p.528-533 DOI: 10.1111/age.12466
The archiving and dissemination of biological structure data.
Berman HM, Burley SK, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. Current opinion in structural biology Volume 40 (2016) p.17-22 DOI: 10.1016/j.sbi.2016.06.018
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Muetze T, Goenawan IH, Wiencko HL, Bernal-Llinares M, Bryan K, Lynn DJ. F1000Research Volume 5 (2016) p.1745 DOI: 10.12688/f1000research.9118.2
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Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost Fda V, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaíno JA. PLoS computational biology Volume 12 (2016) p.e1004947 DOI: 10.1371/journal.pcbi.1004947
Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases.
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Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining.
Boudellioua I, Saidi R, Hoehndorf R, Martin MJ, Solovyev V. PloS one Volume 11 (2016) p.e0158896 DOI: 10.1371/journal.pone.0158896
Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis.
Jakubec D, Laskowski RA, Vondrasek J. PloS one Volume 11 (2016) p.e0158704 DOI: 10.1371/journal.pone.0158704
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Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ. Journal of biomedical semantics Volume 7 (2016) p.44 DOI: 10.1186/s13326-016-0088-7
Letter to the editor for "Update of the human and mouse Fanconi anemia genes".
Nebert DW, Dong H, Bruford EA, Thompson DC, Joenje H, Vasiliou V. Human genomics Volume 10 (2016) p.25 DOI: 10.1186/s40246-016-0081-3
The Evolutionary Fates of a Large Segmental Duplication in Mouse.
Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AM, Didion JP, Yadgary L, Thybert D, Odom DT, Flicek P, McMillan L, de Villena FP. Genetics Volume 204 (2016) p.267-285 DOI: 10.1534/genetics.116.191007
Using the Gene Ontology to Annotate Key Players in Parkinson's Disease.
Foulger RE, Denny P, Hardy J, Martin MJ, Sawford T, Lovering RC. Neuroinformatics Volume 14 (2016) p.297-304 DOI: 10.1007/s12021-015-9293-2
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A High Density Map for Navigating the Human Polycomb Complexome
Hauri S, Comoglio F, Seimiya M, Gerstung M, Glatter T, Hansen K, Aebersold R, Paro R, Gstaiger M, Beisel C. Preprint DOI: 10.1101/059964
Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data.
Rensch T, Villar D, Horvath J, Odom DT, Flicek P. Genome biology Volume 17 (2016) p.139 DOI: 10.1186/s13059-016-0996-y
Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.
Griss J, Perez-Riverol Y, Lewis S, Tabb DL, Dianes JA, Del-Toro N, Rurik M, Walzer MW, Kohlbacher O, Hermjakob H, Wang R, Vizcaíno JA. Nature methods Volume 13 (2016) p.651-656 DOI: 10.1038/nmeth.3902
Epigenome-wide Association Studies and the Interpretation of Disease -Omics.
Birney E, Smith GD, Greally JM. PLoS genetics Volume 12 (2016) p.e1006105 DOI: 10.1371/journal.pgen.1006105
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PASP — a whole-transcriptome poly(A) tail length determination assay for the Illumina platform
Sipos B, Stütz AM, Slodkowicz G, Massingham T, Korbel J, Goldman N. Preprint DOI: 10.1101/060004
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Busby GB, Band G, Si Le Q, Jallow M, Bougama E, Mangano VD, Amenga-Etego LN, Enimil A, Apinjoh T, Ndila CM, Manjurano A, Nyirongo V, Doumba O, Rockett KA, Kwiatkowski DP, Spencer CC, Malaria Genomic Epidemiology Network. eLife Volume 5 (2016) DOI: 10.7554/elife.15266
Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.
Torrente A, Lukk M, Xue V, Parkinson H, Rung J, Brazma A. PloS one Volume 11 (2016) p.e0157484 DOI: 10.1371/journal.pone.0157484
Promiscuous or discriminating: Has the favored mRNA target of Fragile X Mental Retardation Protein been overlooked?
McMahon AC, Rosbash M. Proceedings of the National Academy of Sciences of the United States of America Volume 113 (2016) p.7009-7011 DOI: 10.1073/pnas.1607665113
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Patwardhan A, Lawson CL. Methods in enzymology Volume 579 (2016) p.393-412 DOI: 10.1016/bs.mie.2016.04.015
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.
Cairns J, Freire-Pritchett P, Wingett SW, Várnai C, Dimond A, Plagnol V, Zerbino D, Schoenfelder S, Javierre BM, Osborne C, Fraser P, Spivakov M. Genome biology Volume 17 (2016) p.127 DOI: 10.1186/s13059-016-0992-2
Rising levels of atmospheric oxygen and evolution of Nrf2.
Gacesa R, Dunlap WC, Barlow DJ, Laskowski RA, Long PF. Scientific reports Volume 6 (2016) p.27740 DOI: 10.1038/srep27740
PhenoImageShare: an image annotation and query infrastructure.
Adebayo S, McLeod K, Tudose I, Osumi-Sutherland D, Burdett T, Baldock R, Burger A, Parkinson H. Journal of biomedical semantics Volume 7 (2016) p.35 DOI: 10.1186/s13326-016-0072-2
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Personally tailored cancer management based on knowledge banks of genomic and clinical data
Gerstung M, Papaemmanuil E, Martincorena I, Bullinger L, Gaidzik VI, Paschka P, Heuser M, Thol F, Bolli N, Ganly P, Ganser A, McDermott U, Döhner K, Schlenk RF, Döhner H, Campbell PJ. Preprint DOI: 10.1101/057497
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Touloumis A, Marioni JC, Tavaré S. Bioinformatics (Oxford, England) Volume 32 (2016) p.2193-2195 DOI: 10.1093/bioinformatics/btw224
The Ensembl Variant Effect Predictor.
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. Genome biology Volume 17 (2016) p.122 DOI: 10.1186/s13059-016-0974-4
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.
Tripathi S, Vercruysse S, Chawla K, Christie KR, Blake JA, Huntley RP, Orchard S, Hermjakob H, Thommesen L, Lægreid A, Kuiper M. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw088
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS, Harrow J. Nature communications Volume 7 (2016) p.11778 DOI: 10.1038/ncomms11778
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
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Genomic Classification and Prognosis in Acute Myeloid Leukemia.
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Advancing vector biology research: a community survey for future directions, research applications and infrastructure requirements.
Kohl A, Pondeville E, Schnettler E, Crisanti A, Supparo C, Christophides GK, Kersey PJ, Maslen GL, Takken W, Koenraadt CJ, Oliva CF, Busquets N, Abad FX, Failloux AB, Levashina EA, Wilson AJ, Veronesi E, Pichard M, Arnaud Marsh S, Simard F, Vernick KD. Pathogens and global health Volume 110 (2016) p.164-172 DOI: 10.1080/20477724.2016.1211475
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GENOMICS. A federated ecosystem for sharing genomic, clinical data.
Global Alliance for Genomics and Health. Science (New York, N.Y.) Volume 352 (2016) p.1278-1280 DOI: 10.1126/science.aaf6162
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JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
Roll J, Zirbel CL, Sweeney B, Petrov AI, Leontis N. Nucleic acids research Volume 44 (2016) p.W320-7 DOI: 10.1093/nar/gkw453
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The cellular microscopy phenotype ontology.
Jupp S, Malone J, Burdett T, Heriche JK, Williams E, Ellenberg J, Parkinson H, Rustici G. Journal of biomedical semantics Volume 7 (2016) p.28 DOI: 10.1186/s13326-016-0074-0
HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.
Bryan K, Jarboui MA, Raso C, Bernal-Llinares M, McCann B, Rauch J, Boldt K, Lynn DJ. Journal of proteome research Volume 15 (2016) p.2072-2079 DOI: 10.1021/acs.jproteome.5b01008
Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).
Welch L, Brooksbank C, Schwartz R, Morgan SL, Gaeta B, Kilpatrick AM, Mietchen D, Moore BL, Mulder N, Pauley M, Pearson W, Radivojac P, Rosenberg N, Rosenwald A, Rustici G, Warnow T. PLoS computational biology Volume 12 (2016) p.e1004943 DOI: 10.1371/journal.pcbi.1004943
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A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.
Danecek P, McCarthy SA, HipSci Consortium, Durbin R. PloS one Volume 11 (2016) p.e0155014 DOI: 10.1371/journal.pone.0155014
Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.
Rudolph KL, Schmitt BM, Villar D, White RJ, Marioni JC, Kutter C, Odom DT. PLoS genetics Volume 12 (2016) p.e1006024 DOI: 10.1371/journal.pgen.1006024
Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns.
Digles D, Zdrazil B, Neefs JM, Van Vlijmen H, Herhaus C, Caracoti A, Brea J, Roibás B, Loza MI, Queralt-Rosinach N, Furlong LI, Gaulton A, Bartek L, Senger S, Chichester C, Engkvist O, Evelo CT, Franklin NI, Marren D, Ecker GF, Jacoby E. MedChemComm Volume 7 (2016) p.1237-1244 DOI: 10.1039/c6md00065g
Subtype-specific micro-RNA expression signatures in breast cancer progression.
Haakensen VD, Nygaard V, Greger L, Aure MR, Fromm B, Bukholm IR, Lüders T, Chin SF, Git A, Caldas C, Kristensen VN, Brazma A, Børresen-Dale AL, Hovig E, Helland Å. International journal of cancer Volume 139 (2016) p.1117-1128 DOI: 10.1002/ijc.30142
BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.
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Structure and evolutionary history of a large family of NLR proteins in the zebrafish.
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From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.
Kılıç S, Sagitova DM, Wolfish S, Bely B, Courtot M, Ciufo S, Tatusova T, O'Donovan C, Chibucos MC, Martin MJ, Erill I. Database : the journal of biological databases and curation Volume 2016 (2016) DOI: 10.1093/database/baw055
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Organization, evolution and functions of the human and mouse Ly6/uPAR family genes.
Loughner CL, Bruford EA, McAndrews MS, Delp EE, Swamynathan S, Swamynathan SK. Human genomics Volume 10 (2016) p.10 DOI: 10.1186/s40246-016-0074-2
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Omics Discovery Index - Discovering and Linking Public ‘Omics’ Datasets
Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Mi Park Y, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Nesvizhskii AI, Sansone S, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H. Preprint DOI: 10.1101/049205
Beyond comparisons of means: understanding changes in gene expression at the single-cell level.
Vallejos CA, Richardson S, Marioni JC. Genome biology Volume 17 (2016) p.70 DOI: 10.1186/s13059-016-0930-3
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Ten Simple Rules for Taking Advantage of git and GitHub
Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Veiga Leprevost Fd, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaino JA. Preprint DOI: 10.1101/048744
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Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes.
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