Publications

Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs

Mihalic F, Simonetti L, Giudice G, Sander MR, Lindqvist R, Akprioro Peters MB, Benz C, Kassa E, Badgujar D, Inturi R, Ali M, Krystkowiak I, Sayadi A, Andersson E, Aronsson H, Söderberg O, Dobritzsch D, Petsalaki E, Överby AK, Jemth P, Davey NE, Ivarsson Y.

2022

10.1101/2022.06.19.496705

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues.

Wang S, García-Seisdedos D, Prakash A, Kundu DJ, Collins A, George N, Fexova S, Moreno P, Papatheodorou I, Jones AR, Vizcaíno JA.

2022

10.1371/journal.pcbi.1010174

Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.

Walzer M, García-Seisdedos D, Prakash A, Brack P, Crowther P, Graham RL, George N, Mohammed S, Moreno P, Papatheodorou I, Hubbard SJ, Vizcaíno JA.

2022

10.1038/s41597-022-01380-9

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

Niarakis A, Waltemath D, Glazier J, Schreiber F, Keating SM, Nickerson D, Chaouiya C, Siegel A, Noël V, Hermjakob H, Helikar T, Soliman S, Calzone L.

2022

10.1093/bib/bbac212

AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

Bordin N, Sillitoe I, Nallapareddy V, Rauer C, Lam SD, Waman VP, Sen N, Heinzinger M, Littmann M, Kim S, Velankar S, Steinegger M, Rost B, Orengo C.

2022

10.1101/2022.06.02.494367

Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England.

Vöhringer HS, Sanderson T, Sinnott M, De Maio N, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani CV, Gonçalves S, Jackson DK, Johnston I, Jung AW, Saint C, Sillitoe J, Suciu M, Goldman N, Panovska-Griffiths J, Wellcome Sanger Institute COVID-19 Surveillance Team, COVID-19 Genomics UK (COG-UK) Consortium*, Birney E, Volz E, Funk S, Kwiatkowski D, Chand M, Martincorena I, Barrett JC, Gerstung M.

2022

10.1038/s41586-022-04887-8

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs.

Sen N, Anishchenko I, Bordin N, Sillitoe I, Velankar S, Baker D, Orengo C.

2022

10.1093/bib/bbac187

An open invitation to the Understudied Proteins Initiative.

Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J.

2022

10.1038/s41587-022-01316-z

The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases.

Laurie S, Piscia D, Matalonga L, Corvó A, Fernández-Callejo M, Garcia-Linares C, Hernandez-Ferrer C, Luengo C, Martínez I, Papakonstantinou A, Picó-Amador D, Protasio J, Thompson R, Tonda R, Bayés M, Bullich G, Camps-Puchadas J, Paramonov I, Trotta JR, Alonso A, Attimonelli M, Béroud C, Bros-Facer V, Buske OJ, Cañada-Pallarés A, Fernández JM, Hansson MG, Horvath R, Jacobsen JOB, Kaliyaperumal R, Lair-Préterre S, Licata L, Lopes P, López-Martín E, Mascalzoni D, Monaco L, Pérez-Jurado LA, Posada de la Paz M, Rambla J, Rath A, Riess O, Robinson PN, Salgado D, Smedley D, Spalding D, 't Hoen PAC, Töpf A, Zaharieva I, Graessner H, Gut IG, Lochmüller H, Beltran S.

2022

10.1002/humu.24353

Method for Independent Estimation of the False Localization Rate for Phosphoproteomics.

Ramsbottom KA, Prakash A, Riverol YP, Camacho OM, Martin MJ, Vizcaíno JA, Deutsch EW, Jones AR.

2022

10.1021/acs.jproteome.1c00827

Single-cell transcriptomics of adult macaque hippocampus reveals neural precursor cell populations.

Hao ZZ, Wei JR, Xiao D, Liu R, Xu N, Tang L, Huang M, Shen Y, Xing C, Huang W, Liu X, Xiang M, Liu Y, Miao Z, Liu S.

2022

10.1038/s41593-022-01073-x

The evolution of two transmissible cancers in Tasmanian devils

Stammnitz MR, Gori K, Kwon YM, Harry E, Martin FJ, Billis K, Cheng Y, Baez-Ortega A, Chow W, Comte S, Eggertsson H, Fox S, Hamede R, Jones ME, Lazenby B, Peck S, Pye R, Quail MA, Swift K, Wang J, Wood J, Howe K, Stratton MR, Ning Z, Murchison EP.

2022

10.1101/2022.05.27.493404

Building digital twins of the human immune system: toward a roadmap.

Laubenbacher R, Niarakis A, Helikar T, An G, Shapiro B, Malik-Sheriff RS, Sego TJ, Knapp A, Macklin P, Glazier JA.

2022

10.1038/s41746-022-00610-z

Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR

Beier S, Fiebig A, Pommier C, Liyanage I, Lange M, Kersey PJ, Weise S, Finkers R, Koylass B, Cezard T, Courtot M, Contreras-Moreira B, Naamati G, Dyer S, Scholz U.

2022

10.12688/f1000research.109080.2

Mendelian Randomization.

Birney E.

2022

10.1101/cshperspect.a041302

Author Correction: Tumour gene expression signature in primary melanoma predicts long-term outcomes.

Garg M, Couturier DL, Nsengimana J, Fonseca NA, Wongchenko M, Yan Y, Lauss M, Jönsson GB, Newton-Bishop J, Parkinson C, Middleton MR, Bishop DT, McDonald S, Stefanos N, Tadross J, Vergara IA, Lo S, Newell F, Wilmott JS, Thompson JF, Long GV, Scolyer RA, Corrie P, Adams DJ, Brazma A, Rabbie R.

2022

10.1038/s41467-022-30365-w

Mannose metabolism inhibition sensitizes acute myeloid leukemia cells to cytarabine and FLT3 inhibitor therapy by modulating fatty acid metabolism to drive ferroptotic cell death

Woodley K, Dillingh LS, Giotopoulos G, Madrigal P, Rattigan KM, Philippe C, Asby R, Dembitz V, Magee AS, van de Lagemaat LN, Mapperley C, James SC, Tzelepis K, Rouault-Pierre K, Vassiliou GS, Kranc KR, Helgason G, Huntly BJ, Gallipoli P.

2022

10.1101/2022.05.16.492042

A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics.

Luo X, Bittremieux W, Griss J, Deutsch EW, Sachsenberg T, Levitsky LI, Ivanov MV, Bubis JA, Gabriels R, Webel H, Sanchez A, Bai M, Käll L, Perez-Riverol Y.

2022

10.1021/acs.jproteome.2c00069

ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads.

Hunt M, Swann J, Constantinides B, Fowler PW, Iqbal Z.

2022

10.1093/bioinformatics/btac311

The Quest for Orthologs orthology benchmark service in 2022.

Nevers Y, Jones TEM, Jyothi D, Yates B, Ferret M, Portell-Silva L, Codo L, Cosentino S, Marcet-Houben M, Vlasova A, Poidevin L, Kress A, Hickman M, Persson E, Piližota I, Guijarro-Clarke C, OpenEBench team the Quest for Orthologs Consortium , Iwasaki W, Lecompte O, Sonnhammer E, Roos DS, Gabaldón T, Thybert D, Thomas PD, Hu Y, Emms DM, Bruford E, Capella-Gutierrez S, Martin MJ, Dessimoz C, Altenhoff A.

2022

10.1093/nar/gkac330

Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis.

CRyPTIC Consortium.

2022

10.1183/13993003.00239-2022

Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation.

Kalyuzhnyy A, Eyers PA, Eyers CE, Bowler-Barnett E, Martin MJ, Sun Z, Deutsch EW, Jones AR.

2022

10.1021/acs.jproteome.2c00131

Understudied proteins: opportunities and challenges for functional proteomics.

Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J.

2022

10.1038/s41592-022-01454-x

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Sheriff RSM, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep J, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk D, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR.

2022

10.1093/nar/gkac331

An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia

Provez L, Van Puyvelde B, Corveleyn L, Demeulemeester N, Verhelst S, Lintermans B, Daled S, Roels J, Clement L, Martens L, Deforce D, Van Vlierberghe P, Dhaenens M.

2022

10.1101/2022.05.05.490796

Genomic patterns of malignant peripheral nerve sheath tumour (MPNST) evolution correlate with clinical outcome and are detectable in cell-free DNA

Cortes-Ciriano I, Steele C, Piculell K, Al-Ibraheemi A, Eulo V, Bui M, Chatzipli A, Dickson B, Borcherding D, Feber A, Galor A, Hart J, Jones K, Jordan J, Kim R, Lindsay D, Miller C, Nishida Y, Proszek P, Serrano J, Sundby R, Szymanski J, Ullrich N, Viskochil D, Wang X, Snuderl M, Park P, Flanagan A, Hirbe A, Pillay N, Miller D, Genomics of MPNST (GeM) Consortium.

2022

10.1101/2022.05.03.490481

Use of viral motif mimicry improves the proteome-wide discovery of human linear motifs.

Wadie B, Kleshchevnikov V, Sandaltzopoulou E, Benz C, Petsalaki E.

2022

10.1016/j.celrep.2022.110764

Author Correction: 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.

2022

10.1038/s41586-021-04213-8

How to Best Represent Proteins in Machine Learning-based Prediction of Drug/Compound-Target Interactions

Atas H, Doğan T.

2022

10.1101/2022.05.01.490207

A Simple Standard for Sharing Ontological Mappings (SSSOM).

Matentzoglu N, Balhoff JP, Bello SM, Bizon C, Brush M, Callahan TJ, Chute CG, Duncan WD, Evelo CT, Gabriel D, Graybeal J, Gray A, Gyori BM, Haendel M, Harmse H, Harris NL, Harrow I, Hegde HB, Hoyt AL, Hoyt CT, Jiao D, Jiménez-Ruiz E, Jupp S, Kim H, Koehler S, Liener T, Long Q, Malone J, McLaughlin JA, McMurry JA, Moxon S, Munoz-Torres MC, Osumi-Sutherland D, Overton JA, Peters B, Putman T, Queralt-Rosinach N, Shefchek K, Solbrig H, Thessen A, Tudorache T, Vasilevsky N, Wagner AH, Mungall CJ.

2022

10.1093/database/baac035

Selective clonal persistence of human retroviruses in vivo: Radial chromatin organization, integration site, and host transcription.

Melamed A, Fitzgerald TW, Wang Y, Ma J, Birney E, Bangham CRM.

2022

10.1126/sciadv.abm6210

UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference

Gao M, Qiao C, Huang Y.

2022

10.1101/2022.04.27.489808

phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets.

De Maio N, Boulton W, Weilguny L, Walker CR, Turakhia Y, Corbett-Detig R, Goldman N.

2022

10.1371/journal.pcbi.1010056

A human embryonic limb cell atlas resolved in space and time

Zhang B, He P, Lawrence JE, Wang S, Tuck E, Williams B, Roberts K, Kleshchevnikov V, Mamanova L, Bolt L, Polanski K, Elmentaite R, Fasouli ES, Prete M, He X, Yayon N, Fu Y, Yang H, Liang C, Zhang H, FitzPatrick DR, Firth H, Dean A, Barker RA, Storer MA, Wold BJ, Zhang H, Teichmann SA.

2022

10.1101/2022.04.27.489800

Molecular biology for green recovery-A call for action.

Rodríguez-Martínez M, Nielsen J, Dupont S, Vamathevan J, Glover BJ, Crosswell LC, Rouse B, Luisi BF, Bowler C, Gasser SM, Arendt D, Erb TJ, de Lorenzo V, Heard E, Patil KR.

2022

10.1371/journal.pbio.3001623

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology.

Westbrook JD, Young JY, Shao C, Feng Z, Guranovic V, Lawson CL, Vallat B, Adams PD, Berrisford JM, Bricogne G, Diederichs K, Joosten RP, Keller P, Moriarty NW, Sobolev OV, Velankar S, Vonrhein C, Waterman DG, Kurisu G, Berman HM, Burley SK, Peisach E.

2022

10.1016/j.jmb.2022.167599

The Human Pangenome Project: a global resource to map genomic diversity.

Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, Garrison NA, Graves-Lindsay TA, Ji H, Kenny EE, Koenig BA, Li D, Marschall T, McMichael JF, Novak AM, Purushotham D, Schneider VA, Schultz BI, Smith MW, Sofia HJ, Weissman T, Flicek P, Li H, Miga KH, Paten B, Jarvis ED, Hall IM, Eichler EE, Haussler D, Human Pangenome Reference Consortium.

2022

10.1038/s41586-022-04601-8

Validation analysis of EMDB entries.

Wang Z, Patwardhan A, Kleywegt GJ.

2022

10.1107/s205979832200328x

LY6S, a New IFN-Inducible Human Member of the Ly6a Subfamily Expressed by Spleen Cells and Associated with Inflammation and Viral Resistance.

Shmerling M, Chalik M, Smorodinsky NI, Meeker A, Roy S, Sagi-Assif O, Meshel T, Danilevsky A, Shomron N, Levinger S, Nishry B, Baruchi D, Shargorodsky A, Ziv R, Sarusi-Portuguez A, Lahav M, Ehrlich M, Braschi B, Bruford E, Witz IP, Wreschner DH.

2022

10.4049/immunohorizons.2200018

An atlas of genetic scores to predict multi-omic traits

Xu Y, Ritchie SC, Liang Y, Timmers PRHJ, Pietzner M, Lannelongue L, Lambert SA, Tahir UA, May-Wilson S, Johansson Å, Surendran P, Nath AP, Persyn E, Peters JE, Oliver-Williams C, Deng S, Prins B, Foguet C, Luan J, Bomba L, Soranzo N, Angelantonio ED, Pirastu N, Tai ES, van Dam RM, Davenport EE, Paul DS, Yau C, Gerszten RE, Mälarstig A, Danesh J, Sim X, Langenberg C, Wilson JF, Butterworth AS, Inouye M.

2022

10.1101/2022.04.17.488593

Mondo: Unifying diseases for the world, by the world

Vasilevsky NA, Matentzoglu NA, Toro S, Flack JE, Hegde H, Unni DR, Alyea GF, Amberger JS, Babb L, Balhoff JP, Bingaman TI, Burns GA, Buske OJ, Callahan TJ, Carmody LC, Cordo PC, Chan LE, Chang GS, Christiaens SL, Dumontier M, Failla LE, Flowers MJ, Garrett HA, Goldstein JL, Gration D, Groza T, Hanauer M, Harris NL, Hilton JA, Himmelstein DS, Hoyt CT, Kane MS, Köhler S, Lagorce D, Lai A, Larralde M, Lock A, López Santiago I, Maglott DR, Malheiro AJ, Meldal BHM, Munoz-Torres MC, Nelson TH, Nicholas FW, Ochoa D, Olson DP, Oprea TI, Osumi-Sutherland D, Parkinson H, Pendlington ZM, Rath A, Rehm HL, Remennik L, Riggs ER, Roncaglia P, Ross JE, Shadbolt MF, Shefchek KA, Similuk MN, Sioutos N, Smedley D, Sparks R, Stefancsik R, Stephan R, Storm AL, Stupp D, Stupp GS, Sundaramurthi JC, Tammen I, Tay D, Thaxton CL, Valasek E, Valls-Margarit J, Wagner AH, Welter D, Whetzel PL, Whiteman LL, Wood V, Xu CH, Zankl A, Zhang XA, Chute CG, Robinson PN, Mungall CJ, Hamosh A, Haendel MA.

2022

10.1101/2022.04.13.22273750

Supervised spatial inference of dissociated single-cell data with SageNet

Heidari E, Lohoff T, Tyser RCV, Marioni JC, Robinson MD, Ghazanfar S.

2022

10.1101/2022.04.14.488419

Search and sequence analysis tools services from EMBL-EBI in 2022.

Madeira F, Pearce M, Tivey ARN, Basutkar P, Lee J, Edbali O, Madhusoodanan N, Kolesnikov A, Lopez R.

2022

10.1093/nar/gkac240

DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks

Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O.

2022

10.1101/2022.04.08.487609

A joint NCBI and EMBL-EBI transcript set for clinical genomics and research.

Morales J, Pujar S, Loveland JE, Astashyn A, Bennett R, Berry A, Cox E, Davidson C, Ermolaeva O, Farrell CM, Fatima R, Gil L, Goldfarb T, Gonzalez JM, Haddad D, Hardy M, Hunt T, Jackson J, Joardar VS, Kay M, Kodali VK, McGarvey KM, McMahon A, Mudge JM, Murphy DN, Murphy MR, Rajput B, Rangwala SH, Riddick LD, Thibaud-Nissen F, Threadgold G, Vatsan AR, Wallin C, Webb D, Flicek P, Birney E, Pruitt KD, Frankish A, Cunningham F, Murphy TD.

2022

10.1038/s41586-022-04558-8

ELIXIR biovalidator for semantic validation of life science metadata.

Liyanage I, Burdett T, Droesbeke B, Erdos K, Fernandez R, Gray A, Haseeb M, Penim F, Pommier C, Rocca-Serra P, Courtot M, Coppens F.

2022

10.1093/bioinformatics/btac195

Publisher Correction: Evolution of enhanced innate immune evasion by SARS-CoV-2.

Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, Bischof ML, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hiatt J, Rosales R, McGovern BL, Jahun A, Fabius JM, White K, Goodfellow IG, Takeuchi Y, Bonfanti P, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Kellis M, Swaney DL, García-Sastre A, Jolly C, Towers GJ, Krogan NJ.

2022

10.1038/s41586-022-04653-w

WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans.

Davis P, Zarowiecki M, Arnaboldi V, Becerra A, Cain S, Chan J, Chen WJ, Cho J, da Veiga Beltrame E, Diamantakis S, Gao S, Grigoriadis D, Grove CA, Harris TW, Kishore R, Le T, Lee RYN, Luypaert M, Müller HM, Nakamura C, Nuin P, Paulini M, Quinton-Tulloch M, Raciti D, Rodgers FH, Russell M, Schindelman G, Singh A, Stickland T, Van Auken K, Wang Q, Williams G, Wright AJ, Yook K, Berriman M, Howe KL, Schedl T, Stein L, Sternberg PW.

2022

10.1093/genetics/iyac003

Diversity of microbial defence systems.

Cazares A, Figueroa W, Cazares D.

2022

10.1038/s41579-022-00702-3

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A genotypic analysis.

Walker TM, Miotto P, Köser CU, Fowler PW, Knaggs J, Iqbal Z, Hunt M, Chindelevitch L, Farhat M, Cirillo DM, Comas I, Posey J, Omar SV, Peto TE, Suresh A, Uplekar S, Laurent S, Colman RE, Nathanson CM, Zignol M, Walker AS, CRyPTIC Consortium, Seq&Treat Consortium, Crook DW, Ismail N, Rodwell TC.

2022

10.1016/s2666-5247(21)00301-3

Nanopore ReCappable sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs.

Ugolini C, Mulroney L, Leger A, Castelli M, Criscuolo E, Williamson MK, Davidson AD, Almuqrin A, Giambruno R, Jain M, Frigè G, Olsen H, Tzertzinis G, Schildkraut I, Wulf MG, Corrêa IR, Ettwiller L, Clementi N, Clementi M, Mancini N, Birney E, Akeson M, Nicassio F, Matthews DA, Leonardi T.

2022

10.1093/nar/gkac144

Genetically personalised organ-specific metabolic models in health and disease

Foguet C, Xu Y, Ritchie SC, Lambert SA, Persyn E, Nath AP, Davenport EE, Roberts DJ, Paul DS, Angelantonio ED, Danesh J, Butterworth AS, Yau C, Inouye M.

2022

10.1101/2022.03.25.22272958

A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics.

Van Puyvelde B, Daled S, Willems S, Gabriels R, Gonzalez de Peredo A, Chaoui K, Mouton-Barbosa E, Bouyssié D, Boonen K, Hughes CJ, Gethings LA, Perez-Riverol Y, Bloomfield N, Tate S, Schiltz O, Martens L, Deforce D, Dhaenens M.

2022

10.1038/s41597-022-01216-6

DCATS: differential composition analysis for complex single-cell experimental designs

Lin X, Chau C, Huang Y, Ho JW.

2022

10.1101/2022.03.21.485232

The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.

Fisher ME, Segerdell E, Matentzoglu N, Nenni MJ, Fortriede JD, Chu S, Pells TJ, Osumi-Sutherland D, Chaturvedi P, James-Zorn C, Sundararaj N, Lotay VS, Ponferrada V, Wang DZ, Kim E, Agalakov S, Arshinoff BI, Karimi K, Vize PD, Zorn AM.

2022

10.1186/s12859-022-04636-8

Large-scale analysis reveals the distribution of novel cellular microbes across multiple biomes and kingdoms

Saary P, Kale V, Finn R.

2022

10.21203/rs.3.rs-1441815/v1

Sub-cellular level resolution of common genetic variation in the photoreceptor layer identifies continuum between rare disease and common variation

Currant H, Fitzgerald TW, Patel PJ, Khawaja AP, Webster AR, Mahroo OA, Birney E, UK Biobank Eye and Vision Consortium.

2022

10.1101/2022.03.15.22272407

Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms.

LeDuc RD, Deutsch EW, Binz PA, Fellers RT, Cesnik AJ, Klein JA, Van Den Bossche T, Gabriels R, Yalavarthi A, Perez-Riverol Y, Carver J, Bittremieux W, Kawano S, Pullman B, Bandeira N, Kelleher NL, Thomas PM, Vizcaíno JA.

2022

10.1021/acs.jproteome.1c00771

Wnt and BMP signaling enhance melanocyte regeneration and suppress melanoma cell migration

Katkat E, Demirci Y, Heger G, Papatheodorou I, Brazma A, Ozhan G.

2022

10.1101/2022.03.11.483949

A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae.

Sim CK, Kashaf SS, Stacy A, Proctor DM, Almeida A, Bouladoux N, Chen M, NISC Comparative Sequencing Program, Finn RD, Belkaid Y, Conlan S, Segre JA.

2022

10.1186/s40168-021-01207-6

A panoramic perspective on human phosphosites

Ramasamy P, Vandermarliere E, vranken W, Martens L.

2022

10.1101/2022.03.08.483252

Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation

Hall MB, Rabodoarivelo MS, Koch A, Dippenaar A, George S, Grobbelaar M, Warren R, Walker T, Cox H, Gagneux S, Crook D, Peto T, Rakotosamimanana N, Lapierre SG, Iqbal Z.

2022

10.1101/2022.03.04.22271870

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.

Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David FPA, Brbić M, Spanier K, Leskovec J, McLaughlin CN, Xie Q, Jones RC, Brueckner K, Shim J, Tattikota SG, Schnorrer F, Rust K, Nystul TG, Carvalho-Santos Z, Ribeiro C, Pal S, Mahadevaraju S, Przytycka TM, Allen AM, Goodwin SF, Berry CW, Fuller MT, White-Cooper H, Matunis EL, DiNardo S, Galenza A, O'Brien LE, Dow JAT, FCA Consortium§, Jasper H, Oliver B, Perrimon N, Deplancke B, Quake SR, Luo L, Aerts S, Agarwal D, Ahmed-Braimah Y, Arbeitman M, Ariss MM, Augsburger J, Ayush K, Baker CC, Banisch T, Birker K, Bodmer R, Bolival B, Brantley SE, Brill JA, Brown NC, Buehner NA, Cai XT, Cardoso-Figueiredo R, Casares F, Chang A, Clandinin TR, Crasta S, Desplan C, Detweiler AM, Dhakan DB, Donà E, Engert S, Floc'hlay S, George N, González-Segarra AJ, Groves AK, Gumbin S, Guo Y, Harris DE, Heifetz Y, Holtz SL, Horns F, Hudry B, Hung RJ, Jan YN, Jaszczak JS, Jefferis GSXE, Karkanias J, Karr TL, Katheder NS, Kezos J, Kim AA, Kim SK, Kockel L, Konstantinides N, Kornberg TB, Krause HM, Labott AT, Laturney M, Lehmann R, Leinwand S, Li J, Li JSS, Li K, Li K, Li L, Li T, Litovchenko M, Liu HH, Liu Y, Lu TC, Manning J, Mase A, Matera-Vatnick M, Matias NR, McDonough-Goldstein CE, McGeever A, McLachlan AD, Moreno-Roman P, Neff N, Neville M, Ngo S, Nielsen T, O'Brien CE, Osumi-Sutherland D, Özel MN, Papatheodorou I, Petkovic M, Pilgrim C, Pisco AO, Reisenman C, Sanders EN, Dos Santos G, Scott K, Sherlekar A, Shiu P, Sims D, Sit RV, Slaidina M, Smith HE, Sterne G, Su YH, Sutton D, Tamayo M, Tan M, Tastekin I, Treiber C, Vacek D, Vogler G, Waddell S, Wang W, Wilson RI, Wolfner MF, Wong YE, Xie A, Xu J, Yamamoto S, Yan J, Yao Z, Yoda K, Zhu R, Zinzen RP.

2022

10.1126/science.abk2432

Making European performance and impact assessment frameworks glocal

Melo AM, Oliveira S, Oliveira JS, Martin CS, Leite RB.

2022

10.12688/f1000research.108804.1

Distinct chromosomal “niches” in the genome of S. cerevisiae provide the background for genomic innovation and shape the fate of gene duplicates

Stavropoulou A, Tassios A, Kalyva M, Georgoulopoulos M, Vakirlis N, Iliopoulos I, Nikolaou C.

2022

10.1101/2022.02.26.482092

StabMap: Mosaic single cell data integration using non-overlapping features

Ghazanfar S, Guibentif C, Marioni JC.

2022

10.1101/2022.02.24.481823

A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications

Nassar M, Rogers AB, Talo' F, Sanchez S, Shafique Z, Finn RD, McEntyre J.

2022

10.21203/rs.3.rs-1396476/v1

Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.

Barker CG, Petsalaki E, Giudice G, Sero J, Ekpenyong EN, Bakal C, Petsalaki E.

2022

10.1101/gr.276059.121

Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation.

Scholz AH, Freitag J, Lyal CHC, Sara R, Cepeda ML, Cancio I, Sett S, Hufton AL, Abebaw Y, Bansal K, Benbouza H, Boga HI, Brisse S, Bruford MW, Clissold H, Cochrane G, Coddington JA, Deletoille AC, García-Cardona F, Hamer M, Hurtado-Ortiz R, Miano DW, Nicholson D, Oliveira G, Bravo CO, Rohden F, Seberg O, Segelbacher G, Shouche Y, Sierra A, Karsch-Mizrachi I, da Silva J, Hautea DM, da Silva M, Suzuki M, Tesfaye K, Tiambo CK, Tolley KA, Varshney R, Zambrano MM, Overmann J.

2022

10.1038/s41467-022-28594-0

The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization.

Dudová Z, Conte N, Mason J, Stuchlík D, Peša R, Halmagyi C, Perova Z, Mosaku A, Thorne R, Follette A, Pivarč Ľ, Šašinka R, Usman M, Neuhauser S, Begley DA, Krupke DM, Frassà M, Fiori A, Corsi R, Vezzadini L, Isella C, Bertotti A, Bult C, Parkinson H, Medico E, Meehan T, Křenek A.

2022

10.1186/s12864-022-08367-1

The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.

Fitzgerald T, Brettell I, Leger A, Wolf N, Kusminski N, Monahan J, Barton C, Herder C, Aadepu N, Gierten J, Becker C, Hammouda OT, Hasel E, Lischik C, Lust K, Sokolova N, Suzuki R, Tsingos E, Tavhelidse T, Thumberger T, Watson P, Welz B, Khouja N, Naruse K, Birney E, Wittbrodt J, Loosli F.

2022

10.1186/s13059-022-02623-z

DECIPHER: Supporting the interpretation and sharing of rare disease phenotype-linked variant data to advance diagnosis and research.

Foreman J, Brent S, Perrett D, Bevan AP, Hunt SE, Cunningham F, Hurles ME, Firth HV.

2022

10.1002/humu.24340

Using deep learning to annotate the protein universe.

Bileschi ML, Belanger D, Bryant DH, Sanderson T, Carter B, Sculley D, Bateman A, DePristo MA, Colwell LJ.

2022

10.1038/s41587-021-01179-w

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.

Leger A, Brettell I, Monahan J, Barton C, Wolf N, Kusminski N, Herder C, Aadepu N, Becker C, Gierten J, Hammouda OT, Hasel E, Lischik C, Lust K, Sokolova N, Suzuki R, Tavhelidse T, Thumberger T, Tsingos E, Watson P, Welz B, Naruse K, Loosli F, Wittbrodt J, Birney E, Fitzgerald T.

2022

10.1186/s13059-022-02602-4

Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures

Rausch T, Snajder R, Leger A, Simovic M, Stegle O, Birney E, Bonder MJ, Ernst A, Korbel JO.

2022

10.1101/2022.02.20.480758

CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure

Escobedo N, Cahui RRT, Caruso G, Ríos EG, Hirsh L, Monzon AM, Parisi G, Palopoli N.

2022

10.1101/2022.02.15.480082

PycoMeth: A toolbox for differential methylation testing from Nanopore methylation calls

Snajder R, Stegle O, Bonder MJ.

2022

10.1101/2022.02.16.480699

Editorial: The Transition Era to New Sequencing Technologies and Their Application to Integrative Omics in Molecular Surveillance.

Hölzer M, Escobar-Zepeda A, Linde J, Horn F.

2022

10.3389/fgene.2022.840782

Space omics research in Europe: Contributions, geographical distribution and ESA member state funding schemes.

Deane CS, Space Omics Topical Team, da Silveira WA, Herranz R.

2022

10.1016/j.isci.2022.103920

Brain Regeneration Resembles Brain Cancer at Its Early Wound Healing Stage and Diverges From Cancer Later at Its Proliferation and Differentiation Stages.

Demirci Y, Heger G, Katkat E, Papatheodorou I, Brazma A, Ozhan G.

2022

10.3389/fcell.2022.813314

Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2.

Foix A, López D, Díez-Fuertes F, McConnell MJ, Martín-Galiano AJ.

2022

10.1371/journal.pcbi.1009726

Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome

Madrigal P, Singh NK, Wood JM, Gaudioso E, Hernández-del-Olmo F, Mason CE, Venkateswaran K, Beheshti A.

2022

10.1101/2022.02.07.479455

Deciphering the tangible spatio-temporal spread of a 25 years tuberculosis outbreak boosted by social determinants

López MG, Campos-Herrero MI, Torres-Puente M, Cañas F, Comín J, Copado R, Wintringer P, Iqbal Z, Lagarejos E, Moreno-Molina M, Pérez-Lago L, Pino B, Sante L, de Viedma DG, Samper S, Comas I.

2022

10.1101/2022.02.07.22270243

The discovAIR project: a roadmap towards the Human Lung Cell Atlas.

Luecken MD, Zaragosi LE, Madissoon E, Sikkema L, Firsova AB, De Domenico E, Kümmerle L, Saglam A, Berg M, Gay ACA, Schniering J, Mayr CH, Abalo XM, Larsson L, Sountoulidis A, Teichmann S, van Eunen K, Koppelman GH, Saeb-Parsy K, Leroy S, Powell P, Sarkans U, Timens W, Lundeberg J, van den Berge M, Nilsson M, Horváth P, Denning J, Papatheodorou I, Schultze J, Schiller HB, Barbry P, Petoukhov I, Misharin AV, Adcock I, von Papen M, Theis FJ, Samakovlis C, Meyer KB, Nawijn MC.

2022

10.1183/13993003.02057-2021

Publisher Correction: A catalogue of 1,167 genomes from the human gut archaeome.

Chibani CM, Mahnert A, Borrel G, Almeida A, Werner A, Brugère JF, Gribaldo S, Finn RD, Schmitz RA, Moissl-Eichinger C.

2022

10.1038/s41564-022-01061-8

Profilin 1 deficiency drives mitotic defects and impairs genome stability

Scotto di Carlo F, Russo S, Muyas F, Mangini M, Pazzaglia L, Biamonte F, De Luca AC, Scotlandi K, Cortés-Ciriano I, Gianfrancesco F.

2022

10.1101/2022.02.01.478160

The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients

Muyas F, Gómez Rodriguez MJ, Cortes-Ciriano I, Flores I.

2022

10.1101/2022.01.25.477771

A comprehensive evaluation of consensus spectrum generation methods in proteomics

Luo X, Bittremieux W, Griss J, Deutsch EW, Sachsenberg T, Levitsky LI, Ivanov MV, Bubis JA, Gabriels R, Webel H, Sanchez A, Bai M, Kall L, Perez-Riverol Y.

2022

10.1101/2022.01.25.477699

An organoid CRISPRi screen revealed that SOX9 primes human fetal lung tip progenitors to receive WNT and RTK signals

Sun D, Batlle OL, van den Ameele J, Thomas JC, He P, Lim K, Tang W, Xu C, Meyer KB, Teichmann SA, Marioni JC, Jackson SP, Brand AH, Rawlins EL.

2022

10.1101/2022.01.27.478034

ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads

Hunt M, Swann J, Constantinides B, Fowler PW, Iqbal Z.

2022

10.1101/2022.01.21.477194

In vitro demonstration of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome

Forster SC, Liu J, Kumar N, Gulliver EL, Gould JA, Escobar-Zepeda A, Mkandawire T, Pike LJ, Shao Y, Stares MD, Browne HP, Neville BA, Lawley TD.

2022

10.1101/2022.01.18.476738

Formalizing Insect Morphological Data: A Model-Based, Extensible Insect Anatomy Ontology and Its Potential Applications in Biodiversity Research and Informatics

Girón JC, Tarasov S, González Montaña LA, Matentzoglu N, Smith AD, Koch M, Boudinot BE, Bouchard P, Burks R, Vogt L, Yoder M, Osumi-Sutherland D, Friedrich F, Beutel R, Mikó I.

2022

10.20944/preprints202201.0254.v1

Differential Afa/Dr Fimbriae Expression in the Multidrug-Resistant Escherichia coli ST131 Clone.

Alvarez-Fraga L, Phan MD, Goh KGK, Nhu NTK, Hancock SJ, Allsopp LP, Peters KM, Forde BM, Roberts LW, Sullivan MJ, Totsika M, Beatson SA, Ulett GC, Schembri MA.

2022

10.1128/mbio.03519-21

Data-driven extraction of human kinase-substrate relationships from omics datasets

Petursson B, Petsalaki E.

2022

10.1101/2022.01.15.476449

A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates

He P, Lim K, Sun D, Pett JP, Jeng Q, Polanski K, Dong Z, Bolt L, Richardson L, Mamanova L, Dabrowska M, Wilbrey-Clark A, Madissoon E, Tuong ZK, Dann E, Suo C, Goh Kai’En I, He X, Barker R, Teichmann SA, Marioni JC, Meyer KB, Rawlins EL.

2022

10.1101/2022.01.11.474933

Consensus nomenclature for dyneins and associated assembly factors.

Braschi B, Omran H, Witman GB, Pazour GJ, Pfister KK, Bruford EA, King SM.

2022

10.1083/jcb.202109014

Mendelian gene identification through mouse embryo viability screening

Cacheiro P, Westerberg CH, Mager J, Dickinson ME, Nutter LM, Muñoz-Fuentes V, Hsu C, Van den Veyver IB, Flenniken AM, McKerlie C, Murray SA, Teboul L, Heaney JD, Lloyd KCK, Lanoue L, Braun RE, White JK, Creighton AK, Laurin V, Guo R, Qu D, Wells S, Cleak J, Bunton-Stasyshyn R, Stewart M, Harrisson J, Mason J, Mashhadi HH, Parkinson H, Mallon A, Smedley D, International Mouse Phenotyping Consortium, Genomics England Research Consortium.

2022

10.1101/2022.01.07.22268899

Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations.

Breeze CE, Haugen E, Reynolds A, Teschendorff A, van Dongen J, Lan Q, Rothman N, Bourque G, Dunham I, Beck S, Stamatoyannopoulos J, Franceschini N, Berndt SI.

2022

10.1186/s13059-021-02560-3

Update of the keratin gene family: evolution, tissue-specific expression patterns, and relevance to clinical disorders.

Ho M, Thompson B, Fisk JN, Nebert DW, Bruford EA, Vasiliou V, Bunick CG.

2022

10.1186/s40246-021-00374-9

Identification of Putative β-Galactosidase Genes in the Genome of Lactobacillus helveticus OSU-PECh-4A.

García-Cano I, Escobar-Zepeda A, Ruiz-Ramírez S, Rocha-Mendoza D, Jiménez-Flores R.

2022

10.1128/mra.00766-21

The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements

Botelho J, Cazares A, Schulenburg H.

2022

10.1101/2022.01.03.474784

Single-Cell Analysis Reveals the Immune Characteristics of Myeloid Cells and Memory T Cells in Recovered COVID-19 Patients With Different Severities.

Li X, Garg M, Jia T, Liao Q, Yuan L, Li M, Wu Z, Wu W, Bi Y, George N, Papatheodorou I, Brazma A, Luo H, Fang S, Miao Z, Shu Y.

2022

10.3389/fimmu.2021.781432

SignalP 6.0 predicts all five types of signal peptides using protein language models.

Teufel F, Almagro Armenteros JJ, Johansen AR, Gíslason MH, Pihl SI, Tsirigos KD, Winther O, Brunak S, von Heijne G, Nielsen H.

2022

10.1038/s41587-021-01156-3

The Gene Curation Coalition: A global effort to harmonize gene-disease evidence resources

DiStefano MT, Goehringer S, Babb L, Alkuraya FS, Amberger J, Amin M, Austin-Tse C, Balzotti M, Berg JS, Birney E, Bocchini C, Bruford EA, Coffey AJ, Collins H, Cunningham F, Daugherty LC, Einhorn Y, Firth HV, Fitzpatrick DR, Foulger RE, Goldstein J, Hamosh A, Hurles MR, Leigh SE, Leong IU, Maddirevula S, Martin CL, McDonagh EM, Olry A, Puzriakova A, Radtke K, Ramos EM, Rath A, Riggs ER, Roberts AM, Rodwell C, Snow C, Stark Z, Tahiliani J, Tweedie S, Ware JS, Weller P, Williams E, Wright CF, Yates TM, Rehm HL.

2022

10.1101/2022.01.03.21268593

The reactome pathway knowledgebase 2022.

Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, Griss J, Sevilla C, Matthews L, Gong C, Deng C, Varusai T, Ragueneau E, Haider Y, May B, Shamovsky V, Weiser J, Brunson T, Sanati N, Beckman L, Shao X, Fabregat A, Sidiropoulos K, Murillo J, Viteri G, Cook J, Shorser S, Bader G, Demir E, Sander C, Haw R, Wu G, Stein L, Hermjakob H, D'Eustachio P.

2022

10.1093/nar/gkab1028

Rhea, the reaction knowledgebase in 2022.

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A.

2022

10.1093/nar/gkab1016

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.

Quaglia F, Mészáros B, Salladini E, Hatos A, Pancsa R, Chemes LB, Pajkos M, Lazar T, Peña-Díaz S, Santos J, Ács V, Farahi N, Fichó E, Aspromonte MC, Bassot C, Chasapi A, Davey NE, Davidović R, Dobson L, Elofsson A, Erdős G, Gaudet P, Giglio M, Glavina J, Iserte J, Iglesias V, Kálmán Z, Lambrughi M, Leonardi E, Longhi S, Macedo-Ribeiro S, Maiani E, Marchetti J, Marino-Buslje C, Mészáros A, Monzon AM, Minervini G, Nadendla S, Nilsson JF, Novotný M, Ouzounis CA, Palopoli N, Papaleo E, Pereira PJB, Pozzati G, Promponas VJ, Pujols J, Rocha ACS, Salas M, Sawicki LR, Schad E, Shenoy A, Szaniszló T, Tsirigos KD, Veljkovic N, Parisi G, Ventura S, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D.

2022

10.1093/nar/gkab1082

The impact of AlphaFold2 one year on.

Jones DT, Thornton JM.

2022

10.1038/s41592-021-01365-3

Evaluation of Antimicrobial Effects of Photo-sonodynamic Antimicrobial Chemotherapy Based on Nano-micelle Curcumin on Virulence Gene Expression Patterns in Acinetobacter baumannii.

Pourhajibagher M, Talaei N, Bahador A.

2022

10.2174/1871526522666211220121725

The European Bioinformatics Institute (EMBL-EBI) in 2021.

Cantelli G, Bateman A, Brooksbank C, Petrov AI, Malik-Sheriff RS, Ide-Smith M, Hermjakob H, Flicek P, Apweiler R, Birney E, McEntyre J.

2022

10.1093/nar/gkab1127

The IntAct database: efficient access to fine-grained molecular interaction data.

Del Toro N, Shrivastava A, Ragueneau E, Meldal B, Combe C, Barrera E, Perfetto L, How K, Ratan P, Shirodkar G, Lu O, Mészáros B, Watkins X, Pundir S, Licata L, Iannuccelli M, Pellegrini M, Martin MJ, Panni S, Duesbury M, Vallet SD, Rappsilber J, Ricard-Blum S, Cesareni G, Salwinski L, Orchard S, Porras P, Panneerselvam K, Hermjakob H.

2022

10.1093/nar/gkab1006

A paradigm shift in structural biology.

Subramaniam S, Kleywegt GJ.

2022

10.1038/s41592-021-01361-7

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center.

Amos B, Aurrecoechea C, Barba M, Barreto A, Basenko EY, Bażant W, Belnap R, Blevins AS, Böhme U, Brestelli J, Brunk BP, Caddick M, Callan D, Campbell L, Christensen MB, Christophides GK, Crouch K, Davis K, DeBarry J, Doherty R, Duan Y, Dunn M, Falke D, Fisher S, Flicek P, Fox B, Gajria B, Giraldo-Calderón GI, Harb OS, Harper E, Hertz-Fowler C, Hickman MJ, Howington C, Hu S, Humphrey J, Iodice J, Jones A, Judkins J, Kelly SA, Kissinger JC, Kwon DK, Lamoureux K, Lawson D, Li W, Lies K, Lodha D, Long J, MacCallum RM, Maslen G, McDowell MA, Nabrzyski J, Roos DS, Rund SSC, Schulman SW, Shanmugasundram A, Sitnik V, Spruill D, Starns D, Stoeckert CJ, Tomko SS, Wang H, Warrenfeltz S, Wieck R, Wilkinson PA, Xu L, Zheng J.

2022

10.1093/nar/gkab929

The European Variation Archive: a FAIR resource of genomic variation for all species.

Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, Tsukanov K, Venkataraman S, Flicek P, Parkinson H, Keane TM.

2022

10.1093/nar/gkab960

IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset.

Porras P, Orchard S, Licata L.

2022

10.1007/978-1-0716-2095-3_2

The European Nucleotide Archive in 2021.

Cummins C, Ahamed A, Aslam R, Burgin J, Devraj R, Edbali O, Gupta D, Harrison PW, Haseeb M, Holt S, Ibrahim T, Ivanov E, Jayathilaka S, Kadhirvelu V, Kay S, Kumar M, Lathi A, Leinonen R, Madeira F, Madhusoodanan N, Mansurova M, O'Cathail C, Pearce M, Pesant S, Rahman N, Rajan J, Rinck G, Selvakumar S, Sokolov A, Suman S, Thorne R, Totoo P, Vijayaraja S, Waheed Z, Zyoud A, Lopez R, Burdett T, Cochrane G.

2022

10.1093/nar/gkab1051

Sequence locally, think globally: The Darwin Tree of Life Project.

Darwin Tree of Life Project Consortium.

2022

10.1073/pnas.2115642118

PDBe-KB: collaboratively defining the biological context of structural data.

PDBe-KB consortium.

2022

10.1093/nar/gkab988

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.

Perez-Riverol Y, Bai J, Bandla C, García-Seisdedos D, Hewapathirana S, Kamatchinathan S, Kundu DJ, Prakash A, Frericks-Zipper A, Eisenacher M, Walzer M, Wang S, Brazma A, Vizcaíno JA.

2022

10.1093/nar/gkab1038

AgroLD: A Knowledge Graph Database for Plant Functional Genomics.

Larmande P, Tagny Ngompe G, Venkatesan A, Ruiz M.

2022

10.1007/978-1-0716-2067-0_28

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.

2022

10.1093/nar/gkab889

Complex Portal 2022: new curation frontiers.

Meldal BHM, Perfetto L, Combe C, Lubiana T, Ferreira Cavalcante JV, Bye-A-Jee H, Waagmeester A, Del-Toro N, Shrivastava A, Barrera E, Wong E, Mlecnik B, Bindea G, Panneerselvam K, Willighagen E, Rappsilber J, Porras P, Hermjakob H, Orchard S.

2022

10.1093/nar/gkab991

BioSamples database: FAIRer samples metadata to accelerate research data management.

Courtot M, Gupta D, Liyanage I, Xu F, Burdett T.

2022

10.1093/nar/gkab1046

The European Genome-phenome Archive in 2021.

Freeberg MA, Fromont LA, D'Altri T, Romero AF, Ciges JI, Jene A, Kerry G, Moldes M, Ariosa R, Bahena S, Barrowdale D, Barbero MC, Fernandez-Orth D, Garcia-Linares C, Garcia-Rios E, Haziza F, Juhasz B, Llobet OM, Milla G, Mohan A, Rueda M, Sankar A, Shaju D, Shimpi A, Singh B, Thomas C, de la Torre S, Uyan U, Vasallo C, Flicek P, Guigo R, Navarro A, Parkinson H, Keane T, Rambla J.

2022

10.1093/nar/gkab1059

Ensembl 2022.

Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Austine-Orimoloye O, Azov AG, Barnes I, Bennett R, Berry A, Bhai J, Bignell A, Billis K, Boddu S, Brooks L, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fatima R, Giron CG, Genez T, Martinez JG, Guijarro-Clarke C, Gymer A, Hardy M, Hollis Z, Hourlier T, Hunt T, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Marugán JC, Mohanan S, Mushtaq A, Naven M, Ogeh DN, Parker A, Parton A, Perry M, Piližota I, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Pérez-Silva JG, Stark W, Steed E, Sutinen K, Sukumaran R, Sumathipala D, Suner MM, Szpak M, Thormann A, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Walts B, Willhoft N, Winterbottom A, Wass E, Chakiachvili M, Flint B, Frankish A, Giorgetti S, Haggerty L, Hunt SE, IIsley GR, Loveland JE, Martin FJ, Moore B, Mudge JM, Muffato M, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Dyer S, Harrison PW, Howe KL, Yates AD, Zerbino DR, Flicek P.

2022

10.1093/nar/gkab1049

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.

Yates AD, Allen J, Amode RM, Azov AG, Barba M, Becerra A, Bhai J, Campbell LI, Carbajo Martinez M, Chakiachvili M, Chougule K, Christensen M, Contreras-Moreira B, Cuzick A, Da Rin Fioretto L, Davis P, De Silva NH, Diamantakis S, Dyer S, Elser J, Filippi CV, Gall A, Grigoriadis D, Guijarro-Clarke C, Gupta P, Hammond-Kosack KE, Howe KL, Jaiswal P, Kaikala V, Kumar V, Kumari S, Langridge N, Le T, Luypaert M, Maslen GL, Maurel T, Moore B, Muffato M, Mushtaq A, Naamati G, Naithani S, Olson A, Parker A, Paulini M, Pedro H, Perry E, Preece J, Quinton-Tulloch M, Rodgers F, Rosello M, Ruffier M, Seager J, Sitnik V, Szpak M, Tate J, Tello-Ruiz MK, Trevanion SJ, Urban M, Ware D, Wei S, Williams G, Winterbottom A, Zarowiecki M, Finn RD, Flicek P.

2022

10.1093/nar/gkab1007

PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.

Urban M, Cuzick A, Seager J, Wood V, Rutherford K, Venkatesh SY, Sahu J, Iyer SV, Khamari L, De Silva N, Martinez MC, Pedro H, Yates AD, Hammond-Kosack KE.

2022

10.1093/nar/gkab1037

Expression Atlas update: gene and protein expression in multiple species.

Moreno P, Fexova S, George N, Manning JR, Miao Z, Mohammed S, Muñoz-Pomer A, Fullgrabe A, Bi Y, Bush N, Iqbal H, Kumbham U, Solovyev A, Zhao L, Prakash A, García-Seisdedos D, Kundu DJ, Wang S, Walzer M, Clarke L, Osumi-Sutherland D, Tello-Ruiz MK, Kumari S, Ware D, Eliasova J, Arends MJ, Nawijn MC, Meyer K, Burdett T, Marioni J, Teichmann S, Vizcaíno JA, Brazma A, Papatheodorou I.

2022

10.1093/nar/gkab1030

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.

Varadi M, Anyango S, Deshpande M, Nair S, Natassia C, Yordanova G, Yuan D, Stroe O, Wood G, Laydon A, Žídek A, Green T, Tunyasuvunakool K, Petersen S, Jumper J, Clancy E, Green R, Vora A, Lutfi M, Figurnov M, Cowie A, Hobbs N, Kohli P, Kleywegt G, Birney E, Hassabis D, Velankar S.

2022

10.1093/nar/gkab1061

A catalogue of 1,167 genomes from the human gut archaeome.

Chibani CM, Mahnert A, Borrel G, Almeida A, Werner A, Brugère JF, Gribaldo S, Finn RD, Schmitz RA, Moissl-Eichinger C.

2021

10.1038/s41564-021-01020-9

CoDNaS-RNA: a database of Conformational Diversity in the Native State of RNA.

Buitrón MG, Cahui RRT, Ríos EG, Hirsh L, Parisi G, Fornasari MS, Palopoli N.

2021

10.1093/bioinformatics/btab858

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions.

Saheb Kashaf S, Proctor DM, Deming C, Saary P, Hölzer M, NISC Comparative Sequencing Program, Taylor ME, Kong HH, Segre JA, Almeida A, Finn RD.

2021

10.1038/s41564-021-01011-w

Evolution of enhanced innate immune evasion by SARS-CoV-2.

Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, Bischof ML, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hiatt J, Rosales R, McGovern BL, Jahun A, Fabius JM, White K, Goodfellow IG, Takeuchi Y, Bonfanti P, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Kellis M, Swaney DL, García-Sastre A, Jolly C, Towers GJ, Krogan NJ.

2021

10.1038/s41586-021-04352-y

How to interpret AlphaFold structures

Bateman A, Velankar S, Tunyasuvakool K, Ovchinnikov S, Beltrao P, Mészáros B.

2021

10.6019/tol.alphafold-w.2021.00001.1

A guide to analysing binding sites in protein structures

Armstrong D.

2021

10.6019/tol.bindingsites-w.2021.00001.1

Submitting your genome wide association study data to the GWAS Catalog

Sollis E.

2021

10.6019/tol.gwas_catalog-w.2021.00001.1

A guide to exploring drug-like compounds and their biological targets using ChEMBL

Hunter F, Manners E.

2021

10.6019/tol.guide-chembl-w.2021.00001.1

A guide to proteomics data analysis using UniProt and InterPro

Bowler-Barnett E, Paysan-Lafosse T, Denny P.

2021

10.6019/tol.guide-uniprot-interpro-w.2021.00001.1

Introduction to CATH database: Quick tour

Waman V, Silitoe I, Mishra A, Orengo C.

2021

10.6019/tol.cathdb-t.2021.00001.1

A guide to organising data associated to a publication using BioStudies

Sarkans U.

2021

10.6019/tol.guide-biostudies-w.2021.00001.1

The BioImage Archive - building a home for life-sciences microscopy data

Hartley M, Kleywegt GJ, Patwardhan A, Sarkans U, Swedlow JR, Brazma A.

2021

10.1101/2021.12.17.473169

Preprints 101 for authors

Levchenko M, Puebla I, Pal Singh S.

2021

10.6019/tol.preprints-w.2021.00001.1

Open access: Finding and accessing open data

Sarkans U, Swan A.

2021

10.6019/tol.openaccessfinding-w.2021.00001.1

Open access: Let's talk about open access, open data and open software

Avles R, Burdett T, Levchenko M, Orchard S, Swan A.

2021

10.6019/tol.openaccessdiscussion-w.2021.00001.1

EMBL-EBI Tools: An introduction

Swan A, Pearce M, Madhusoodanan N, Zaru R, Griss J, Perry E, Nuka G.

2021

10.6019/tol.ebitools-t.2021.00001.1

A guide to...: Introducing concepts and resources in bioinformatics

Sarkans U, Madhusoodanan N, Mushtaq A, Petrov A, Griffiths-Jones S, Ontiveros-Palacios N, Nawrocki E, Griss J, Meldal B, Bowler-Barnett E, Paysan-Lafosse T, Armstrong D, Manners E, Hunter F, Cornu H, O’Donovan C, Harrus D, Zaru R, Pearce M, Eduardo Ribas C, Sweeney B, Swan A, Mishra A.

2021

10.6019/tol.guidewebinarseries-t.2021.00001.1

Single-Cell Atlas of Common Variable Immunodeficiency reveals germinal center-associated epigenetic dysregulation in B cell responses

Rodríguez-Ubreva J, Arutyunyan A, Bonder MJ, Pino-Molina LD, Clark SJ, de la Calle-Fabregat C, Garcia-Alonso L, Handfield L, Ciudad L, Andrés-León E, Krueger F, Català-Moll F, Rodríguez-Cortez VC, Polanski K, Mamanova L, van Dongen S, Kiselev VY, Martínez-Saavedra MT, Heyn H, Martín J, Warnatz K, López-Granados E, Rodríguez-Gallego C, Stegle O, Kelsey G, Vento-Tormo R, Ballestar E.

2021

10.1101/2021.12.20.473453

Open access: publications and preprints

Levchenko M.

2021

10.6019/tol.openaccesspublications-w.2021.00001.1

A guide to EBI Search

Pearce M.

2021

10.6019/tol.ebisearch-w.2021.00001.1

Retrieving biological data from EMBL-EBI resources using Dbfetch

Madhusoodanan N, Madeira F.

2021

10.6019/tol.dbfetch-w.2021.00001.1

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

Wang S, García-Seisdedos D, Prakash A, Kundu DJ, Collins A, George N, Fexova S, Moreno P, Papatheodorou I, Jones AR, Vizcaíno JA.

2021

10.1101/2021.12.20.473413

Introduction to exploring genome-phenome data with EGA

Shaju D, Kerry G.

2021

10.6019/tol.ega-w.2021.00001.1

A guide to sequence similarity search for biomolecular sequences

Madhusoodanan N.

2021

10.6019/tol.seqsimilaritysearch-w.2021.00001.1

A guide to the maintenance of life science data by biocurators

O'Donovan C, Meldal B, Harrus D, Zaru R.

2021

10.6019/tol.biocurators-w.2021.00001.1

BioSamples: a FAIR sample metadata archive

Xu F.

2021

10.6019/tol.biosamples-w.2021.00001.1

The future of preprint peer review

Levchenko M, Pariente N, Giraud T, Shannon P, Lemberger T.

2021

10.6019/tol.preprintpeer-w.2021.00001.1

3D-Strudel - a novel model-dependent map-feature validation method for high-resolution cryo-EM structures

Istrate A, Wang Z, Murshudov GN, Patwardhan A, Kleywegt GJ.

2021

10.1101/2021.12.16.472999

LY6S, a New Interferon-Inducible Human Member of the Ly6a-Subfamily Expressed by Spleen Cells and Associated with Inflammation and Viral Resistance

Shmerling M, Chalik M, Smorodinsky NI, Meeker A, Roy S, Sagi-Assif O, Meshel T, Danilevsky A, Shomron N, Levinger S, Nishry B, Baruchi D, Shargorodsky A, Ziv R, Sarusi-Portuguez A, Lahav M, Ehrlich M, Braschi B, Bruford E, Witz IP, Wreschner DH.

2021

10.1101/2021.12.16.472998

Towards a structurally resolved human protein interaction network

Elofsson A, Burke D, Bryant P, Barrio-Hernandez I, Memon D, Pozzati G, Shenoy A, Zhu W, Dunham A, Albanese P, Keller A, Scheltema R, Bruce J, Leitner A, Kundrotas P, Beltrao P.

2021

10.21203/rs.3.rs-1098605/v1

Transcriptional differences between JAK2-V617F and wild-type bone marrow cells in patients with myeloproliferative neoplasms.

Van Egeren D, Kamaz B, Liu S, Nguyen M, Reilly CR, Kalyva M, DeAngelo DJ, Galinsky I, Wadleigh M, Winer ES, Luskin MR, Stone RM, Garcia JS, Hobbs GS, Michor F, Cortes-Ciriano I, Mullally A, Hormoz S.

2021

10.1016/j.exphem.2021.12.364

Genetic, parental and lifestyle factors influence telomere length

Andreu-Sánchez S, Aubert G, Ripoll-Cladellas A, Henkelman S, Zhernakova DV, Sinha T, Kurilshikov A, Cenit MC, Bonder MJ, Franke L, Wijmenga C, Fu J, van der Wijst MG, Melé M, Lansdorp P, Zhernakova A, Lifelines cohort study.

2021

10.1101/2021.12.14.472541

Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides.

Umer HM, Audain E, Zhu Y, Pfeuffer J, Sachsenberg T, Lehtiö J, Branca R, Perez-Riverol Y.

2021

10.1093/bioinformatics/btab838

Conformational variation in enzyme catalysis: A structural study on catalytic residues

Riziotis IG, Ribeiro AJM, Borkakoti N, Thornton JM.

2021

10.1101/2021.12.12.472283

RNA modifications detection by comparative Nanopore direct RNA sequencing.

Leger A, Amaral PP, Pandolfini L, Capitanchik C, Capraro F, Miano V, Migliori V, Toolan-Kerr P, Sideri T, Enright AJ, Tzelepis K, van Werven FJ, Luscombe NM, Barbieri I, Ule J, Fitzgerald T, Birney E, Leonardi T, Kouzarides T.

2021

10.1038/s41467-021-27393-3

Mapping the Melanoma Plasma Proteome (MPP) Using Single-Shot Proteomics Interfaced with the WiMT Database.

Almeida N, Rodriguez J, Pla Parada I, Perez-Riverol Y, Woldmar N, Kim Y, Oskolas H, Betancourt L, Valdés JG, Sahlin KB, Pizzatti L, Szasz AM, Kárpáti S, Appelqvist R, Malm J, B Domont G, C S Nogueira F, Marko-Varga G, Sanchez A.

2021

10.3390/cancers13246224

Large Scale Discovery of Microbial Fibrillar Adhesins and Identification of Novel Members of Adhesive Domain Families

Monzon V, Bateman A.

2021

10.1101/2021.12.07.471604

A crowdsourcing open platform for literature curation in UniProt.

Wang Y, Wang Q, Huang H, Huang W, Chen Y, McGarvey PB, Wu CH, Arighi CN, UniProt Consortium.

2021

10.1371/journal.pbio.3001464

geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.

Missarova A, Jain J, Butler A, Ghazanfar S, Stuart T, Brusko M, Wasserfall C, Nick H, Brusko T, Atkinson M, Satija R, Marioni JC.

2021

10.1186/s13059-021-02548-z

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Waterhouse RM, Adam-Blondon A, Agosti D, Baldrian P, Balech B, Corre E, Davey RP, Lantz H, Pesole G, Quast C, Glöckner FO, Raes N, Sandionigi A, Santamaria M, Addink W, Vohradsky J, Nunes-Jorge A, Willassen NP, Lanfear J.

2021

10.12688/f1000research.73825.1

Target 2035 - update on the quest for a probe for every protein.

Müller S, Ackloo S, Al Chawaf A, Al-Lazikani B, Antolin A, Baell JB, Beck H, Beedie S, Betz UAK, Bezerra GA, Brennan PE, Brown D, Brown PJ, Bullock AN, Carter AJ, Chaikuad A, Chaineau M, Ciulli A, Collins I, Dreher J, Drewry D, Edfeldt K, Edwards AM, Egner U, Frye SV, Fuchs SM, Hall MD, Hartung IV, Hillisch A, Hitchcock SH, Homan E, Kannan N, Kiefer JR, Knapp S, Kostic M, Kubicek S, Leach AR, Lindemann S, Marsden BD, Matsui H, Meier JL, Merk D, Michel M, Morgan MR, Mueller-Fahrnow A, Owen DR, Perry BG, Rosenberg SH, Saikatendu KS, Schapira M, Scholten C, Sharma S, Simeonov A, Sundström M, Superti-Furga G, Todd MH, Tredup C, Vedadi M, von Delft F, Willson TM, Winter GE, Workman P, Arrowsmith CH.

2021

10.1039/d1md00228g

Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches

Thornlow B, Kramer A, Ye C, De Maio N, McBroome J, Hinrichs AS, Lanfear R, Turakhia Y, Corbett-Detig R.

2021

10.1101/2021.12.02.471004

Cysteine and iron accelerate the formation of ribose-5-phosphate, providing insights into the evolutionary origins of the metabolic network structure.

Piedrafita G, Varma SJ, Castro C, Messner CB, Szyrwiel L, Griffin JL, Ralser M.

2021

10.1371/journal.pbio.3001468

Accounting for spatial sampling patterns in Bayesian phylogeography.

Guindon S, De Maio N.

2021

10.1073/pnas.2105273118

A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees.

McBroome J, Thornlow B, Hinrichs AS, Kramer A, De Maio N, Goldman N, Haussler D, Corbett-Detig R, Turakhia Y.

2021

10.1093/molbev/msab264

Enhancing the interoperability of glycan data flow between ChEBI, PubChem and GlyGen.

Navelkar R, Owen G, Mutherkrishnan V, Thiessen P, Cheng T, Bolton E, Edwards N, Tiemeyer M, Campbell MP, Martin M, Vora J, Kahsay R, Mazumder R.

2021

10.1093/glycob/cwab078

Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature.

Lange M, Alako BTF, Cochrane G, Ghaffar M, Mascher M, Habekost PK, Hillebrand U, Scholz U, Schorch F, Freitag J, Scholz AH.

2021

10.1093/gigascience/giab084

COVID-19 Disease Map, a computational knowledge repository of 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, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, 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 JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, 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, Senff-Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, 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, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Willighagen 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, COVID-19 Disease Map Community.

2021

10.15252/msb.202110851

Myth-busting the provider-user relationship for digital sequence information.

Scholz AH, Lange M, Habekost P, Oldham P, Cancio I, Cochrane G, Freitag J.

2021

10.1093/gigascience/giab085

REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.

Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A.

2021

10.1038/s41592-021-01166-8

A global view of standards for open image data formats and repositories.

Swedlow JR, Kankaanpää P, Sarkans U, Goscinski W, Galloway G, Malacrida L, Sullivan RP, Härtel S, Brown CM, Wood C, Keppler A, Paina F, Loos B, Zullino S, Longo DL, Aime S, Onami S.

2021

10.1038/s41592-021-01113-7

The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Khalifa A, Krawitz PM, Köhler S, Laraway BJ, Lehväslaiho H, Lloyd KC, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Schofield PN, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C, Haendel MA, Robinson PN.

2021

10.1101/2021.11.27.21266944

What makes a megaplasmid?

Hall JPJ, Botelho J, Cazares A, Baltrus DA.

2021

10.1098/rstb.2020.0472

Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases.

Doğan T, Akhan Güzelcan E, Baumann M, Koyas A, Atas H, Baxendale IR, Martin M, Cetin-Atalay R.

2021

10.1371/journal.pcbi.1009171

Nanopore ReCappable Sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs

Ugolini C, Mulroney L, Leger A, Castelli M, Criscuolo E, Williamson MK, Davidson AD, Almuqrin A, Giambruno R, Jain M, Frige G, Olsen H, Tzertzinis G, Schildkraut I, Wulf MG, Corrêa IR, Ettwiller L, Clementi N, Clementi M, Mancini N, Birney E, Akeson M, Nicassio F, Matthews DA, Leonardi T.

2021

10.1101/2021.11.24.469860

A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics

Van Puyvelde B, Daled S, Willems S, Gabriels R, de Peredo AG, Chaoui K, Mouton-Barbosa E, Bouyssié D, Boonen K, Hughes CJ, Gethings LA, Perez-Riverol Y, Bloomfield N, Tate S, Schiltz O, Martens L, Deforce D, Dhaenens M.

2021

10.1101/2021.11.24.469852

Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor-A tutorial.

Hunt SE, Moore B, Amode RM, Armean IM, Lemos D, Mushtaq A, Parton A, Schuilenburg H, Szpak M, Thormann A, Perry E, Trevanion SJ, Flicek P, Yates AD, Cunningham F.

2021

10.1002/humu.24298

PDBsum extras: SARS-CoV-2 and AlphaFold models.

Laskowski RA, Thornton JM.

2021

10.1002/pro.4238

Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions.

Carrascoza F, Antczak M, Miao Z, Westhof E, Szachniuk M.

2021

10.1261/rna.078685.121

Ten Simple Rules for FAIR Sharing of Experimental and Clinical Data with the Modeling Community

König M, Grzegorzewski J, Golebiewski M, Hermjakob H, Hucka M, Olivier B, Keating S, Nickerson D, Schreiber F, Sheriff R, Waltemath D.

2021

10.20944/preprints202108.0303.v2

Characterizing and explaining impact of disease-associated mutations in proteins without known structures or structural homologues

Sen N, Anishchenko I, Bordin N, Sillitoe I, Velankar S, Baker D, Orengo C.

2021

10.1101/2021.11.17.468998

Multiple adaptive solutions to face climatic constraints: novel insights in the debate over the role of convergence in local adaptation

Benjelloun B, Leempoel K, Boyer F, Stucki S, Streeter I, Orozco-terWengel P, Alberto FJ, Servin B, Biscarini F, Alberti A, Engelen S, Stella A, Colli L, Coissac E, Bruford MW, Ajmone-Marsan P, Negrini R, Clarke L, Flicek P, Chikhi A, Joost S, Taberlet P, Pompanon F.

2021

10.1101/2021.11.18.469099

Metagenomics approach for Polymyxa betae genome assembly enables comparative analysis towards deciphering the intracellular parasitic lifestyle of the plasmodiophorids.

Decroës A, Li JM, Richardson L, Mutasa-Gottgens E, Lima-Mendez G, Mahillon M, Bragard C, Finn RD, Legrève A.

2021

10.1016/j.ygeno.2021.11.018

Cardiac Investigations in Sudden Unexpected Death in DEPDC5-Related Epilepsy.

Bacq A, Roussel D, Bonduelle T, Zagaglia S, Maletic M, Ribierre T, Adle-Biassette H, Marchal C, Jennesson M, An I, Genomics England Research Consortium, Picard F, Navarro V, Sisodiya SM, Baulac S.

2021

10.1002/ana.26256

Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean.

Royo-Llonch M, Sánchez P, Ruiz-González C, Salazar G, Pedrós-Alió C, Sebastián M, Labadie K, Paoli L, M Ibarbalz F, Zinger L, Churcheward B, Tara Oceans Coordinators, Chaffron S, Eveillard D, Karsenti E, Sunagawa S, Wincker P, Karp-Boss L, Bowler C, Acinas SG.

2021

10.1038/s41564-021-00979-9

The Data Use Ontology to streamline responsible access to human biomedical datasets.

Lawson J, Cabili MN, Kerry G, Boughtwood T, Thorogood A, Alper P, Bowers SR, Boyles RR, Brookes AJ, Brush M, Burdett T, Clissold H, Donnelly S, Dyke SOM, Freeberg MA, Haendel MA, Hata C, Holub P, Jeanson F, Jene A, Kawashima M, Kawashima S, Konopko M, Kyomugisha I, Li H, Linden M, Rodriguez LL, Morita M, Mulder N, Muller J, Nagaie S, Nasir J, Ogishima S, Ota Wang V, Paglione LD, Pandya RN, Parkinson H, Philippakis AA, Prasser F, Rambla J, Reinold K, Rushton GA, Saltzman A, Saunders G, Sofia HJ, Spalding JD, Swertz MA, Tulchinsky I, van Enckevort EJ, Varma S, Voisin C, Yamamoto N, Yamasaki C, Zass L, Guidry Auvil JM, Nyrönen TH, Courtot M.

2021

10.1016/j.xgen.2021.100028

Selective clonal persistence of human retroviruses in vivo: radial chromatin organization, integration site and host transcription

Melamed A, Fitzgerald TW, Wang Y, Ma J, Birney E, Bangham CRM.

2021

10.1101/2021.11.10.467892

Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.

Blackwell GA, Hunt M, Malone KM, Lima L, Horesh G, Alako BTF, Thomson NR, Iqbal Z.

2021

10.1371/journal.pbio.3001421

Towards a structurally resolved human protein interaction network

Burke DF, Bryant P, Barrio-Hernandez I, Memon D, Pozzati G, Shenoy A, Zhu W, Dunham AS, Albanese P, Keller A, Scheltema RA, Bruce JE, Leitner A, Kundrotas P, Beltrao P, Elofsson A.

2021

10.1101/2021.11.08.467664

Cell type ontologies of the Human Cell Atlas.

Osumi-Sutherland D, Xu C, Keays M, Levine AP, Kharchenko PV, Regev A, Lein E, Teichmann SA.

2021

10.1038/s41556-021-00787-7

Anatomical structures, cell types and biomarkers of the Human Reference Atlas.

Börner K, Teichmann SA, Quardokus EM, Gee JC, Browne K, Osumi-Sutherland D, Herr BW, Bueckle A, Paul H, Haniffa M, Jardine L, Bernard A, Ding SL, Miller JA, Lin S, Halushka MK, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G.

2021

10.1038/s41556-021-00788-6

Validation analysis of EMDB entries

Wang Z, Patwardhan A, Kleywegt GJ.

2021

10.1101/2021.11.02.466942

MS2Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates

Declercq A, Bouwmeester R, Hirschler A, Carapito C, Degroeve S, Degroeve S, Martens L, Gabriels R.

2021

10.1101/2021.11.02.466886

100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care - Preliminary Report.

100,000 Genomes Project Pilot Investigators, Smedley D, Smith KR, Martin A, Thomas EA, McDonagh EM, Cipriani V, Ellingford JM, Arno G, Tucci A, Vandrovcova J, Chan G, Williams HJ, Ratnaike T, Wei W, Stirrups K, Ibanez K, Moutsianas L, Wielscher M, Need A, Barnes MR, Vestito L, Buchanan J, Wordsworth S, Ashford S, Rehmström K, Li E, Fuller G, Twiss P, Spasic-Boskovic O, Halsall S, Floto RA, Poole K, Wagner A, Mehta SG, Gurnell M, Burrows N, James R, Penkett C, Dewhurst E, Gräf S, Mapeta R, Kasanicki M, Haworth A, Savage H, Babcock M, Reese MG, Bale M, Baple E, Boustred C, Brittain H, de Burca A, Bleda M, Devereau A, Halai D, Haraldsdottir E, Hyder Z, Kasperaviciute D, Patch C, Polychronopoulos D, Matchan A, Sultana R, Ryten M, Tavares ALT, Tregidgo C, Turnbull C, Welland M, Wood S, Snow C, Williams E, Leigh S, Foulger RE, Daugherty LC, Niblock O, Leong IUS, Wright CF, Davies J, Crichton C, Welch J, Woods K, Abulhoul L, Aurora P, Bockenhauer D, Broomfield A, Cleary MA, Lam T, Dattani M, Footitt E, Ganesan V, Grunewald S, Compeyrot-Lacassagne S, Muntoni F, Pilkington C, Quinlivan R, Thapar N, Wallis C, Wedderburn LR, Worth A, Bueser T, Compton C, Deshpande C, Fassihi H, Haque E, Izatt L, Josifova D, Mohammed S, Robert L, Rose S, Ruddy D, Sarkany R, Say G, Shaw AC, Wolejko A, Habib B, Burns G, Hunter S, Grocock RJ, Humphray SJ, Robinson PN, Haendel M, Simpson MA, Banka S, Clayton-Smith J, Douzgou S, Hall G, Thomas HB, O'Keefe RT, Michaelides M, Moore AT, Malka S, Pontikos N, Browning AC, Straub V, Gorman GS, Horvath R, Quinton R, Schaefer AM, Yu-Wai-Man P, Turnbull DM, McFarland R, Taylor RW, O'Connor E, Yip J, Newland K, Morris HR, Polke J, Wood NW, Campbell C, Camps C, Gibson K, Koelling N, Lester T, Németh AH, Palles C, Patel S, Roy NBA, Sen A, Taylor J, Cacheiro P, Jacobsen JO, Seaby EG, Davison V, Chitty L, Douglas A, Naresh K, McMullan D, Ellard S, Temple IK, Mumford AD, Wilson G, Beales P, Bitner-Glindzicz M, Black G, Bradley JR, Brennan P, Burn J, Chinnery PF, Elliott P, Flinter F, Houlden H, Irving M, Newman W, Rahman S, Sayer JA, Taylor JC, Webster AR, Wilkie AOM, Ouwehand WH, Raymond FL, Chisholm J, Hill S, Bentley D, Scott RH, Fowler T, Rendon A, Caulfield M.

2021

10.1056/nejmoa2035790

The contribution of common regulatory and protein-coding TYR variants in the genetic architecture of albinism

Michaud V, Lasseaux E, Green DJ, Gerrard DT, Plaisant C, Fitzgerald T, Birney E, Arveiler B, Black GC, Sergouniotis PI, UK Biobank Eye and Vision Consortium.

2021

10.1101/2021.11.01.21265733

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SOM, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Guidry Auvil JM, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CWL, Hobb AE, Hoffmann MM, Hoffman OM, Holub P, Hsu JS, Hubaux J-P, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJM, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor S-S, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Liyanage IU, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O'Connor BD, Oesterle S, Ogishima S, Wang VO, Paglione LAD, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Varmathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E.

2021

10.1016/j.xgen.2021.100029

Updates to HCOP: the HGNC comparison of orthology predictions tool.

Yates B, Gray KA, Jones TEM, Bruford EA.

2021

10.1093/bib/bbab155

Author Correction: 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.

2021

10.1038/s41590-021-01036-7

The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification.

Wagner AH, Babb L, Alterovitz G, Baudis M, Brush M, Cameron DL, Cline M, Griffith M, Griffith OL, Hunt SE, Kreda D, Lee JM, Li S, Lopez J, Moyer E, Nelson T, Patel RY, Riehle K, Robinson PN, Rynearson S, Schuilenburg H, Tsukanov K, Walsh B, Konopko M, Rehm HL, Yates AD, Freimuth RR, Hart RK.

2021

10.1016/j.xgen.2021.100027

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SOM, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Auvil JMG, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CWL, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJM, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Udara Liyanage I, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O'Connor BD, Oesterle S, Ogishima S, Wang VO, Paglione LAD, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E.

2021

10.1016/j.xgen.2021.100029

The gene regulation knowledge commons: the action area of GREEKC.

Kuiper M, Bonello J, Fernández-Breis JT, Bucher P, Futschik ME, Gaudet P, Kulakovskiy IV, Licata L, Logie C, Lovering RC, Makeev VJ, Orchard S, Panni S, Perfetto L, Sant D, Schulz S, Vercruysse S, Zerbino DR, Lægreid A, GRECO Consortium.

2021

10.1016/j.bbagrm.2021.194768

Tuberculosis in badgers where the bovine tuberculosis epidemic is expanding in cattle in England.

Swift BMC, Barron ES, Christley R, Corbetta D, Grau-Roma L, Jewell C, O'Cathail C, Mitchell A, Phoenix J, Prosser A, Rees C, Sorley M, Verin R, Bennett M.

2021

10.1038/s41598-021-00473-6

ELIXIR Software Management Plan for Life Sciences

Alves R, Bampalikis D, Castro LJ, Fernández JM, Harrow J, Kuzak M, Martin E, Psomopoulos FE, Via A.

2021

10.37044/osf.io/k8znb

Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.

Garg M, Li X, Moreno P, Papatheodorou I, Shu Y, Brazma A, Miao Z.

2021

10.1038/s41598-021-00121-z

A method for independent estimation of false localisation rate for phosphoproteomics

Ramsbottom KA, Prakash A, Riverol YP, Camacho OM, Martin M, Vizcaíno JA, Deutsch EW, Jones AR.

2021

10.1101/2021.10.18.464791

High-throughput functional characterization of protein phosphorylation sites in yeast.

Viéitez C, Busby BP, Ochoa D, Mateus A, Memon D, Galardini M, Yildiz U, Trovato M, Jawed A, Geiger AG, Oborská-Oplová M, Potel CM, Vonesch SC, Szu Tu C, Shahraz M, Stein F, Steinmetz LM, Panse VG, Noh KM, Savitski MM, Typas A, Beltrao P.

2021

10.1038/s41587-021-01051-x

Correction: Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images.

Currant H, Hysi P, Fitzgerald TW, Gharahkhani P, Bonnemaijer PWM, Senabouth A, Hewitt AW, UK Biobank Eye and Vision Consortium, International Glaucoma Genetics Consortium, Atan D, Aung T, Charng J, Choquet H, Craig J, Khaw PT, Klaver CCW, Kubo M, Ong JS, Pasquale LR, Reisman CA, Daniszewski M, Powell JE, Pébay A, Simcoe MJ, Thiadens AAHJ, van Duijn CM, Yazar S, Jorgenson E, MacGregor S, Hammond CJ, Mackey DA, Wiggs JL, Foster PJ, Patel PJ, Birney E, Khawaja AP.

2021

10.1371/journal.pgen.1009858

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.

2021

10.1016/j.bbagrm.2021.194765

Genomic reconstruction of the SARS-CoV-2 epidemic in England.

Vöhringer HS, Sanderson T, Sinnott M, De Maio N, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani CV, Gonçalves S, Jackson DK, Johnston I, Jung AW, Saint C, Sillitoe J, Suciu M, Goldman N, Panovska-Griffiths J, Wellcome Sanger Institute COVID-19 Surveillance Team, COVID-19 Genomics UK (COG-UK) Consortium*, Birney E, Volz E, Funk S, Kwiatkowski D, Chand M, Martincorena I, Barrett JC, Gerstung M.

2021

10.1038/s41586-021-04069-y

Path4Drug: Data Science Workflow for Identification of Tissue-Specific Biological Pathways Modulated by Toxic Drugs.

Füzi B, Gurinova J, Hermjakob H, Ecker GF, Sheriff R.

2021

10.3389/fphar.2021.708296

Brain Data Standards Ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex

Tan SZK, Kir H, Aevermann B, Gillespie T, Hawrylycz M, Lein E, Matentzoglu N, Miller J, Mollenkopf TS, Mungall CJ, Ray PL, Sanchez REA, Scheuermann RH, Staats B, Zhang YH, Osumi-Sutherland D.

2021

10.1101/2021.10.10.463703

Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication.

Zhu F, Yin ZT, Wang Z, Smith J, Zhang F, Martin F, Ogeh D, Hincke M, Lin FB, Burt DW, Zhou ZK, Hou SS, Zhao QS, Li XQ, Ding SR, Li GS, Yang FX, Hao JP, Zhang Z, Lu LZ, Yang N, Hou ZC.

2021

10.1038/s41467-021-26272-1

DECIPHER: Supporting the interpretation and sharing of rare disease phenotype-linked variant data to advance diagnosis and research

Foreman J, Brent S, Perrett D, Bevan A, Hunt S, Cunningham F, Hurles M, Firth H.

2021

10.22541/au.163389792.27006605/v1

Author Correction: Macroscale patterns of oceanic zooplankton composition and size structure.

Brandão MC, Benedetti F, Martini S, Soviadan YD, Irisson JO, Romagnan JB, Elineau A, Desnos C, Jalabert L, Freire AS, Picheral M, Guidi L, Gorsky G, Bowler C, Karp-Boss L, Henry N, de Vargas C, Sullivan MB, Tara Oceans Consortium Coordinators, Stemmann L, Lombard F.

2021

10.1038/s41598-021-99772-1

A proteomics sample metadata representation for multiomics integration and big data analysis.

Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y.

2021

10.1038/s41467-021-26111-3

The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life

McKenna V, Archibald JM, Beinart R, Dawson MN, Hentschel U, Keeling PJ, Lopez JV, Martín-Durán JM, Petersen JM, Sigwart JD, Simakov O, Sutherland KR, Sweet M, Talbot N, Thompson AW, Bender S, Harrison PW, Rajan J, Cochrane G, Berriman M, Lawniczak M, Blaxter M.

2021

10.12688/wellcomeopenres.17222.1

HUGO Gene Nomenclature Committee (HGNC) recommendations for the designation of gene fusions.

Bruford EA, Antonescu CR, Carroll AJ, Chinnaiyan A, Cree IA, Cross NCP, Dalgleish R, Gale RP, Harrison CJ, Hastings RJ, Huret JL, Johansson B, Le Beau M, Mecucci C, Mertens F, Verhaak R, Mitelman F.

2021

10.1038/s41375-021-01436-6

The production of 4,182 mouse lines identifies experimental and biological variables impacting Cas9-mediated mutant mouse line production

Elrick H, Peterson KA, Wood JA, Lanza DG, Acar EF, Teboul L, Ryder EJ, Ayabe S, Birling M, Caulder A, Chiani F, Codner GF, Doe B, Duddy G, Gambadoro A, Gertsenstein M, Gomez-Segura A, Goodwin LO, Ju C, Kasparek P, King R, Lee D, Lee H, Lintott LG, Liu Z, Lorenzo I, Mackenzie M, Marschall S, Matthews P, Ruhe M, Santos L, Seavitt JR, Seisenberger C, Wardle-Jones H, Willis BJ, Zhang J, Zhao J, Zhou F, Adams DJ, Bradley A, Braun RE, DeMayo FJ, Dickinson ME, Gao X, Hérault Y, Hrabĕ de Angelis M, Lloyd KCK, Mallon A, Mammano F, McKerlie C, Meehan T, Parkinson H, Ramirez-Solis R, Sedlacek R, Seong JK, Skarnes WC, Smedley D, Tamura M, Wells S, White JK, Wurst W, Yoshiki A, Murray SA, Heaney JD, Nutter LMJ, International Mouse Phenotyping Consortium.

2021

10.1101/2021.10.06.463037

Citrobacter amalonaticus Inhibits the Growth of Citrobacter rodentium in the Gut Lumen.

Mullineaux-Sanders C, Carson D, Hopkins EGD, Glegola-Madejska I, Escobar-Zepeda A, Browne HP, Lawley TD, Frankel G.

2021

10.1128/mbio.02410-21

The International Human Genome Project.

Birney E.

2021

10.1093/hmg/ddab198

COVID19 Disease Map, a computational knowledge repository of 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, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, 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 JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, 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, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, 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, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël 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, COVID-19 Disease Map Community.

2021

10.15252/msb.202110387

AlphaFold heralds a data-driven revolution in biology and medicine.

Thornton JM, Laskowski RA, Borkakoti N.

2021

10.1038/s41591-021-01533-0

Sequencing-based genome-wide association studies reporting standards.

McMahon A, Lewis E, Buniello A, Cerezo M, Hall P, Sollis E, Parkinson H, Hindorff LA, Harris LW, MacArthur JAL.

2021

10.1016/j.xgen.2021.100005

A Minimally Morphologically Destructive Approach for DNA Retrieval and Whole-Genome Shotgun Sequencing of Pinned Historic Dipteran Vector Species.

Korlević P, McAlister E, Mayho M, Makunin A, Flicek P, Lawniczak MKN.

2021

10.1093/gbe/evab226

The growing need for controlled data access models in clinical proteomics and metabolomics.

Keane TM, O'Donovan C, Vizcaíno JA.

2021

10.1038/s41467-021-26110-4

Cell type-specific novel long non-coding RNA and circular RNA in the BLUEPRINT hematopoietic transcriptomes atlas.

Grassi L, Izuogu OG, Jorge NAN, 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 JHA, Yaspo ML, Stunnenberg HG, Ouwehand WH, Passetti F, Turro E, Frontini M.

2021

10.3324/haematol.2019.238147

The risks of using unapproved gene symbols.

Braschi B, Seal RL, Tweedie S, Jones TEM, Bruford EA.

2021

10.1016/j.ajhg.2021.09.004

Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases.

Saverimuttu SCC, Kramarz B, Rodríguez-López M, Garmiri P, Attrill H, Thurlow KE, Makris M, de Miranda Pinheiro S, Orchard S, Lovering RC.

2021

10.1093/database/baab067

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.

Jackson R, Matentzoglu N, Overton JA, Vita R, Balhoff JP, Buttigieg PL, Carbon S, Courtot M, Diehl AD, Dooley DM, Duncan WD, Harris NL, Haendel MA, Lewis SE, Natale DA, Osumi-Sutherland D, Ruttenberg A, Schriml LM, Smith B, Stoeckert CJ, Vasilevsky NA, Walls RL, Zheng J, Mungall CJ, Peters B.

2021

10.1093/database/baab069

Differential abundance testing on single-cell data using k-nearest neighbor graphs.

Dann E, Henderson NC, Teichmann SA, Morgan MD, Marioni JC.

2021

10.1038/s41587-021-01033-z

Quality control and removal of technical variation of NMR metabolic biomarker data in ∼120,000 UK Biobank participants

Ritchie SC, Surendran P, Karthikeyan S, Lambert SA, Bolton T, Pennells L, Danesh J, Di Angelantonio E, Butterworth AS, Inouye M.

2021

10.1101/2021.09.24.21264079

A structural biology community assessment of AlphaFold 2 applications

Akdel M, Pires DEV, Porta Pardo E, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Ruiz Serra V, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Lindorff-Larsen K, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P.

2021

10.1101/2021.09.26.461876

K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes.

Contreras-Moreira B, Filippi CV, Naamati G, García Girón C, Allen JE, Flicek P.

2021

10.1002/tpg2.20143

Correction: Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease.

Audain E, Wilsdon A, Breckpot J, Izarzugaza JMG, Fitzgerald TW, Kahlert AK, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H, Bak M, Bassett AS, Benson DW, Berger F, Daehnert I, Devriendt K, Dittrich S, Daubeney PE, Garg V, Hackmann K, Hoff K, Hofmann P, Dombrowsky G, Pickardt T, Bauer U, Keavney BD, Klaassen S, Kramer HH, Marshall CR, Milewicz DM, Lemaire S, Coselli JS, Mitchell ME, Tomita-Mitchell A, Prakash SK, Stamm K, Stewart AFR, Silversides CK, Siebert R, Stiller B, Rosenfeld JA, Vater I, Postma AV, Caliebe A, Brook JD, Andelfinger G, Hurles ME, Thienpont B, Larsen LA, Hitz MP.

2021

10.1371/journal.pgen.1009809

Ten simple rules to make your computing more environmentally sustainable.

Lannelongue L, Grealey J, Bateman A, Inouye M.

2021

10.1371/journal.pcbi.1009324

A generalisable approach to drug susceptibility prediction for M. tuberculosis using machine learning and whole-genome sequencing

The CRyPTIC consortium, Lachapelle AS.

2021

10.1101/2021.09.14.458035

Variant calling across 505 openly consented samples from four Gambian populations on GRCh38

Lowy E, Fairley S, Flicek P.

2021

10.12688/wellcomeopenres.17001.1

Genome-wide association studies of global Mycobacterium tuberculosis resistance to thirteen antimicrobials in 10,228 genomes

The CRyPTIC Consortium, Earle SG, Wilson DJ.

2021

10.1101/2021.09.14.460272

A data compendium of Mycobacterium tuberculosis antibiotic resistance

Brankin A, Malone KM, The CRyPTIC Consortium.

2021

10.1101/2021.09.14.460274

Pleiotropy data resource as a primer for investigating co-morbidities/multi-morbidities and their role in disease.

Muñoz-Fuentes V, Haselimashhadi H, Santos L, Westerberg H, Parkinson H, Mason J.

2021

10.1007/s00335-021-09917-w

Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes

Hunt M, Letcher B, Malone K, Nguyen G, Hall M, Colquhoun R, Lima L, Schatz M, Ramakrishnan S, Iqbal Z, CRyPTIC consortium.

2021

10.1101/2021.09.15.460475

Breast cancer risks associated with missense variants in breast cancer susceptibility genes

Dorling L, Carvalho S, Allen J, Parsons MT, Fortuno C, González-Neira A, Heijl SM, Adank MA, Ahearn TU, Andrulis IL, Auvinen P, Becher H, Beckmann MW, Behrens S, Bermisheva M, Bogdanova NV, Bojesen SE, Bolla MK, Bremer M, Briceno I, Camp NJ, Campbell A, Castelao JE, Chang-Claude J, Chanock SJ, Chenevix-Trench G, Collée JM, Czene K, Dennis J, Dörk T, Eriksson M, Evans DG, Fasching PA, Figueroa J, Flyger H, Gabrielson M, Gago-Dominguez M, García-Closas M, Giles GG, Glendon G, Guénel P, Gündert M, Hadjisavvas A, Hahnen E, Hall P, Hamann U, Harkness EF, Hartman M, Hogervorst FB, Hollestelle A, Hoppe R, Howell A, Jakubowska A, Jung A, Khusnutdinova E, Kim S, Ko Y, Kristensen VN, Lakeman IM, Li J, Lindblom A, Loizidou MA, Lophatananon A, Lubiński J, Luccarini C, Madsen MJ, Mannermaa A, Manoochehri M, Margolin S, Mavroudis D, Milne RL, Mohd Taib NA, Muir K, Nevanlinna H, Newman WG, Oosterwijk JC, Park SK, Peterlongo P, Radice P, Saloustros E, Sawyer EJ, Schmutzler RK, Shah M, Sim X, Southey MC, Surowy H, Suvanto M, Tomlinson I, Torres D, Truong T, van Asperen CJ, Waltes R, Wang Q, Yang XR, Pharoah PD, Schmidt MK, Benitez J, Vroling B, Dunning AM, Teo SH, Kvist A, de la Hoya M, Devilee P, Spurdle AB, Vreeswijk MP, Easton DF, NBCS Collaborators, kConFab Investigators, SGBCC Investigators.

2021

10.1101/2021.09.02.21262369

Pandora: 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.

2021

10.1186/s13059-021-02473-1

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.

Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A, Czaplewski C, Giełdoń A, Kogut M, Lipska AG, Liwo A, Lubecka EA, Maszota-Zieleniak M, Sieradzan AK, Ślusarz R, Wesołowski PA, Zięba K, Del Carpio Muñoz CA, Ichiishi E, Harmalkar A, Gray JJ, Bonvin AMJJ, Ambrosetti F, Vargas Honorato R, Jandova Z, Jiménez-García B, Koukos PI, Van Keulen S, Van Noort CW, Réau M, Roel-Touris J, Kotelnikov S, Padhorny D, Porter KA, Alekseenko A, Ignatov M, Desta I, Ashizawa R, Sun Z, Ghani U, Hashemi N, Vajda S, Kozakov D, Rosell M, Rodríguez-Lumbreras LA, Fernandez-Recio J, Karczynska A, Grudinin S, Yan Y, Li H, Lin P, Huang SY, Christoffer C, Terashi G, Verburgt J, Sarkar D, Aderinwale T, Wang X, Kihara D, Nakamura T, Hanazono Y, Gowthaman R, Guest JD, Yin R, Taherzadeh G, Pierce BG, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Sun Y, Zhu S, Shen Y, Park T, Woo H, Yang J, Kwon S, Won J, Seok C, Kiyota Y, Kobayashi S, Harada Y, Takeda-Shitaka M, Kundrotas PJ, Singh A, Vakser IA, Dapkūnas J, Olechnovič K, Venclovas Č, Duan R, Qiu L, Xu X, Zhang S, Zou X, Wodak SJ.

2021

10.1002/prot.26222

Identifying genetic determinants of inflammatory pain in mice using a large-scale gene-targeted screen.

Wotton JM, Peterson E, Flenniken AM, Bains RS, Veeraragavan S, Bower LR, Bubier JA, Parisien M, Bezginov A, Haselimashhadi H, Mason J, Moore MA, Stewart ME, Clary DA, Delbarre DJ, Anderson LC, D'Souza A, Goodwin LO, Harrison ME, Huang Z, Mckay M, Qu D, Santos L, Srinivasan S, Urban R, Vukobradovic I, Ward CS, Willett AM, Braun RE, Brown SDM, Dickinson ME, Heaney JD, Kumar V, Lloyd KCK, Mallon AM, McKerlie C, Murray SA, Nutter LMJ, Parkinson H, Seavitt JR, Wells S, Samaco RC, Chesler EJ, Smedley D, Diatchenko L, Baumbauer KM, Young EE, Bonin RP, Mandillo S, White JK, International Mouse Phenotyping Consortium.

2021

10.1097/j.pain.0000000000002481

An integrated view of baseline protein expression in human tissues

Prakash A, García-Seisdedos D, Wang S, Kundu DJ, Collins A, George N, Moreno P, Papatheodorou I, Jones AR, Vizcaíno JA.

2021

10.1101/2021.09.10.459811

Fission stories: Using PomBase to understand Schizosaccharomyces pombe biology

Harris MA, Rutherford KM, Hayles J, Lock A, Bähler J, Oliver SG, Mata J, Wood V.

2021

10.1101/2021.09.07.459264

Deep learning for bioimage analysis in developmental biology.

Hallou A, Yevick HG, Dumitrascu B, Uhlmann V.

2021

10.1242/dev.199616

Distinctive prokaryotic microbiomes in sympatric plant roots from a Yucatan cenote.

Escobar-Zepeda A, Rosas-Escobar P, Marquez Valdelamar L, de la Torre P, Partida-Martinez LP, Remegaldo R, Sanchez-Flores A, Vergara F.

2021

10.1186/s13104-021-05746-x

Gramtools enables multiscale variation analysis with genome graphs.

Letcher B, Hunt M, Iqbal Z.

2021

10.1186/s13059-021-02474-0

Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis.

Lohoff T, Ghazanfar S, Missarova A, Koulena N, Pierson N, Griffiths JA, Bardot ES, Eng CL, Tyser RCV, Argelaguet R, Guibentif C, Srinivas S, Briscoe J, Simons BD, Hadjantonakis AK, Göttgens B, Reik W, Nichols J, Cai L, Marioni JC.

2021

10.1038/s41587-021-01006-2

CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq

Cuomo AS, Heinen T, Vagiaki D, Horta D, Marioni JC, Stegle O.

2021

10.1101/2021.09.01.458524

Correction to: Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases.

Zurek B, Ellwanger K, Vissers LELM, Schüle R, Synofzik M, Töpf A, de Voer RM, Laurie S, Matalonga L, Gilissen C, Ossowski S, 't Hoen PAC, Vitobello A, Schulze-Hentrich JM, Riess O, Brunner HG, Brookes AJ, Rath A, Bonne G, Gumus G, Verloes A, Hoogerbrugge N, Evangelista T, Harmuth T, Swertz M, Spalding D, Hoischen A, Beltran S, Graessner H, Solve-RD consortium.

2021

10.1038/s41431-021-00936-4

Correction to: Solving patients with rare diseases through programmatic reanalysis of genome-phenome data.

Matalonga L, Hernández-Ferrer C, Piscia D, Solve-RD SNV-indel working group, Schüle R, Synofzik M, Töpf A, Vissers LELM, de Voer R, Solve-RD DITF-GENTURIS, Solve-RD DITF-ITHACA, Solve-RD DITF-euroNMD, Solve-RD DITF-RND, Tonda R, Laurie S, Fernandez-Callejo M, Picó D, Garcia-Linares C, Papakonstantinou A, Corvó A, Joshi R, Diez H, Gut I, Hoischen A, Graessner H, Beltran S, Solve-RD Consortium.

2021

10.1038/s41431-021-00934-6

Correction: Solving unsolved rare neurological diseases-a Solve-RD viewpoint.

Schüle R, Timmann D, Erasmus CE, Reichbauer J, Wayand M, Solve-RD-DITF-RND, van de Warrenburg B, Schöls L, Wilke C, Bevot A, Zuchner S, Beltran S, Laurie S, Matalonga L, Graessner H, Synofzik M, Solve-RD Consortium.

2021

10.1038/s41431-021-00935-5

Desiderata for the development of next-generation electronic health record phenotype libraries.

Chapman M, Mumtaz S, Rasmussen LV, Karwath A, Gkoutos GV, Gao C, Thayer D, Pacheco JA, Parkinson H, Richesson RL, Jefferson E, Denaxas S, Curcin V.

2021

10.1093/gigascience/giab059

ISA API: An open platform for interoperable life science experimental metadata.

Johnson D, Batista 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 SA, Rocca-Serra P.

2021

10.1093/gigascience/giab060

Modernized uniform representation of carbohydrate molecules in the Protein Data Bank.

Shao C, Feng Z, Westbrook JD, Peisach E, Berrisford J, Ikegawa Y, Kurisu G, Velankar S, Burley SK, Young JY.

2021

10.1093/glycob/cwab039

CROssBAR: comprehensive resource of biomedical relations with 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.

2021

10.1093/nar/gkab543

Personalized profiles for disease risk must capture all facets of health.

McCarthy M, Birney E.

2021

10.1038/d41586-021-02401-0

The Enzyme Portal: an integrative tool for enzyme information and analysis.

Zaru R, Onwubiko J, Ribeiro AJM, Cochrane K, Tyzack JD, Muthukrishnan V, Pravda L, Thornton JM, O'Donovan C, Velanker S, Orchard S, Leach A, Martin MJ.

2021

10.1111/febs.16168

The value of primary transcripts to the clinical and non-clinical genomics community: Survey results and roadmap for improvements.

Morales J, McMahon AC, Loveland J, Perry E, Frankish A, Hunt S, Armean IM, Flicek P, Cunningham F.

2021

10.1002/mgg3.1786

New restraints and validation approaches for nucleic acid structures in PDB-REDO.

de Vries I, Kwakman T, Lu XJ, Hekkelman ML, Deshpande M, Velankar S, Perrakis A, Joosten RP.

2021

10.1107/s2059798321007610

Integration of transcription coregulator complexes with sequence-specific DNA-binding factor interactomes.

Velthuijs N, Meldal B, Geessinck Q, Porras P, Medvedeva Y, Zubritskiy A, Orchard S, Logie C.

2021

10.1016/j.bbagrm.2021.194749

CNest: A Novel Copy Number Association Discovery Method Uncovers 862 New Associations from 200,629 Whole Exome Sequence Datasets in the UK Biobank

Fitzgerald T, Birney E.

2021

10.1101/2021.08.19.456963

Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries.

Moore B, Carvajal-López P, Chauke PA, Cristancho M, Dominguez Del Angel V, Fernandez-Valverde SL, Ghouila A, Gopalasingam P, Guerfali FZ, Matimba A, Morgan SL, Oliveira G, Ras V, Reyes A, De Las Rivas J, Mulder N.

2021

10.1371/journal.pcbi.1009218

Pout2Prot: an efficient tool to create protein (sub)groups from Percolator output files

Schallert K, Verschaffelt P, Mesuere B, Benndorf D, Martens L, Bossche TVD.

2021

10.1101/2021.08.11.455803

Measuring outcomes and impact from the BioHackathon Europe

Garcia Castro LJ, Martin C, Lazarov G, Cernoskova D, Takatsuki T, Harrow J, Rebholz-Schuhmann D.

2021

10.37044/osf.io/3dxhg

geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq

Missarova A, Jain J, Butler A, Ghazanfar S, Stuart T, Brusko M, Wasserfall C, Nick H, Brusko T, Atkinson M, Satija R, Marioni J.

2021

10.1101/2021.08.10.455720

Transcription factors: Bridge between cell signaling and gene regulation.

Weidemüller P, Kholmatov M, Petsalaki E, Zaugg JB.

2021

10.1002/pmic.202000034

Genetic variants associated with cross-disorder and disorder-specific risk for psychiatric disorders are enriched at epigenetically active sites in peripheral lymphoid cells

Lynall M, Soskic B, Hayhurst J, Schwartzentruber J, Levey DF, Pathak GA, Polimanti R, Gelernter J, Stein MB, Trynka G, Clatworthy MR, Bullmore E.

2021

10.1101/2021.08.04.21261606

Late diagnoses of Dravet syndrome: How many individuals are we missing?

Silvennoinen K, Puvirajasinghe C, Hudgell K, Sidhu MK, Martins Custodio H, Genomics England Research Consortium, Jones WD, Balestrini S, Sisodiya SM.

2021

10.1002/epi4.12525

Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region

Turkahia Y, Thornlow B, Hinrichs A, McBroome J, Ayala N, Ye C, De Maio N, Haussler D, Lanfear R, Corbett-Detig R.

2021

10.1101/2021.08.04.455157

Identifying genomic regions and candidate genes selected during the breeding of rice in Vietnam

Higgins J, Santos B, Khanh TD, Trung KH, Duong TD, Phuong Doai NT, Hall A, Dyer S, Ham LH, Caccamo M, De Vega J.

2021

10.1101/2021.08.04.455072

Development and evaluation of a decision prediction tool for the reduction of fungicide applications for the control of strawberry powdery mildew epidemics

Dodgson JLA, Liu B, Wileman HJ, Mutasa-Gottgens ES, Hall AM.

2021

10.1101/2021.08.04.455115

Paenarthrobacter sp. GOM3 Is a Novel Marine Species With Monoaromatic Degradation Relevance.

Rosas-Díaz J, Escobar-Zepeda A, Adaya L, Rojas-Vargas J, Cuervo-Amaya DH, Sánchez-Reyes A, Pardo-López L.

2021

10.3389/fmicb.2021.713702

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Pardo-Palacios F, Reese F, Carbonell-Sala S, Diekhans M, Liang C, Wang D, Williams B, Adams M, Behera A, Lagarde J, Li H, Prjibelski A, Balderrama-Gutierrez G, Çelik MH, De María M, Denslow N, Garcia-Reyero N, Goetz S, Hunter M, Loveland J, Menor C, Moraga D, Mudge J, Takahashi H, Tang A, Youngworth I, Carninci P, Guigó R, Tilgner H, Wold B, Vollmers C, Sheynkman G, Frankish A, Au KF, Conesa A, Mortazavi A, Brooks AN.

2021

10.21203/rs.3.rs-777702/v1

Macroscale patterns of oceanic zooplankton composition and size structure.

Brandão MC, Benedetti F, Martini S, Soviadan YD, Irisson JO, Romagnan JB, Elineau A, Desnos C, Jalabert L, Freire AS, Picheral M, Guidi L, Gorsky G, Bowler C, Karp-Boss L, Henry N, de Vargas C, Sullivan MB, Tara Oceans Consortium Coordinators, Stemmann L, Lombard F.

2021

10.1038/s41598-021-94615-5

Myth-busting the provider-user relationship for digital sequence information

Scholz AH, Lange M, Habekost P, Oldham P, Cancio I, Cochrane G, Freitag J.

2021

10.1101/2021.08.02.454535

Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology.

Harrill JA, Viant MR, Yauk CL, Sachana M, Gant TW, Auerbach SS, Beger RD, Bouhifd M, O'Brien J, Burgoon L, Caiment F, Carpi D, Chen T, Chorley BN, Colbourne J, Corvi R, Debrauwer L, O'Donovan C, Ebbels TMD, Ekman DR, Faulhammer F, Gribaldo L, Hilton GM, Jones SP, Kende A, Lawson TN, Leite SB, Leonards PEG, Luijten M, Martin A, Moussa L, Rudaz S, Schmitz O, Sobanski T, Strauss V, Vaccari M, Vijay V, Weber RJM, Williams AJ, Williams A, Thomas RS, Whelan M.

2021

10.1016/j.yrtph.2021.105020

Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease.

Audain E, Wilsdon A, Breckpot J, Izarzugaza JMG, Fitzgerald TW, Kahlert AK, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H, Bak M, Bassett AS, Benson DW, Berger F, Daehnert I, Devriendt K, Dittrich S, Daubeney PE, Garg V, Hackmann K, Hoff K, Hofmann P, Dombrowsky G, Pickardt T, Bauer U, Keavney BD, Klaassen S, Kramer HH, Marshall CR, Milewicz DM, Lemaire S, Coselli JS, Mitchell ME, Tomita-Mitchell A, Prakash SK, Stamm K, Stewart AFR, Silversides CK, Siebert R, Stiller B, Rosenfeld JA, Vater I, Postma AV, Caliebe A, Brook JD, Andelfinger G, Hurles ME, Thienpont B, Larsen LA, Hitz MP.

2021

10.1371/journal.pgen.1009679

Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution.

Stark Z, Foulger RE, Williams E, Thompson BA, Patel C, Lunke S, Snow C, Leong IUS, Puzriakova A, Daugherty LC, Leigh S, Boustred C, Niblock O, Rueda-Martin A, Gerasimenko O, Savage K, Bellamy W, Lin VSK, Valls R, Gordon L, Brittain HK, Thomas ERA, Taylor Tavares AL, McEntagart M, White SM, Tan TY, Yeung A, Downie L, Macciocca I, Savva E, Lee C, Roesley A, De Fazio P, Deller J, Deans ZC, Hill SL, Caulfield MJ, North KN, Scott RH, Rendon A, Hofmann O, McDonagh EM.

2021

10.1016/j.ajhg.2021.06.020

PathExNET: A tool for extracting pathway expression networks from gene expression statistics.

Minadakis G, Muñoz-Pomer Fuentes A, Tsouloupas G, Papatheodorou I, Spyrou GM.

2021

10.1016/j.csbj.2021.07.033

VisBOL2-Improving Web-Based Visualization for Synthetic Biology Designs.

Hatch B, Meng L, Mante J, McLaughlin JA, Scott-Brown J, Myers CJ.

2021

10.1021/acssynbio.1c00147

EyeG2P: an automated variant filtering approach improves efficiency of diagnostic genomic testing for inherited ophthalmic disorders

Lenassi E, Carvalho A, Thormann A, Fletcher T, Hardcastle C, Hunt SE, Sergouniotis PI, Michaelides M, Webster AR, Cunningham F, Ramsden S, FitzPatrick DR, Black GC, Ellingford JM.

2021

10.1101/2021.07.23.21261017

PDBeCIF: an open-source mmCIF/CIF parsing and processing package.

van Ginkel G, Pravda L, Dana JM, Varadi M, Keller P, Anyango S, Velankar S.

2021

10.1186/s12859-021-04271-9

Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lung cancer

Memon D, Rizvi H, Fromm G, Lihm J, Schoenfeld AJ, Sauter JL, Luo J, Chow A, Bhanot UK, McCarthy C, Ye D, Vanderbilt CM, Liu C, Abu-Akeel M, Plodkowski AJ, McGranahan N, Łuksza M, Greenbaum BD, Merghoub T, Minn AJ, Beltrao P, Schreiber TH, Miller ML, Hellmann MD.

2021

10.1101/2021.07.21.452854

Highly accurate protein structure prediction for the human proteome.

Tunyasuvunakool K, Adler J, Wu Z, Green T, Zielinski M, Žídek A, Bridgland A, Cowie A, Meyer C, Laydon A, Velankar S, Kleywegt GJ, Bateman A, Evans R, Pritzel A, Figurnov M, Ronneberger O, Bates R, Kohl SAA, Potapenko A, Ballard AJ, Romera-Paredes B, Nikolov S, Jain R, Clancy E, Reiman D, Petersen S, Senior AW, Kavukcuoglu K, Birney E, Kohli P, Jumper J, Hassabis D.

2021

10.1038/s41586-021-03828-1

BashTheBug: a crowd of volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates

Fowler PW, Wright C, Spiers H, Zhu T, Baeten EM, Hoosdally SW, Cruz ALG, Roohi A, Kouchaki S, Walker TM, Peto TE, Miller G, Lintott C, Clifton D, Crook DW, Walker AS, The Zooniverse Volunteer Community, The CRyPTIC Consortium.

2021

10.1101/2021.07.20.453060

The PROTACtable genome.

Schneider M, Radoux CJ, Hercules A, Ochoa D, Dunham I, Zalmas LP, Hessler G, Ruf S, Shanmugasundaram V, Hann MM, Thomas PJ, Queisser MA, Benowitz AB, Brown K, Leach AR.

2021

10.1038/s41573-021-00245-x

Network expansion of genetic associations defines a pleiotropy map of human cell biology

Barrio-Hernandez I, Schwartzentruber J, Shrivastava A, del-Toro N, Zhang Q, Bradley G, Hermjakob H, Orchard S, Dunham I, Anderson CA, Porras P, Beltrao P.

2021

10.1101/2021.07.19.452924

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.

2021

10.3389/fimmu.2021.669357

Discovery of fibrillar adhesins across bacterial species.

Monzon V, Lafita A, Bateman A.

2021

10.1186/s12864-021-07586-2

Refget: standardised access to reference sequences.

Yates AD, Adams J, Chaturvedi S, Davies RM, Laird M, Leinonen R, Nag R, Sheffield NC, Hofmann O, Keane TM.

2021

10.1093/bioinformatics/btab524

Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity.

Bui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE, Human Cell Atlas Lung Biological Network.

2021

10.1038/s41467-021-24467-0

Individual COVID-19 disease trajectories revealed by plasma proteomics.

Memon D, Barrio-Hernandez I, Beltrao P.

2021

10.15252/emmm.202114532

A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases.

Magraner-Pardo L, Laskowski RA, Pons T, Thornton JM.

2021

10.1038/s41598-021-93715-6

Using host genetics to infer the global spread and evolutionary history of HCV subtype 3a.

Lin SK, De Maio N, Pedergnana V, Wu CH, Thézé J, Wilson DJ, Barnes E, Ansari MA.

2021

10.1093/ve/veab065

UCSC Cell Browser: Visualize Your Single-Cell Data.

Speir ML, Bhaduri A, Markov NS, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA, Raney BJ, Seninge L, Kent WJ, Haeussler M.

2021

10.1093/bioinformatics/btab503

Mapping the human genetic architecture of COVID-19.

COVID-19 Host Genetics Initiative.

2021

10.1038/s41586-021-03767-x

MaxDIA enables library-based and library-free data-independent acquisition proteomics.

Sinitcyn P, Hamzeiy H, Salinas Soto F, Itzhak D, McCarthy F, Wichmann C, Steger M, Ohmayer U, Distler U, Kaspar-Schoenefeld S, Prianichnikov N, Yılmaz Ş, Rudolph JD, Tenzer S, Perez-Riverol Y, Nagaraj N, Humphrey SJ, Cox J.

2021

10.1038/s41587-021-00968-7

Dense optical flow software to quantify cellular contractility.

Scalzo S, Afonso MQL, da Fonseca NJ, Jesus ICG, Alves AP, Mendonça CATF, Teixeira VP, Biagi D, Cruvinel E, Santos AK, Miranda K, Marques FAM, Mesquita ON, Kushmerick C, Campagnole-Santos MJ, Agero U, Guatimosim S.

2021

10.1016/j.crmeth.2021.100044

Profiles of Glucose Metabolism in Different Prediabetes Phenotypes, Classified by Fasting Glycemia, 2-Hour OGTT, Glycated Hemoglobin, and 1-Hour OGTT: An IMI DIRECT Study.

Tura A, Grespan E, Göbl CS, Koivula RW, Franks PW, Pearson ER, Walker M, Forgie IM, Giordano GN, Pavo I, Ruetten H, Dermitzakis ET, McCarthy MI, Pedersen O, Schwenk JM, Adamski J, De Masi F, Tsirigos KD, Brunak S, Viñuela A, Mahajan A, McDonald TJ, Kokkola T, Vangipurapu J, Cederberg H, Laakso M, Rutters F, Elders PJM, Koopman ADM, Beulens JW, Ridderstråle M, Hansen TH, Allin KH, Hansen T, Vestergaard H, Mari A, IMI DIRECT Consortium.

2021

10.2337/db21-0227

Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly

Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David F, Brbić M, Leskovec J, McLaughlin CN, Xie Q, Jones RC, Brueckner K, Shim J, Tattikota SG, Schnorrer F, Rust K, Nystul TG, Carvalho-Santos Z, Ribeiro C, Pal S, Przytycka TM, Allen AM, Goodwin SF, Berry CW, Fuller MT, White-Cooper H, Matunis EL, DiNardo S, Galenza A, O’Brien LE, Dow JAT, Jasper H, Oliver B, Perrimon N, Deplancke B, Quake SR, Luo L, Aerts S, FCA Consortium.

2021

10.1101/2021.07.04.451050

Predicted Impact of the Viral Mutational Landscape on the Cytotoxic Response against SARS-CoV-2

Foix A, López D, McConnell MJ, Martín-Galiano AJ.

2021

10.1101/2021.07.04.451040

ionbot: a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification

Degroeve S, Gabriels R, Velghe K, Bouwmeester R, Tichshenko N, Martens L.

2021

10.1101/2021.07.02.450686

Exploring amino acid functions in a deep mutational landscape.

Dunham AS, Beltrao P.

2021

10.15252/msb.202110305

The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.

Harrison PW, Lopez R, Rahman N, Allen SG, Aslam R, Buso N, Cummins C, Fathy Y, Felix E, Glont M, Jayathilaka S, Kadam S, Kumar M, Lauer KB, Malhotra G, Mosaku A, Edbali O, Park YM, Parton A, Pearce M, Estrada Pena JF, Rossetto J, Russell C, Selvakumar S, Sitjà XP, Sokolov A, Thorne R, Ventouratou M, Walter P, Yordanova G, Zadissa A, Cochrane G, Blomberg N, Apweiler R.

2021

10.1093/nar/gkab417

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.

Sehnal D, Bittrich S, Deshpande M, Svobodová R, Berka K, Bazgier V, Velankar S, Burley SK, Koča J, Rose AS.

2021

10.1093/nar/gkab314

Ten Years of Collaborative Progress in the Quest for Orthologs.

Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I, QFO Consortium.

2021

10.1093/molbev/msab098

Identifiers.org: Compact Identifier services in the cloud.

Bernal-Llinares M, Ferrer-Gómez J, Juty N, Goble C, Wimalaratne SM, Hermjakob H.

2021

10.1093/bioinformatics/btaa864

Acquisition of alveolar fate and differentiation competence by human fetal lung epithelial progenitor cells

Lim K, Tang W, Sun D, He P, Teichmann SA, Marioni JC, Meyer KB, Rawlins EL.

2021

10.1101/2021.06.30.450501

Exploring the conformational space of a receptor for drug design: An ERα case study.

Schneider M, Pons JL, Labesse G.

2021

10.1016/j.jmgm.2021.107974

A minimally morphologically destructive approach for DNA retrieval and whole genome shotgun sequencing of pinned historic Dipteran vector species

Korlević P, McAlister E, Mayho M, Makunin A, Flicek P, Lawniczak MKN.

2021

10.1101/2021.06.28.450148

Universal Spectrum Identifier for mass spectra.

Deutsch EW, Perez-Riverol Y, Carver J, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Binz PA, Pullman B, Sun Z, Shofstahl J, Bittremieux W, Mak TD, Klein J, Zhu Y, Lam H, Vizcaíno JA, Bandeira N.

2021

10.1038/s41592-021-01184-6

Genetic Variability of the SARS-CoV-2 Pocketome.

Yazdani S, De Maio N, Ding Y, Shahani V, Goldman N, Schapira M.

2021

10.1021/acs.jproteome.1c00206

Distribution and molecular evolution of the anti-CRISPR family AcrIF7

Figueroa W, Cazares A, Cazares D, Wu Y, de la Cruz A, Welch M, Kameyama L, Nobrega FL, Guarneros G.

2021

10.1101/2021.06.27.450086

ELIXIR: Providing a Sustainable Infrastructure for Life Science Data at European Scale.

Harrow J, Drysdale R, Smith A, Repo S, Lanfear J, Blomberg N.

2021

10.1093/bioinformatics/btab481

Use of viral motif mimicry improves the proteome-wide discovery of human linear motifs

Wadie B, Kleshchevnikov V, Sandaltzopoulou E, Benz C, Petsalaki E.

2021

10.1101/2021.06.25.449930

MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.

Murigneux V, Roberts LW, Forde BM, Phan MD, Nhu NTK, Irwin AD, Harris PNA, Paterson DL, Schembri MA, Whiley DM, Beatson SA.

2021

10.1186/s12864-021-07767-z

Annotating and prioritising genomic variants using the Ensembl Variant Effect Predictor - a tutorial

Hunt S, Moore B, Amode M, Armean I, Lemos D, Mushtaq A, Parton A, Schuilenburg H, Szpak M, Thormann A, Perry E, Trevanion S, Flicek P, Cunningham F, Yates A.

2021

10.22541/au.162460842.27880071/v1

Optimizing expression quantitative trait locus mapping workflows for single-cell studies.

Cuomo ASE, Alvari G, Azodi CB, single-cell eQTLGen consortium, McCarthy DJ, Bonder MJ.

2021

10.1186/s13059-021-02407-x

Transferability of genetic loci and polygenic scores for cardiometabolic traits in British Pakistanis and Bangladeshis

Huang QQ, Sallah N, Dunca D, Trivedi B, Hunt KA, Hodgson S, Lambert SA, Arciero E, Wright J, Griffiths C, Trembath RC, Hemingway H, Inouye M, Finer S, van Heel DA, Lumbers T, Martin HC, Kuchenbaecker K, Genes & Health Research team.

2021

10.1101/2021.06.22.21259323

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.

Dillon MR, Bolyen E, Adamov A, Belk A, Borsom E, Burcham Z, Debelius JW, Deel H, Emmons A, Estaki M, Herman C, Keefe CR, Morton JT, Oliveira RRM, Sanchez A, Simard A, Vázquez-Baeza Y, Ziemski M, Miwa HE, Kerere TA, Coote C, Bonneau R, Knight R, Oliveira G, Gopalasingam P, Kaehler BD, Cope EK, Metcalf JL, Robeson Ii MS, Bokulich NA, Caporaso JG.

2021

10.1371/journal.pcbi.1009056

Activation and detoxification of cassava cyanogenic glucosides by the whitefly Bemisia tabaci.

Easson MLAE, Malka O, Paetz C, Hojná A, Reichelt M, Stein B, van Brunschot S, Feldmesser E, Campbell L, Colvin J, Winter S, Morin S, Gershenzon J, Vassão DG.

2021

10.1038/s41598-021-92553-w

Big Data Analysis of Electronic Health Records: Clinically interpretable representations of older adult inpatient trajectories using time-series numerical data and Hidden Markov Models

Herrero-Zazo M, Fitzgerald T, Taylor V, Street H, Chaudhry AN, Bradley J, Birney E, Keevil VL.

2021

10.1101/2021.06.18.21258885

Investigation of clinical characteristics and genome associations in the ‘UK Lipoedema’ cohort

Grigoriadis D, Sackey E, Riches K, van Zanten M, Brice G, England R, Mills M, Dobbins SE, Jeffery S, Dong L, Savage DB, Mortimer PS, Keeley V, Pittman A, Gordon K, Ostergaard P, Lipoedema Consortium, Genomics England Research Consortium.

2021

10.1101/2021.06.15.21258988

Enhancing the interoperability of glycan data flow between ChEBI, PubChem, and GlyGen.

Navelkar R, Owen G, Mutherkrishnan V, Thiessen P, Bolton E, Cheng T, Edwards N, Tiemeyer M, Campbell M, Martin M, Vora J, Kahsay R, Mazumder R.

2021

10.1101/2021.06.17.448729

The FAANG Data Portal: Global, Open-Access, "FAIR", and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes.

Harrison PW, Sokolov A, Nayak A, Fan J, Zerbino D, Cochrane G, Flicek P.

2021

10.3389/fgene.2021.639238

Using Genomic Concordance to Estimate COVID-19 Transmission Risk Across Different Community Settings in England 2020/21

Chen C, Packer S, Hughes G, Edeghere O, Oliver I, Birney E.

2021

10.2139/ssrn.3867682

Protein Domain-Based Prediction of Compound–Target Interactions and Experimental Validation on LIM Kinases

Doğan T, Akhan Güzelcan E, Baumann M, Koyas A, Atas H, Baxendale I, Martin M, Cetin-Atalay R.

2021

10.1101/2021.06.14.448307

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Gonzalez JM, Magrane M, Martinez T, Schulz JF, Yang YT, Albà MM, Baranov PV, Bazzini A, Bruford E, Martin MJ, Carvunis A, Chen J, Couso JP, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Menschaert G, Ohler U, Roucou X, Saghatelian A, Weissman J, van Heesch S.

2021

10.1101/2021.06.10.447896

SignalP 6.0 achieves signal peptide prediction across all types using protein language models

Teufel F, Armenteros JJA, Johansen AR, Gíslason MH, Pihl SI, Tsirigos KD, Winther O, Brunak S, von Heijne G, Nielsen H.

2021

10.1101/2021.06.09.447770

Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas

Walzer M, García-Seisdedos D, Prakash A, Brack P, Crowther P, Graham RL, George N, Mohammed S, Moreno P, Papathedourou I, Hubbard SJ, Vizcaíno JA.

2021

10.1101/2021.06.08.447493

R2DT is a framework for predicting and visualising RNA secondary structure using templates.

Sweeney BA, Hoksza D, Nawrocki EP, Ribas CE, Madeira F, Cannone JJ, Gutell R, Maddala A, Meade CD, Williams LD, Petrov AS, Chan PP, Lowe TM, Finn RD, Petrov AI.

2021

10.1038/s41467-021-23555-5

Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival

Sousa A, Dugourd A, Memon D, Petursson B, Petsalaki E, Saez-Rodriguez J, Beltrao P.

2021

10.1101/2021.06.09.447741

Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides

Umer HM, Zhu Y, Pfeuffer J, Sachsenberg T, Lehtiö J, Branca R, Perez-Riverol Y.

2021

10.1101/2021.06.08.447496

A map of transcriptional heterogeneity and regulatory variation in human microglia.

Young AMH, Kumasaka N, Calvert F, Hammond TR, Knights A, Panousis N, Park JS, Schwartzentruber J, Liu J, Kundu K, Segel M, Murphy NA, McMurran CE, Bulstrode H, Correia J, Budohoski KP, Joannides A, Guilfoyle MR, Trivedi R, Kirollos R, Morris R, Garnett MR, Timofeev I, Jalloh I, Holland K, Mannion R, Mair R, Watts C, Price SJ, Kirkpatrick PJ, Santarius T, Mountjoy E, Ghoussaini M, Soranzo N, Bayraktar OA, Stevens B, Hutchinson PJ, Franklin RJM, Gaffney DJ.

2021

10.1038/s41588-021-00875-2

Crowdsourced mapping of unexplored target space of kinase inhibitors.

Cichońska A, Ravikumar B, Allaway RJ, Wan F, Park S, Isayev O, Li S, Mason M, Lamb A, Tanoli Z, Jeon M, Kim S, Popova M, Capuzzi S, Zeng J, Dang K, Koytiger G, Kang J, Wells CI, Willson TM, IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium, Oprea TI, Schlessinger A, Drewry DH, Stolovitzky G, Wennerberg K, Guinney J, Aittokallio T.

2021

10.1038/s41467-021-23165-1

PDBe Aggregated API: Programmatic access to an integrative knowledge graph of molecular structure data.

Nair S, Váradi M, Nadzirin N, Pravda L, Anyango S, Mir S, Berrisford J, Armstrong D, Gutmanas A, Velankar S.

2021

10.1093/bioinformatics/btab424

Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas

Börner K, Teichmann SA, Quardokus EM, Gee J, Browne K, Osumi-Sutherland D, Herr BW, Bueckle A, Paul H, Haniffa MA, Jardine L, Bernard A, Ding S, Miller JA, Lin S, Halushka M, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G.

2021

10.1101/2021.05.31.446440

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 JWB, Plevin MJ, Baumann CG, Bateman A, Potts JR.

2021

10.1073/pnas.2101349118

Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases.

Zurek B, Ellwanger K, Vissers LELM, Schüle R, Synofzik M, Töpf A, de Voer RM, Laurie S, Matalonga L, Gilissen C, Ossowski S, 't Hoen PAC, Vitobello A, Schulze-Hentrich JM, Riess O, Brunner HG, Brookes AJ, Rath A, Bonne G, Gumus G, Verloes A, Hoogerbrugge N, Evangelista T, Harmuth T, Swertz M, Spalding D, Hoischen A, Beltran S, Graessner H, Solve-RD consortium.

2021

10.1038/s41431-021-00859-0

Erratum to: Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes.

Tagirdzhanova G, Saary P, Tingley JP, Díaz-Escandón D, Abbott DW, Finn RD, Spribille T.

2021

10.1093/gbe/evab129

Solving patients with rare diseases through programmatic reanalysis of genome-phenome data.

Matalonga L, Hernández-Ferrer C, Piscia D, Solve-RD SNV-indel working group, Schüle R, Synofzik M, Töpf A, Vissers LELM, de Voer R, Solve-RD DITF-GENTURIS, Solve-RD DITF-ITHACA, Solve-RD DITF-euroNMD, Solve-RD DITF-RND, Tonda R, Laurie S, Fernandez-Callejo M, Picó D, Garcia-Linares C, Papakonstantinou A, Corvó A, Joshi R, Diez H, Gut I, Hoischen A, Graessner H, Beltran S, Solve-RD Consortia.

2021

10.1038/s41431-021-00852-7

A phylogenetic approach for weighting genetic sequences.

De Maio N, Alekseyenko AV, Coleman-Smith WJ, Pardi F, Suchard MA, Tamuri AU, Truszkowski J, Goldman N.

2021

10.1186/s12859-021-04183-8

Genomic reconstruction of the SARS-CoV-2 epidemic in England

Vöhringer HS, Sanderson T, Sinnott M, Maio ND, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani C, Gonçalves S, Jackson D, Johnston I, Jung AW, Saint C, Sillitoe J, Suciu M, Goldman N, Panovska-Griffiths J, Birney E, Volz E, Funk S, Kwiatkowski D, Chand M, Martincorena I, Barrett JC, Gerstung M, The Wellcome Sanger Institute Covid-19 Surveillance Team, The COVID-19 Genomics UK (COG-UK) Consortium.

2021

10.1101/2021.05.22.21257633

Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries.

Milne R, Morley KI, Almarri MA, Anwer S, Atutornu J, Baranova EE, Bevan P, Cerezo M, Cong Y, Costa A, 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, 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, Wang N, West AV, Yoshizawa G, Middleton A.

2021

10.1186/s13073-021-00903-0

Abnormal neonatal sodium handling in skin precedes hypertension in the SAME rat.

Mullins L, Ivy J, Ward M, Tenstad O, Wiig H, Kitada K, Manning J, Rakova N, Muller D, Mullins J.

2021

10.1007/s00424-021-02582-7

A proteomics sample metadata representation for multiomics integration, and big data analysis

Dai C, Füllgrabe A, Pfeuffer J, Solovyeva E, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky L, Perez-Riverol Y.

2021

10.1101/2021.05.21.445143

An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities.

O'Sullivan DM, Doyle RM, Temisak S, Redshaw N, Whale AS, Logan G, Huang J, Fischer N, Amos GCA, Preston MD, Marchesi JR, Wagner J, Parkhill J, Motro Y, Denise H, Finn RD, Harris KA, Kay GL, O'Grady J, Ransom-Jones E, Wu H, Laing E, Studholme DJ, Benavente ED, Phelan J, Clark TG, Moran-Gilad J, Huggett JF.

2021

10.1038/s41598-021-89881-2

Mapping Rora expression in resting and activated CD4+ T cells.

Haim-Vilmovsky L, Henriksson J, Walker JA, Miao Z, Natan E, Kar G, Clare S, Barlow JL, Charidemou E, Mamanova L, Chen X, Proserpio V, Pramanik J, Woodhouse S, Protasio AV, Efremova M, Griffin JL, Berriman M, Dougan G, Fisher J, Marioni JC, McKenzie ANJ, Teichmann SA.

2021

10.1371/journal.pone.0251233

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Leger A, Brettell I, Monahan J, Barton C, Wolf N, Kusminski N, Herder C, Aadepu N, Becker C, Gierten J, Hammouda OT, Hasel E, Lischik C, Lust K, Suzuki R, Tavhelidse T, Thumberger T, Thumberger T, Tsingos E, Watson P, Welz B, Naruse K, Loosli F, Wittbrodt J, Birney E, Fitzgerald T.

2021

10.1101/2021.05.17.444424

Diagnostic accuracy of non-invasive tests for advanced fibrosis in patients with NAFLD: an individual patient data meta-analysis.

Mózes FE, Lee JA, Selvaraj EA, Jayaswal ANA, Trauner M, Boursier J, Fournier C, Staufer K, Stauber RE, Bugianesi E, Younes R, Gaia S, Lupșor-Platon M, Petta S, Shima T, Okanoue T, Mahadeva S, Chan WK, Eddowes PJ, Hirschfield GM, Newsome PN, Wong VW, de Ledinghen V, Fan J, Shen F, Cobbold JF, Sumida Y, Okajima A, Schattenberg JM, Labenz C, Kim W, Lee MS, Wiegand J, Karlas T, Yılmaz Y, Aithal GP, Palaniyappan N, Cassinotto C, Aggarwal S, Garg H, Ooi GJ, Nakajima A, Yoneda M, Ziol M, Barget N, Geier A, Tuthill T, Brosnan MJ, Anstee QM, Neubauer S, Harrison SA, Bossuyt PM, Pavlides M, LITMUS Investigators.

2021

10.1136/gutjnl-2021-324243

The Medaka Inbred Kiyosu-Karlsruhe (MIKK) Panel

Fitzgerald T, Brettell I, Leger A, Wolf N, Kusminski N, Monahan J, Barton C, Herder C, Aadepu N, Gierten J, Becker C, Hammouda OT, Hasel E, Lischik C, Lust K, Suzuki R, Tsingos E, Tavhelidse T, Thumberger T, Watson P, Welz B, Khouja N, Naruse K, Birney E, Wittbrodt J, Loosli F.

2021

10.1101/2021.05.17.444412

Functional conservation in genes and pathways linking ageing and immunity.

Fabian DK, Fuentealba M, Dönertaş HM, Partridge L, Thornton JM.

2021

10.1186/s12979-021-00232-1

Diagnostic accuracy of elastography and magnetic resonance imaging in patients with NAFLD: A systematic review and meta-analysis.

Selvaraj EA, Mózes FE, Jayaswal ANA, Zafarmand MH, Vali Y, Lee JA, Levick CK, Young LAJ, Palaniyappan N, Liu CH, Aithal GP, Romero-Gómez M, Brosnan MJ, Tuthill TA, Anstee QM, Neubauer S, Harrison SA, Bossuyt PM, Pavlides M, LITMUS Investigators.

2021

10.1016/j.jhep.2021.04.044

The genome sequence of the brown trout, Salmo trutta Linnaeus 1758.

Hansen T, Fjelldal PG, Lien S, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan J, Fedrigo O, Mountcastle J, Jarvis E, McCarthy SA, Chow W, Howe K, Torrance J, Wood J, Sims Y, Haggerty L, Challis R, Threlfall J, Mead D, Durbin R, Blaxter M.

2021

10.12688/wellcomeopenres.16838.1

Target-Based Evaluation of "Drug-Like" Properties and Ligand Efficiencies.

Leeson PD, Bento AP, Gaulton A, Hersey A, Manners EJ, Radoux CJ, Leach AR.

2021

10.1021/acs.jmedchem.1c00416

Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images.

Currant H, Hysi P, Fitzgerald TW, Gharahkhani P, Bonnemaijer PWM, Senabouth A, Hewitt AW, UK Biobank Eye and Vision Consortium, International Glaucoma Genetics Consortium, Atan D, Aung T, Charng J, Choquet H, Craig J, Khaw PT, Klaver CCW, Kubo M, Ong JS, Pasquale LR, Reisman CA, Daniszewski M, Powell JE, Pébay A, Simcoe MJ, Thiadens AAHJ, van Duijn CM, Yazar S, Jorgenson E, MacGregor S, Hammond CJ, Mackey DA, Wiggs JL, Foster PJ, Patel PJ, Birney E, Khawaja AP.

2021

10.1371/journal.pgen.1009497

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei.

Hawkey J, Paranagama K, Baker KS, Bengtsson RJ, Weill FX, Thomson NR, Baker S, Cerdeira L, Iqbal Z, Hunt M, Ingle DJ, Dallman TJ, Jenkins C, Williamson DA, Holt KE.

2021

10.1038/s41467-021-22700-4

Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature

Lange M, Alako BT, Cochrane G, Ghaffar M, Mascher M, Habekost P, Hillebrand U, Scholz U, Zunder F, Freitag J, Scholz AH.

2021

10.1101/2021.05.10.443393

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic.

Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D, Corbett-Detig R.

2021

10.1038/s41588-021-00862-7

Solving unsolved rare neurological diseases-a Solve-RD viewpoint.

Schüle R, Timmann D, Erasmus CE, Reichbauer J, Wayand M, Solve-RD-DITF-RND, van de Warrenburg B, Schöls L, Wilke C, Bevot A, Zuchner S, Beltran S, Laurie S, Matalonga L, Graessner H, Synofzik M, Solve-RD Consortium.

2021

10.1038/s41431-021-00901-1

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.

2021

10.1021/acs.jproteome.1c00096

IntAct App: a Cytoscape application for molecular interaction network visualisation and analysis.

Ragueneau E, Shrivastava A, Morris JH, Del-Toro N, Hermjakob H, Porras P.

2021

10.1093/bioinformatics/btab319

Anticholinergic burden in older adult inpatients: patterns from admission to discharge and associations with hospital outcomes.

Herrero-Zazo M, Berry R, Bines E, Bhattacharya D, Myint PK, Keevil VL.

2021

10.1177/20420986211012592

Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities".

Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia JM, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, Galazka JM, Gibbons SM, Hays D, Hervey J, Hu B, Hurwitz BL, Jaiswal P, Joachimiak MP, Kinkel L, Ladau J, Martin SL, McCue LA, Miller K, Mouncey N, Mungall C, Pafilis E, Reddy TBK, Richardson L, Roux S, Schriml LM, Shaffer JP, Sundaramurthi JC, Thompson LR, Timme RE, Zheng J, Wood-Charlson EM, Eloe-Fadrosh EA.

2021

10.1128/msystems.00273-21

Computational principles and challenges in single-cell data integration.

Argelaguet R, Cuomo ASE, Stegle O, Marioni JC.

2021

10.1038/s41587-021-00895-7

Genomic sequences and RNA binding proteins predict RNA splicing kinetics in various single-cell contexts

Hou R, Huang Y.

2021

10.1101/2021.05.02.442314

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.

2021

10.1093/bioinformatics/btaa713

Which image-based phenotypes are most promising for using AI to understand cellular functions and why?

Lundberg E, Funke J, Uhlmann V, Gerlich D, Walter T, Carpenter A, Coehlo LP.

2021

10.1016/j.cels.2021.04.012

Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes.

Smyshlyaev G, Bateman A, Barabas O.

2021

10.15252/msb.20209880

Author Correction: Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts.

Woo XY, Giordano J, Srivastava A, Zhao ZM, Lloyd MW, de Bruijn R, Suh YS, Patidar R, Chen L, Scherer S, Bailey MH, Yang CH, Cortes-Sanchez E, Xi Y, Wang J, Wickramasinghe J, Kossenkov AV, Rebecca VW, Sun H, Mashl RJ, Davies SR, Jeon R, Frech C, Randjelovic J, Rosains J, Galimi F, Bertotti A, Lafferty A, O'Farrell AC, Modave E, Lambrechts D, Ter Brugge P, Serra V, Marangoni E, El Botty R, Kim H, Kim JI, Yang HK, Lee C, Dean DA, Davis-Dusenbery B, Evrard YA, Doroshow JH, Welm AL, Welm BE, Lewis MT, Fang B, Roth JA, Meric-Bernstam F, Herlyn M, Davies MA, Ding L, Li S, Govindan R, Isella C, Moscow JA, Trusolino L, Byrne AT, Jonkers J, Bult CJ, Medico E, Chuang JH, PDXNET Consortium, EurOPDX Consortium.

2021

10.1038/s41588-021-00811-4

Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2.

De Maio N, Walker CR, Turakhia Y, Lanfear R, Corbett-Detig R, Goldman N.

2021

10.1093/gbe/evab087

Copy number aberrations drive kinase rewiring, leading to genetic vulnerabilities in cancer.

Memon D, Gill MB, Papachristou EK, Ochoa D, D'Santos CS, Miller ML, Beltrao P.

2021

10.1016/j.celrep.2021.109155

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.

2021

10.1093/bioinformatics/btaa858

Accessing Livestock Resources in Ensembl.

Martin FJ, Gall A, Szpak M, Flicek P.

2021

10.3389/fgene.2021.650228

Towards complete and error-free genome assemblies of all vertebrate species.

Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED.

2021

10.1038/s41586-021-03451-0

A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage.

Zou X, Koh GCC, Nanda AS, Degasperi A, Urgo K, Roumeliotis TI, Agu CA, Badja C, Momen S, Young J, Amarante TD, Side L, Brice G, Perez-Alonso V, Rueda D, Gomez C, Bushell W, Harris R, Choudhary JS, Genomics England Research Consortium, Jiricny J, Skarnes WC, Nik-Zainal S.

2021

10.1038/s43018-021-00200-0

Adaptive introgression of the beta-globin cluster in two Andean waterfowl.

Graham AM, Peters JL, Wilson RE, Muñoz-Fuentes V, Green AJ, Dorfsman DA, Valqui TH, Winker K, McCracken KG.

2021

10.1038/s41437-021-00437-6

An integrated landscape of protein expression in human cancer.

Jarnuczak AF, Najgebauer H, Barzine M, Kundu DJ, Ghavidel F, Perez-Riverol Y, Papatheodorou I, Brazma A, Vizcaíno JA.

2021

10.1038/s41597-021-00890-2

Principled Design and Implementation of Steerable Detectors.

Fageot J, Uhlmann V, Puspoki Z, Beck B, Unser M, Depeursinge A.

2021

10.1109/tip.2021.3072499

Single-cell multi-omics analysis of the immune response in COVID-19.

Stephenson E, Reynolds G, Botting RA, Calero-Nieto FJ, Morgan MD, Tuong ZK, Bach K, Sungnak W, Worlock KB, Yoshida M, Kumasaka N, Kania K, Engelbert J, Olabi B, Spegarova JS, Wilson NK, Mende N, Jardine L, Gardner LCS, Goh I, Horsfall D, McGrath J, Webb S, Mather MW, Lindeboom RGH, Dann E, Huang N, Polanski K, Prigmore E, Gothe F, Scott J, Payne RP, Baker KF, Hanrath AT, Schim van der Loeff ICD, Barr AS, Sanchez-Gonzalez A, Bergamaschi L, Mescia F, Barnes JL, Kilich E, de Wilton A, Saigal A, Saleh A, Janes SM, Smith CM, Gopee N, Wilson C, Coupland P, Coxhead JM, Kiselev VY, van Dongen S, Bacardit J, King HW, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID-19 BioResource Collaboration, Rostron AJ, Simpson AJ, Hambleton S, Laurenti E, Lyons PA, Meyer KB, Nikolić MZ, Duncan CJA, Smith KGC, Teichmann SA, Clatworthy MR, Marioni JC, Göttgens B, Haniffa M.

2021

10.1038/s41591-021-01329-2

Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data.

Saheb Kashaf S, Almeida A, Segre JA, Finn RD.

2021

10.1038/s41596-021-00508-2

Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease.

Watt S, Vasquez L, Walter K, Mann AL, Kundu K, Chen L, Sims Y, Ecker S, Burden F, Farrow S, Farr B, Iotchkova V, Elding H, Mead D, Tardaguila M, Ponstingl H, Richardson D, Datta A, Flicek P, Clarke L, Downes K, Pastinen T, Fraser P, Frontini M, Javierre BM, Spivakov M, Soranzo N.

2021

10.1038/s41467-021-22548-8

Visualization of loop extrusion by DNA nanoscale tracing in single human cells

Beckwith K, Ødegård-Fougner Ø, Morero N, Barton C, Schueder F, Tang W, Alexander S, Peters J, Jungmann R, Jungmann R, Birney E, Ellenberg J.

2021

10.1101/2021.04.12.439407

DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species.

Hu Y, Tattikota SG, Liu Y, Comjean A, Gao Y, Forman C, Kim G, Rodiger J, Papatheodorou I, Dos Santos G, Mohr SE, Perrimon N.

2021

10.1016/j.csbj.2021.04.021

Sensitive and specific spectral library searching with COSS and Percolator

Shiferaw GA, Gabriels R, Bouwmeester R, Van Den Bossche T, Van Den Bossche T, Vandermarliere E, Martens L, Volders P.

2021

10.1101/2021.04.09.438700

Genomic sequence characteristics and the empiric accuracy of short-read sequencing

Marin M, Vargas R, Harris M, Jeffrey B, Epperson LE, Durbin D, Strong M, Salfinger M, Iqbal Z, Akhundova I, Vashakidze S, Crudu V, Rosenthal A, Farhat MR.

2021

10.1101/2021.04.08.438862

Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19.

Gaziano L, Giambartolomei C, Pereira AC, Gaulton A, Posner DC, Swanson SA, Ho YL, Iyengar SK, Kosik NM, Vujkovic M, Gagnon DR, Bento AP, Barrio-Hernandez I, Rönnblom L, Hagberg N, Lundtoft C, Langenberg C, Pietzner M, Valentine D, Gustincich S, Tartaglia GG, Allara E, Surendran P, Burgess S, Zhao JH, Peters JE, Prins BP, Angelantonio ED, Devineni P, Shi Y, Lynch KE, DuVall SL, Garcon H, Thomann LO, Zhou JJ, Gorman BR, Huffman JE, O'Donnell CJ, Tsao PS, Beckham JC, Pyarajan S, Muralidhar S, Huang GD, Ramoni R, Beltrao P, Danesh J, Hung AM, Chang KM, Sun YV, Joseph J, Leach AR, Edwards TL, Cho K, Gaziano JM, Butterworth AS, Casas JP, VA Million Veteran Program COVID-19 Science Initiative.

2021

10.1038/s41591-021-01310-z

Common genetic associations between age-related diseases.

Dönertaş HM, Fabian DK, Valenzuela MF, Partridge L, Thornton JM.

2021

10.1038/s43587-021-00051-5

A decoupled, modular and scriptable architecture for tools to curate data platforms.

Langenstein M, Hermjakob H, Llinares MB.

2021

10.1093/bioinformatics/btab233

Linked electronic health records for research on a nationwide cohort of more than 54 million people in England: data resource.

Wood A, Denholm R, Hollings S, Cooper J, Ip S, Walker V, Denaxas S, Akbari A, Banerjee A, Whiteley W, Lai A, Sterne J, Sudlow C, CVD-COVID-UK consortium.

2021

10.1136/bmj.n826

Cells of the human intestinal tract mapped across space and time

Elmentaite R, Kumasaka N, King H, Roberts K, Dabrowska M, Pritchard S, Bolt L, Vieira S, Mamanova L, Huang N, Goh Kai’En I, Stephenson E, Engelbert J, Botting R, Fleming A, Dann E, Lisgo S, Katan M, Leonard S, Oliver T, Hook C, Nayak K, Perrone F, Campos L, Dominguez-Conde C, Polanski K, Van Dongen S, Patel M, Morgan M, Marioni J, Bayraktar O, Meyer K, Zilbauer M, Uhlig H, Clatworthy M, Mahbubani K, Saeb Parsy K, Haniffa M, James K, Teichmann S.

2021

10.1101/2021.04.07.438755

Author Correction: Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes.

Schwartzentruber J, Cooper S, Liu JZ, Barrio-Hernandez I, Bello E, Kumasaka N, Young AMH, Franklin RJM, Johnson T, Estrada K, Gaffney DJ, Beltrao P, Bassett A.

2021

10.1038/s41588-021-00822-1

A resource of targeted mutant mouse lines for 5,061 genes.

Birling MC, Yoshiki A, Adams DJ, Ayabe S, Beaudet AL, Bottomley J, Bradley A, Brown SDM, Bürger A, Bushell W, Chiani F, Chin HG, Christou S, Codner GF, DeMayo FJ, Dickinson ME, Doe B, Donahue LR, Fray MD, Gambadoro A, Gao X, Gertsenstein M, Gomez-Segura A, Goodwin LO, Heaney JD, Hérault Y, de Angelis MH, Jiang ST, Justice MJ, Kasparek P, King RE, Kühn R, Lee H, Lee YJ, Liu Z, Lloyd KCK, Lorenzo I, Mallon AM, McKerlie C, Meehan TF, Fuentes VM, Newman S, Nutter LMJ, Oh GT, Pavlovic G, Ramirez-Solis R, Rosen B, Ryder EJ, Santos LA, Schick J, Seavitt JR, Sedlacek R, Seisenberger C, Seong JK, Skarnes WC, Sorg T, Steel KP, Tamura M, Tocchini-Valentini GP, Wang CL, Wardle-Jones H, Wattenhofer-Donzé M, Wells S, Wiles MV, Willis BJ, Wood JA, Wurst W, Xu Y, International Mouse Phenotyping Consortium (IMPC), Teboul L, Murray SA.

2021

10.1038/s41588-021-00825-y

Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes.

Tagirdzhanova G, Saary P, Tingley JP, Díaz-Escandón D, Abbott DW, Finn RD, Spribille T.

2021

10.1093/gbe/evab047

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis.

Moreno P, Huang N, Manning JR, Mohammed S, Solovyev A, Polanski K, Bacon W, Chazarra R, Talavera-López C, Doyle MA, Marnier G, Grüning B, Rasche H, George N, Fexova SK, Alibi M, Miao Z, Perez-Riverol Y, Haeussler M, Brazma A, Teichmann S, Meyer KB, Papatheodorou I.

2021

10.1038/s41592-021-01102-w

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.

2021

10.1093/nar/gkab077

The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation.

Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, McMahon A, Abraham G, Chapman M, Parkinson H, Danesh J, MacArthur JAL, Inouye M.

2021

10.1038/s41588-021-00783-5

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine.

Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni JC, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T, LifeTime Community Working Groups.

2021

10.1038/s41586-021-03287-8

Recommendations for the FAIRification of genomic track metadata

Gundersen S, Boddu S, Capella-Gutierrez S, Drabløs F, Fernández JM, Kompova R, Taylor K, Titov D, Zerbino D, Hovig E.

2021

10.12688/f1000research.28449.1

A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages.

Dellicour S, Durkin K, Hong SL, Vanmechelen B, Martí-Carreras J, Gill MS, Meex C, Bontems S, André E, Gilbert M, Walker C, Maio N, Faria NR, Hadfield J, Hayette MP, Bours V, Wawina-Bokalanga T, Artesi M, Baele G, Maes P.

2021

10.1093/molbev/msaa284

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).

Touré V, Vercruysse S, Acencio ML, Lovering RC, Orchard S, Bradley G, Casals-Casas C, Chaouiya C, Del-Toro N, Flobak Å, Gaudet P, Hermjakob H, Hoyt CT, Licata L, Lægreid A, Mungall CJ, Niknejad A, Panni S, Perfetto L, Porras P, Pratt D, Saez-Rodriguez J, Thieffry D, Thomas PD, Türei D, Kuiper M.

2021

10.1093/bioinformatics/btaa622

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.

MacDougall A, Volynkin V, Saidi R, Poggioli D, Zellner H, Hatton-Ellis E, Joshi V, O'Donovan C, Orchard S, Auchincloss AH, Baratin D, Bolleman J, Coudert E, de Castro E, Hulo C, Masson P, Pedruzzi I, Rivoire C, Arighi C, Wang Q, Chen C, Huang H, Garavelli J, Vinayaka CR, Yeh LS, Natale DA, Laiho K, Martin MJ, Renaux A, Pichler K, The UniProt Consortium.

2021

10.1093/bioinformatics/btaa663

Transposable Element Landscape in Drosophila Populations Selected for Longevity.

Fabian DK, Dönertaş HM, Fuentealba M, Partridge L, Thornton JM.

2021

10.1093/gbe/evab031

The small DUF1127 protein CcaF1 from Rhodobacter sphaeroides is an RNA-binding protein involved in sRNA maturation and RNA turnover.

Grützner J, Billenkamp F, Spanka DT, Rick T, Monzon V, Förstner KU, Klug G.

2021

10.1093/nar/gkab146

Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders.

Ochoa R, Laskowski RA, Thornton JM, Cossio P.

2021

10.3389/fmolb.2021.636562

MQuad enables clonal substructure discovery using single cell mitochondrial variants

Kwok AWC, Qiao C, Huang R, Sham M, Ho JWK, Huang Y.

2021

10.1101/2021.03.27.437331

GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning

Gröschel MI, Owens M, Freschi L, Vargas R, Marin MG, Phelan J, Iqbal Z, Dixit A, Farhat MR.

2021

10.1101/2021.03.27.437319

The value of primary transcripts to the clinical and non-clinical genomics community: survey results and roadmap for improvements.

Morales J, McMahon A, Loveland J, Perry E, Frankish A, Hunt S, Armean I, Flicek P, Cunningham F.

2021

10.22541/au.161674625.52543047/v1

Efficient masking of plant genomes by combining kmer counting and curated repeats

Contreras-Moreira B, Filippi CV, Naamati G, Girón CG, Allen JE, Flicek P.

2021

10.1101/2021.03.22.436504

Exploring Leishmania-Host Interaction with Reactome, a Database of Biological Pathways and Processes

Murillo J, Jassal B, Gómez MA, Hermjakob H.

2021

10.1101/2021.03.23.436718

The SARS-CoV-2 replication-transcription complex is a priority target for broad-spectrum pan-coronavirus drugs

Yazdani S, De Maio N, Ding Y, Shahani V, Goldman N, Schapira M.

2021

10.1101/2021.03.23.436637

Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research.

Kern C, Wang Y, Xu X, Pan Z, Halstead M, Chanthavixay G, Saelao P, Waters S, Xiang R, Chamberlain A, Korf I, Delany ME, Cheng HH, Medrano JF, Van Eenennaam AL, Tuggle CK, Ernst C, Flicek P, Quon G, Ross P, Zhou H.

2021

10.1038/s41467-021-22100-8

Deciphering Bedaquiline and Clofazimine Resistance in Tuberculosis: An Evolutionary Medicine Approach

Sonnenkalb L, Carter J, Spitaleri A, Iqbal Z, Hunt M, Malone K, Utpatel C, Cirillo DM, Rodrigues C, Nilgiriwala KS, Fowler PW, Merker M, Niemann S, the CRyPTIC Consortium.

2021

10.1101/2021.03.19.436148

Representation learning of RNA velocity reveals robust cell transitions

Qiao C, Huang Y.

2021

10.1101/2021.03.19.436127

A proteome-wide genetic investigation identifies several SARS-CoV-2-exploited host targets of clinical relevance

Karim MA, Shilts J, Schwartzentruber J, Hayhurst J, Buniello A, Mohammed ESE, Zheng J, Holmes MV, Ochoa D, Carmona M, Maranville J, Gaunt TR, Emilsson V, Gudnason V, McDonagh EM, Wright GJ, Ghoussaini M, Dunham I.

2021

10.1101/2021.03.15.21253625

Suppression of insulin-induced gene 1 (INSIG1) function promotes hepatic lipid remodelling and restrains NASH progression.

Azzu V, Vacca M, Kamzolas I, Hall Z, Leslie J, Carobbio S, Virtue S, Davies SE, Lukasik A, Dale M, Bohlooly-Y M, Acharjee A, Lindén D, Bidault G, Petsalaki E, Griffin JL, Oakley F, Allison MED, Vidal-Puig A.

2021

10.1016/j.molmet.2021.101210

phastSim: efficient simulation of sequence evolution for pandemic-scale datasets

De Maio N, Boulton W, Weilguny L, Walker CR, Turakhia Y, Corbett-Detig R, Goldman N.

2021

10.1101/2021.03.15.435416

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

Martens L, Bouwmeester R, Gabriels R, Hulstaert N, Degroeve S.

2021

10.21203/rs.3.rs-275246/v1

Refget: standardised access to reference sequences

Yates AD, Adams J, Chaturvedi S, Davies RM, Laird M, Leinonen R, Nag R, Sheffield NC, Hofmann O, Keane T.

2021

10.1101/2021.03.11.434800

Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future.

Bandeira N, Deutsch EW, Kohlbacher O, Martens L, Vizcaíno JA.

2021

10.1016/j.mcpro.2021.100071

The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.

Olafson PU, Aksoy S, Attardo GM, Buckmeier G, Chen X, Coates CJ, Davis M, Dykema J, Emrich SJ, Friedrich M, Holmes CJ, Ioannidis P, Jansen EN, Jennings EC, Lawson D, Martinson EO, Maslen GL, Meisel RP, Murphy TD, Nayduch D, Nelson DR, Oyen KJ, Raszick TJ, Ribeiro JMC, Robertson HM, Rosendale AJ, Sackton TB, Saelao P, Swiger SL, Sze SH, Tarone AM, Taylor DB, Warren WC, Waterhouse RM, Weirauch MT, Werren JH, Wilson RK, Zdobnov EM, Benoit JB.

2021

10.1186/s12915-021-00975-9

Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics.

Bonder MJ, Smail C, Gloudemans MJ, Frésard L, Jakubosky D, D'Antonio M, Li X, Ferraro NM, Carcamo-Orive I, Mirauta B, Seaton DD, Cai N, Vakili D, Horta D, Zhao C, Zastrow DB, Bonner DE, HipSci Consortium, iPSCORE consortium, Undiagnosed Diseases Network, PhLiPS consortium, Wheeler MT, Kilpinen H, Knowles JW, Smith EN, Frazer KA, Montgomery SB, Stegle O.

2021

10.1038/s41588-021-00800-7

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation.

Jerber J, Seaton DD, Cuomo ASE, Kumasaka N, Haldane J, Steer J, Patel M, Pearce D, Andersson M, Bonder MJ, Mountjoy E, Ghoussaini M, Lancaster MA, HipSci Consortium, Marioni JC, Merkle FT, Gaffney DJ, Stegle O.

2021

10.1038/s41588-021-00801-6

Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences

Blackwell GA, Hunt M, Malone KM, Lima L, Horesh G, Alako BT, Thomson NR, Iqbal Z.

2021

10.1101/2021.03.02.433662

Iron limitation by transferrin promotes simultaneous cheating of pyoverdine and exoprotease in Pseudomonas aeruginosa.

Tostado-Islas O, Mendoza-Ortiz A, Ramírez-García G, Cabrera-Takane ID, Loarca D, Pérez-González C, Jasso-Chávez R, Jiménez-Cortés JG, Hoshiko Y, Maeda T, Cazares A, García-Contreras R.

2021

10.1038/s41396-021-00938-6

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.

Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Torlai Triglia E, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams T, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo ASE, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CGK, NHLBI LungMap Consortium, Human Cell Atlas Lung Biological Network.

2021

10.1038/s41591-020-01227-z

Short-range template switching in great ape genomes explored using pair hidden Markov models.

Walker CR, Scally A, De Maio N, Goldman N.

2021

10.1371/journal.pgen.1009221

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank.

Feng Z, Westbrook JD, Sala R, Smart OS, Bricogne G, Matsubara M, Yamada I, Tsuchiya S, Aoki-Kinoshita KF, Hoch JC, Kurisu G, Velankar S, Burley SK, Young JY.

2021

10.1016/j.str.2021.02.004

Want to track pandemic variants faster? Fix the bioinformatics bottleneck.

Hodcroft EB, De Maio N, Lanfear R, MacCannell DR, Minh BQ, Schmidt HA, Stamatakis A, Goldman N, Dessimoz C.

2021

10.1038/d41586-021-00525-x

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.

Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, Baumbach J, Beerenwinkel N, Brandt C, Cacciabue M, Chuguransky S, Drechsel O, Finn RD, Fritz A, Fuchs S, Hattab G, Hauschild AC, Heider D, Hoffmann M, Hölzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, Kühnert D, Lasso G, Libin P, List M, Löchel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki EP, O'Toole ÁN, Ontiveros-Palacios N, Petrov AI, Rangel-Pineros G, Redaschi N, Reimering S, Reinert K, Reyes A, Richardson L, Robertson DL, Sadegh S, Singer JB, Theys K, Upton C, Welzel M, Williams L, Marz M.

2021

10.1093/bib/bbaa232

Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.

Niarakis A, Kuiper M, Ostaszewski M, Malik Sheriff RS, Casals-Casas C, Thieffry D, Freeman TC, Thomas P, Touré V, Noël V, Stoll G, Saez-Rodriguez J, Naldi A, Oshurko E, Xenarios I, Soliman S, Chaouiya C, Helikar T, Calzone L.

2021

10.1093/bib/bbaa046

Publisher Correction: The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors.

Harland LTG, Simon CS, Senft AD, Costello I, Greder L, Imaz-Rosshandler I, Göttgens B, Marioni JC, Bikoff EK, Porcher C, de Bruijn MFTR, Robertson EJ.

2021

10.1038/s41556-021-00645-6

Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis

The CRyPTIC Consortium, Fowler PW, Barilar I, Battaglia S, Borroni E, Brandao AP, Brankin A, Cabibbe AM, Carter J, Cirillo DM, Claxton P, Clifton DA, Cohen T, Coronel J, Crook DW, Dreyer V, Earle SG, Escuyer V, Ferrazoli L, Gao GF, Gardy J, Gharbia S, Ghisi KT, Ghodousi A, Gibertoni Cruz AL, Grandjean L, Grazian C, Groenheit R, Guthrie JL, He W, Hoffmann H, Hoosdally SJ, Hunt M, Iqbal Z, Ismail NA, Jarrett L, Joseph L, Jou R, Kambli P, Khot R, Knaggs J, Koch A, Kohlerschmidt D, Kouchaki S, Lachapelle AS, Lalvani A, Lapierre SG, Laurenson IF, Letcher B, Lin W, Liu C, Liu D, Malone KM, Mandal A, Mansjö M, Matias D, Meintjes G, de Freitas Mendes F, Merker M, Mihalic M, Millard J, Miotto P, Mistry N, Moore D, Musser KA, Ngcamu D, Nhung HN, Niemann S, Nilgiriwala KS, Nimmo C, Okozi N, Oliveira RS, Omar SV, Paton N, Peto TE, Watanabe Pinhata JM, Plesnik S, Puyen ZM, Rabodoarivelo MS, Rakotosamimanana N, Rancoita PM, Rathod P, Robinson E, Rodger G, Rodrigues C, Rodwell TC, Roohi A, Santos-Lazaro D, Shah S, Kohl TA, Smith G, Solano W, Spitaleri A, Supply P, Surve U, Tahseen S, Thuong NTT, Thwaites G, Todt K, Trovato A, Utpatel C, Van Rie A, Vijay S, Walker TM, Walker AS, Warren R, Werngren J, Wijkander M, Wilkinson RJ, Wilson DJ, Wintringer P, Xiao Y, Yang Y, Yanlin Z, Yao S, Zhu B.

2021

10.1101/2021.02.24.21252386

An ancestral 10-bp repeat expansion in VWA1 causes recessive hereditary motor neuropathy.

Pagnamenta AT, Kaiyrzhanov R, Zou Y, Da'as SI, Maroofian R, Donkervoort S, Dominik N, Lauffer M, Ferla MP, Orioli A, Giess A, Tucci A, Beetz C, Sedghi M, Ansari B, Barresi R, Basiri K, Cortese A, Elgar G, Fernandez-Garcia MA, Yip J, Foley AR, Gutowski N, Jungbluth H, Lassche S, Lavin T, Marcelis C, Marks P, Marini-Bettolo C, Medne L, Moslemi AR, Sarkozy A, Reilly MM, Muntoni F, Millan F, Muraresku CC, Need AC, Nemeth AH, Neuhaus SB, Norwood F, O'Donnell M, O'Driscoll M, Rankin J, Yum SW, Zolkipli-Cunningham Z, Brusius I, Wunderlich G, Genomics England Research Consortium, Karakaya M, Wirth B, Fakhro KA, Tajsharghi H, Bönnemann CG, Taylor JC, Houlden H.

2021

10.1093/brain/awaa420

Drug-Resistant Tuberculosis in Pet Ring-Tailed Lemur, Madagascar.

LaFleur M, Reuter KE, Hall MB, Rasoanaivo HH, McKernan S, Ranaivomanana P, Michel A, Rabodoarivelo MS, Iqbal Z, Rakotosamimanana N, Lapierre SG.

2021

10.3201/eid2703.202924

Haplotype-resolved diverse human genomes and integrated analysis of structural variation.

Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE.

2021

10.1126/science.abf7117

Guidelines for FAIR sharing of preclinical safety and off-target pharmacology data.

Briggs K, Bosc N, Camara T, Diaz C, Drew P, Drewe WC, Kors J, Van Mulligen E, Pastor M, Pognan F, Quintana JR, Sarntivijai S, Steger-Hartmann T.

2021

10.14573/altex.2011181

A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae

Sim CK, Kashaf SS, Conlan S, Stacy A, Proctor DM, Almeida A, Bouladoux N, Chen M, Finn RD, Belkaid Y, Segre JA, NISC Comparative Sequencing Program.

2021

10.1101/2021.02.24.432587

Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries.

Gharahkhani P, Jorgenson E, Hysi P, Khawaja AP, Pendergrass S, Han X, Ong JS, Hewitt AW, Segrè AV, Rouhana JM, Hamel AR, Igo RP, Choquet H, Qassim A, Josyula NS, Cooke Bailey JN, Bonnemaijer PWM, Iglesias A, Siggs OM, Young TL, Vitart V, Thiadens AAHJ, Karjalainen J, Uebe S, Melles RB, Nair KS, Luben R, Simcoe M, Amersinghe N, Cree AJ, Hohn R, Poplawski A, Chen LJ, Rong SS, Aung T, Vithana EN, NEIGHBORHOOD consortium, ANZRAG consortium, Biobank Japan project, FinnGen study, UK Biobank Eye and Vision Consortium, GIGA study group, 23 and Me Research Team, Tamiya G, Shiga Y, Yamamoto M, Nakazawa T, Currant H, Birney E, Wang X, Auton A, Lupton MK, Martin NG, Ashaye A, Olawoye O, Williams SE, Akafo S, Ramsay M, Hashimoto K, Kamatani Y, Akiyama M, Momozawa Y, Foster PJ, Khaw PT, Morgan JE, Strouthidis NG, Kraft P, Kang JH, Pang CP, Pasutto F, Mitchell P, Lotery AJ, Palotie A, van Duijn C, Haines JL, Hammond C, Pasquale LR, Klaver CCW, Hauser M, Khor CC, Mackey DA, Kubo M, Cheng CY, Craig JE, MacGregor S, Wiggs JL.

2021

10.1038/s41467-020-20851-4

A missense variant effect prediction and annotation resource for SARS-CoV-2

Dunham A, Jang GM, Muralidharan M, Swaney D, Beltrao P.

2021

10.1101/2021.02.24.432721

BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers.

Bai J, Bandla C, Guo J, Vera Alvarez R, Bai M, Vizcaíno JA, Moreno P, Grüning B, Sallou O, Perez-Riverol Y.

2021

10.1021/acs.jproteome.0c00904

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.

Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia JM, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, Galazka JM, Gibbons SM, Hays D, Hervey J, Hu B, Hurwitz BL, Jaiswal P, Joachimiak MP, Kinkel L, Ladau J, Martin SL, McCue LA, Miller K, Mouncey N, Mungall C, Pafilis E, Reddy TBK, Richardson L, Roux S, Schriml LM, Shaffer JP, Sundaramurthi JC, Thompson LR, Timme RE, Zheng J, Wood-Charlson EM, Eloe-Fadrosh EA.

2021

10.1128/msystems.01194-20

Standardized nomenclature and open science in Human Genomics.

Vasiliou V, Veselkov K, Bruford E, Reichardt JKV.

2021

10.1186/s40246-021-00312-9

MAIP: a web service for predicting blood-stage malaria inhibitors.

Bosc N, Felix E, Arcila R, Mendez D, Saunders MR, Green DVS, Ochoada J, Shelat AA, Martin EJ, Iyer P, Engkvist O, Verras A, Duffy J, Burrows J, Gardner JMF, Leach AR.

2021

10.1186/s13321-021-00487-2

Reconstructing the Lineage Histories and Differentiation Trajectories of Individual Cancer Cells in Myeloproliferative Neoplasms.

Van Egeren D, Escabi J, Nguyen M, Liu S, Reilly CR, Patel S, Kamaz B, Kalyva M, DeAngelo DJ, Galinsky I, Wadleigh M, Winer ES, Luskin MR, Stone RM, Garcia JS, Hobbs GS, Camargo FD, Michor F, Mullally A, Cortes-Ciriano I, Hormoz S.

2021

10.1016/j.stem.2021.02.001

LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions.

Roller M, Stamper E, Villar D, Izuogu O, Martin F, Redmond AM, Ramachanderan R, Harewood L, Odom DT, Flicek P.

2021

10.1186/s13059-021-02260-y

Tumour gene expression signature in primary melanoma predicts long-term outcomes.

Garg M, Couturier DL, Nsengimana J, Fonseca NA, Wongchenko M, Yan Y, Lauss M, Jönsson GB, Newton-Bishop J, Parkinson C, Middleton MR, Bishop DT, McDonald S, Stefanos N, Tadross J, Vergara IA, Lo S, Newell F, Wilmott JS, Thompson JF, Long GV, Scolyer RA, Corrie P, Adams DJ, Brazma A, Rabbie R.

2021

10.1038/s41467-021-21207-2

Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care.

Roberts LW, Forde BM, Hurst T, Ling W, Nimmo GR, Bergh H, George N, Hajkowicz K, McNamara JF, Lipman J, Permana B, Schembri MA, Paterson D, Beatson SA, Harris PNA.

2021

10.1099/mgen.0.000530

Toward Understanding the Biochemical Determinants of Protein Degradation Rates.

Correa Marrero M, Barrio-Hernandez I.

2021

10.1021/acsomega.0c05318

Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in cutaneous T-cell lymphoma.

Jones CL, Degasperi A, Grandi V, Amarante TD, Genomics England Research Consortium, Mitchell TJ, Nik-Zainal S, Whittaker SJ.

2021

10.1038/s41598-021-83352-4

Data Sharing Under the General Data Protection Regulation: Time to Harmonize Law and Research Ethics?

Vlahou A, Hallinan D, Apweiler R, Argiles A, Beige J, Benigni A, Bischoff R, Black PC, Boehm F, Céraline J, Chrousos GP, Delles C, Evenepoel P, Fridolin I, Glorieux G, van Gool AJ, Heidegger I, Ioannidis JPA, Jankowski J, Jankowski V, Jeronimo C, Kamat AM, Masereeuw R, Mayer G, Mischak H, Ortiz A, Remuzzi G, Rossing P, Schanstra JP, Schmitz-Dräger BJ, Spasovski G, Staessen JA, Stamatialis D, Stenvinkel P, Wanner C, Williams SB, Zannad F, Zoccali C, Vanholder R.

2021

10.1161/hypertensionaha.120.16340

Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes.

Schwartzentruber J, Cooper S, Liu JZ, Barrio-Hernandez I, Bello E, Kumasaka N, Young AMH, Franklin RJM, Johnson T, Estrada K, Gaffney DJ, Beltrao P, Bassett A.

2021

10.1038/s41588-020-00776-w

Identification of phenotype-specific networks from paired gene expression-cell shape imaging data

Barker CG, Petsalaki E, Giudice G, Sero J, Ekpenyong EN, Bakal C, Petsalaki E.

2021

10.1101/2021.02.11.430597

ELIXIR-EXCELERATE: establishing Europe's data infrastructure for the life science research of the future.

Harrow J, Hancock J, ELIXIR-EXCELERATE Community, Blomberg N.

2021

10.15252/embj.2020107409

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.

2021

10.1038/s41594-020-00555-5

High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K, Fairley S, Runnels A, Winterkorn L, Lowy E, Flicek P, Germer S, Brand H, Hall IM, Talkowski ME, Narzisi G, Zody MC, The Human Genome Structural Variation Consortium.

2021

10.1101/2021.02.06.430068

Using data from the 100,000 Genomes Project to resolve conflicting interpretations of a recurrent TUBB2A mutation.

Ragoussis V, Pagnamenta AT, Haines RL, Giacopuzzi E, McClatchey MA, Sampson JR, Suri M, Gardham A, Cobben JM, Osio D, Fry AE, Genomics England Research Consortium, Taylor JC.

2021

10.1136/jmedgenet-2020-107528

Crypt4GH: a file format standard enabling native access to encrypted data.

Senf A, Davies R, Haziza F, Marshall J, Troncoso-Pastoriza J, Hofmann O, Keane TM.

2021

10.1093/bioinformatics/btab087

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Herzik MA, Hoh SW, Hou J, Hung LW, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W.

2021

10.1038/s41592-020-01051-w

Data-driven identification of ageing-related diseases from electronic health records.

Kuan V, Fraser HC, Hingorani M, Denaxas S, Gonzalez-Izquierdo A, Direk K, Nitsch D, Mathur R, Parisinos CA, Lumbers RT, Sofat R, Wong ICK, Casas JP, Thornton JM, Hemingway H, Partridge L, Hingorani AD.

2021

10.1038/s41598-021-82459-y

MicroPIPE: An end-to-end solution for high-quality complete bacterial genome construction

Murigneux V, Roberts LW, Forde BM, Phan M, Nhu NTK, Irwin AD, Harris PNA, Paterson DL, Schembri MA, Whiley DM, Beatson SA.

2021

10.1101/2021.02.02.429319

Enabling multiscale variation analysis with genome graphs

Letcher B, Hunt M, Iqbal Z.

2021

10.1101/2021.02.03.429603

Global spread and evolutionary history of HCV subtype 3a

lin S, De Maio N, Pedergnana V, Wu C, Thézé J, Barnes E, Ansari MA.

2021

10.1101/2021.02.03.429581

A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation.

Cazares D, Cazares A, Figueroa W, Guarneros G, Edwards RA, Vinuesa P.

2021

10.1128/msystems.00773-20

ChIPflow: from raw data to epigenomic dynamics

Daunesse M, Legendre R, Varet H, Pain A, Chica C.

2021

10.1101/2021.02.02.429342

The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment.

De Maio N.

2021

10.1093/sysbio/syaa050

SARS-CoV-2 infection remodels the host protein thermal stability landscape.

Selkrig J, Stanifer M, Mateus A, Mitosch K, Barrio-Hernandez I, Rettel M, Kim H, Voogdt CGP, Walch P, Kee C, Kurzawa N, Stein F, Potel C, Jarzab A, Kuster B, Bartenschlager R, Boulant S, Beltrao P, Typas A, Savitski MM.

2021

10.15252/msb.202010188

Cell type-specific modulation of healthspan by Forkhead family transcription factors in the nervous system.

Bolukbasi E, Woodling NS, Ivanov DK, Adcott J, Foley A, Rajasingam A, Gittings LM, Aleyakpo B, Niccoli T, Thornton JM, Partridge L.

2021

10.1073/pnas.2011491118

Longevity, clonal relationship, and transcriptional program of celiac disease-specific plasma cells.

Lindeman I, Zhou C, Eggesbø LM, Miao Z, Polak J, Lundin KEA, Jahnsen J, Qiao SW, Iversen R, Sollid LM.

2021

10.1084/jem.20200852

Twelve years of SAMtools and BCFtools.

Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H.

2021

10.1093/gigascience/giab008

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.

2021

10.15252/msb.20209982

Massive expansion of human gut bacteriophage diversity.

Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD.

2021

10.1016/j.cell.2021.01.029

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.

2021

10.1093/gigascience/giab007

Drug Safety Data Curation and Modeling in ChEMBL: Boxed Warnings and Withdrawn Drugs.

Hunter FMI, Bento AP, Bosc N, Gaulton A, Hersey A, Leach AR.

2021

10.1021/acs.chemrestox.0c00296

Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 2: a discussion of chemical and biological data.

Bender A, Cortes-Ciriano I.

2021

10.1016/j.drudis.2020.11.037

The CovR regulatory network drives the evolution of Group B Streptococcus virulence

Mazzuoli M, Daunesse M, Varet H, Rosinski-Chupin I, Legendre R, Sismeiro O, Gominet M, Kaminski P, Glaser P, Chica C, Trieu-Cuot P, Firon A.

2021

10.1101/2021.01.25.428120

Meta-analysis reveals consistent immune response patterns in COVID-19 infected patients at single-cell resolution

Garg M, Li X, Moreno P, Papatheodorou I, Shu Y, Brazma A, Miao Z.

2021

10.1101/2021.01.24.427089

Identifying causative mechanisms linking early-life stress to psycho-cardio-metabolic multi-morbidity: The EarlyCause project.

Mariani N, Borsini A, Cecil CAM, Felix JF, Sebert S, Cattaneo A, Walton E, Milaneschi Y, Cochrane G, Amid C, Rajan J, Giacobbe J, Sanz Y, Agustí A, Sorg T, Herault Y, Miettunen J, Parmar P, Cattane N, Jaddoe V, Lötjönen J, Buisan C, González Ballester MA, Piella G, Gelpi JL, Lamers F, Penninx BWJH, Tiemeier H, von Tottleben M, Thiel R, Heil KF, Järvelin MR, Pariante C, Mansuy IM, Lekadir K.

2021

10.1371/journal.pone.0245475

Optimising expression quantitative trait locus mapping workflows for single-cell studies

Cuomo AS, Alvari G, Azodi CB, McCarthy DJ, Bonder MJ, single-cell eQTLGen consortium.

2021

10.1101/2021.01.20.427401

A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases and prostate cancer progression

Magraner-Pardo L, Laskowski RA, Pons T, Thornton JM.

2021

10.1101/2021.01.21.427605

Correlative multimodal imaging: Building a community.

Walter A, Kleywegt GJ, Verkade P.

2021

10.1016/bs.mcb.2020.12.010

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain.

Joglekar A, Prjibelski A, Mahfouz A, Collier P, Lin S, Schlusche AK, Marrocco J, Williams SR, Haase B, Hayes A, Chew JG, Weisenfeld NI, Wong MY, Stein AN, Hardwick SA, Hunt T, Wang Q, Dieterich C, Bent Z, Fedrigo O, Sloan SA, Risso D, Jarvis ED, Flicek P, Luo W, Pitt GS, Frankish A, Smit AB, Ross ME, Tilgner HU.

2021

10.1038/s41467-020-20343-5

Sustainable data analysis with Snakemake.

Mölder F, Jablonski KP, Letcher B, Hall MB, Tomkins-Tinch CH, Sochat V, Forster J, Lee S, Twardziok SO, Kanitz A, Wilm A, Holtgrewe M, Rahmann S, Nahnsen S, Köster J.

2021

10.12688/f1000research.29032.2

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

Wagner AH, Babb L, Alterovitz G, Baudis M, Brush M, Cameron DL, Cline M, Griffith M, Griffith OL, Hunt S, Kreda D, Lee J, Lopez J, Moyer E, Nelson T, Patel RY, Riehle K, Robinson PN, Rynearson S, Schuilenburg H, Tsukanov K, Walsh B, Konopko M, Rehm H, Yates AD, Freimuth RR, Hart RK.

2021

10.1101/2021.01.15.426843

Structural and dynamical analysis of integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19

Bannerman BP, Julvez J, Oarga A, Moreno P, Blundell TL, Floto RA.

2021

10.21203/rs.3.rs-46892/v2

Mutation rates and selection on synonymous mutations in SARS-CoV-2

De Maio N, Walker CR, Turakhia Y, Lanfear R, Corbett-Detig R, Goldman N.

2021

10.1101/2021.01.14.426705

Data-deposition protocols for correlative soft X-ray tomography and super-resolution structured illumination microscopy applications.

Iudin A, Sarkans U, Koronfel MA, Fish T, Dobbie I, Harkiolaki M, Patwardhan A, Kleywegt GJ.

2021

10.1016/j.xpro.2020.100253

Recognizing the value of software: a software citation guide

Katz DS, Chue Hong NP, Clark T, Muench A, Stall S, Bouquin D, Cannon M, Edmunds S, Faez T, Feeney P, Fenner M, Friedman M, Grenier G, Harrison M, Heber J, Leary A, MacCallum C, Murray H, Pastrana E, Perry K, Schuster D, Stockhause M, Yeston J.

2021

10.12688/f1000research.26932.2

The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors.

Harland LTG, Simon CS, Senft AD, Costello I, Greder L, Imaz-Rosshandler I, Göttgens B, Marioni JC, Bikoff EK, Porcher C, de Bruijn MFTR, Robertson EJ.

2021

10.1038/s41556-020-00611-8

Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts.

Woo XY, Giordano J, Srivastava A, Zhao ZM, Lloyd MW, de Bruijn R, Suh YS, Patidar R, Chen L, Scherer S, Bailey MH, Yang CH, Cortes-Sanchez E, Xi Y, Wang J, Wickramasinghe J, Kossenkov AV, Rebecca VW, Sun H, Mashl RJ, Davies SR, Jeon R, Frech C, Randjelovic J, Rosains J, Galimi F, Bertotti A, Lafferty A, O'Farrell AC, Modave E, Lambrechts D, Ter Brugge P, Serra V, Marangoni E, El Botty R, Kim H, Kim JI, Yang HK, Lee C, Dean DA, Davis-Dusenbery B, Evrard YA, Doroshow JH, Welm AL, Welm BE, Lewis MT, Fang B, Roth JA, Meric-Bernstam F, Herlyn M, Davies MA, Ding L, Li S, Govindan R, Isella C, Moscow JA, Trusolino L, Byrne AT, Jonkers J, Bult CJ, Medico E, Chuang JH, PDXNET Consortium, EurOPDX Consortium.

2021

10.1038/s41588-020-00750-6

Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk.

Kalkauskas A, Perron U, Sun Y, Goldman N, Baele G, Guindon S, De Maio N.

2021

10.1371/journal.pcbi.1008561

Structure-function investigation of a new VUI-202012/01 SARS-CoV-2 variant

Singh J, Ehtesham NZ, Rahman SA, Hasnain SE.

2021

10.1101/2021.01.01.425028

Transcriptomics data availability and reusability in the transition from microarray to next-generation sequencing

Rustici G, Williams E, Barzine M, Brazma A, Bumgarner R, Chierici M, Furlanello C, Greger L, Jurman G, Miller M, Ouellette BF, Quackenbush J, Reich M, Stoeckert CJ, Taylor RC, Trutane SC, Weller J, Wilhelm B, Winegarden N.

2021

10.1101/2020.12.31.425022

Cellsnp-lite: an efficient tool for genotyping single cells

Huang X, Huang Y.

2021

10.1101/2020.12.31.424913

The Protein Data Bank Archive.

Velankar S, Burley SK, Kurisu G, Hoch JC, Markley JL.

2021

10.1007/978-1-0716-1406-8_1

Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses.

Dugourd A, Kuppe C, Sciacovelli M, Gjerga E, Gabor A, Emdal KB, Vieira V, Bekker-Jensen DB, Kranz J, Bindels EMJ, Costa ASH, Sousa A, Beltrao P, Rocha M, Olsen JV, Frezza C, Kramann R, Saez-Rodriguez J.

2021

10.15252/msb.20209730

Pfam: The protein families database in 2021.

Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, Tosatto SCE, Paladin L, Raj S, Richardson LJ, Finn RD, Bateman A.

2021

10.1093/nar/gkaa913

High-performance macromolecular data delivery and visualization for the web. Corrigendum.

Sehnal D, Svobodová R, Berka K, Rose AS, Burley SK, Velankar S, Koča J.

2021

10.1107/s205979832001606x

The InterPro protein families and domains database: 20 years on.

Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD.

2021

10.1093/nar/gkaa977

Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space.

Weber CC, Perron U, Casey D, Yang Z, Goldman N.

2021

10.1093/sysbio/syaa036

Sequence and Structure-Based Analysis of Specificity Determinants in Eukaryotic Protein Kinases.

Bradley D, Viéitez C, Rajeeve V, Selkrig J, Cutillas PR, Beltrao P.

2021

10.1016/j.celrep.2020.108602

Rfam 14: expanded coverage of metagenomic, viral and microRNA families.

Kalvari I, Nawrocki EP, Ontiveros-Palacios N, Argasinska J, Lamkiewicz K, Marz M, Griffiths-Jones S, Toffano-Nioche C, Gautheret D, Weinberg Z, Rivas E, Eddy SR, Finn RD, Bateman A, Petrov AI.

2021

10.1093/nar/gkaa1047

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.

RNAcentral Consortium.

2021

10.1093/nar/gkaa921

The European Nucleotide Archive in 2020.

Harrison PW, Ahamed A, Aslam R, Alako BTF, Burgin J, Buso N, Courtot M, Fan J, Gupta D, Haseeb M, Holt S, Ibrahim T, Ivanov E, Jayathilaka S, Balavenkataraman Kadhirvelu V, Kumar M, Lopez R, Kay S, Leinonen R, Liu X, O'Cathail C, Pakseresht A, Park Y, Pesant S, Rahman N, Rajan J, Sokolov A, Vijayaraja S, Waheed Z, Zyoud A, Burdett T, Cochrane G.

2021

10.1093/nar/gkaa1028

PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.

Lazar T, Martínez-Pérez E, Quaglia F, Hatos A, Chemes LB, Iserte JA, Méndez NA, Garrone NA, Saldaño TE, Marchetti J, Rueda AJV, Bernadó P, Blackledge M, Cordeiro TN, Fagerberg E, Forman-Kay JD, Fornasari MS, Gibson TJ, Gomes GW, Gradinaru CC, Head-Gordon T, Jensen MR, Lemke EA, Longhi S, Marino-Buslje C, Minervini G, Mittag T, Monzon AM, Pappu RV, Parisi G, Ricard-Blum S, Ruff KM, Salladini E, Skepö M, Svergun D, Vallet SD, Varadi M, Tompa P, Tosatto SCE, Piovesan D.

2021

10.1093/nar/gkaa1021

From ArrayExpress to BioStudies.

Sarkans U, Füllgrabe A, Ali A, Athar A, Behrangi E, Diaz N, Fexova S, George N, Iqbal H, Kurri S, Munoz J, Rada J, Papatheodorou I, Brazma A.

2021

10.1093/nar/gkaa1062

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.

Tello-Ruiz MK, Naithani S, Gupta P, Olson A, Wei S, Preece J, Jiao Y, Wang B, Chougule K, Garg P, Elser J, Kumari S, Kumar V, Contreras-Moreira B, Naamati G, George N, Cook J, Bolser D, D'Eustachio P, Stein LD, Gupta A, Xu W, Regala J, Papatheodorou I, Kersey PJ, Flicek P, Taylor C, Jaiswal P, Ware D.

2021

10.1093/nar/gkaa979

Europe PMC in 2020.

Ferguson C, Araújo D, Faulk L, Gou Y, Hamelers A, Huang Z, Ide-Smith M, Levchenko M, Marinos N, Nambiar R, Nassar M, Parkin M, Pi X, Rahman F, Rogers F, Roochun Y, Saha S, Selim M, Shafique Z, Sharma S, Stephenson D, Talo' F, Thouvenin A, Tirunagari S, Vartak V, Venkatesan A, Yang X, McEntyre J.

2021

10.1093/nar/gkaa994

Genenames.org: the HGNC and VGNC resources in 2021.

Tweedie S, Braschi B, Gray K, Jones TEM, Seal RL, Yates B, Bruford EA.

2021

10.1093/nar/gkaa980

The European Bioinformatics Institute: empowering cooperation in response to a global health crisis.

Cantelli G, Cochrane G, Brooksbank C, McDonagh E, Flicek P, McEntyre J, Birney E, Apweiler R.

2021

10.1093/nar/gkaa1077

Ensembl 2021.

Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, El Houdaigui B, Fatima R, Gall A, Garcia Giron C, Grego T, Guijarro-Clarke C, Haggerty L, Hemrom A, Hourlier T, Izuogu OG, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Gonzalez Martinez J, Marugán JC, Maurel T, McMahon AC, Mohanan S, Moore B, Muffato M, Oheh DN, Paraschas D, Parker A, Parton A, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Steed E, Szpak M, Szuba M, Taylor K, Thormann A, Threadgold G, Walts B, Winterbottom A, Chakiachvili M, Chaubal A, De Silva N, Flint B, Frankish A, Hunt SE, IIsley GR, Langridge N, Loveland JE, Martin FJ, Mudge JM, Morales J, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Cunningham F, Yates AD, Zerbino DR, Flicek P.

2021

10.1093/nar/gkaa942

Definition of the Metagenomic Profile of Ocean Water Samples From the Gulf of Mexico Based on Comparison With Reference Samples From Sites Worldwide.

Loza A, García-Guevara F, Segovia L, Escobar-Zepeda A, Sanchez-Olmos MDC, Merino E, Sanchez-Flores A, Pardo-Lopez L, Juarez K, Gutierrez-Rios RM.

2021

10.3389/fmicb.2021.781497

The international nucleotide sequence database collaboration.

Arita M, Karsch-Mizrachi I, Cochrane G.

2021

10.1093/nar/gkaa967

Open Targets Platform: supporting systematic drug-target identification and prioritisation.

Ochoa D, Hercules A, Carmona M, Suveges D, Gonzalez-Uriarte A, Malangone C, Miranda A, Fumis L, Carvalho-Silva D, Spitzer M, Baker J, Ferrer J, Raies A, Razuvayevskaya O, Faulconbridge A, Petsalaki E, Mutowo P, Machlitt-Northen S, Peat G, McAuley E, Ong CK, Mountjoy E, Ghoussaini M, Pierleoni A, Papa E, Pignatelli M, Koscielny G, Karim M, Schwartzentruber J, Hulcoop DG, Dunham I, McDonagh EM.

2021

10.1093/nar/gkaa1027

UniProt: the universal protein knowledgebase in 2021.

UniProt Consortium.

2021

10.1093/nar/gkaa1100

GENCODE 2021.

Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Howe KL, Hunt T, Izuogu OG, Johnson R, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Riera FC, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Wolf MY, Xu J, Yang YT, Yates A, Zerbino D, Zhang Y, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Tress ML, Flicek P.

2021

10.1093/nar/gkaa1087

Opinion: Standardizing gene product nomenclature-a call to action.

Fujiyoshi K, Bruford EA, Mroz P, Sims CL, O'Leary TJ, Lo AWI, Chen N, Patel NR, Patel KP, Seliger B, Song M, Monzon FA, Carter AB, Gulley ML, Mockus SM, Phung TL, Feilotter H, Williams HE, Ogino S.

2021

10.1073/pnas.2025207118

The Gene Ontology resource: enriching a GOld mine.

Gene Ontology Consortium.

2021

10.1093/nar/gkaa1113

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.

2020

10.1371/journal.pone.0242933

An automated protocol for modelling peptide substrates to proteases.

Ochoa R, Magnitov M, Laskowski RA, Cossio P, Thornton JM.

2020

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.

2020

10.1371/journal.pgen.1009190

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.

2020

10.1101/2020.12.24.424326

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.

2020

10.1101/2020.12.24.424174

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.

2020

10.1101/2020.12.21.423773

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.

2020

10.1101/2020.12.18.422865

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.

2020

10.1101/2020.12.17.423357

Metagenomics Bioinformatics

Mitchell A, Finn R, Kale V.

2020

10.6019/tol.metagenomics-t.2019.00001.1

Exploring metabolite metabolism using the Enzyme Portal

Zaru R.

2020

10.6019/tol.enzymeportal-w.2020.00001.1

Discovering scientific evidence using Europe PMC SciLite annotation

Araujo D.

2020

10.6019/tol.epmc-scilite-w.2020.00001.1

Finding the data behind research articles with Europe PMC

Araujo D.

2020

10.6019/tol.epmcfind-w.2020.00001.1

Searching and browsing scientific publications with the new Europe PMC

Araujo D.

2020

10.6019/tol.europepmc_new-w.2020.00001.1

The Ensembl Rapid Release genome browser

Moore B.

2020

10.6019/tol.ensembl-rapid-release-w.2020.00001.1

Using Europe PMC for effective literature research

Araujo D.

2020

10.6019/tol.epmclit-w.2020.00001.1

Open with purpose: How and why to make your data open

Morgan S.

2020

10.6019/tol.openaccess-w.2020.00001.1

PDBe Graph Database: A Neo4J-driven integrative knowledge graph for structural data

Nair S.

2020

10.6019/tol.pdbe-graphdatabase-w.2020.00001.1

The International Mouse Phenotyping Consortium (IMPC): a large-scale functional catalogue of mammalian genes

Munoz Fuentes V, Haseli H.

2020

10.6019/tol.impc-w.2020.00001.1

Understanding InterPro families, domains and functions

Paysan-Lafosse T.

2020

10.6019/tol.understanding-interpro-w.2020.00001.1

Genome3D annotations in InterPro

Paysan-Lafosse T.

2020

10.6019/tol.genome3d-t.2019.00001.1

Using the InterPro website in your research

Paysan-Lafosse T.

2020

10.6019/tol.interprowebsite-w.2020.00001.1

MGnify today: analysing microbiome data

Kale V.

2020

10.6019/tol.mgnify-analysis-w.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.

2020

10.1016/j.drudis.2020.12.009

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.

2020

10.1101/2020.12.16.423064

De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Mari RS, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Chaisson MJ, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier A, Abel H, Hall I, Flicek P, Stegle O, Gerstein MB, Tubio JM, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE.

2020

10.1101/2020.12.16.423102

Processes Underlying Glycemic Deterioration in Type 2 Diabetes: An IMI DIRECT Study.

Bizzotto R, Jennison C, Jones AG, Kurbasic A, Tura A, Kennedy G, Bell JD, Thomas EL, Frost G, Eriksen R, Koivula RW, Brage S, Kaye J, Hattersley AT, Heggie A, McEvoy D, 't Hart LM, Beulens JW, Elders P, Musholt PB, Ridderstråle M, Hansen TH, Allin KH, Hansen T, Vestergaard H, Lundgaard AT, Thomsen HS, De Masi F, Tsirigos KD, Brunak S, Viñuela A, Mahajan A, McDonald TJ, Kokkola T, Forgie IM, Giordano GN, Pavo I, Ruetten H, Dermitzakis E, McCarthy MI, Pedersen O, Schwenk JM, Adamski J, Franks PW, Walker M, Pearson ER, Mari A, IMI DIRECT consortium.

2020

10.2337/dc20-1567

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.

2020

10.1101/2020.12.09.20246397

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.

2020

10.1016/j.devcel.2020.11.013

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.

2020

10.1101/2020.12.11.419523

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.

2020

10.1038/s41598-020-78031-9

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.

2020

10.1101/2020.12.07.415539

MM-PBSA and the Importance of the Dielectric Constant for Kinase Drug Design

Schneider M, Labesse G.

2020

10.26434/chemrxiv.13347368.v1

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.

2020

10.1016/j.jprot.2020.104070

Discovery of Fibrillar Adhesins across Bacterial Species

Monzon V, Lafita A, Bateman A.

2020

10.1101/2020.12.07.414375

Metabolomics: The Stethoscope for the Twenty-First Century.

Ashrafian H, Sounderajah V, Glen R, Ebbels T, Blaise BJ, Kalra D, Kultima K, Spjuth O, Tenori L, Salek RM, Kale N, Haug K, Schober D, Rocca-Serra P, O'Donovan C, Steinbeck C, Cano I, de Atauri P, Cascante M.

2020

10.1159/000513545

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.

2020

10.1101/2020.12.03.410100

Biocuration - mapping resources and needs

Holinski A, Burke ML, Morgan SL, McQuilton P, Palagi PM.

2020

10.12688/f1000research.25413.2

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.

2020

10.1084/jem.20192275

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.

2020

10.1038/s41587-020-00744-z

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.

2020

10.1093/bioinformatics/btaa805

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.

2020

10.1038/s41467-020-19942-z

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.

2020

10.1038/s41591-020-01186-5

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.

2020

10.1371/journal.pgen.1009083

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.

2020

10.1038/s41467-020-20128-w

High-performance macromolecular data delivery and visualization for the web.

Sehnal D, Svobodová R, Berka K, Rose AS, Burley SK, Velankar S, Koča J.

2020

10.1107/s2059798320014515

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.

2020

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.

2020

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.

2020

10.1186/s13059-020-02197-8

Mining a GWAS of Severe Covid-19.

Karim M, Dunham I, Ghoussaini M.

2020

10.1056/nejmc2025747

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.

2020

10.1101/2020.11.19.20234120

Milo: differential abundance testing on single-cell data using k-NN graphs

Dann E, Henderson NC, Teichmann SA, Morgan MD, Marioni JC.

2020

10.1101/2020.11.23.393769

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.

2020

10.1101/2020.11.21.392621

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.

2020

10.1101/2020.11.20.391896

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.

2020

10.21203/rs.3.rs-105193/v1

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, Espinal-Centeno A, Varela-Rodríguez L, Gomez-Zepeda D, Caballero-Pérez J, García-Medel PL, Brieba LG, Ordaz-Ortiz JJ, Cruz-Ramirez A.

2020

10.3389/fcell.2020.562940

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.

2020

10.1371/journal.pgen.1009175

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.

2020

10.1016/j.stem.2020.10.017

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.

2020

10.1101/2020.11.16.384834

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.

2020

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.

2020

10.3389/fmicb.2020.590294

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.

2020

10.1101/2020.11.12.380378

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.

2020

10.1101/2020.11.11.378869

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.

2020

10.1038/s41586-020-2896-2

Short-range template switching in great ape genomes explored using a pair hidden Markov model

Walker CR, Scally A, De Maio N, Goldman N.

2020

10.1101/2020.11.09.374694

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.

2020

10.1101/2020.11.06.371716

Computational identification of splicing phenotypes from single cell transcriptomic experiments

Huang Y, Sanguinetti G.

2020

10.1101/2020.11.04.368019

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.

2020

10.1101/2020.11.03.367086

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.

2020

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.

2020

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.

2020

10.1101/2020.10.30.361162

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, Chen C, Ragkousi K, Praher D, Fredman D, Moran Y, Gibson MC, Technau U.

2020

10.1101/2020.10.30.359448

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.

2020

10.21203/rs.3.rs-41814/v2

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.

2020

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, 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.

2020

10.1101/2020.10.26.356014

Evaluation of Methods for Protein Representation Learning: A Quantitative Analysis

Unsal S, Ataş H, Albayrak M, Turhan K, Acar AC, Doğan T.

2020

10.1101/2020.10.28.359828

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.

2020

10.1101/2020.10.28.359232

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.

2020

10.1371/journal.pone.0240824

Databiology Lab CORONAHACK: Collection of Public COVID-19 Data

Pérez JC, Contreras JMC, de Blas Pérez C, Alvarez FL.

2020

10.1101/2020.10.22.328864

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.

2020

10.1101/2020.10.20.347013

BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management.

Sehnal D, Bittrich S, Velankar S, Koča J, Svobodová R, Burley SK, Rose AS.

2020

10.1371/journal.pcbi.1008247

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.

2020

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, Vizcaíno JA, Choudhary JS, Brazma A, Viksna J.

2020

10.1002/pmic.202000009

OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS.

Netz E, Dijkstra TMH, Sachsenberg T, Zimmermann L, Walzer M, Monecke T, Ficner R, Dybkov O, Urlaub H, Kohlbacher O.

2020

10.1074/mcp.tir120.002186

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.

2020

10.1038/s42003-020-01302-8

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.

2020

10.1016/j.str.2020.09.011

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.

2020

10.1126/science.abe9403

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.

2020

10.1038/s41586-020-2766-y

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).

2020

10.1007/s11306-020-01728-5

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.

2020

10.3389/fcell.2020.584604

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.

2020

10.1038/s41436-020-00980-3

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.

2020

10.12688/f1000research.24427.1

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.

2020

10.20944/preprints202010.0118.v1

How to use the MEROPS database and website to help understand peptidase specificity.

Rawlings ND, Bateman A.

2020

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.

2020

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.

2020

10.1126/science.aba8347

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.

2020

10.1038/s41591-020-1079-x

CEN-tools: an integrative platform to identify the contexts of essential genes.

Sharma S, Dincer C, Weidemüller P, Wright GJ, Petsalaki E.

2020

10.15252/msb.20209698

In conversation with Janet Thornton.

Dhillon P, Thornton JM.

2020

10.1111/febs.15567

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.

2020

10.1093/gigascience/giaa102

A decoupled, modular and scriptable architecture for tools to curate data platforms

Langenstein M, Hermjakob H, Llinares MB.

2020

10.1101/2020.09.28.282699

Overview of the expression of key regeneration genes in embryo development and matured tissues in Axolotl (Ambystoma mexicanum)

Shah H, Caballero J.

2020

10.1101/2020.09.24.312462

Functional signatures of evolutionarily young CTCF binding sites.

Azazi D, Mudge JM, Odom DT, Flicek P.

2020

10.1186/s12915-020-00863-8

Secondary structure of the SARS-CoV-2 5'-UTR.

Miao Z, Tidu A, Eriani G, Martin F.

2020

10.1080/15476286.2020.1814556

Toward a Sample Metadata Standard in Public Proteomics Repositories.

Perez-Riverol Y, European Bioinformatics Community for Mass Spectrometry.

2020

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.

2020

10.1038/s41467-020-18151-y

Deep microbial community profiling along the fermentation process of pulque, a biocultural resource of Mexico.

Rocha-Arriaga C, Espinal-Centeno A, Martinez-Sánchez S, Caballero-Pérez J, Alcaraz LD, Cruz-Ramírez A.

2020

10.1016/j.micres.2020.126593

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.

2020

10.1016/j.ajhg.2020.08.023

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.

2020

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.

2020

10.1101/2020.09.17.301614

A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

McGrath JM(, Funk A, Galewski P, Ou S, Townsend B, Davenport K, Daligault H, Johnson S, Lee J, Hastie A, Darracq A, Willems G, Barnes S, Liachko I, Sullivan S, Koren S, Phillippy A, Wang J, Liu T, Pulman J, Childs K, Yocum A, Fermin D, Mutasa-Göttgens E, Stevanato P, Taguchi K, Dorn K.

2020

10.1101/2020.09.15.298315

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.

2020

10.1101/2020.09.14.296889

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.

2020

10.1101/2020.09.14.20193870

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.

2020

10.1038/s41592-020-0955-0

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.

2020

10.12688/f1000research.26098.1

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.

2020

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.

2020

10.1101/2020.09.10.290924

Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC.

Saary P, Mitchell AL, Finn RD.