Publications for 2020

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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Periscope Proteins are variable length regulators of bacterial cell surface interactions
Whelan F, Lafita A, Gilburt J, Dégut C, Griffiths SC, Jenkins HT, St John AN, Paci E, Moir JW, Plevin MJ, Baumann CG, Bateman A, Potts JR. Preprint DOI: 10.1101/2020.12.24.424174
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A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data
Douglass EF, Allaway RJ, Szalai B, Wang W, Tian T, Fernández-Torras A, Realubit R, Karan C, Zheng S, Pessia A, Tanoli Z, Jafari M, Wan F, Li S, Xiong Y, Duran-Frigola M, Bertoni M, Badia-i-Mompel P, Mateo L, Guitart-Pla O, Chung V, Tang J, Zeng J, Aloy P, Saez-Rodriguez J, Guinney J, Gerhard DS, Califano A, DREAM CTD-squared Pancancer Drug Activity Challenge Consortium. Preprint DOI: 10.1101/2020.12.21.423514
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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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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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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
Genome3D annotations in InterPro
Paysan-Lafosse T. DOI: 10.6019/tol.genome3d-t.2019.00001.1
Using the InterPro website in your research
Paysan-Lafosse T. DOI: 10.6019/tol.interprowebsite-w.2020.00001.1
Understanding InterPro families, domains and functions
Paysan-Lafosse T. DOI: 10.6019/tol.understanding-interpro-w.2020.00001.1
Finding the data behind research articles with Europe PMC
Araujo D. DOI: 10.6019/tol.epmcfind-w.2020.00001.1
MGnify today: analysing microbiome data
Kale V. DOI: 10.6019/tol.mgnify-analysis-w.2020.00001.1
Using Europe PMC for effective literature research
Araujo D. DOI: 10.6019/tol.epmclit-w.2020.00001.1
Discovering scientific evidence using Europe PMC SciLite annotation
Araujo D. DOI: 10.6019/tol.epmc-scilite-w.2020.00001.1
Metagenomics Bioinformatics
Mitchell A, Finn R, Kale V. DOI: 10.6019/tol.metagenomics-t.2019.00001.1
Searching and browsing scientific publications with the new Europe PMC
Araujo D. DOI: 10.6019/tol.europepmc_new-w.2020.00001.1
The Ensembl Rapid Release genome browser
Moore B. DOI: 10.6019/tol.ensembl-rapid-release-w.2020.00001.1
Introduction to the Complex Portal
Meldel B. DOI: 10.6019/tol.complexportal-w.2020.00001.1
eQTL Catalogue: a compendium of uniformly processed human expression and splicing QTLs
Zerbino D. DOI: 10.6019/tol.eqtlcatalogue-t.2020.00001.1
Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 1: Ways to make an impact, and why we are not there yet.
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
Bonfield JK, Marshall J, Danecek P, Li H, Ohan V, Whitwham A, Keane T, Davies RM. Preprint DOI: 10.1101/2020.12.16.423064
Diverse Routes toward Early Somites in the Mouse Embryo.
Guibentif C, Griffiths JA, Imaz-Rosshandler I, Ghazanfar S, Nichols J, Wilson V, Göttgens B, Marioni JC. Developmental cell Volume 56 (2021) p.141-153.e6 DOI: 10.1016/j.devcel.2020.11.013
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A genomic epidemiology study of multidrug-resistant Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii in two intensive care units in Hanoi, Vietnam
Roberts LW, Hoi LT, Khokhar FA, Hoa NT, Van Giang T, Bui C, Ninh TH, Co DX, Binh NG, Long HB, Huong DT, Bryan JE, Herrick A, Feltwell T, Nadjm B, van Doorn HR, Parkhill J, Trung NV, Van Kinh N, Iqbal Z, Török ME. Preprint DOI: 10.1101/2020.12.09.20246397
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The Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection
Salz R, Bouwmeester R, Gabriels R, Degroeve S, Martens L, Volders P, ’t Hoen PA. Preprint DOI: 10.1101/2020.12.11.419523
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Spatial multi-omic map of human myocardial infarction
Kuppe C, Ramirez Flores RO, Li Z, Hannani M, Tanevski J, Halder M, Cheng M, Ziegler S, Zhang X, Preisker F, Kaesler N, Xu Y, Hoogenboezem RM, Bindels EM, Schneider RK, Milting H, Costa IG, Saez-Rodriguez J, Kramann R. Preprint DOI: 10.1101/2020.12.08.411686
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Deep learning prediction of BRAF-RAS gene expression signature identifies noninvasive follicular thyroid neoplasms with papillary-like nuclear features.
Dolezal JM, Trzcinska A, Liao CY, Kochanny S, Blair E, Agrawal N, Keutgen XM, Angelos P, Cipriani NA, Pearson AT. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc Volume 34 (2021) p.862-874 DOI: 10.1038/s41379-020-00724-3
Urinary metabolic phenotyping for Alzheimer's disease.
Kurbatova N, Garg M, Whiley L, Chekmeneva E, Jiménez B, Gómez-Romero M, Pearce J, Kimhofer T, D'Hondt E, Soininen H, Kłoszewska I, Mecocci P, Tsolaki M, Vellas B, Aarsland D, Nevado-Holgado A, Liu B, Snowden S, Proitsi P, Ashton NJ, Hye A, Legido-Quigley C, Lewis MR, Nicholson JK, Holmes E, Brazma A, Lovestone S. Scientific reports Volume 10 (2020) p.21745 DOI: 10.1038/s41598-020-78031-9
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Universal Spectrum Identifier for mass spectra
Deutsch EW, Perez-Riverol Y, Carver J, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Binz P, Pullman B, Sun Z, Shofstahl J, Bittremieux W, Mak TD, Klein J, Zhu Y, Lam H, Vizcaíno JA, Bandeira N. Preprint DOI: 10.1101/2020.12.07.415539
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Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling
Mazein A, Rougny A, Karr JR, Saez Rodriguez J, Ostaszewski M, Schneider R. Preprint DOI: 10.1101/2020.12.08.416719
Deep learning embedder method and tool for mass spectra similarity search.
Qin C, Luo X, Deng C, Shu K, Zhu W, Griss J, Hermjakob H, Bai M, Perez-Riverol Y. Journal of proteomics Volume 232 (2021) p.104070 DOI: 10.1016/j.jprot.2020.104070
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Discovery of Fibrillar Adhesins across Bacterial Species
Monzon V, Lafita A, Bateman A. Preprint DOI: 10.1101/2020.12.07.414375
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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
De Maio N, Alekseyenko AV, Coleman-Smith WJ, Pardi F, Suchard MA, Tamuri AU, Truszkowski J, Goldman N. Preprint DOI: 10.1101/2020.12.03.410100
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Biocuration - mapping resources and needs
Holinski A, Burke ML, Morgan SL, McQuilton P, Palagi PM. Preprint DOI: 10.12688/f1000research.25413.2
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
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
Towards a unified open access dataset of molecular interactions.
Porras P, Barrera E, Bridge A, Del-Toro N, Cesareni G, Duesbury M, Hermjakob H, Iannuccelli M, Jurisica I, Kotlyar M, Licata L, Lovering RC, Lynn DJ, Meldal B, Nanduri B, Paneerselvam K, Panni S, Pastrello C, Pellegrini M, Perfetto L, Rahimzadeh N, Ratan P, Ricard-Blum S, Salwinski L, Shirodkar G, Shrivastava A, Orchard S. Nature communications Volume 11 (2020) p.6144 DOI: 10.1038/s41467-020-19942-z
Guidelines for reporting single-cell RNA-seq experiments.
Füllgrabe A, George N, Green M, Nejad P, Aronow B, Fexova SK, Fischer C, Freeberg MA, Huerta L, Morrison N, Scheuermann RH, Taylor D, Vasilevsky N, Clarke L, Gehlenborg N, Kent J, Marioni J, Teichmann S, Brazma A, Papatheodorou I. Nature biotechnology Volume 38 (2020) p.1384-1386 DOI: 10.1038/s41587-020-00744-z
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
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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
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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Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19.
Bernardes JP, Mishra N, Tran F, Bahmer T, Best L, Blase JI, Bordoni D, Franzenburg J, Geisen U, Josephs-Spaulding J, Köhler P, Künstner A, Rosati E, Aschenbrenner AC, Bacher P, Baran N, Boysen T, Brandt B, Bruse N, Dörr J, Dräger A, Elke G, Ellinghaus D, Fischer J, Forster M, Franke A, Franzenburg S, Frey N, Friedrichs A, Fuß J, Glück A, Hamm J, Hinrichsen F, Hoeppner MP, Imm S, Junker R, Kaiser S, Kan YH, Knoll R, Lange C, Laue G, Lier C, Lindner M, Marinos G, Markewitz R, Nattermann J, Noth R, Pickkers P, Rabe KF, Renz A, Röcken C, Rupp J, Schaffarzyk A, Scheffold A, Schulte-Schrepping J, Schunk D, Skowasch D, Ulas T, Wandinger KP, Wittig M, Zimmermann J, Busch H, Hoyer BF, Kaleta C, Heyckendorf J, Kox M, Rybniker J, Schreiber S, Schultze JL, Rosenstiel P, HCA Lung Biological Network, Deutsche COVID-19 Omics Initiative (DeCOI). Immunity Volume 53 (2020) p.1296-1314.e9 DOI: 10.1016/j.immuni.2020.11.017
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
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
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
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The evolution of relapse of adult T cell acute lymphoblastic leukemia.
Sentís I, Gonzalez S, Genescà E, García-Hernández V, Muiños F, Gonzalez C, López-Arribillaga E, Gonzalez J, Fernandez-Ibarrondo L, Mularoni L, Espinosa L, Bellosillo B, Ribera JM, Bigas A, Gonzalez-Perez A, Lopez-Bigas N. Genome biology Volume 21 (2020) p.284 DOI: 10.1186/s13059-020-02192-z
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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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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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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
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COVID-19-associated olfactory dysfunction reveals SARS-CoV-2 neuroinvasion and persistence in the olfactory system
De Melo GD, Lazarini F, Levallois S, Hautefort C, Michel V, Larrous F, Verillaud B, Aparicio C, Wagner S, Gheusi G, Kergoat L, Kornobis E, Cokelaer T, Hervochon R, Madec Y, Roze E, Salmon D, Bourhy H, Lecuit M, Lledo P. Preprint DOI: 10.1101/2020.11.18.388819
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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
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
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
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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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
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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.
Doyle SR, Tracey A, Laing R, Holroyd N, Bartley D, Bazant W, Beasley H, Beech R, Britton C, Brooks K, Chaudhry U, Maitland K, Martinelli A, Noonan JD, Paulini M, Quail MA, Redman E, Rodgers FH, Sallé G, Shabbir MZ, Sankaranarayanan G, Wit J, Howe KL, Sargison N, Devaney E, Berriman M, Gilleard JS, Cotton JA. Communications biology Volume 3 (2020) p.656 DOI: 10.1038/s42003-020-01377-3
*
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
*
Identifying temporal and spatial patterns of variation from multi-modal data using MEFISTO
Velten B, Braunger JM, Arnol D, Argelaguet R, Stegle O. Preprint DOI: 10.1101/2020.11.03.366674
*
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
*
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
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
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
*
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
*
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
*
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
*
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
*
COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Cristóbal Monraz Gómez L, Somers J, Hoch M, Gupta SK, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Leon MPd, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker J, Zucker J, Oxford K, Teuton J, Kocakaya E, Yağmur Summak G, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Ribeiro AS, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel J, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, Waard Ad, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Medina ME, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, Meulder BD, Dugourd A, Naldi A, Noë V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D’Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R, the COVID-19 Disease Map Community. Preprint DOI: 10.1101/2020.10.26.356014
*
A GO catalogue of human DNA-binding transcription factors
Lovering RC, Gaudet P, Acencio ML, Ignatchenko A, Jolma A, Fornes O, Kuiper M, Kulakovskiy IV, Lægreid A, Martin MJ, Logie C. Preprint DOI: 10.1101/2020.10.28.359232
*
SplineDist: Automated Cell Segmentation With Spline Curves
Mandal S, Uhlmann V. Preprint DOI: 10.1101/2020.10.27.357640
*
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
Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study.
Galardini M, Clermont O, Baron A, Busby B, Dion S, Schubert S, Beltrao P, Denamur E. PLoS genetics Volume 16 (2020) p.e1009065 DOI: 10.1371/journal.pgen.1009065
A novel computational approach for predicting complex phenotypes in Drosophila (starvation-sensitive and sterile) by deriving their gene expression signatures from public data.
Ivanov DK, Bostelmann G, Lan-Leung B, Williams J, Partridge L, Escott-Price V, Thornton JM. PloS one Volume 15 (2020) p.e0240824 DOI: 10.1371/journal.pone.0240824
*
Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice
Fuentealba M, Fabian DK, Dönertaş HM, Thornton JM, Partridge L. Preprint DOI: 10.1101/2020.10.20.347013
Selection of Oncogenic Mutant Clones in Normal Human Skin Varies with Body Site.
Fowler JC, King C, Bryant C, Hall MWJ, Sood R, Ong SH, Earp E, Fernandez-Antoran D, Koeppel J, Dentro SC, Shorthouse D, Durrani A, Fife K, Rytina E, Milne D, Roshan A, Mahububani K, Saeb-Parsy K, Hall BA, Gerstung M, Jones PH. Cancer discovery Volume 11 (2021) p.340-361 DOI: 10.1158/2159-8290.cd-20-1092
*
Too sweet: cheminformatics for deglycosylation in natural products
Schaub J, Zielesny A, Steinbeck C, Sorokina M. Preprint DOI: 10.21203/rs.3.rs-50194/v3
BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management.
Sehnal D, Bittrich S, Velankar S, Koča J, Svobodová R, Burley SK, Rose AS. PLoS computational biology Volume 16 (2020) p.e1008247 DOI: 10.1371/journal.pcbi.1008247
MDeePred: Novel Multi-Channel protein featurization for deep learning based binding affinity prediction in drug discovery.
Rifaioglu AS, Cetin Atalay R, Cansen Kahraman D, Doğan T, Martin M, Atalay V. Bioinformatics (Oxford, England) (2020) DOI: 10.1093/bioinformatics/btaa858
A high-stringency blueprint of the human proteome.
Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS. Nature communications Volume 11 (2020) p.5301 DOI: 10.1038/s41467-020-19045-9
Using Deep Learning to Extrapolate Protein Expression Measurements.
Barzine MP, Freivalds K, Wright JC, Opmanis M, Rituma D, Ghavidel FZ, Jarnuczak AF, Celms E, Čerāns K, Jonassen I, Lace L, Antonio Vizcaíno J, Choudhary JS, Brazma A, Viksna J. Proteomics Volume 20 (2020) p.e2000009 DOI: 10.1002/pmic.202000009
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, QCRG Structural Biology Consortium, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Zoonomia Consortium, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ. Science (New York, N.Y.) Volume 370 (2020) DOI: 10.1126/science.abe9403
Network integration and modelling of dynamic drug responses at multi-omics levels.
Selevsek N, Caiment F, Nudischer R, Gmuender H, Agarkova I, Atkinson FL, Bachmann I, Baier V, Barel G, Bauer C, Boerno S, Bosc N, Clayton O, Cordes H, Deeb S, Gotta S, Guye P, Hersey A, Hunter FMI, Kunz L, Lewalle A, Lienhard M, Merken J, Minguet J, Oliveira B, Pluess C, Sarkans U, Schrooders Y, Schuchhardt J, Smit I, Thiel C, Timmermann B, Verheijen M, Wittenberger T, Wolski W, Zerck A, Heymans S, Kuepfer L, Roth A, Schlapbach R, Niederer S, Herwig R, Kleinjans J. Communications biology Volume 3 (2020) p.573 DOI: 10.1038/s42003-020-01302-8
*
Multiple Drug-Induced Stress Responses Inhibit Formation of Escherichia coli Biofilms.
Teteneva NA, Mart'yanov SV, Esteban-López M, Kahnt J, Glatter T, Netrusov AI, Plakunov VK, Sourjik V. Applied and environmental microbiology Volume 86 (2020) DOI: 10.1128/aem.01113-20
Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry.
Leitner A, Bonvin AMJJ, Borchers CH, Chalkley RJ, Chamot-Rooke J, Combe CW, Cox J, Dong MQ, Fischer L, Götze M, Gozzo FC, Heck AJR, Hoopmann MR, Huang L, Ishihama Y, Jones AR, Kalisman N, Kohlbacher O, Mechtler K, Moritz RL, Netz E, Novak P, Petrotchenko E, Sali A, Scheltema RA, Schmidt C, Schriemer D, Sinz A, Sobott F, Stengel F, Thalassinos K, Urlaub H, Viner R, Vizcaíno JA, Wilkins MR, Rappsilber J. Structure (London, England : 1993) Volume 28 (2020) p.1259-1268 DOI: 10.1016/j.str.2020.09.011
Transparency and reproducibility in artificial intelligence.
Haibe-Kains B, Adam GA, Hosny A, Khodakarami F, Massive Analysis Quality Control (MAQC) Society Board of Directors, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Aerts HJWL. Nature Volume 586 (2020) p.E14-E16 DOI: 10.1038/s41586-020-2766-y
*
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research
Salgado D, Armean IM, Baudis M, Beltran S, Capella-Gutierrez S, Carvalho-Silva D, Dominguez Del Angel V, Dopazo J, Furlong LI, Gao B, Garcia L, Gerloff D, Gut I, Gyenesei A, Habermann N, Hancock JM, Hanauer M, Hovig E, Johansson LF, Keane T, Korbel J, Lauer KB, Laurie S, Leskošek B, Lloyd D, Marques-Bonet T, Mei H, Monostory K, Piñero J, Poterlowicz K, Rath A, Samarakoon P, Sanz F, Saunders G, Sie D, Swertz MA, Tsukanov K, Valencia A, Vidak M, Yenyxe González C, Ylstra B, Béroud C. Preprint DOI: 10.12688/f1000research.24887.1
Dissemination and analysis of the quality assurance (QA) and quality control (QC) practices of LC-MS based untargeted metabolomics practitioners.
Evans AM, O'Donovan C, Playdon M, Beecher C, Beger RD, Bowden JA, Broadhurst D, Clish CB, Dasari S, Dunn WB, Griffin JL, Hartung T, Hsu PC, Huan T, Jans J, Jones CM, Kachman M, Kleensang A, Lewis MR, Monge ME, Mosley JD, Taylor E, Tayyari F, Theodoridis G, Torta F, Ubhi BK, Vuckovic D, Metabolomics Quality Assurance, Quality Control Consortium (mQACC). Metabolomics : Official journal of the Metabolomic Society Volume 16 (2020) p.113 DOI: 10.1007/s11306-020-01728-5
*
Heterozygous lamin B1 and lamin B2 variants cause primary microcephaly and define a novel laminopathy.
Parry DA, Martin CA, Greene P, Marsh JA, Genomics England Research Consortium, Blyth M, Cox H, Donnelly D, Greenhalgh L, Greville-Heygate S, Harrison V, Lachlan K, McKenna C, Quigley AJ, Rea G, Robertson L, Suri M, Jackson AP. Genetics in medicine : official journal of the American College of Medical Genetics Volume 23 (2021) p.408-414 DOI: 10.1038/s41436-020-00980-3
Comparative Transcriptome Analysis of the Regenerating Zebrafish Telencephalon Unravels a Resource With Key Pathways During Two Early Stages and Activation of Wnt/β-Catenin Signaling at the Early Wound Healing Stage.
Demirci Y, Cucun G, Poyraz YK, Mohammed S, Heger G, Papatheodorou I, Ozhan G. Frontiers in cell and developmental biology Volume 8 (2020) p.584604 DOI: 10.3389/fcell.2020.584604
*
Annotation and curation of human genomic variations: an ELIXIR Implementation Study
David A, Barbié V, Attimonelli M, Preste R, Makkonen E, Marjonen H, Lindstedt M, Kristiansson K, Hunt SE, Cunningham F, Lappalainen I, Sternberg MJ. Preprint DOI: 10.12688/f1000research.24427.1
Identifiers.org - Compact Identifier Services in the Cloud.
Llinares MB, Gomez JF, Juty N, Goble C, Wimalaratne SM, Hermjakob H. Bioinformatics (Oxford, England) (2020) DOI: 10.1093/bioinformatics/btaa864
*
Distinct human gut microbial taxonomic signatures uncovered with different sample processing and microbial cell disruption methods for metaproteomic analysis
García-Durán C, Martínez López R, Zapico I, Pérez E, Romeu E, Arroyo J, Hernáez ML, Pitarch A, Monteoliva L, Gil C. Preprint DOI: 10.1101/2020.10.08.331066
*
From FAANG to Fork: Application of Highly Annotated Genomes to Improve Farmed Animal Production
Clark EL, Archibald AL, Daetwyler HD, Groenen MA, Harrison PW, Houston RD, Kuehn C, Lien S, Macqueen DJ, Reecy JM, Robledo D, Watson M, Tuggle CK, Giuffra E. Preprint DOI: 10.20944/preprints202010.0118.v1
Ten simple rules for annotating sequencing experiments.
Stevens I, Mukarram AK, Hörtenhuber M, Meehan TF, Rung J, Daub CO. PLoS computational biology Volume 16 (2020) p.e1008260 DOI: 10.1371/journal.pcbi.1008260
Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure.
Akdemir KC, Le VT, Kim JM, Killcoyne S, King DA, Lin YP, Tian Y, Inoue A, Amin SB, Robinson FS, Nimmakayalu M, Herrera RE, Lynn EJ, Chan K, Seth S, Klimczak LJ, Gerstung M, Gordenin DA, O'Brien J, Li L, Deribe YL, Verhaak RG, Campbell PJ, Fitzgerald R, Morrison AJ, Dixon JR, Andrew Futreal P. Nature genetics Volume 52 (2020) p.1178-1188 DOI: 10.1038/s41588-020-0708-0
How to use the MEROPS database and website to help understand peptidase specificity.
Rawlings ND, Bateman A. Protein science : a publication of the Protein Society Volume 30 (2021) p.83-92 DOI: 10.1002/pro.3948
*
Transposable element expression at unique loci in single cells with CELLO-seq
Berrens RV, Yang A, Laumer CE, Lun AT, Bieberich F, Law C, Lan G, Imaz M, Gaffney D, Marioni JC. Preprint DOI: 10.1101/2020.10.02.322073
Extensive heterogeneity in somatic mutation and selection in the human bladder.
Lawson ARJ, Abascal F, Coorens THH, Hooks Y, O'Neill L, Latimer C, Raine K, Sanders MA, Warren AY, Mahbubani KTA, Bareham B, Butler TM, Harvey LMR, Cagan A, Menzies A, Moore L, Colquhoun AJ, Turner W, Thomas B, Gnanapragasam V, Williams N, Rassl DM, Vöhringer H, Zumalave S, Nangalia J, Tubío JMC, Gerstung M, Saeb-Parsy K, Stratton MR, Campbell PJ, Mitchell TJ, Martincorena I. Science (New York, N.Y.) Volume 370 (2020) p.75-82 DOI: 10.1126/science.aba8347
CEN-tools: an integrative platform to identify the contexts of essential genes.
Sharma S, Dincer C, Weidemüller P, Wright GJ, Petsalaki E. Molecular systems biology Volume 16 (2020) p.e9698 DOI: 10.15252/msb.20209698
A single-cell RNA-sequencing training and analysis suite using the Galaxy framework.
Tekman M, Batut B, Ostrovsky A, Antoniewski C, Clements D, Ramirez F, Etherington GJ, Hotz HR, Scholtalbers J, Manning JR, Bellenger L, Doyle MA, Heydarian M, Huang N, Soranzo N, Moreno P, Mautner S, Papatheodorou I, Nekrutenko A, Taylor J, Blankenberg D, Backofen R, Grüning B. GigaScience Volume 9 (2020) DOI: 10.1093/gigascience/giaa102
IL10RA modulates crizotinib sensitivity in NPM1-ALK+ anaplastic large cell lymphoma.
Prokoph N, Probst NA, Lee LC, Monahan JM, Matthews JD, Liang HC, Bahnsen K, Montes-Mojarro IA, Karaca-Atabay E, Sharma GG, Malik V, Larose H, Forde SD, Ducray SP, Lobello C, Wang Q, Luan SL, Pospíšilová Š, Gambacorti-Passerini C, Burke GAA, Pervez S, Attarbaschi A, Janíková A, Pacquement H, Landman-Parker J, Lambilliotte A, Schleiermacher G, Klapper W, Jauch R, Woessmann W, Vassal G, Kenner L, Merkel O, Mologni L, Chiarle R, Brugières L, Geoerger B, Barbieri I, Turner SD. Blood Volume 136 (2020) p.1657-1669 DOI: 10.1182/blood.2019003793
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 J, 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.1663 DOI: 10.1038/s41591-020-1079-x
In conversation with Janet Thornton.
Dhillon P, Thornton JM. The FEBS journal Volume 287 (2020) p.4106-4113 DOI: 10.1111/febs.15567
*
A decoupled, modular and scriptable architecture for tools to curate data platforms
Langenstein M, Hermjakob H, Llinares MB. Preprint DOI: 10.1101/2020.09.28.282699
*
Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii.
Anopheles gambiae 1000 Genomes Consortium. Genome research Volume 30 (2020) p.1533-1546 DOI: 10.1101/gr.262790.120
*
Overview of the expression of key regeneration genes in embryo development and matured tissues in Axolotl (Ambystoma mexicanum)
Shah H, Caballero J. Preprint DOI: 10.1101/2020.09.24.312462
Functional signatures of evolutionarily young CTCF binding sites.
Azazi D, Mudge JM, Odom DT, Flicek P. BMC biology Volume 18 (2020) p.132 DOI: 10.1186/s12915-020-00863-8
Secondary structure of the SARS-CoV-2 5'-UTR.
Miao Z, Tidu A, Eriani G, Martin F. RNA biology Volume 18 (2021) p.447-456 DOI: 10.1080/15476286.2020.1814556
Toward a Sample Metadata Standard in Public Proteomics Repositories.
Perez-Riverol Y, European Bioinformatics Community for Mass Spectrometry. Journal of proteome research Volume 19 (2020) p.3906-3909 DOI: 10.1021/acs.jproteome.0c00376
*
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.4748 DOI: 10.1038/s41467-020-18151-y
*
Open Targets Genetics: An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci
Mountjoy E, Schmidt EM, Carmona M, Peat G, Miranda A, Fumis L, Hayhurst J, Buniello A, Schwartzentruber J, Karim MA, Wright D, Hercules A, Papa E, Fauman E, Barrett JC, Todd JA, Ochoa D, Dunham I, Ghoussaini M. Preprint DOI: 10.1101/2020.09.16.299271
*
Mutational signatures in countries affected by SARS-CoV-2: Implications in host-pathogen interactome
Singh J, Singh H, Hasnain SE, Rahman S. Preprint DOI: 10.1101/2020.09.17.301614
*
Global Public Perceptions of Genomic Data Sharing: What Shapes the Willingness to Donate DNA and Health Data?
Middleton A, Milne R, Almarri MA, Anwer S, Atutornu J, Baranova EE, Bevan P, Cerezo M, Cong Y, Critchley C, Fernow J, Goodhand P, Hasan Q, Hibino A, Houeland G, Howard HC, Hussain SZ, Malmgren CI, Izhevskaya VL, Jędrzejak A, Jinhong C, Kimura M, Kleiderman E, Leach B, Liu K, Mascalzoni D, Mendes Á, Minari J, Wang N, Nicol D, Niemiec E, Patch C, Pollard J, Prainsack B, Rivière M, Robarts L, Roberts J, Romano V, Sheerah HA, Smith J, Soulier A, Steed C, Stefànsdóttir V, Tandre C, Thorogood A, Voigt TH, West AV, Yoshizawa G, Morley KI. American journal of human genetics Volume 107 (2020) p.743-752 DOI: 10.1016/j.ajhg.2020.08.023
*
Coconut Online: Collection of Open Natural Products Database
Sorokina M, Merseburger P, Rajan K, Yirik MA, Steinbeck C. Preprint DOI: 10.21203/rs.3.rs-75600/v1
*
Elucidating the Joint Genetic Architecture of Mood Disorder and Schizophrenia
Lam M, Thompson M, Li B, Edwards AC, Chen C, Ge T, Cai N, Bigdeli T, Lencz T, Kendler K, Huang H. Preprint DOI: 10.1101/2020.09.14.20193870
*
CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations
Doğan T, Atas H, Joshi V, Atakan A, Rifaioglu AS, Nalbat E, Nightingale A, Saidi R, Volynkin V, Zellner H, Cetin-Atalay R, Martin M, Atalay V. Preprint DOI: 10.1101/2020.09.14.296889
*
COVID-19 and beyond: a call for action and audacious solidarity to all the citizens and nations, it is humanity’s fight
Auffray C, Balling R, Blomberg N, Bonaldo MC, Boutron B, Brahmachari S, Bréchot C, Cesario A, Chen S, Clément K, Danilenko D, Di Meglio A, Gelemanović A, Goble C, Gojobori T, Goldman JD, Goldman M, Guo Y, Heath J, Hood L, Hunter P, Jin L, Kitano H, Knoppers B, Lancet D, Larue C, Lathrop M, Laville M, Lindner AB, Magnan A, Metspalu A, Morin E, Ng LF, Nicod L, Noble D, Nottale L, Nowotny H, Ochoa T, Okeke IN, Oni T, Openshaw P, Oztürk M, Palkonen S, Paweska JT, Pison C, Polymeropoulos MH, Pristipino C, Protzer U, Roca J, Rozman D, Santolini M, Sanz F, Scambia G, Segal E, Serageldin I, Soares MB, Sterk P, Sugano S, Superti-Furga G, Supple D, Tegner J, Uhlen M, Urbani A, Valencia A, Valentini V, van der Werf S, Vinciguerra M, Wolkenhauer O, Wouters E. Preprint DOI: 10.12688/f1000research.26098.1
MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets.
Choi M, Carver J, Chiva C, Tzouros M, Huang T, Tsai TH, Pullman B, Bernhardt OM, Hüttenhain R, Teo GC, Perez-Riverol Y, Muntel J, Müller M, Goetze S, Pavlou M, Verschueren E, Wollscheid B, Nesvizhskii AI, Reiter L, Dunkley T, Sabidó E, Bandeira N, Vitek O. Nature methods Volume 17 (2020) p.981-984 DOI: 10.1038/s41592-020-0955-0
*
Understanding and predicting ciprofloxacin minimum inhibitory concentration in Escherichia coli with machine learning.
Pataki BÁ, Matamoros S, van der Putten BCL, Remondini D, Giampieri E, Aytan-Aktug D, Hendriksen RS, Lund O, Csabai I, Schultsz C, SPS COMPARE ML-AMR group. Scientific reports Volume 10 (2020) p.15026 DOI: 10.1038/s41598-020-71693-5
*
R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types
Sweeney BA, Hoksza D, Nawrocki EP, Ribas CE, Madeira F, Cannone JJ, Gutell R, Maddala A, Meade C, Williams LD, Petrov AS, Chan PP, Lowe TM, Finn RD, Petrov AI. Preprint DOI: 10.1101/2020.09.10.290924
*
A vast resource of allelic expression data spanning human tissues.
Castel SE, Aguet F, Mohammadi P, GTEx Consortium, Ardlie KG, Lappalainen T. Genome biology Volume 21 (2020) p.234 DOI: 10.1186/s13059-020-02122-z
Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC.
Saary P, Mitchell AL, Finn RD. Genome biology Volume 21 (2020) p.244 DOI: 10.1186/s13059-020-02155-4
*
A Quantitative Proteome Map of the Human Body.
Jiang L, Wang M, Lin S, Jian R, Li X, Chan J, Dong G, Fang H, Robinson AE, GTEx Consortium, Snyder MP. Cell Volume 183 (2020) p.269-283.e19 DOI: 10.1016/j.cell.2020.08.036
*
Host adaptation in gut Firmicutes is associated with sporulation loss and altered colonisation patterns
Browne HP, Almeida A, Kumar N, Vervier K, Adoum AT, Viciani E, Dawson NJ, Forster SC, Cormie C, Goulding D, Lawley TD. Preprint DOI: 10.1101/2020.09.09.289504
*
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. Preprint DOI: 10.1101/2020.09.08.287557
*
UVA radiation could be a significant contributor to sunlight inactivation of SARS-CoV-2
Luzzatto-Fegiz P, Temprano-Coleto F, Peaudecerf FJ, Landel JR, Zhu Y, McMurry JA. Preprint DOI: 10.1101/2020.09.07.286666
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 587 (2020) p.377-386 DOI: 10.1038/s41586-020-2715-9
Genomic copy number predicts esophageal cancer years before transformation.
Killcoyne S, Gregson E, Wedge DC, Woodcock DJ, Eldridge MD, de la Rue R, Miremadi A, Abbas S, Blasko A, Kosmidou C, Januszewicz W, Jenkins AV, Gerstung M, Fitzgerald RC. Nature medicine Volume 26 (2020) p.1726-1732 DOI: 10.1038/s41591-020-1033-y
Biocuration - mapping resources and needs.
Holinski A, Burke ML, Morgan SL, McQuilton P, Palagi PM. F1000Research Volume 9 (2020) DOI: 10.12688/f1000research.25413.2
*
Massive expansion of human gut bacteriophage diversity
Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD. Preprint DOI: 10.1101/2020.09.03.280214
Effect of sequence padding on the performance of deep learning models in archaeal protein functional prediction.
Lopez-Del Rio A, Martin M, Perera-Lluna A, Saidi R. Scientific reports Volume 10 (2020) p.14634 DOI: 10.1038/s41598-020-71450-8
An open source chemical structure curation pipeline using RDKit.
Bento AP, Hersey A, Félix E, Landrum G, Gaulton A, Atkinson F, Bellis LJ, De Veij M, Leach AR. Journal of cheminformatics Volume 12 (2020) p.51 DOI: 10.1186/s13321-020-00456-1
The Polygenic and Monogenic Basis of Blood Traits and Diseases.
Vuckovic D, Bao EL, Akbari P, Lareau CA, Mousas A, Jiang T, Chen MH, Raffield LM, Tardaguila M, Huffman JE, Ritchie SC, Megy K, Ponstingl H, Penkett CJ, Albers PK, Wigdor EM, Sakaue S, Moscati A, Manansala R, Lo KS, Qian H, Akiyama M, Bartz TM, Ben-Shlomo Y, Beswick A, Bork-Jensen J, Bottinger EP, Brody JA, van Rooij FJA, Chitrala KN, Wilson PWF, Choquet H, Danesh J, Di Angelantonio E, Dimou N, Ding J, Elliott P, Esko T, Evans MK, Felix SB, Floyd JS, Broer L, Grarup N, Guo MH, Guo Q, Greinacher A, Haessler J, Hansen T, Howson JMM, Huang W, Jorgenson E, Kacprowski T, Kähönen M, Kamatani Y, Kanai M, Karthikeyan S, Koskeridis F, Lange LA, Lehtimäki T, Linneberg A, Liu Y, Lyytikäinen LP, Manichaikul A, Matsuda K, Mohlke KL, Mononen N, Murakami Y, Nadkarni GN, Nikus K, Pankratz N, Pedersen O, Preuss M, Psaty BM, Raitakari OT, Rich SS, Rodriguez BAT, Rosen JD, Rotter JI, Schubert P, Spracklen CN, Surendran P, Tang H, Tardif JC, Ghanbari M, Völker U, Völzke H, Watkins NA, Weiss S, VA Million Veteran Program, Cai N, Kundu K, Watt SB, Walter K, Zonderman AB, Cho K, Li Y, Loos RJF, Knight JC, Georges M, Stegle O, Evangelou E, Okada Y, Roberts DJ, Inouye M, Johnson AD, Auer PL, Astle WJ, Reiner AP, Butterworth AS, Ouwehand WH, Lettre G, Sankaran VG, Soranzo N. Cell Volume 182 (2020) p.1214-1231.e11 DOI: 10.1016/j.cell.2020.08.008
*
Optimising biomedical relationship extraction with BioBERT
Giles O, Karlsson A, Masiala S, White S, Cesareni G, Perfetto L, Mullen J, Hughes M, Harland L, Malone J. Preprint DOI: 10.1101/2020.09.01.277277
Publisher Correction: The tuatara genome reveals ancient features of amniote evolution.
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 MD, Newcomb RD, 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, Bond DM, Paterson JM, Mulcahy DG, Gonzalez VL, Barbieri CG, DeMeo DP, Pabinger S, Van Stijn T, Clarke S, Ryder O, Edwards SV, Salzberg SL, Anderson L, Nelson N, Stone C, Ngatiwai Trust Board. Nature Volume 585 (2020) p.E3 DOI: 10.1038/s41586-020-2661-6
Exploring Non-Coding RNAs in RNAcentral.
Sweeney BA, Tagmazian AA, Ribas CE, Finn RD, Bateman A, Petrov AI. Current protocols in bioinformatics Volume 71 (2020) p.e104 DOI: 10.1002/cpbi.104
Two Cases of Recessive Intellectual Disability Caused by NDST1 and METTL23 Variants.
Khan A, Miao Z, Umair M, Ullah A, Alshabeeb MA, Bilal M, Ahmad F, Rappold GA, Ansar M, Carapito R. Genes Volume 11 (2020) DOI: 10.3390/genes11091021
Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development.
Burrows N, Bashford-Rogers RJM, Bhute VJ, Peñalver A, Ferdinand JR, Stewart BJ, Smith JEG, Deobagkar-Lele M, Giudice G, Connor TM, Inaba A, Bergamaschi L, Smith S, Tran MGB, Petsalaki E, Lyons PA, Espeli M, Huntly BJP, Smith KGC, Cornall RJ, Clatworthy MR, Maxwell PH. Nature immunology Volume 21 (2020) p.1408-1420 DOI: 10.1038/s41590-020-0772-8
*
An Open Source Chemical Structure Curation Pipeline using RDKit
Bento AP, Hersey A, Felix E, Landrum G, Gaulton A, Atkinson F, Bellis LJ, Veij MD, Leach AR. Preprint DOI: 10.21203/rs.3.rs-34715/v2
*
Deep spatial profiling of COVID19 brains reveals neuroinflammation by compartmentalized local immune cell interactions and targets for intervention
Bengsch B, Schwabenland M, Salié H, Tanevski J, Killmer S, Matschke J, Püschel K, Mei H, Boettler T, Neumann-Haefelin C, Hofmann M, Saez-Rodriguez J, Knobeloch K, Blank T, Thimme R, Glatzel M, Prinz M. Preprint DOI: 10.21203/rs.3.rs-63687/v1
*
Sex differences in oncogenic mutational processes.
Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, PCAWG Tumour Subtypes and Clinical Translation, Boutros PC, PCAWG Consortium. Nature communications Volume 11 (2020) p.4330 DOI: 10.1038/s41467-020-17359-2
*
Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference.
Hop PJ, Luijk R, Daxinger L, van Iterson M, Dekkers KF, Jansen R, BIOS Consortium, van Meurs JBJ, 't Hoen PAC, Ikram MA, van Greevenbroek MMJ, Boomsma DI, Slagboom PE, Veldink JH, van Zwet EW, Heijmans BT. Genome biology Volume 21 (2020) p.220 DOI: 10.1186/s13059-020-02114-z
Analysis of mutational signatures in C. elegans: Implications for cancer genome analysis.
Meier B, Volkova NV, Gerstung M, Gartner A. DNA repair Volume 95 (2020) p.102957 DOI: 10.1016/j.dnarep.2020.102957
*
Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development
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 S, Hunt T, Bent Z, Fedrigo O, Sloan SA, Risso D, Jarvis ED, Flicek P, Luo W, Pitt GS, Frankish A, Smit AB, Ross ME, Tilgner HU. Preprint DOI: 10.1101/2020.08.27.268730
Acetylation of Surface Carbohydrates in Bacterial Pathogens Requires Coordinated Action of a Two-Domain Membrane-Bound Acyltransferase.
Pearson CR, Tindall SN, Herman R, Jenkins HT, Bateman A, Thomas GH, Potts JR, Van der Woude MW. mBio Volume 11 (2020) DOI: 10.1128/mbio.01364-20
*
Reconstructing the lineage histories and differentiation trajectories of individual cancer cells in JAK2-mutant 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. Preprint DOI: 10.1101/2020.08.24.265058
*
Cell state diversity promotes metastasis through heterotypic cluster formation in melanoma
Campbell NR, Rao A, Zhang M, Baron M, Heilmann S, Deforet M, Kenny C, Ferretti L, Huang T, Garg M, Nsengimana J, Montal E, Tagore M, Hunter M, Newton-Bishop J, Middleton MR, Corrie P, Adams DJ, Rabbie R, Levesque MP, Cornell RA, Yanai I, Xavier JB, White RM. Preprint DOI: 10.1101/2020.08.24.265140
*
Predicting gene regulatory networks from cell atlases
Møller AF, Natarajan KN. Preprint DOI: 10.1101/2020.08.21.261735
Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma.
Ordoñez R, Kulis M, Russiñol N, Chapaprieta V, Carrasco-Leon A, García-Torre B, Charalampopoulou S, Clot G, Beekman R, Meydan C, Duran-Ferrer M, Verdaguer-Dot N, Vilarrasa-Blasi R, Soler-Vila P, Garate L, Miranda E, San José-Enériz E, Rodriguez-Madoz JR, Ezponda T, Martínez-Turrilas R, Vilas-Zornoza A, Lara-Astiaso D, Dupéré-Richer D, Martens JHA, El-Omri H, Taha RY, Calasanz MJ, Paiva B, San Miguel J, Flicek P, Gut I, Melnick A, Mitsiades CS, Licht JD, Campo E, Stunnenberg HG, Agirre X, Prosper F, Martin-Subero JI. Genome research Volume 30 (2020) p.1217-1227 DOI: 10.1101/gr.265520.120
Genetic and functional insights into the fractal structure of the heart.
Meyer HV, Dawes TJW, Serrani M, Bai W, Tokarczuk P, Cai J, de Marvao A, Henry A, Lumbers RT, Gierten J, Thumberger T, Wittbrodt J, Ware JS, Rueckert D, Matthews PM, Prasad SK, Costantino ML, Cook SA, Birney E, O'Regan DP. Nature Volume 584 (2020) p.589-594 DOI: 10.1038/s41586-020-2635-8
*
The Use of Frailty Scoring to Predict Early Physical Activity Levels After Cardiac Surgery.
Abdullahi YS, Salmasi MY, Moscarelli M, Parlanti A, Marotta M, Varone E, Solinas M, Sheriff RM, Casula RP, Athanasiou T. The Annals of thoracic surgery Volume 111 (2021) p.36-43 DOI: 10.1016/j.athoracsur.2020.06.029
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.1623-1635 DOI: 10.1038/s41591-020-1038-6
*
LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications
Alvarez-Jarreta J, Rodrigues PR, Fahy E, O’Connor A, Price A, Gaud C, Andrews S, Benton P, Siuzdak G, Hawksworth JI, Valdivia-Garcia M, Allen SM, O’Donnell VB. Preprint DOI: 10.1101/2020.08.16.250878
Transcription and DNA Methylation Patterns of Blood-Derived CD8+ T Cells Are Associated With Age and Inflammatory Bowel Disease But Do Not Predict Prognosis.
Gasparetto M, Payne F, Nayak K, Kraiczy J, Glemas C, Philip-McKenzie Y, Ross A, Edgar RD, Zerbino DR, Salvestrini C, Torrente F, Ventham NT, Kalla R, Satsangi J, Sarkies P, Heuschkel R, Zilbauer M. Gastroenterology Volume 160 (2021) p.232-244.e7 DOI: 10.1053/j.gastro.2020.08.017
*
Genomic surveillance, characterisation and intervention of a carbapenem-resistant Acinetobacter baumannii 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. Preprint DOI: 10.1101/2020.08.10.20166652
Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation.
Ortmann D, Brown S, Czechanski A, Aydin S, Muraro D, Huang Y, Tomaz RA, Osnato A, Canu G, Wesley BT, Skelly DA, Stegle O, Choi T, Churchill GA, Baker CL, Rugg-Gunn PJ, Munger SC, Reinholdt LG, Vallier L. Cell stem cell Volume 27 (2020) p.470-481.e6 DOI: 10.1016/j.stem.2020.07.019
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) (2020) DOI: 10.1093/bioinformatics/btaa713
*
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. Preprint DOI: 10.1101/2020.08.07.239855
Population-scale proteome variation in human induced pluripotent stem cells.
Mirauta BA, Seaton DD, Bensaddek D, Brenes A, Bonder MJ, Kilpinen H, HipSci Consortium, Stegle O, Lamond AI. eLife Volume 9 (2020) DOI: 10.7554/elife.57390
Evolution and dissemination of L and M plasmid lineages carrying antibiotic resistance genes in diverse Gram-negative bacteria.
Blackwell GA, Doughty EL, Moran RA. Plasmid Volume 113 (2021) p.102528 DOI: 10.1016/j.plasmid.2020.102528
Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci.
Cavadas B, Camacho R, Ferreira JC, Ferreira RM, Figueiredo C, Brazma A, Fonseca NA, Pereira L. Microorganisms Volume 8 (2020) DOI: 10.3390/microorganisms8081196
*
Understanding the Binding Specificity of G-Protein Coupled Receptors toward G-Proteins and Arrestins: Application to the Dopamine Receptor Family.
Preto AJ, Barreto CAV, Baptista SJ, Almeida JG, Lemos A, Melo A, Cordeiro MNDS, Kurkcuoglu Z, Melo R, Moreira IS. Journal of chemical information and modeling Volume 60 (2020) p.3969-3984 DOI: 10.1021/acs.jcim.0c00371
The tuatara genome reveals ancient features of amniote evolution.
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 MD, Newcomb RD, 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, Bond DM, Paterson JM, Mulcahy DG, Gonzalez VL, Barbieri CG, DeMeo DP, Pabinger S, Van Stijn T, Clarke S, Ryder O, Edwards SV, Salzberg SL, Anderson L, Nelson N, Stone C, Ngatiwai Trust Board. Nature Volume 584 (2020) p.403-409 DOI: 10.1038/s41586-020-2561-9
*
DYNC2H1 hypomorphic or retina-predominant variants cause nonsyndromic retinal degeneration.
Vig A, Poulter JA, Ottaviani D, Tavares E, Toropova K, Tracewska AM, Mollica A, Kang J, Kehelwathugoda O, Paton T, Maynes JT, Wheway G, Arno G, Genomics England Research Consortium, Khan KN, McKibbin M, Toomes C, Ali M, Di Scipio M, Li S, Ellingford J, Black G, Webster A, Rydzanicz M, Stawiński P, Płoski R, Vincent A, Cheetham ME, Inglehearn CF, Roberts A, Heon E. Genetics in medicine : official journal of the American College of Medical Genetics Volume 22 (2020) p.2041-2051 DOI: 10.1038/s41436-020-0915-1
*
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.
Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, De Domenico E, Wendisch D, Grasshoff M, Kapellos TS, Beckstette M, Pecht T, Saglam A, Dietrich O, Mei HE, Schulz AR, Conrad C, Kunkel D, Vafadarnejad E, Xu CJ, Horne A, Herbert M, Drews A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, Müller-Redetzky H, Heim KM, Machleidt F, Uhrig A, Bosquillon de Jarcy L, Jürgens L, Stegemann M, Glösenkamp CR, Volk HD, Goffinet C, Landthaler M, Wyler E, Georg P, Schneider M, Dang-Heine C, Neuwinger N, Kappert K, Tauber R, Corman V, Raabe J, Kaiser KM, Vinh MT, Rieke G, Meisel C, Ulas T, Becker M, Geffers R, Witzenrath M, Drosten C, Suttorp N, von Kalle C, Kurth F, Händler K, Schultze JL, Aschenbrenner AC, Li Y, Nattermann J, Sawitzki B, Saliba AE, Sander LE, Deutsche COVID-19 OMICS Initiative (DeCOI). Cell Volume 182 (2020) p.1419-1440.e23 DOI: 10.1016/j.cell.2020.08.001
*
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis
Türei D, Valdeolivas A, Gul L, Palacio-Escat N, Ivanova O, Gábor A, Módos D, Korcsmáros T, Saez-Rodriguez J. Preprint DOI: 10.1101/2020.08.03.221242
Guidelines for human gene nomenclature.
Bruford EA, Braschi B, Denny P, Jones TEM, Seal RL, Tweedie S. Nature genetics Volume 52 (2020) p.754-758 DOI: 10.1038/s41588-020-0669-3
*
Publisher Correction: Whole-genome sequencing of a sporadic primary immunodeficiency cohort.
Thaventhiran JED, Lango Allen H, Burren OS, Rae W, Greene D, Staples E, Zhang Z, Farmery JHR, Simeoni I, Rivers E, Maimaris J, Penkett CJ, Stephens J, Deevi SVV, Sanchis-Juan A, Gleadall NS, Thomas MJ, Sargur RB, Gordins P, Baxendale HE, Brown M, Tuijnenburg P, Worth A, Hanson S, Linger RJ, Buckland MS, Rayner-Matthews PJ, Gilmour KC, Samarghitean C, Seneviratne SL, Sansom DM, Lynch AG, Megy K, Ellinghaus E, Ellinghaus D, Jorgensen SF, Karlsen TH, Stirrups KE, Cutler AJ, Kumararatne DS, Chandra A, Edgar JDM, Herwadkar A, Cooper N, Grigoriadou S, Huissoon AP, Goddard S, Jolles S, Schuetz C, Boschann F, Primary Immunodeficiency Consortium for the NIHR Bioresource, Lyons PA, Hurles ME, Savic S, Burns SO, Kuijpers TW, Turro E, Ouwehand WH, Thrasher AJ, Smith KGC. Nature Volume 584 (2020) p.E2 DOI: 10.1038/s41586-020-2556-6
*
GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 Genomes.
Wilson DJ, CRyPTIC Consortium. Molecular biology and evolution Volume 37 (2020) p.2450-2460 DOI: 10.1093/molbev/msaa069
TB1: from domestication gene to tool for many trades.
Igartua E, Contreras-Moreira B, Casas AM. Journal of experimental botany Volume 71 (2020) p.4621-4624 DOI: 10.1093/jxb/eraa308
SBML Level 3: an extensible format for the exchange and reuse of biological models.
Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M, SBML Level 3 Community members. Molecular systems biology Volume 16 (2020) p.e9110 DOI: 10.15252/msb.20199110
*
Why do pathway methods work better than they should?
Szalai B, Saez-Rodriguez J. Preprint DOI: 10.1101/2020.07.30.228296
*
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Nature Volume 583 (2020) p.699-710 DOI: 10.1038/s41586-020-2493-4
Transcriptional activity and strain-specific history of mouse pseudogenes.
Sisu C, Muir P, Frankish A, Fiddes I, Diekhans M, Thybert D, Odom DT, Flicek P, Keane TM, Hubbard T, Harrow J, Gerstein M. Nature communications Volume 11 (2020) p.3695 DOI: 10.1038/s41467-020-17157-w
*
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes
Yao G, Zhang W, Yang M, Yang H, Wang J, Zhang H, Wei L, Xie Z, Li W. Preprint DOI: 10.1101/2020.07.29.221010
Overview of PAX gene family: analysis of human tissue-specific variant expression and involvement in human disease.
Thompson B, Davidson EA, Liu W, Nebert DW, Bruford EA, Zhao H, Dermitzakis ET, Thompson DC, Vasiliou V. Human genetics Volume 140 (2021) p.381-400 DOI: 10.1007/s00439-020-02212-9
Perspectives on ENCODE.
ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. Nature Volume 583 (2020) p.693-698 DOI: 10.1038/s41586-020-2449-8
Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri.
Kenny NJ, Francis WR, Rivera-Vicéns RE, Juravel K, de Mendoza A, Díez-Vives C, Lister R, Bezares-Calderón LA, Grombacher L, Roller M, Barlow LD, Camilli S, Ryan JF, Wörheide G, Hill AL, Riesgo A, Leys SP. Nature communications Volume 11 (2020) p.3676 DOI: 10.1038/s41467-020-17397-w
*
Genetic variation affects morphological retinal phenotypes extracted from UK Biobank Optical Coherence Tomography images
Currant H, Hysi P, Fitzgerald TW, Gharahkhani P, Bonnemaijer PWM, Atan D, Aung T, Charng J, Choquet H, Craig J, Hewitt AW, Khaw PT, Klaver CCW, Kubo M, Ong J, Pasquale LR, Reisman CA, 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, UK Biobank Eye and Vision Consortium, International Glaucoma Genetics Consortium. Preprint DOI: 10.1101/2020.07.20.20157180
*
What the Phage: A scalable workflow for the identification and analysis of phage sequences
Marquet M, Hölzer M, Pletz MW, Viehweger A, Makarewicz O, Ehricht R, Brandt C. Preprint DOI: 10.1101/2020.07.24.219899
Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.
Yang M, Petralia F, Li Z, Li H, Ma W, Song X, Kim S, Lee H, Yu H, Lee B, Bae S, Heo E, Kaczmarczyk J, Stępniak P, Warchoł M, Yu T, Calinawan AP, Boutros PC, Payne SH, Reva B, NCI-CPTAC-DREAM Consortium, Boja E, Rodriguez H, Stolovitzky G, Guan Y, Kang J, Wang P, Fenyö D, Saez-Rodriguez J. Cell systems Volume 11 (2020) p.186-195.e9 DOI: 10.1016/j.cels.2020.06.013
A framework to assess the quality and impact of bioinformatics training across ELIXIR.
Gurwitz KT, Singh Gaur P, Bellis LJ, Larcombe L, Alloza E, Balint BL, Botzki A, Dimec J, Dominguez Del Angel V, Fernandes PL, Korpelainen E, Krause R, Kuzak M, Le Pera L, Leskošek B, Lindvall JM, Marek D, Martinez PA, Muyldermans T, Nygård S, Palagi PM, Peterson H, Psomopoulos F, Spiwok V, van Gelder CWG, Via A, Vidak M, Wibberg D, Morgan SL, Rustici G. PLoS computational biology Volume 16 (2020) p.e1007976 DOI: 10.1371/journal.pcbi.1007976
Cell type specific novel lncRNAs and circRNAs in the BLUEPRINT haematopoietic transcriptomes atlas.
Grassi L, Izuogu OG, Jorge NA, Seyres D, Bustamante M, Burden F, Farrow S, Farahi N, Martin FJ, Frankish A, Mudge JM, Kostadima M, Petersen R, Lambourne JJ, Rowlston S, Martin-Rendon E, Clarke L, Downes K, Estivill X, Flicek P, Martens JH, Yaspo ML, Stunnenberg HG, Ouwehand WH, Passetti F, Turro E, Frontini M. Haematologica (2020) DOI: 10.3324/haematol.2019.238147
*
Author Correction: Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA in humans.
Wei W, Pagnamenta AT, Gleadall N, Sanchis-Juan A, Stephens J, Broxholme J, Tuna S, Odhams CA, Genomics England Research Consortium, NIHR BioResource, Fratter C, Turro E, Caulfield MJ, Taylor JC, Rahman S, Chinnery PF. Nature communications Volume 11 (2020) p.3741 DOI: 10.1038/s41467-020-17572-z
*
DreamAI: algorithm for the imputation of proteomics data
Ma W, Kim S, Chowdhury S, Li Z, Yang M, Yoo S, Petralia F, Jacobsen J, Li JJ, Ge X, Li K, Yu T, Edwards N, Payne S, Boutros PC, Rodriguez H, Stolovitzky G, Zhu J, Kang J, Fenyo D, Saez-Rodriguez J, Wang P. Preprint DOI: 10.1101/2020.07.21.214205
*
BioContainers Registry: searching for bioinformatics tools, packages and containers
Bai J, Bandla C, Guo J, Alvarez RV, Vizcaíno JA, Bai M, Moreno P, Grüning BA, Sallou O, Perez-Riverol Y. Preprint DOI: 10.1101/2020.07.21.187609
*
Modelling structural rearrangements in proteins using Euclidean distance matrices
Lafita A, Bateman A. Preprint DOI: 10.12688/f1000research.25235.1
A unified catalog of 204,938 reference genomes from the human gut microbiome.
Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, Pollard KS, Sakharova E, Parks DH, Hugenholtz P, Segata N, Kyrpides NC, Finn RD. Nature biotechnology Volume 39 (2021) p.105-114 DOI: 10.1038/s41587-020-0603-3
*
Dynamics of cell-free tumour DNA correlate with treatment response of head and neck cancer patients receiving radiochemotherapy.
Hilke FJ, Muyas F, Admard J, Kootz B, Nann D, Welz S, Rieß O, Zips D, Ossowski S, Schroeder C, Clasen K. Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology Volume 151 (2020) p.182-189 DOI: 10.1016/j.radonc.2020.07.027
Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.
Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R, Schneider R. Scientific data Volume 7 (2020) p.247 DOI: 10.1038/s41597-020-00589-w
Tumors induce de novo steroid biosynthesis in T cells to evade immunity.
Mahata B, Pramanik J, van der Weyden L, Polanski K, Kar G, Riedel A, Chen X, Fonseca NA, Kundu K, Campos LS, Ryder E, Duddy G, Walczak I, Okkenhaug K, Adams DJ, Shields JD, Teichmann SA. Nature communications Volume 11 (2020) p.3588 DOI: 10.1038/s41467-020-17339-6
The Concerted Action of Two B3-Like Prophage Genes Excludes Superinfecting Bacteriophages by Blocking DNA Entry into Pseudomonas aeruginosa.
Carballo-Ontiveros MA, Cazares A, Vinuesa P, Kameyama L, Guarneros G. Journal of virology Volume 94 (2020) DOI: 10.1128/jvi.00953-20
*
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 A, Dougan G, Sjöling Å. Preprint DOI: 10.1101/2020.07.16.203430
*
Prophage-encoded phage defense proteins with cognate self-immunity
Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD. Preprint DOI: 10.1101/2020.07.13.199331
*
scMET: Bayesian modelling of DNA methylation heterogeneity at single-cell resolution
Kapourani C, Argelaguet R, Sanguinetti G, Vallejos CA. Preprint DOI: 10.1101/2020.07.10.196816
*
Identifying Causative Mechanisms Linking Early-Life Stress to Psycho-Cardio-Metabolic Multi-Morbidity: The EarlyCause Project
Mariani N, Borsini A, Cecil CA, 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, Ballester MAG, Piella G, Gelpi JL, Lamers F, Penninx BW, Tiemeier H, von Tottleben M, Thiel R, Heil KF, Järvelin M, Pariante C, Mansuy IM, Lekadir K. Preprint DOI: 10.1101/2020.07.08.181958
A user guide for the online exploration and visualization of PCAWG data.
Goldman MJ, 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. Nature communications Volume 11 (2020) p.3400 DOI: 10.1038/s41467-020-16785-6
The EU-ToxRisk method documentation, data processing and chemical testing pipeline for the regulatory use of new approach methods.
Krebs A, van Vugt-Lussenburg BMA, Waldmann T, Albrecht W, Boei J, Ter Braak B, Brajnik M, Braunbeck T, Brecklinghaus T, Busquet F, Dinnyes A, Dokler J, Dolde X, Exner TE, Fisher C, Fluri D, Forsby A, Hengstler JG, Holzer AK, Janstova Z, Jennings P, Kisitu J, Kobolak J, Kumar M, Limonciel A, Lundqvist J, Mihalik B, Moritz W, Pallocca G, Ulloa APC, Pastor M, Rovida C, Sarkans U, Schimming JP, Schmidt BZ, Stöber R, Strassfeld T, van de Water B, Wilmes A, van der Burg B, Verfaillie CM, von Hellfeld R, Vrieling H, Vrijenhoek NG, Leist M. Archives of toxicology Volume 94 (2020) p.2435-2461 DOI: 10.1007/s00204-020-02802-6
A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program.
Alda-Catalinas C, Bredikhin D, Hernando-Herraez I, Santos F, Kubinyecz O, Eckersley-Maslin MA, Stegle O, Reik W. Cell systems Volume 11 (2020) p.25-41.e9 DOI: 10.1016/j.cels.2020.06.004
*
Genetic risk factors for death with SARS-CoV-2 from the UK Biobank
Lu C, Gam R, Pandurangan AP, Gough J. Preprint DOI: 10.1101/2020.07.01.20144592
*
The RESOLUTE consortium: unlocking SLC transporters for drug discovery.
Superti-Furga G, Lackner D, Wiedmer T, Ingles-Prieto A, Barbosa B, Girardi E, Goldmann U, Gürtl B, Klavins K, Klimek C, Lindinger S, Liñeiro-Retes E, Müller AC, Onstein S, Redinger G, Reil D, Sedlyarov V, Wolf G, Crawford M, Everley R, Hepworth D, Liu S, Noell S, Piotrowski M, Stanton R, Zhang H, Corallino S, Faedo A, Insidioso M, Maresca G, Redaelli L, Sassone F, Scarabottolo L, Stucchi M, Tarroni P, Tremolada S, Batoulis H, Becker A, Bender E, Chang YN, Ehrmann A, Müller-Fahrnow A, Pütter V, Zindel D, Hamilton B, Lenter M, Santacruz D, Viollet C, Whitehurst C, Johnsson K, Leippe P, Baumgarten B, Chang L, Ibig Y, Pfeifer M, Reinhardt J, Schönbett J, Selzer P, Seuwen K, Bettembourg C, Biton B, Czech J, de Foucauld H, Didier M, Licher T, Mikol V, Pommereau A, Puech F, Yaligara V, Edwards A, Bongers BJ, Heitman LH, IJzerman AP, Sijben HJ, van Westen GJP, Grixti J, Kell DB, Mughal F, Swainston N, Wright-Muelas M, Bohstedt T, Burgess-Brown N, Carpenter L, Dürr K, Hansen J, Scacioc A, Banci G, Colas C, Digles D, Ecker G, Füzi B, Gamsjäger V, Grandits M, Martini R, Troger F, Altermatt P, Doucerain C, Dürrenberger F, Manolova V, Steck AL, Sundström H, Wilhelm M, Steppan CM. Nature reviews. Drug discovery Volume 19 (2020) p.429-430 DOI: 10.1038/d41573-020-00056-6
*
Building trust in preprints: recommendations for servers and other stakeholders
Beck J, Ferguson C, Funk K, Hanson B, Harrison M, Ide-Smith M, Lammey R, Levchenko M, Mendonça A, Parkin M, Penfold N, Pfeiffer N, Polka J, Puebla I, Rieger OY, Rittman M. Preprint DOI: 10.31219/osf.io/8dn4w
Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens.
Gonçalves E, Segura-Cabrera A, Pacini C, Picco G, Behan FM, Jaaks P, Coker EA, van der Meer D, Barthorpe A, Lightfoot H, Mironenko T, Beck A, Richardson L, Yang W, Lleshi E, Hall J, Tolley C, Hall C, Mali I, Thomas F, Morris J, Leach AR, Lynch JT, Sidders B, Crafter C, Iorio F, Fawell S, Garnett MJ. Molecular systems biology Volume 16 (2020) p.e9405 DOI: 10.15252/msb.20199405
The Quest for Orthologs benchmark service and consensus calls in 2020.
Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernández-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernández JM, Codó L, For Orthologs Consortium TQ, Gelpi JL, Huerta-Cepas J, Iwasaki W, Kelly S, Lecompte O, Muffato M, Martin MJ, Capella-Gutierrez S, Thomas PD, Sonnhammer E, Dessimoz C. Nucleic acids research Volume 48 (2020) p.W538-W545 DOI: 10.1093/nar/gkaa308
*
Unifying the known and unknown microbial coding sequence space
Vanni C, Schechter MS, Acinas SG, Barberán A, Buttigieg PL, Casamayor EO, Delmont TO, Duarte CM, Eren AM, Finn RD, Kottmann R, Mitchell A, Sanchez P, Siren K, Steinegger M, Glöckner FO, Fernandez-Guerra A. Preprint DOI: 10.1101/2020.06.30.180448
*
Locating patterns in Nanopore currents using time-warped signal representation of consensus nucleotides for demultiplexing and motif detection.
Kang ASW, Enright AJ. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference Volume 2020 (2020) p.82-86 DOI: 10.1109/embc44109.2020.9176358
The omics discovery REST interface.
Dass G, Vu MT, Xu P, Audain E, Hitz MP, Grüning BA, Hermjakob H, Perez-Riverol Y. Nucleic acids research Volume 48 (2020) p.W380-W384 DOI: 10.1093/nar/gkaa326
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets.
Marchet C, Iqbal Z, Gautheret D, Salson M, Chikhi R. Bioinformatics (Oxford, England) Volume 36 (2020) p.i177-i185 DOI: 10.1093/bioinformatics/btaa487
*
Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states
Girbig M, Misiaszek AD, Vorländer MK, Lafita A, Grötsch H, Baudin F, Bateman A, Müller CW. Preprint DOI: 10.1101/2020.06.29.177642
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).
Waltemath D, Golebiewski M, Blinov ML, Gleeson P, Hermjakob H, Hucka M, Inau ET, Keating SM, König M, Krebs O, Malik-Sheriff RS, Nickerson D, Oberortner E, Sauro HM, Schreiber F, Smith L, Stefan MI, Wittig U, Myers CJ. Journal of integrative bioinformatics Volume 17 (2020) DOI: 10.1515/jib-2020-0005
The Global Phosphorylation Landscape of SARS-CoV-2 Infection.
Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ. Cell Volume 182 (2020) p.685-712.e19 DOI: 10.1016/j.cell.2020.06.034
*
Large-scale association analyses identify host factors influencing human gut microbiome composition
Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Roy CIL, Raygoza Garay JA, Finnicum CT, Liu X, Zhernakova DV, Bonder MJ, Hansen TH, Frost F, Rühlemann MC, Turpin W, Moon J, Kim H, Lüll K, Barkan E, Shah SA, Fornage M, Szopinska-Tokov J, Wallen ZD, Borisevich D, Agreus L, Andreasson A, Bang C, Bedrani L, Bell JT, Bisgaard H, Boehnke M, Boomsma DI, Burk RD, Claringbould A, Croitoru K, Davies GE, van Duijn CM, Duijts L, Falony G, Fu J, van der Graaf A, Hansen T, Homuth G, Hughes DA, Ijzerman RG, Jackson MA, Jaddoe VW, Joossens M, Jørgensen T, Keszthelyi D, Knight R, Laakso M, Laudes M, Launer LJ, Lieb W, Lusis AJ, Masclee AA, Moll HA, Mujagic Z, Qibin Q, Rothschild D, Shin H, Sørensen SJ, Steves CJ, Thorsen J, Timpson NJ, Tito RY, Vieira-Silva S, Völker U, Völzke H, Võsa U, Wade KH, Walter S, Watanabe K, Weiss S, Weiss FU, Weissbrod O, Westra H, Willemsen G, Payami H, Jonkers DM, Vasquez AA, de Geus EJ, Meyer KA, Stokholm J, Segal E, Org E, Wijmenga C, Kim H, Kaplan RC, Spector TD, Uitterlinden AG, Rivadeneira F, Franke A, Lerch MM, Franke L, Sanna S, D’Amato M, Pedersen O, Paterson AD, Kraaij R, Raes J, Zhernakova A. Preprint DOI: 10.1101/2020.06.26.173724
*
Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
Audain E, Wilsdon A, Breckpot J, Izarzugaza J, Fitzgerald T, Kahlert A, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H, Bak M, Bassett A, Belmont J, Benson D, Berger F, Daehnert I, Devriendt K, Dittrich S, Daubeney P, Garg V, Hackmann K, Hoff K, Hofmann P, Dombrowsky G, Pickardt T, Bauer U, Keavney B, Klaassen S, Kramer H, Marshall C, Milewicz D, Lemaire S, Coselli J, Mitchell M, Tomita-Mitchell A, Prakash S, Stamm K, Stewart A, Silversides C, Siebert R, Stiller B, Rosenfeld J, Vater I, Postma A, Caliebe A, Brook J, Andelfinger G, Hurles M, Thienpont B, Larsen L, Hitz M. Preprint DOI: 10.1101/2020.06.25.169573
*
Intestinal transkingdom analysis on the impact of antibiotic perturbation in health and critical illness
Haak BW, Argelaguet R, Kinsella CM, Kullberg RF, Lankelma JM, Hakvoort TB, Hugenholtz F, Kostidis S, Giera M, de Jonge WJ, Schultz MJ, van Gool T, van der Poll T, de Vos WM, van den Hoek L, Wiersinga WJ. Preprint DOI: 10.1101/2020.06.25.171553
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 SV, Davies SE, Drews RM, Ewing A, Kaiser VB, Khamseh A, López-Arribillaga E, Redmond AM, Santoyo-Lopez J, Sentís I, Talmane L, Yates AD, Liver Cancer Evolution Consortium, Semple CA, López-Bigas N, Flicek P, Odom DT, Taylor MS. Nature Volume 583 (2020) p.265-270 DOI: 10.1038/s41586-020-2435-1
*
Whole-genome sequencing of patients with rare diseases in a national health system.
Turro E, Astle WJ, Megy K, Gräf S, Greene D, Shamardina O, Allen HL, Sanchis-Juan A, Frontini M, Thys C, Stephens J, Mapeta R, Burren OS, Downes K, Haimel M, Tuna S, Deevi SVV, Aitman TJ, Bennett DL, Calleja P, Carss K, Caulfield MJ, Chinnery PF, Dixon PH, Gale DP, James R, Koziell A, Laffan MA, Levine AP, Maher ER, Markus HS, Morales J, Morrell NW, Mumford AD, Ormondroyd E, Rankin S, Rendon A, Richardson S, Roberts I, Roy NBA, Saleem MA, Smith KGC, Stark H, Tan RYY, Themistocleous AC, Thrasher AJ, Watkins H, Webster AR, Wilkins MR, Williamson C, Whitworth J, Humphray S, Bentley DR, NIHR BioResource for the 100,000 Genomes Project, Kingston N, Walker N, Bradley JR, Ashford S, Penkett CJ, Freson K, Stirrups KE, Raymond FL, Ouwehand WH. Nature Volume 583 (2020) p.96-102 DOI: 10.1038/s41586-020-2434-2
*
Bacterial retrons encode tripartite toxin/antitoxin systems
Bobonis J, Mateus A, Pfalz B, Garcia-Santamarina S, Galardini M, Kobayashi C, Stein F, Savitski MM, Elfenbein JR, Andrews-Polymenis H, Typas A. Preprint DOI: 10.1101/2020.06.22.160168
*
Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2-Mediated Myocarditis.
Tucker NR, Chaffin M, Bedi KC, Papangeli I, Akkad AD, Arduini A, Hayat S, Eraslan G, Muus C, Bhattacharyya RP, Stegmann CM, Human Cell Atlas Lung Biological Network, Margulies KB, Ellinor PT, Human Cell Atlas Lung Biological Network Consortium Members. Circulation Volume 142 (2020) p.708-710 DOI: 10.1161/circulationaha.120.047911
*
Detection of differential RNA modifications from direct RNA sequencing of human cell lines
Pratanwanich PN, Yao F, Chen Y, Koh CW, Hendra C, Poon P, Goh YT, Yap PML, Yuan CJ, Chng WJ, Ng S, Thiery A, Goh WS, Göke J. Preprint DOI: 10.1101/2020.06.18.160010
*
Functional Characterization of the Lin28/let-7 Circuit during Forelimb Regeneration in Ambystoma mexicanum and its Influence on Metabolic Reprogramming
Varela-Rodríguez H, Abella-Quintana DG, Varela-Rodríguez L, Gomez-Zepeda D, Espinal-Centeno A, Caballero-Pérez J, Ordaz-Ortiz JJ, Cruz-Ramírez A. Preprint DOI: 10.1101/2020.06.18.160291
COVID-19 pandemic reveals the peril of ignoring metadata standards.
Schriml LM, Chuvochina M, Davies N, Eloe-Fadrosh EA, Finn RD, Hugenholtz P, Hunter CI, Hurwitz BL, Kyrpides NC, Meyer F, Mizrachi IK, Sansone SA, Sutton G, Tighe S, Walls R. Scientific data Volume 7 (2020) p.188 DOI: 10.1038/s41597-020-0524-5
*
Common genetic associations between age-related diseases
Dönertaş HM, Fabian DK, Valenzuela MF, Partridge L, Thornton JM. Preprint DOI: 10.1101/2020.06.16.20132621
Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli.
Wang Y, Huang JM, Zhou YL, Almeida A, Finn RD, Danchin A, He LS. BMC genomics Volume 21 (2020) p.408 DOI: 10.1186/s12864-020-06807-4
*
The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions
Perfetto L, Pastrello C, Del-Toro N, Duesbury M, Iannuccelli M, Kotlyar M, Licata L, Meldal B, Panneerselvam K, Panni S, Rahimzadeh N, Ricard-Blum S, Salwinski L, Shrivastava A, Cesareni G, Pellegrini M, Orchard S, Jurisica I, Hermjakob H, Porras P. Preprint DOI: 10.1101/2020.06.16.153817
*
Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution
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 L, 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. Preprint DOI: 10.1101/2020.06.12.147033
*
A comprehensive and centralized database for exploring omics data in Autoimmune Diseases
Martorell-Marugán J, Lopez-Dominguez R, Garcia-Moreno A, Toro-Dominguez D, Villatoro-Garcia JA, Barturen G, Martin-Gomez A, Troule K, Gomez-Lopez G, Al-Shahrour F, Gonzalez-Rumayor V, Peña-Chilet M, Dopazo J, Saez-Rodriguez J, Alarcon-Riquelme ME, Carmona-Saez P. Preprint DOI: 10.1101/2020.06.10.144972
Population Structure, Stratification, and Introgression of Human Structural Variation.
Almarri MA, Bergström A, Prado-Martinez J, Yang F, Fu B, Dunham AS, Chen Y, Hurles ME, Tyler-Smith C, Xue Y. Cell Volume 182 (2020) p.189-199.e15 DOI: 10.1016/j.cell.2020.05.024
*
Properties of structural variants and short tandem repeats associated with gene expression and complex traits.
Jakubosky D, D'Antonio M, Bonder MJ, Smail C, Donovan MKR, Young Greenwald WW, Matsui H, i2QTL Consortium, D'Antonio-Chronowska A, Stegle O, Smith EN, Montgomery SB, DeBoever C, Frazer KA. Nature communications Volume 11 (2020) p.2927 DOI: 10.1038/s41467-020-16482-4
*
Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats.
Jakubosky D, Smith EN, D'Antonio M, Jan Bonder M, Young Greenwald WW, D'Antonio-Chronowska A, Matsui H, i2QTL Consortium, Stegle O, Montgomery SB, DeBoever C, Frazer KA. Nature communications Volume 11 (2020) p.2928 DOI: 10.1038/s41467-020-16481-5
Caenorhabditis elegans AF4/FMR2 Family Homolog affl-2 Regulates Heat-Shock-Induced Gene Expression.
Walton SJ, Wang H, Quintero-Cadena P, Bateman A, Sternberg PW. Genetics Volume 215 (2020) p.1039-1054 DOI: 10.1534/genetics.120.302923
*
A consensus Covid-19 immune signature combines immuno-protection with discrete sepsis-like traits associated 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 J, Gee S, En Chan JN, Ryan S, Bugallo-Blanco E, Peterson P, Kisand K, Haljasmägi L, Martinez L, Merrick B, Bisnauthsing K, Brooks K, Ibrahim M, Mason J, Gomez FL, Babalola K, Abdul- Jawad S, Cason J, Mant C, Doores KJ, Seow J, Graham C, Rosa FD, Edgeworth J, Shankar-Hari M, Hayday AC. Preprint DOI: 10.1101/2020.06.08.20125112
*
A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework
Tekman M, Batut B, Ostrovsky A, Antoniewski C, Clements D, Ramirez F, Etherington GJ, Hotz H, Scholtalbers J, Manning JR, Bellenger L, Doyle MA, Heydarian M, Huang N, Soranzo N, Moreno P, Mautner S, Papatheodorou I, Nekrutenko A, Taylor J, Blankenberg D, Backofen R, Grüning B. Preprint DOI: 10.1101/2020.06.06.137570
Spatiotemporal proteomics uncovers cathepsin-dependent macrophage cell death during Salmonella infection.
Selkrig J, Li N, Hausmann A, Mangan MSJ, Zietek M, Mateus A, Bobonis J, Sueki A, Imamura H, El Debs B, Sigismondo G, Florea BI, Overkleeft HS, Kopitar-Jerala N, Turk B, Beltrao P, Savitski MM, Latz E, Hardt WD, Krijgsveld J, Typas A. Nature microbiology Volume 5 (2020) p.1119-1133 DOI: 10.1038/s41564-020-0736-7
*
Strain and lineage-level methylome heterogeneity in the multi-drug resistant pathogenic Escherichia coli ST101 clone
Ashcroft MM, Forde BM, Phan M, Peters KM, Roberts LW, Chan K, Chong TM, Yin W, Paterson DL, Walsh TR, Schembri MA, Beatson SA. Preprint DOI: 10.1101/2020.06.07.138552
*
Linking T cell receptor sequence to transcriptional profiles with clonotype neighbor graph analysis (CoNGA)
Schattgen SA, Guion K, Crawford JC, Souquette A, Barrio AM, Stubbington MJ, Thomas PG, Bradley P. Preprint DOI: 10.1101/2020.06.04.134536
*
Systematic analysis of mutational spectra associated with DNA repair deficiency in C. elegans
Meier B, Volkova N, Hong Y, Bertolini S, González-Huici V, Petrova T, Boulton S, Campbell P, Gerstung M, Gartner A. Preprint DOI: 10.1101/2020.06.04.133306
*
Analysis of tRNACys processing under salt stress in Bacillus subtilis spore outgrowth using RNA sequencing data
Arvizu Hernández I, Hernández Flores JL, Caballero Pérez J, Gutiérrez Sánchez H, Ramos López MÁ, Romero Gómez S, Cruz Hernández A, Saldaña Gutierrez C, Álvarez Hidalgo E, Jones GH, Campos Guillén J. Preprint DOI: 10.12688/f1000research.23780.1
*
Secreted inhibitors drive the loss of regeneration competence in Xenopus limbs
Aztekin C, Hiscock TW, Gurdon JB, Jullien J, Marioni JC, Simons BD. Preprint DOI: 10.1101/2020.06.01.127654
Using Reactome to build an autophagy mechanism knowledgebase.
Varusai TM, Jupe S, Sevilla C, Matthews L, Gillespie M, Stein L, Wu G, D'Eustachio P, Metzakopian E, Hermjakob H. Autophagy (2020) p.1-12 DOI: 10.1080/15548627.2020.1761659
*
INSIGHT: a population scale COVID-19 testing strategy combining point-of-care diagnosis with centralised high-throughput sequencing
Wu Q, Suo C, Brown T, Wang T, Teichmann SA, Bassett AR. Preprint DOI: 10.1101/2020.06.01.127019
*
Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies.
Eduati F, Jaaks P, Wappler J, Cramer T, Merten CA, Garnett MJ, Saez-Rodriguez J. Molecular systems biology Volume 16 (2020) p.e9690 DOI: 10.15252/msb.209690
An improved pig reference genome sequence to enable pig genetics and genomics research.
Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, Girón CG, Griffin DK, Hall R, Hannum G, Hourlier T, Howe K, Hume DA, Izuogu O, Kim K, Koren S, Liu H, Manchanda N, Martin FJ, Nonneman DJ, O'Connor RE, Phillippy AM, Rohrer GA, Rosen BD, Rund LA, Sargent CA, Schook LB, Schroeder SG, Schwartz AS, Skinner BM, Talbot R, Tseng E, Tuggle CK, Watson M, Smith TPL, Archibald AL. GigaScience Volume 9 (2020) DOI: 10.1093/gigascience/giaa051
*
Corrigendum: OMA standalone: orthology inference among public and custom genomes and transcriptomes
Altenhoff A, Levy J, Zarowiecki M, Tomiczek B, Vesztrocy A, Dalquen D, Müller S, Telford M, Glover N, Dylus D, Dessimoz C. Genome research Volume 30 (2020) p.9382-9382
GlyGen data model and processing workflow.
Kahsay R, Vora J, Navelkar R, Mousavi R, Fochtman BC, Holmes X, Pattabiraman N, Ranzinger R, Mahadik R, Williamson T, Kulkarni S, Agarwal G, Martin M, Vasudev P, Garcia L, Edwards N, Zhang W, Natale DA, Ross K, Aoki-Kinoshita KF, Campbell MP, York WS, Mazumder R. Bioinformatics (Oxford, England) Volume 36 (2020) p.3941-3943 DOI: 10.1093/bioinformatics/btaa238
Unraveling tumor-immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy.
Jiménez-Sánchez A, Cybulska P, Mager KL, Koplev S, Cast O, Couturier DL, Memon D, Selenica P, Nikolovski I, Mazaheri Y, Bykov Y, Geyer FC, Macintyre G, Gavarró LM, Drews RM, Gill MB, Papanastasiou AD, Sosa RE, Soslow RA, Walther T, Shen R, Chi DS, Park KJ, Hollmann T, Reis-Filho JS, Markowetz F, Beltrao P, Vargas HA, Zamarin D, Brenton JD, Snyder A, Weigelt B, Sala E, Miller ML. Nature genetics Volume 52 (2020) p.582-593 DOI: 10.1038/s41588-020-0630-5
*
Metabolic control of tumour extracellular matrix production in cancer-associated fibroblasts
Kay EJ, Paterson K, Sumpton D, Stepanova E, Boldrini C, Hernandez-Fernaud JR, Dhayade S, Gjerga E, Shaw R, Neilson LJ, Koulouras G, McGregor G, Lilla S, Jamieson C, Hedley A, Johnson RM, Park M, Miller C, Kamphorst JJ, Loayza-Puch F, Saez-Rodriguez J, Blyth K, Zagnoni M, Zanivan S. Preprint DOI: 10.1101/2020.05.30.125237
*
LINE elements are a reservoir of regulatory potential in mammalian genomes
Roller M, Stamper E, Villar D, Izuogu O, Martin F, Redmond A, Ramachanderan R, Harewood L, Odom DT, Flicek P. Preprint DOI: 10.1101/2020.05.31.126169
*
The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues.
Muyas F, Zapata L, Guigó R, Ossowski S. Genome medicine Volume 12 (2020) p.49 DOI: 10.1186/s13073-020-00746-1
*
Evaluating drug targets through human loss-of-function genetic variation.
Minikel EV, Karczewski KJ, Martin HC, Cummings BB, Whiffin N, Rhodes D, Alföldi J, Trembath RC, van Heel DA, Daly MJ, Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Schreiber SL, MacArthur DG. Nature Volume 581 (2020) p.459-464 DOI: 10.1038/s41586-020-2267-z
*
Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes.
Wang Q, Pierce-Hoffman E, Cummings BB, Alföldi J, Francioli LC, Gauthier LD, Hill AJ, O'Donnell-Luria AH, Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Karczewski KJ, MacArthur DG. Nature communications Volume 11 (2020) p.2539 DOI: 10.1038/s41467-019-12438-5
*
Characterising the loss-of-function impact of 5' untranslated region variants in 15,708 individuals.
Whiffin N, Karczewski KJ, Zhang X, Chothani S, Smith MJ, Evans DG, Roberts AM, Quaife NM, Schafer S, Rackham O, Alföldi J, O'Donnell-Luria AH, Francioli LC, Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Cook SA, Barton PJR, MacArthur DG, Ware JS. Nature communications Volume 11 (2020) p.2523 DOI: 10.1038/s41467-019-10717-9
*
A structural variation reference for medical and population genetics.
Collins RL, Brand H, Karczewski KJ, Zhao X, Alföldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H, Watts NA, Solomonson M, O'Donnell-Luria A, Baumann A, Munshi R, Walker M, Whelan CW, Huang Y, Brookings T, Sharpe T, Stone MR, Valkanas E, Fu J, Tiao G, Laricchia KM, Ruano-Rubio V, Stevens C, Gupta N, Cusick C, Margolin L, Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Taylor KD, Lin HJ, Rich SS, Post WS, Chen YI, Rotter JI, Nusbaum C, Philippakis A, Lander E, Gabriel S, Neale BM, Kathiresan S, Daly MJ, Banks E, MacArthur DG, Talkowski ME. Nature Volume 581 (2020) p.444-451 DOI: 10.1038/s41586-020-2287-8
*
Exploring amino acid functions in a deep mutational landscape
Dunham A, Beltrao P. Preprint DOI: 10.1101/2020.05.26.116756
*
Transcript expression-aware annotation improves rare variant interpretation.
Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH, Poterba T, Seed C, Solomonson M, Alföldi J, Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Daly MJ, MacArthur DG. Nature Volume 581 (2020) p.452-458 DOI: 10.1038/s41586-020-2329-2
*
Sex and Power: sexual dimorphism in trait variability and its eco-evolutionary and statistical implications
Zajitschek S, Zajitschek F, Bonduriansky R, Brooks R, Cornwell W, Falster D, Lagisz M, Mason J, Senior AM, Noble DAW, Nakagawa S. Preprint DOI: 10.1101/2020.05.23.106146
*
A Consensus Transcriptional Landscape of Human End-Stage Heart Failure
Flores ROR, Lanzer JD, Holland CH, Leuschner F, Most P, Schultz J, Levinson RT, Saez-Rodriguez J. Preprint DOI: 10.1101/2020.05.23.20110858
*
The Polygenic Score Catalog: an open database for reproducibility and systematic evaluation
Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, Abraham G, Chapman M, Parkinson H, Danesh J, MacArthur JA, Inouye M. Preprint DOI: 10.1101/2020.05.20.20108217
*
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, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Lee C, Ko BJ, Kim J, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan C, Burt D, George JM, Biegler M, Iorns D, Digby A, Eason D, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW, Svardal H, Wagner M, Naylor GJ, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Korlach J, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, 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 RH, Lewin H, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli K, Shapiro B, Johnson WE, Di Palma F, Margues-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Hausler D, O’Brien SJ, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Preprint DOI: 10.1101/2020.05.22.110833
*
Integrated cross-study datasets of genetic dependencies in cancer
Pacini C, Dempster JM, Boyle I, Gonçalves E, Najgebauer H, Karakoc E, van der Meer D, Barthorpe A, Lightfoot H, Jaaks P, McFarland JM, Garnett MJ, Tsherniak A, Iorio F. Preprint DOI: 10.1101/2020.05.22.110247
*
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 A, 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 E, O'Toole ÁN, Palacios-Ontiveros N, Petrov AI, Rangel-Piñeros 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. Preprint DOI: 10.20944/preprints202005.0376.v1
*
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
Jerber J, Seaton D, Cuomo A, Kumasaka N, Haldane J, Steer J, Patel M, Pearce D, Andersson M, Bonder M, Mountjoy E, Ghoussaini M, Lancaster M, Marioni J, Merkle F, Stegle O, Gaffney D, HipSci Consortium. Preprint DOI: 10.1101/2020.05.21.103820
Identification of male heterogametic sex-determining regions on the Atlantic herring Clupea harengus genome.
Í Kongsstovu S, Dahl HA, Gislason H, Homrum E, Jacobsen JA, Flicek P, Mikalsen SO. Journal of fish biology Volume 97 (2020) p.190-201 DOI: 10.1111/jfb.14349
*
De Novo SOX6 Variants Cause a Neurodevelopmental Syndrome Associated with ADHD, Craniosynostosis, and Osteochondromas.
Tolchin D, Yeager JP, Prasad P, Dorrani N, Russi AS, Martinez-Agosto JA, Haseeb A, Angelozzi M, Santen GWE, Ruivenkamp C, Mercimek-Andrews S, Depienne C, Kuechler A, Mikat B, Ludecke HJ, Bilan F, Le Guyader G, Gilbert-Dussardier B, Keren B, Heide S, Haye D, Van Esch H, Keldermans L, Ortiz D, Lancaster E, Krantz ID, Krock BL, Pechter KB, Arkader A, Medne L, DeChene ET, Calpena E, Melistaccio G, Wilkie AOM, Suri M, Foulds N, Genomics England Research Consortium, Begtrup A, Henderson LB, Forster C, Reed P, McDonald MT, McConkie-Rosell A, Thevenon J, Le Tanno P, Coutton C, Tsai ACH, Stewart S, Maver A, Gorazd R, Pichon O, Nizon M, Cogné B, Isidor B, Martin-Coignard D, Stoeva R, Lefebvre V, Le Caignec C. American journal of human genetics Volume 106 (2020) p.830-845 DOI: 10.1016/j.ajhg.2020.04.015
Ten simple rules for making training materials FAIR.
Garcia L, Batut B, Burke ML, Kuzak M, Psomopoulos F, Arcila R, Attwood TK, Beard N, Carvalho-Silva D, Dimopoulos AC, Del Angel VD, Dumontier M, Gurwitz KT, Krause R, McQuilton P, Le Pera L, Morgan SL, Rauste P, Via A, Kahlem P, Rustici G, van Gelder CWG, Palagi PM. PLoS computational biology Volume 16 (2020) p.e1007854 DOI: 10.1371/journal.pcbi.1007854
*
PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection
Hölzer M, Marz M. Preprint DOI: 10.1101/2020.05.18.102731
Putative cell type discovery from single-cell gene expression data.
Miao Z, Moreno P, Huang N, Papatheodorou I, Brazma A, Teichmann SA. Nature methods Volume 17 (2020) p.621-628 DOI: 10.1038/s41592-020-0825-9
Progress, Challenges, and Surprises in Annotating the Human Genome.
Zerbino DR, Frankish A, Flicek P. Annual review of genomics and human genetics Volume 21 (2020) p.55-79 DOI: 10.1146/annurev-genom-121119-083418
Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium.
Colom B, Alcolea MP, Piedrafita G, Hall MWJ, Wabik A, Dentro SC, Fowler JC, Herms A, King C, Ong SH, Sood RK, Gerstung M, Martincorena I, Hall BA, Jones PH. Nature genetics Volume 52 (2020) p.604-614 DOI: 10.1038/s41588-020-0624-3
*
OpenStats: A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput Phenotypic Data
Haselimashhadi H, Mason JC, Mallon A, Smedley D, Meehan TF, Parkinson H. Preprint DOI: 10.1101/2020.05.13.091157
*
Repeated global migrations on different plant hosts by the tropical pathogenPhytophthora palmivora
Wang J, Coffey MD, De Maio N, Goss EM. Preprint DOI: 10.1101/2020.05.13.093211
*
EpiDope: A Deep neural network for linear B-cell epitope prediction
Collatz M, Mock F, Hölzer M, Barth E, Sachse K, Marz M. Preprint DOI: 10.1101/2020.05.12.090019
*
Tara Oceans: towards global ocean ecosystems biology.
Sunagawa S, Acinas SG, Bork P, Bowler C, Tara Oceans Coordinators, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C. Nature reviews. Microbiology Volume 18 (2020) p.428-445 DOI: 10.1038/s41579-020-0364-5
*
Calcification of abdominal aorta is an underappreciated cardiovascular disease risk factor
Sethi A, Taylor L, Ruby JG, Venkataraman J, Cule M, Melamud E. Preprint DOI: 10.1101/2020.05.07.20094706
Effects of the COVID-19 pandemic on life scientists.
Korbel JO, Stegle O. Genome biology Volume 21 (2020) p.113 DOI: 10.1186/s13059-020-02031-1
Dysregulation at multiple points of the kynurenine pathway is a ubiquitous feature of renal cancer: implications for tumour immune evasion.
Hornigold N, Dunn KR, Craven RA, Zougman A, Trainor S, Shreeve R, Brown J, Sewell H, Shires M, Knowles M, Fukuwatari T, Maher ER, Burns J, Bhattarai S, Menon M, Brazma A, Scelo G, Feulner L, Riazalhosseini Y, Lathrop M, Harris A, Selby PJ, Banks RE, Vasudev NS. British journal of cancer Volume 123 (2020) p.137-147 DOI: 10.1038/s41416-020-0874-y
*
CEN-tools: An integrative platform to identify the ‘contexts’ of essential genes
Sharma S, Dincer C, Weidemüller P, Wright GJ, Petsalaki E. Preprint DOI: 10.1101/2020.05.10.087668
MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data.
Argelaguet R, Arnol D, Bredikhin D, Deloro Y, Velten B, Marioni JC, Stegle O. Genome biology Volume 21 (2020) p.111 DOI: 10.1186/s13059-020-02015-1
*
Explainable multi-view framework for dissecting inter-cellular signaling from highly multiplexed spatial data
Tanevski J, Gabor A, Flores ROR, Schapiro D, Saez-Rodriguez J. Preprint DOI: 10.1101/2020.05.08.084145
*
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, De Maio N, Faria NR, Hadfield J, Hayette M, Bours V, Wawina-Bokalanga T, Artesi M, Baele G, Maes P. Preprint DOI: 10.1101/2020.05.05.078758
*
Improving reporting standards for polygenic scores in risk prediction studies
Wand H, Lambert SA, Tamburro C, Iacocca MA, O’Sullivan JW, Sillari C, Kullo IJ, Rowley R, Dron JS, Brockman D, Venner E, McCarthy MI, Antoniou AC, Easton DF, Hegele RA, Khera AV, Chatterjee N, Kooperberg C, Edwards K, Vlessis K, Kinnear K, Danesh JN, Parkinson H, Ramos EM, Roberts MC, Ormond KE, Khoury MJ, Janssens ACJ, Goddard KA, Kraft P, MacArthur JAL, Inouye M, Wojcik G. Preprint DOI: 10.1101/2020.04.23.20077099
*
A phenome-wide association and Mendelian Randomisation study of polygenic risk for depression in UK Biobank.
Shen X, Howard DM, Adams MJ, Hill WD, Clarke TK, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Deary IJ, Whalley HC, McIntosh AM. Nature communications Volume 11 (2020) p.2301 DOI: 10.1038/s41467-020-16022-0
*
Exploring the conformational space of a receptor for drug design: an ERα case study
Schneider M, Pons J, Labesse G. Preprint DOI: 10.1101/2020.05.06.081000
*
Whole-genome sequencing of a sporadic primary immunodeficiency cohort.
Thaventhiran JED, Lango Allen H, Burren OS, Rae W, Greene D, Staples E, Zhang Z, Farmery JHR, Simeoni I, Rivers E, Maimaris J, Penkett CJ, Stephens J, Deevi SVV, Sanchis-Juan A, Gleadall NS, Thomas MJ, Sargur RB, Gordins P, Baxendale HE, Brown M, Tuijnenburg P, Worth A, Hanson S, Linger RJ, Buckland MS, Rayner-Matthews PJ, Gilmour KC, Samarghitean C, Seneviratne SL, Sansom DM, Lynch AG, Megy K, Ellinghaus E, Ellinghaus D, Jorgensen SF, Karlsen TH, Stirrups KE, Cutler AJ, Kumararatne DS, Chandra A, Edgar JDM, Herwadkar A, Cooper N, Grigoriadou S, Huissoon AP, Goddard S, Jolles S, Schuetz C, Boschann F, Primary Immunodeficiency Consortium for the NIHR Bioresource, Lyons PA, Hurles ME, Savic S, Burns SO, Kuijpers TW, Turro E, Ouwehand WH, Thrasher AJ, Smith KGC. Nature Volume 583 (2020) p.90-95 DOI: 10.1038/s41586-020-2265-1
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.
Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R, Schneider R. Scientific data Volume 7 (2020) p.136 DOI: 10.1038/s41597-020-0477-8
*
Chromosomal arrangement of synthetic lethal gene pairs: repulsion or attraction?
Hosseini S, Wadie B, Petsalaki E. Preprint DOI: 10.1101/2020.05.05.078626
*
A statistical framework for assessing pharmacological response and biomarkers using uncertainty estimates
Wang D, Hensman J, Kutkaite G, Toh TS, Dry JR, Saez-Rodriguez J, Garnett MJ, Menden MP, Dondelinger F, GDSC Screening Team. Preprint DOI: 10.1101/2020.05.01.072983
*
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 S, Iversen R, Sollid LM. Preprint DOI: 10.1101/2020.04.30.058560
Prediction of Signed Protein Kinase Regulatory Circuits.
Invergo BM, Petursson B, Akhtar N, Bradley D, Giudice G, Hijazi M, Cutillas P, Petsalaki E, Beltrao P. Cell systems Volume 10 (2020) p.384-396.e9 DOI: 10.1016/j.cels.2020.04.005
*
Issues with SARS-CoV-2 sequencing data
De Maio N, Walker C, Borges R, Weilguny L, Slodkowicz G, Goldman N. Preprint
*
Masking strategies for SARS-CoV-2 alignments
De Maio N, Walker C, Borges R, Weilguny L, Slodkowicz G, Goldman N. Preprint
Mutational signatures are jointly shaped by DNA damage and repair.
Volkova NV, Meier B, González-Huici V, Bertolini S, Gonzalez S, Vöhringer H, Abascal F, Martincorena I, Campbell PJ, Gartner A, Gerstung M. Nature communications Volume 11 (2020) p.2169 DOI: 10.1038/s41467-020-15912-7
The open targets post-GWAS analysis pipeline.
Peat G, Jones W, Nuhn M, Marugán JC, Newell W, Dunham I, Zerbino D. Bioinformatics (Oxford, England) Volume 36 (2020) p.2936-2937 DOI: 10.1093/bioinformatics/btaa020
CELLector: Genomics-Guided Selection of Cancer In Vitro Models.
Najgebauer H, Yang M, Francies HE, Pacini C, Stronach EA, Garnett MJ, Saez-Rodriguez J, Iorio F. Cell systems Volume 10 (2020) p.424-432.e6 DOI: 10.1016/j.cels.2020.04.007
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. Nature Volume 583 (2020) p.459-468 DOI: 10.1038/s41586-020-2286-9
*
Data Forensic Determination of the Accuracy of International COVID-19 Reporting: Using Zipf's Law for Pandemic Investigation
Iorliam A, Ho AT, Tirunagari S, Windridge D. Preprint DOI: 10.20944/preprints202004.0531.v1
*
Antibody repertoire and gene expression dynamics of diverse human B cell states during affinity maturation
King HW, Orban N, Riches JC, Clear AJ, Warnes G, Teichmann SA, James LK. Preprint DOI: 10.1101/2020.04.28.054775
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.
Low WY, Tearle R, Liu R, Koren S, Rhie A, Bickhart DM, Rosen BD, Kronenberg ZN, Kingan SB, Tseng E, Thibaud-Nissen F, Martin FJ, Billis K, Ghurye J, Hastie AR, Lee J, Pang AWC, Heaton MP, Phillippy AM, Hiendleder S, Smith TPL, Williams JL. Nature communications Volume 11 (2020) p.2071 DOI: 10.1038/s41467-020-15848-y
Structural analysis of pathogenic missense mutations in GABRA2 and identification of a novel de novo variant in the desensitization gate.
Sanchis-Juan A, Hasenahuer MA, Baker JA, McTague A, Barwick K, Kurian MA, Duarte ST, NIHR BioResource, Carss KJ, Thornton J, Raymond FL. Molecular genetics & genomic medicine Volume 8 (2020) p.e1106 DOI: 10.1002/mgg3.1106
*
The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)
Touré V, Vercruysse S, Acencio ML, Lovering R, Orchard S, Bradley G, Casals-Casas C, Chaouiya C, del-Toro N, Flobak Å, Gaudet P, Hermjakob H, Licata L, Lægreid A, Mungall C, Niknejad A, Panni S, Perfetto L, Porras P, Pratt D, Thieffry D, Thomas P, Türei D, Saez-Rodriguez J, Kuiper M. Preprint DOI: 10.20944/preprints202004.0480.v1
*
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.
Ziegler CGK, Allon SJ, Nyquist SK, Mbano IM, Miao VN, Tzouanas CN, Cao Y, Yousif AS, Bals J, Hauser BM, Feldman J, Muus C, Wadsworth MH, Kazer SW, Hughes TK, Doran B, Gatter GJ, Vukovic M, Taliaferro F, Mead BE, Guo Z, Wang JP, Gras D, Plaisant M, Ansari M, Angelidis I, Adler H, Sucre JMS, Taylor CJ, Lin B, Waghray A, Mitsialis V, Dwyer DF, Buchheit KM, Boyce JA, Barrett NA, Laidlaw TM, Carroll SL, Colonna L, Tkachev V, Peterson CW, Yu A, Zheng HB, Gideon HP, Winchell CG, Lin PL, Bingle CD, Snapper SB, Kropski JA, Theis FJ, Schiller HB, Zaragosi LE, Barbry P, Leslie A, Kiem HP, Flynn JL, Fortune SM, Berger B, Finberg RW, Kean LS, Garber M, Schmidt AG, Lingwood D, Shalek AK, Ordovas-Montanes J, HCA Lung Biological Network. Electronic address: lung-network@humancellatlas.org, HCA Lung Biological Network. Cell Volume 181 (2020) p.1016-1035.e19 DOI: 10.1016/j.cell.2020.04.035
*
Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses
Dugourd A, Kuppe C, Sciacovelli M, Gjerga E, Emdal KB, Bekker-Jensen DB, Kranz J, Bindels EMJ, Costa ASH, Olsen JV, Frezza C, Kramann R, Saez-Rodriguez J. Preprint DOI: 10.1101/2020.04.23.057893
*
Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns
Wood V, Carbon S, Harris MA, Lock A, Engel SR, Hill DP, Van Auken K, Attrill H, Feuermann M, Gaudet P, Lovering RC, Poux S, Rutherford KM, Mungall CJ. Preprint DOI: 10.1101/2020.04.21.045195
*
SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes.
Sungnak W, Huang N, Bécavin C, Berg M, Queen R, Litvinukova M, Talavera-López C, Maatz H, Reichart D, Sampaziotis F, Worlock KB, Yoshida M, Barnes JL, HCA Lung Biological Network. Nature medicine Volume 26 (2020) p.681-687 DOI: 10.1038/s41591-020-0868-6
Sex chromosome evolution in parasitic nematodes of humans.
Foster JM, Grote A, Mattick J, Tracey A, Tsai YC, Chung M, Cotton JA, Clark TA, Geber A, Holroyd N, Korlach J, Li Y, Libro S, Lustigman S, Michalski ML, Paulini M, Rogers MB, Teigen L, Twaddle A, Welch L, Berriman M, Dunning Hotopp JC, Ghedin E. Nature communications Volume 11 (2020) p.1964 DOI: 10.1038/s41467-020-15654-6
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community).
Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, Wierenga R, Salminen T, Schneider B. F1000Research Volume 9 (2020) DOI: 10.12688/f1000research.20559.1
*
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)
Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AM, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, Wierenga R, Salminen T, Schneider B. Preprint DOI: 10.12688/f1000research.20559.1
*
Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
Muus C, Luecken MD, Eraslan G, Waghray A, Heimberg G, Sikkema L, Kobayashi Y, Vaishnav ED, Subramanian A, Smilie C, Jagadeesh K, 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, Samuel J, Andrusivova AZ, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Deprez M, Fischer DS, Gillich A, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Jaiswal A, Jiang P, Kapellos T, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Lu J, Ludwig LS, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Marquette C, Mbano I, McAdams AM, Metzger RJ, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp J, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith N, Sountoulidis A, Strunz M, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon K, Wadsworth MH, Waldman J, Wang X, Yan W, Zhao W, Ziegler CGK, The NHLBI LungMAP Consortium, The Human Cell Atlas Lung Biological Network. Preprint DOI: 10.1101/2020.04.19.049254
*
ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis
Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. Preprint DOI: 10.1101/2020.04.16.044958
*
GATA3 Mediates a Fast, Irreversible Commitment to BMP4-Driven Differentiation in Human Embryonic Stem Cells.
Gunne-Braden A, Sullivan A, Gharibi B, Sheriff RSM, Maity A, Wang YF, Edwards A, Jiang M, Howell M, Goldstone R, Wollman R, East P, Santos SDM. Cell stem cell Volume 26 (2020) p.693-706.e9 DOI: 10.1016/j.stem.2020.03.005
A unified nomenclature for vertebrate olfactory receptors.
Olender T, Jones TEM, Bruford E, Lancet D. BMC evolutionary biology Volume 20 (2020) p.42 DOI: 10.1186/s12862-020-01607-6
*
User-friendly, scalable tools and workflows for single-cell analysis
Moreno P, Huang N, Manning J, Mohammed S, Solovyev A, Polanski K, Chazarra R, Talavera-Lopez C, Doyle M, Marnier G, Grüning B, Rasche H, Bacon W, Perez-Riverol Y, Haeussler M, Meyer K, Teichmann S, Papatheodorou I. Preprint DOI: 10.1101/2020.04.08.032698
BlobToolKit - Interactive Quality Assessment of Genome Assemblies.
Challis R, Richards E, Rajan J, Cochrane G, Blaxter M. G3 (Bethesda, Md.) Volume 10 (2020) p.1361-1374 DOI: 10.1534/g3.119.400908
*
Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA in humans.
Wei W, Pagnamenta AT, Gleadall N, Sanchis-Juan A, Stephens J, Broxholme J, Tuna S, Odhams CA, Genomics England Research Consortium, NIHR BioResource, Fratter C, Turro E, Caulfield MJ, Taylor JC, Rahman S, Chinnery PF. Nature communications Volume 11 (2020) p.1740 DOI: 10.1038/s41467-020-15336-3
Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.
Mereu E, Lafzi A, Moutinho C, Ziegenhain C, McCarthy DJ, Álvarez-Varela A, Batlle E, Sagar, Grün D, Lau JK, Boutet SC, Sanada C, Ooi A, Jones RC, Kaihara K, Brampton C, Talaga Y, Sasagawa Y, Tanaka K, Hayashi T, Braeuning C, Fischer C, Sauer S, Trefzer T, Conrad C, Adiconis X, Nguyen LT, Regev A, Levin JZ, Parekh S, Janjic A, Wange LE, Bagnoli JW, Enard W, Gut M, Sandberg R, Nikaido I, Gut I, Stegle O, Heyn H. Nature biotechnology Volume 38 (2020) p.747-755 DOI: 10.1038/s41587-020-0469-4
*
Genomic and Phenotypic Analyses of Acinetobacter baumannii Isolates From Three Tertiary Care Hospitals in Thailand.
Loraine J, Heinz E, Soontarach R, Blackwell GA, Stabler RA, Voravuthikunchai SP, Srimanote P, Kiratisin P, Thomson NR, Taylor PW. Frontiers in microbiology Volume 11 (2020) p.548 DOI: 10.3389/fmicb.2020.00548
*
KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species
Hassani-Pak K, Singh A, Brandizi M, Hearnshaw J, Amberkar S, Phillips AL, Doonan JH, Rawlings C. Preprint DOI: 10.1101/2020.04.02.017004
Genomics of MPNST (GeM) Consortium: Rationale and Study Design for Multi-Omic Characterization of NF1-Associated and Sporadic MPNSTs.
Miller DT, Cortés-Ciriano I, Pillay N, Hirbe AC, Snuderl M, Bui MM, Piculell K, Al-Ibraheemi A, Dickson BC, Hart J, Jones K, Jordan JT, Kim RH, Lindsay D, Nishida Y, Ullrich NJ, Wang X, Park PJ, Flanagan AM. Genes Volume 11 (2020) DOI: 10.3390/genes11040387
Hotspots API: A Python Package for the Detection of Small Molecule Binding Hotspots and Application to Structure-Based Drug Design.
Curran PR, Radoux CJ, Smilova MD, Sykes RA, Higueruelo AP, Bradley AR, Marsden BD, Spring DR, Blundell TL, Leach AR, Pitt WR, Cole JC. Journal of chemical information and modeling Volume 60 (2020) p.1911-1916 DOI: 10.1021/acs.jcim.9b00996
*
Precursor intensity-based label-free quantification software tools for proteomic and multiomic analysis within the Galaxy Platform
Mehta S, Easterly C, Sajulga R, Millikin RJ, Argentini A, Eguinoa I, Martens L, Shortreed MR, Smith LM, McGowan T, Kumar P, Johnson JE, Griffin TJ, Jagtap P. Preprint DOI: 10.1101/2020.04.01.003988
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases.
Chen Q, Britto R, Erill I, Jeffery CJ, Liberzon A, Magrane M, Onami JI, Robinson-Rechavi M, Sponarova J, Zobel J, Verspoor K. Genomics, proteomics & bioinformatics Volume 18 (2020) p.91-103 DOI: 10.1016/j.gpb.2018.11.006
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences.
Drysdale R, Cook CE, Petryszak R, Baillie-Gerritsen V, Barlow M, Gasteiger E, Gruhl F, Haas J, Lanfear J, Lopez R, Redaschi N, Stockinger H, Teixeira D, Venkatesan A, Elixir Core Data Resource Forum, Blomberg N, Durinx C, McEntyre J. Bioinformatics (Oxford, England) Volume 36 (2020) p.2636-2642 DOI: 10.1093/bioinformatics/btz959
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.
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 AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Sheriff RSM, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. Nature biotechnology Volume 38 (2020) p.504 DOI: 10.1038/s41587-020-0477-4
*
CD8+ T-cell transcription and DNA methylation show age specific differences and lack correlation with clinical outcome in pediatric Inflammatory Bowel Disease
Gasparetto M, Payne F, Nayak K, Kraiczy J, Glemas C, Philip-McKenzie Y, Ross A, Edgar R, Zerbino D, Salvestrini C, Torrente F, Sarkies P, Heuschkel R, Zilbauer M. Preprint DOI: 10.1101/2020.03.30.015446
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 BÁ, Pakseresht N, Rossello M, Silvester N, Amid C, Aarestrup FM, Koopmans M, Cochrane G, Csabai I, Lund O, Schultsz C, The Compare Ml-Amr Group. Microbial genomics Volume 6 (2020) DOI: 10.1099/mgen.0.000342
*
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets
Marchet C, Iqbal Z, Gautheret D, Salson M, Chikhi R. Preprint DOI: 10.1101/2020.03.29.014159
*
DeepLC can predict retention times for peptides that carry as-yet unseen modifications
Bouwmeester R, Gabriels R, Hulstaert N, Martens L, Degroeve S. Preprint DOI: 10.1101/2020.03.28.013003
A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat.
Adamski NM, Borrill P, Brinton J, Harrington SA, 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, Maccaferrri M, Naamati G, Pozniak CJ, Ramirez-Gonzalez RH, Sansaloni C, Trevaskis B, Wingen LU, Wulff BB, Uauy C. eLife Volume 9 (2020) DOI: 10.7554/elife.55646
Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions.
Müller PM, Rademacher J, Bagshaw RD, Wortmann C, Barth C, van Unen J, Alp KM, Giudice G, Eccles RL, Heinrich LE, Pascual-Vargas P, Sanchez-Castro M, Brandenburg L, Mbamalu G, Tucholska M, Spatt L, Czajkowski MT, Welke RW, Zhang S, Nguyen V, Rrustemi T, Trnka P, Freitag K, Larsen B, Popp O, Mertins P, Gingras AC, Roth FP, Colwill K, Bakal C, Pertz O, Pawson T, Petsalaki E, Rocks O. Nature cell biology Volume 22 (2020) p.498-511 DOI: 10.1038/s41556-020-0488-x
*
Molecular Analyses of Over Hundred Sixty Clinical Isolates of SARS-CoV-2: Insights on Likely Origin, Evolution and Spread, and Possible Intervention
Jamal S, Singh J, Sheikh JA, Singh H, Khubaib M, Kohli S, Dobrindt U, Rahman SA, Ehtesham NZ, Hasnain SE. Preprint DOI: 10.20944/preprints202003.0320.v1
Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.
Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, HipSci Consortium, Vallier L, Marioni JC, Chhatriwala M, Stegle O. Nature communications Volume 11 (2020) p.1572 DOI: 10.1038/s41467-020-15098-y
*
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O’Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJ, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, Zastrow Mv, Taunton J, Schwartz O, Vignuzzi M, d’Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. Preprint DOI: 10.1101/2020.03.22.002386
*
Pitfalls in re-analysis of observational omics studies: a post-mortem of the human pathology atlas
Gilis J, Taelman S, Davey L, Martens L, Clement L. Preprint DOI: 10.1101/2020.03.16.994038
Wikidata as a knowledge graph for the life sciences.
Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith OL, Hanspers K, Hermjakob H, Hudson TS, 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. eLife Volume 9 (2020) DOI: 10.7554/elife.52614
Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.
McCarthy DJ, Rostom R, Huang Y, Kunz DJ, Danecek P, Bonder MJ, Hagai T, Lyu R, HipSci Consortium, Wang W, Gaffney DJ, Simons BD, Stegle O, Teichmann SA. Nature methods Volume 17 (2020) p.414-421 DOI: 10.1038/s41592-020-0766-3
Modeling protein interactions and complexes in CAPRI: Seventh CAPRI evaluation meeting, April 3-5 EMBL-EBI, Hinxton, UK.
Wodak SJ, Velankar S, Sternberg MJE. Proteins Volume 88 (2020) p.913-915 DOI: 10.1002/prot.25883
Phosphoproteomics identifies a bimodal EPHA2 receptor switch that promotes embryonic stem cell differentiation.
Fernandez-Alonso R, Bustos F, Budzyk M, Kumar P, Helbig AO, Hukelmann J, Lamond AI, Lanner F, Zhou H, Petsalaki E, Findlay GM. Nature communications Volume 11 (2020) p.1357 DOI: 10.1038/s41467-020-15173-4
*
Efficient and Flexible Integration of Variant Characteristics in Rare Variant Association Studies Using Integrated Nested Laplace Approximation
Susak H, Serra-Saurina L, Janssen RR, Domènech L, Bosio M, Muyas F, Estivill X, Escaramís G, Ossowski S. Preprint DOI: 10.1101/2020.03.12.988584
*
Genomic loci susceptible to systematic sequencing bias in clinical whole genomes.
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
Temporal changes in the gene expression heterogeneity during brain development and aging.
Işıldak U, Somel M, Thornton JM, Dönertaş HM. Scientific reports Volume 10 (2020) p.4080 DOI: 10.1038/s41598-020-60998-0
*
Converting networks to predictive logic models from perturbation signalling data with CellNOpt
Gjerga E, Trairatphisan P, Gabor A, Koch H, Chevalier C, Ceccarelli F, Dugourd A, Mitsos A, Saez-Rodriguez J. Preprint DOI: 10.1101/2020.03.04.976852
*
Motif analysis in co-expression networks reveals regulatory elements in plants: The peach as a model
Ksouri N, Castro-Mondragón JA, Montardit-Tardà F, van Helden J, Contreras-Moreira B, Gogorcena Y. Preprint DOI: 10.1101/2020.02.28.970137
Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals.
Slodkowicz G, Goldman N. Proceedings of the National Academy of Sciences of the United States of America Volume 117 (2020) p.5977-5986 DOI: 10.1073/pnas.1916786117
Soft windowing application to improve analysis of high-throughput phenotyping data.
Haselimashhadi H, Mason JC, Munoz-Fuentes V, López-Gómez F, Babalola K, Acar EF, Kumar V, White J, Flenniken AM, King R, Straiton E, Seavitt JR, Gaspero A, Garza A, Christianson AE, Hsu CW, Reynolds CL, Lanza DG, Lorenzo I, Green JR, Gallegos JJ, Bohat R, Samaco RC, Veeraragavan S, Kim JK, Miller G, Fuchs H, Garrett L, Becker L, Kang YK, Clary D, Cho SY, Tamura M, Tanaka N, Soo KD, Bezginov A, About GB, Champy MF, Vasseur L, Leblanc S, Meziane H, Selloum M, Reilly PT, Spielmann N, Maier H, Gailus-Durner V, Sorg T, Hiroshi M, Yuichi O, Heaney JD, Dickinson ME, Wolfgang W, Tocchini-Valentini GP, Lloyd KCK, McKerlie C, Seong JK, Yann H, de Angelis MH, Brown SDM, Smedley D, Flicek P, Mallon AM, Parkinson H, Meehan TF. Bioinformatics (Oxford, England) Volume 36 (2020) p.1492-1500 DOI: 10.1093/bioinformatics/btz744
Differential evolution in 3'UTRs leads to specific gene expression in Staphylococcus.
Menendez-Gil P, Caballero CJ, Catalan-Moreno A, Irurzun N, Barrio-Hernandez I, Caldelari I, Toledo-Arana A. Nucleic acids research Volume 48 (2020) p.2544-2563 DOI: 10.1093/nar/gkaa047
*
Enzyme annotation in UniProtKB using Rhea.
Morgat A, Lombardot T, Coudert E, Axelsen K, Neto TB, Gehant S, Bansal P, Bolleman J, Gasteiger E, de Castro E, Baratin D, Pozzato M, Xenarios I, Poux S, Redaschi N, Bridge A, UniProt Consortium. Bioinformatics (Oxford, England) Volume 36 (2020) p.1896-1901 DOI: 10.1093/bioinformatics/btz817
*
Interim 2019/20 influenza vaccine effectiveness: six European studies, September 2019 to January 2020.
Rose A, Kissling E, Emborg HD, Larrauri A, McMenamin J, Pozo F, Trebbien R, Mazagatos C, Whitaker H, Valenciano M, European IVE group. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin Volume 25 (2020) DOI: 10.2807/1560-7917.es.2020.25.10.2000153
MEMOTE for standardized genome-scale metabolic model testing.
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 AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Malik Sheriff RS, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. Nature biotechnology Volume 38 (2020) p.272-276 DOI: 10.1038/s41587-020-0446-y
*
Microbiota Characterization of Agricultural Green Waste-Based Suppressive Composts Using Omics and Classic Approaches
Scotti R, Mitchell AL, Pane C, Finn RD, Zaccardelli M. Agriculture Volume 10 (2020) p.61 DOI: 10.3390/agriculture10030061
*
Genomic copy number predicts oesophageal cancer years before transformation
Killcoyne S, Gregson E, Wedge DC, Woodcock DJ, Eldridge M, de la Rue R, Miremadi A, Abbas S, Blasko A, Januszewicz W, Varanou Jenkins A, Gerstung M, Fitzgerald RC. Preprint DOI: 10.1101/2020.02.27.967612
*
Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli.
Pleguezuelos-Manzano C, Puschhof J, Rosendahl Huber A, van Hoeck A, Wood HM, Nomburg J, Gurjao C, Manders F, Dalmasso G, Stege PB, Paganelli FL, Geurts MH, Beumer J, Mizutani T, Miao Y, van der Linden R, van der Elst S, Genomics England Research Consortium, Garcia KC, Top J, Willems RJL, Giannakis M, Bonnet R, Quirke P, Meyerson M, Cuppen E, van Boxtel R, Clevers H. Nature Volume 580 (2020) p.269-273 DOI: 10.1038/s41586-020-2080-8
*
Tumour gene expression signature in primary melanoma predicts long-term outcomes: A prospective multicentre study
Garg M, Couturier D, Nsengimana J, Fonseca NA, Wongchenko M, Yan Y, Lauss M, Jönsson GB, Newton-Bishop J, Parkinson C, Middleton MR, Bishop T, Corrie P, Adams DJ, Brazma A, Rabbie R. Preprint DOI: 10.1101/2020.02.24.961771
BioHackathon 2015: Semantics of data for life sciences and reproducible research.
Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, Bolleman JT, Bolton E, Bonnal RJP, Bono H, Burger K, Chiba H, Cohen KB, Deutsch EW, Fernández-Breis JT, Fu G, Fujisawa T, Fukushima A, García A, Goto N, Groza T, Hercus C, Hoehndorf R, Itaya K, Juty N, Kawashima T, Kim JH, Kinjo AR, Kotera M, Kozaki K, Kumagai S, Kushida T, Lütteke T, Matsubara M, Miyamoto J, Mohsen A, Mori H, Naito Y, Nakazato T, Nguyen-Xuan J, Nishida K, Nishida N, Nishide H, Ogishima S, Ohta T, Okuda S, Paten B, Perret JL, Prathipati P, Prins P, Queralt-Rosinach N, Shinmachi D, Suzuki S, Tabata T, Takatsuki T, Taylor K, Thompson M, Uchiyama I, Vieira B, Wei CH, Wilkinson M, Yamada I, Yamanaka R, Yoshitake K, Yoshizawa AC, Dumontier M, Kosaki K, Takagi T. F1000Research Volume 9 (2020) p.136 DOI: 10.12688/f1000research.18236.1
*
BioHackathon 2015: Semantics of data for life sciences and reproducible research
Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim J, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, Bolleman JT, Bolton E, Bonnal RJP, Bono H, Burger K, Chiba H, Cohen KB, Deutsch EW, Fernández-Breis JT, Fu G, Fujisawa T, Fukushima A, García A, Goto N, Groza T, Hercus C, Hoehndorf R, Itaya K, Juty N, Kawashima T, Kim J, Kinjo AR, Kotera M, Kozaki K, Kumagai S, Kushida T, Lütteke T, Matsubara M, Miyamoto J, Mohsen A, Mori H, Naito Y, Nakazato T, Nguyen-Xuan J, Nishida K, Nishida N, Nishide H, Ogishima S, Ohta T, Okuda S, Paten B, Perret J, Prathipati P, Prins P, Queralt-Rosinach N, Shinmachi D, Suzuki S, Tabata T, Takatsuki T, Taylor K, Thompson M, Uchiyama I, Vieira B, Wei C, Wilkinson M, Yamada I, Yamanaka R, Yoshitake K, Yoshizawa AC, Dumontier M, Kosaki K, Takagi T. Preprint DOI: 10.12688/f1000research.18236.1
*
Widespread patterns of gene loss in the evolution of the animal kingdom.
Guijarro-Clarke C, Holland PWH, Paps J. Nature ecology & evolution Volume 4 (2020) p.519-523 DOI: 10.1038/s41559-020-1129-2
*
A unified nomenclature for vertebrate olfactory receptors
Olender T, Jones TE, Bruford E, Lancet D. Preprint DOI: 10.21203/rs.2.14887/v2
*
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. Preprint DOI: 10.1101/2020.02.18.954057
Comparison of sequencing methods and data processing pipelines for whole genome sequencing and minority single nucleotide variant (mSNV) analysis during an influenza A/H5N8 outbreak.
Poen MJ, Pohlmann A, Amid C, Bestebroer TM, Brookes SM, Brown IH, Everett H, Schapendonk CME, Scheuer RD, Smits SL, Beer M, Fouchier RAM, Ellis RJ. PloS one Volume 15 (2020) p.e0229326 DOI: 10.1371/journal.pone.0229326
*
Extensive genomic and transcriptomic variation defines the chromosome-scale assembly ofHaemonchus contortus, a model gastrointestinal worm
Doyle SR, Tracey A, Laing R, Holroyd N, Bartley D, Bazant W, Beasley H, Beech R, Britton C, Brooks K, Chaudhry U, Maitland K, Martinelli A, Noonan JD, Paulini M, Quail MA, Redman E, Rodgers FH, Sallé G, Shabbir MZ, Sankaranarayanan G, Wit J, Howe KL, Sargison N, Devaney E, Berriman M, Gilleard JS, Cotton JA. Preprint DOI: 10.1101/2020.02.18.945246
Towards a European health research and innovation cloud (HRIC).
Aarestrup FM, Albeyatti A, Armitage WJ, Auffray C, Augello L, Balling R, Benhabiles N, Bertolini G, Bjaalie JG, Black M, Blomberg N, Bogaert P, Bubak M, Claerhout B, Clarke L, De Meulder B, D'Errico G, Di Meglio A, Forgo N, Gans-Combe C, Gray AE, Gut I, Gyllenberg A, Hemmrich-Stanisak G, Hjorth L, Ioannidis Y, Jarmalaite S, Kel A, Kherif F, Korbel JO, Larue C, Laszlo M, Maas A, Magalhaes L, Manneh-Vangramberen I, Morley-Fletcher E, Ohmann C, Oksvold P, Oxtoby NP, Perseil I, Pezoulas V, Riess O, Riper H, Roca J, Rosenstiel P, Sabatier P, Sanz F, Tayeb M, Thomassen G, Van Bussel J, Van den Bulcke M, Van Oyen H. Genome medicine Volume 12 (2020) p.18 DOI: 10.1186/s13073-020-0713-z
*
Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri
Kenny NJ, Francis WR, Rivera-Vicéns RE, Juravel K, de Mendoza A, Díez-Vives C, Lister R, Bezares-Calderon L, Grombacher L, Roller M, Barlow LD, Camilli S, Ryan JF, Wörheide G, Hill AL, Riesgo A, Leys SP. Preprint DOI: 10.1101/2020.02.18.954784
*
Widespread targeting of development-related host transcription factors by phytoplasma effectors
Marrero MC, Capdevielle S, Huang W, Busscher M, Busscher-Lange J, de Ridder D, van Dijk AD, Hogenhout SA, Immink RG. Preprint DOI: 10.1101/2020.02.13.946517
Publisher Correction: Butler enables rapid cloud-based analysis of thousands of human genomes.
Yakneen S, Waszak SM, PCAWG Technical Working Group, Gertz M, Korbel JO, PCAWG Consortium. Nature biotechnology (2020) DOI: 10.1038/s41587-020-0448-9
Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit Using Difference Maps.
Joseph AP, Lagerstedt I, Jakobi A, Burnley T, Patwardhan A, Topf M, Winn M. Journal of chemical information and modeling Volume 60 (2020) p.2552-2560 DOI: 10.1021/acs.jcim.9b01103
*
The Omics Discovery REST interface
Dass G, Vu M, Xu P, Audain E, Hitz M, Hermjakob H, Perez-Riverol Y. Preprint DOI: 10.1101/2020.02.10.939967
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.
Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, HipSci Consortium, Vallier L, Marioni JC, Chhatriwala M, Stegle O. Nature communications Volume 11 (2020) p.810 DOI: 10.1038/s41467-020-14457-z
Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes.
Sundaram V, Wysocka J. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 375 (2020) p.20190347 DOI: 10.1098/rstb.2019.0347
*
Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis (MUFFIN)
Van Damme R, Hölzer M, Viehweger A, Müller B, Bongcam-Rudloff E, Brandt C. Preprint DOI: 10.1101/2020.02.08.939843
*
Freshwater monitoring by nanopore sequencing
Urban L, Holzer A, Baronas JJ, Hall M, Braeuninger-Weimer P, Scherm MJ, Kunz DJ, Perera SN, Martin-Herranz DE, Tipper ET, Salter SJ, Stammnitz MR. Preprint DOI: 10.1101/2020.02.06.936302
*
BOSS-RUNS: a flexible and practical dynamic read sampling framework for nanopore sequencing
De Maio N, Manser C, Munro R, Birney E, Loose M, Goldman N. Preprint DOI: 10.1101/2020.02.07.938670
Eleven grand challenges in single-cell data science.
Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Raczkowski L, Reinders M, Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A. Genome biology Volume 21 (2020) p.31 DOI: 10.1186/s13059-020-1926-6
*
Multi-organ transcriptomic landscape of Ambystoma velasci metamorphosis
Janet P, Juan C, Annie E, Gilberto M, Hilda L, Enrique S, Denhi S, Jesus C, Alfredo C. Preprint DOI: 10.1101/2020.02.06.937896
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, PCAWG Evolution & Heterogeneity Working Group, Spellman PT, Wedge DC, Van Loo P, PCAWG Consortium. Nature Volume 578 (2020) p.122-128 DOI: 10.1038/s41586-019-1907-7
*
Pan-cancer analysis of whole genomes.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Nature Volume 578 (2020) p.82-93 DOI: 10.1038/s41586-020-1969-6
*
Genomic basis for RNA alterations in cancer.
PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, PCAWG Transcriptome Working Group, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, PCAWG Consortium. Nature Volume 578 (2020) p.129-136 DOI: 10.1038/s41586-020-1970-0
*
Inferring structural variant cancer cell fraction.
Cmero M, Yuan K, Ong CS, Schröder J, PCAWG Evolution and Heterogeneity Working Group, Corcoran NM, Papenfuss T, Hovens CM, Markowetz F, Macintyre G, PCAWG Consortium. Nature communications Volume 11 (2020) p.730 DOI: 10.1038/s41467-020-14351-8
*
Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig.
Rubanova Y, Shi R, Harrigan CF, Li R, Wintersinger J, Sahin N, Deshwar A, PCAWG Evolution and Heterogeneity Working Group, Morris Q, PCAWG Consortium. Nature communications Volume 11 (2020) p.731 DOI: 10.1038/s41467-020-14352-7
*
Patterns of somatic structural variation in human cancer genomes.
Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Campbell PJ, PCAWG Consortium. Nature Volume 578 (2020) p.112-121 DOI: 10.1038/s41586-019-1913-9
*
Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer.
Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA, PCAWG Structural Variation Working Group, PCAWG Consortium. Nature genetics Volume 52 (2020) p.294-305 DOI: 10.1038/s41588-019-0564-y
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, Creighton CJ, PCAWG Consortium. Nature communications Volume 11 (2020) p.736 DOI: 10.1038/s41467-019-13885-w
*
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.
Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PAW, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine K, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH, PCAWG Structural Variation Working Group, Campbell PJ, Tubio JMC, PCAWG Consortium. Nature genetics Volume 52 (2020) p.306-319 DOI: 10.1038/s41588-019-0562-0
*
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G, PCAWG Consortium. Nature Volume 578 (2020) p.102-111 DOI: 10.1038/s41586-020-1965-x
Butler enables rapid cloud-based analysis of thousands of human genomes.
Yakneen S, Waszak SM, PCAWG Technical Working Group, Gertz M, Korbel JO, PCAWG Consortium. Nature biotechnology Volume 38 (2020) p.288-292 DOI: 10.1038/s41587-019-0360-3
*
A large cross-ancestry meta-analysis of genome-wide association studies identifies 69 novel risk loci for primary open-angle glaucoma and includes a genetic link with Alzheimer’s disease
Gharahkhani P, Jorgenson E, Hysi P, Khawaja AP, Pendergrass S, Han X, Ong JS, Hewitt AW, Segre A, Igo RP, Choquet H, Qassim A, Josyula NS, Cooke Bailey JN, Bonnemaijer P, Iglesias A, Siggs OM, Young T, Vitart V, Thiadens AA, Karjalainen J, Uebe S, Melles RB, Nair KS, Luben R, Simcoe M, Amersinghe N, Cree AJ, Hohn R, Poplawski A, Chen (CUHK) LJ, Cheng C, Vithana EN, Tamiya G, Shiga Y, Yamamoto M, Nakazawa T, Rouhana J, Currant H, Birney E, Wang X, Auton A, Ashaye A, Olawoye O, Williams SE, Akafo S, Ramsay M, Hashimoto K, Kamatani Y, Akiama M, Momozawa Y, Foster PJ, Khaw PT, Morgan JE, Strouthidis NG, Kraft P, Kang JH, Pui Pang (CUHK) CC, Pasutto F, Mitchell P, Lotery AJ, Palotie A, van Duijn C, Haines J, Hammond C, Pasquale LR, Klaver CC, Hauser M, Khor CC, Mackey DA, Kubo M, Aung T, Craig J, MacGregor S, Wiggs J, NEIGHBORHOOD consortium, ANZRAG consortium, Biobank Japan project, FinnGen study, UK Biobank Eye and Vision Consortium, GIGA study group, 23andMe Research Team. Preprint DOI: 10.1101/2020.01.30.927822
Population genetic structure and predominance of cyclical parthenogenesis in the bird cherry-oat aphid Rhopalosiphum padi in England.
Morales-Hojas R, Gonzalez-Uriarte A, Alvira Iraizoz F, Jenkins T, Alderson L, Kruger T, Hall MJ, Greenslade A, Shortall CR, Bell JR. Evolutionary applications Volume 13 (2020) p.1009-1025 DOI: 10.1111/eva.12917
The Deep Genome Project.
Lloyd KCK, Adams DJ, Baynam G, Beaudet AL, Bosch F, Boycott KM, Braun RE, Caulfield M, Cohn R, Dickinson ME, Dobbie MS, Flenniken AM, Flicek P, Galande S, Gao X, Grobler A, Heaney JD, Herault Y, de Angelis MH, Lupski JR, Lyonnet S, Mallon AM, Mammano F, MacRae CA, McInnes R, McKerlie C, Meehan TF, Murray SA, Nutter LMJ, Obata Y, Parkinson H, Pepper MS, Sedlacek R, Seong JK, Shiroishi T, Smedley D, Tocchini-Valentini G, Valle D, Wang CL, Wells S, White J, Wurst W, Xu Y, Brown SDM. Genome biology Volume 21 (2020) p.18 DOI: 10.1186/s13059-020-1931-9
Caenorhabditis elegans phosphatase complexes in UniProtKB and Complex Portal.
Bye-A-Jee H, Zaru R, Magrane M, Orchard S, UniProt Consortium. The FEBS journal Volume 287 (2020) p.2664-2684 DOI: 10.1111/febs.15213
Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies.
Eduati F, Jaaks P, Wappler J, Cramer T, Merten CA, Garnett MJ, Saez-Rodriguez J. Molecular systems biology Volume 16 (2020) p.e8664 DOI: 10.15252/msb.20188664
Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines.
Bush SJ, Foster D, Eyre DW, Clark EL, De Maio N, Shaw LP, Stoesser N, Peto TEA, Crook DW, Walker AS. GigaScience Volume 9 (2020) DOI: 10.1093/gigascience/giaa007
Human and mouse essentiality screens as a resource for disease gene discovery.
Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LMJ, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu CW, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon AM, Lloyd KCK, Brown SDM, Parkinson H, Meehan TF, Smedley D, Genomics England Research Consortium, International Mouse Phenotyping Consortium. Nature communications Volume 11 (2020) p.655 DOI: 10.1038/s41467-020-14284-2
*
Approaches for Containerized Scientific Workflows in Cloud Environments with Applications in Life Science
Spjuth O, Capuccini M, Carone M, Larsson A, Schaal W, Novella JA, Stein O, Ekmefjord M, Di Tommaso P, Floden E, Notredame C, Moreno P, Emami Khoonsari P, Herman S, Kultima K, Lampa S. Preprint DOI: 10.20944/preprints202001.0378.v1
*
Functional signatures of evolutionarily young CTCF binding sites
Azazi D, Mudge JM, Odom DT, Flicek P. Preprint DOI: 10.1101/2020.01.31.928119
*
The effects of common structural variants on 3D chromatin structure.
Shanta O, Noor A, Human Genome Structural Variation Consortium (HGSVC), Sebat J. BMC genomics Volume 21 (2020) p.95 DOI: 10.1186/s12864-020-6516-1
Single-cell transcriptomics identifies CD44 as a marker and regulator of endothelial to haematopoietic transition.
Oatley M, Bölükbası ÖV, Svensson V, Shvartsman M, Ganter K, Zirngibl K, Pavlovich PV, Milchevskaya V, Foteva V, Natarajan KN, Baying B, Benes V, Patil KR, Teichmann SA, Lancrin C. Nature communications Volume 11 (2020) p.586 DOI: 10.1038/s41467-019-14171-5
*
eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs
Kerimov N, Hayhurst JD, Peikova K, Manning JR, Walter P, Kolberg L, Samoviča M, Sakthivel MP, Kuzmin I, Trevanion SJ, Trevanion SJ, Burdett T, Jupp S, Parkinson H, Papatheodorou I, Yates A, Zerbino DR, Alasoo K. Preprint DOI: 10.1101/2020.01.29.924266
*
Graphene oxide and GST-omega enzyme: An interaction that affects arsenic metabolism in the shrimp Litopenaeus vannamei.
Josende ME, Nunes SM, de Oliveira Lobato R, González-Durruthy M, Kist LW, Bogo MR, Wasielesky W, Sahoo S, Nascimento JP, Furtado CA, Fattorini D, Regoli F, Machado K, Werhli AV, Monserrat JM, Ventura-Lima J. The Science of the total environment Volume 716 (2020) p.136893 DOI: 10.1016/j.scitotenv.2020.136893
*
Genome-wide meta-analysis, fine-mapping, and integrative prioritization identify new Alzheimer’s disease risk genes
Schwartzentruber J, Cooper S, Liu JZ, Barrio-Hernandez I, Bello E, Kumasaka N, Johnson T, Estrada K, Gaffney DJ, Beltrao P, Bassett A. Preprint DOI: 10.1101/2020.01.22.20018424
Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D.
Kennedy SA, Jarboui MA, Srihari S, Raso C, Bryan K, Dernayka L, Charitou T, Bernal-Llinares M, Herrera-Montavez C, Krstic A, Matallanas D, Kotlyar M, Jurisica I, Curak J, Wong V, Stagljar I, LeBihan T, Imrie L, Pillai P, Lynn MA, Fasterius E, Al-Khalili Szigyarto C, Breen J, Kiel C, Serrano L, Rauch N, Rukhlenko O, Kholodenko BN, Iglesias-Martinez LF, Ryan CJ, Pilkington R, Cammareri P, Sansom O, Shave S, Auer M, Horn N, Klose F, Ueffing M, Boldt K, Lynn DJ, Kolch W. Nature communications Volume 11 (2020) p.499 DOI: 10.1038/s41467-019-14224-9
The thrombospondin module 1 domain of the matricellular protein CCN3 shows an atypical disulfide pattern and incomplete CWR layers.
Xu ER, Lafita A, Bateman A, Hyvönen M. Acta crystallographica. Section D, Structural biology Volume 76 (2020) p.124-134 DOI: 10.1107/s2059798319016747
*
Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli
Wang Y, Huang J, Zhou Y, Almeida A, Finn RD, Danchin A, He L. Preprint DOI: 10.1101/2020.01.21.914887
*
Deciphering the Signaling Network Landscape of Breast Cancer Improves Drug Sensitivity Prediction
Tognetti M, Gabor A, Yang M, Cappelletti V, Windhager J, Charmpi K, de Souza N, Beyer A, Picotti P, Saez-Rodriguez J, Bodenmiller B. Preprint DOI: 10.1101/2020.01.21.907691
*
Biobtree: A tool to search and map bioinformatics identifiers and special keywords
Gur T. Preprint DOI: 10.12688/f1000research.17927.4
*
Phosphorylation-Dependent Assembly of a 14-3-3 Mediated Signaling Complex During Red Blood Cell Invasion by Plasmodium falciparum Merozoites
More KR, Kaur I, Gianetto QG, Invergo BM, Chaze T, Jain R, Huon C, Gutenbrunner P, Weisser H, Matondo M, Choudhary JS, Langsley G, Singh S, Chitnis CE. Preprint DOI: 10.1101/2020.01.17.911107
Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics.
Arıkan M, Mitchell AL, Finn RD, Gürel F. Journal of food science Volume 85 (2020) p.455-464 DOI: 10.1111/1750-3841.14992
*
Effect of Sequence Padding on the Performance of Protein-Based Deep Learning Models
Rio AL, Martin M, Perera-Lluna A, Saidi R. Preprint DOI: 10.21203/rs.2.21336/v1
*
Coevolved Positions Represent Key Functional Properties in the Trypsin-Like Serine Proteases Protein Family.
Querino Lima Afonso M, da Fonseca NJ, de Oliveira LC, Lobo FP, Bleicher L. Journal of chemical information and modeling Volume 60 (2020) p.1060-1068 DOI: 10.1021/acs.jcim.9b00903
The DNA polymerases of Drosophila melanogaster.
Marygold SJ, Attrill H, Speretta E, Warner K, Magrane M, Berloco M, Cotterill S, McVey M, Rong Y, Yamaguchi M. Fly Volume 14 (2020) p.49-61 DOI: 10.1080/19336934.2019.1710076
*
Generalized calibration across LC-setups for generic prediction of small molecule retention times
Bouwmeester R, Martens L, Degroeve S. Preprint DOI: 10.1101/2020.01.14.905844
*
Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens
Gonçalves E, Segura-Cabrera A, Pacini C, Picco G, Behan FM, Jaaks P, Coker EA, van der Meer D, Barthorpe A, Lightfoot H, Leach AR, Lynch JT, Sidders B, Crafter C, Iorio F, Fawell S, Garnett MJ, GDSC Screening Team. Preprint DOI: 10.1101/2020.01.14.905729
High-throughput discovery of genetic determinants of circadian misalignment.
Zhang T, Xie P, Dong Y, Liu Z, Zhou F, Pan D, Huang Z, Zhai Q, Gu Y, Wu Q, Tanaka N, Obata Y, Bradley A, Lelliott CJ, Sanger Institute Mouse Genetics Project, Nutter LMJ, McKerlie C, Flenniken AM, Champy MF, Sorg T, Herault Y, Angelis MH, Durner VG, Mallon AM, Brown SDM, Meehan T, Parkinson HE, Smedley D, Lloyd KCK, Yan J, Gao X, Seong JK, Wang CL, Sedlacek R, Liu Y, Rozman J, Yang L, Xu Y. PLoS genetics Volume 16 (2020) p.e1008577 DOI: 10.1371/journal.pgen.1008577
*
A Learning-Based Formulation of Parametric Curve Fitting for Bioimage Analysis
Mandal S, Uhlmann V. Preprint DOI: 10.1101/2020.01.10.901702
Modeling protein-protein, protein-peptide, and protein-oligosaccharide complexes: CAPRI 7th edition.
Lensink MF, Nadzirin N, Velankar S, Wodak SJ. Proteins Volume 88 (2020) p.916-938 DOI: 10.1002/prot.25870
DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations.
Rifaioglu AS, Nalbat E, Atalay V, Martin MJ, Cetin-Atalay R, Doğan T. Chemical science Volume 11 (2020) p.2531-2557 DOI: 10.1039/c9sc03414e
Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains.
Kentepozidou E, Aitken SJ, Feig C, Stefflova K, Ibarra-Soria X, Odom DT, Roller M, Flicek P. Genome biology Volume 21 (2020) p.5 DOI: 10.1186/s13059-019-1894-x
Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies.
Waterhouse RM, Aganezov S, Anselmetti Y, Lee J, Ruzzante L, Reijnders MJMF, 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. BMC biology Volume 18 (2020) p.1 DOI: 10.1186/s12915-019-0728-3
*
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
*
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
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
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
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
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
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
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
*
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
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 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
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
*
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
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
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
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
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
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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
Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data.
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
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
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
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
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
MetaboLights: a resource evolving in response to the needs of its scientific community.
Haug K, Cochrane K, Nainala VC, Williams M, Chang J, Jayaseelan KV, O'Donovan C. Nucleic acids research Volume 48 (2020) p.D440-D444 DOI: 10.1093/nar/gkz1019
PHI-base: the pathogen-host interactions database.
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
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
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions.
Perfetto L, Pastrello C, Del-Toro N, Duesbury M, Iannuccelli M, Kotlyar M, Licata L, Meldal B, Panneerselvam K, Panni S, Rahimzadeh N, Ricard-Blum S, Salwinski L, Shrivastava A, Cesareni G, Pellegrini M, Orchard S, Jurisica I, Hermjakob H, Porras P. Database : the journal of biological databases and curation Volume 2020 (2020) DOI: 10.1093/database/baaa096
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