Publications | EMBL’s European Bionformatics Institute

Publications

EMBL-EBI researchers publish regularly in top-tier life science journals and strive to make their research and data open access.

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2022 PPR Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs

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

2022 CTX-AGR-MED Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England.

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

2022 CTX-AGR-MED The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases.

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

2022 PPR The evolution of two transmissible cancers in Tasmanian devils

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

2022 CTX-AGR-MED Author Correction: Tumour gene expression signature in primary melanoma predicts long-term outcomes.

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

2022 PPR Mannose metabolism inhibition sensitizes acute myeloid leukemia cells to cytarabine and FLT3 inhibitor therapy by modulating fatty acid metabolism to drive ferroptotic cell death

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

2022 CTX-AGR-MED The Quest for Orthologs orthology benchmark service in 2022.

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

2022 CTX-AGR-MED BioSimulators: a central registry of simulation engines and services for recommending specific tools.

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

2022 PPR Genomic patterns of malignant peripheral nerve sheath tumour (MPNST) evolution correlate with clinical outcome and are detectable in cell-free DNA

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

2022 CTX-AGR-MED Author Correction: Perspectives on ENCODE.

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

2022 CTX-AGR-MED A Simple Standard for Sharing Ontological Mappings (SSSOM).

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

2022 PPR A human embryonic limb cell atlas resolved in space and time

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

2022 CTX-AGR-MED Molecular biology for green recovery-A call for action.

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

2022 CTX-AGR-MED PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology.

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

2022 CTX-AGR-MED The Human Pangenome Project: a global resource to map genomic diversity.

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

2022 CTX-AGR-MED LY6S, a New IFN-Inducible Human Member of the Ly6a Subfamily Expressed by Spleen Cells and Associated with Inflammation and Viral Resistance.

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

2022 PPR An atlas of genetic scores to predict multi-omic traits

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

2022 PPR Mondo: Unifying diseases for the world, by the world

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

2022 CTX-AGR-MED A joint NCBI and EMBL-EBI transcript set for clinical genomics and research.

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

2022 CTX-AGR-MED Publisher Correction: Evolution of enhanced innate immune evasion by SARS-CoV-2.

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

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

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

2022 CTX-AGR-MED The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A genotypic analysis.

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

2022 CTX-AGR-MED Nanopore ReCappable sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs.

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

2022 CTX-AGR-MED A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics.

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

2022 CTX-AGR-MED Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.

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

2022 CTX-AGR-MED Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation.

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

2022 CTX-AGR-MED The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization.

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

2022 CTX-AGR-MED The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.

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

2022 CTX-AGR-MED Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.

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

2022 CTX-AGR-MED The discovAIR project: a roadmap towards the Human Lung Cell Atlas.

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

2022 PPR Formalizing Insect Morphological Data: A Model-Based, Extensible Insect Anatomy Ontology and Its Potential Applications in Biodiversity Research and Informatics

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

2022 PPR A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates

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

2022 PPR Mendelian gene identification through mouse embryo viability screening

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

2022 PPR The Gene Curation Coalition: A global effort to harmonize gene-disease evidence resources

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

2022 CTX-AGR-MED The reactome pathway knowledgebase 2022.

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

2022 CTX-AGR-MED Rhea, the reaction knowledgebase in 2022.

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

2022 CTX-AGR-MED DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.

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

2022 CTX-AGR-MED The European Bioinformatics Institute (EMBL-EBI) in 2021.

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

2022 CTX-AGR-MED The IntAct database: efficient access to fine-grained molecular interaction data.

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

2022 CTX-AGR-MED VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center.

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

2022 CTX-AGR-MED The European Nucleotide Archive in 2021.

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

2022 CTX-AGR-MED The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data.

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

2022 CTX-AGR-MED Complex Portal 2022: new curation frontiers.

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

2022 CTX-AGR-MED The European Genome-phenome Archive in 2021.

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

2022 CTX-AGR-MED Ensembl 2022.

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

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

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

2022 CTX-AGR-MED Expression Atlas update: gene and protein expression in multiple species.

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

2022 CTX-AGR-MED AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.

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

2021 CTX-AGR-MED Evolution of enhanced innate immune evasion by SARS-CoV-2.

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

2021 CTX-AGR-MED How to interpret AlphaFold structures

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

2021 CTX-AGR-MED Preprints 101 for authors

Preprints 101 for authors

Levchenko M, Puebla I, Pal Singh S.

2021

10.6019/tol.preprints-w.2021.00001.1

2021 CTX-AGR-MED EMBL-EBI Tools: An introduction

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

2021 CTX-AGR-MED A guide to...: Introducing concepts and resources in bioinformatics

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

2021 PPR Single-Cell Atlas of Common Variable Immunodeficiency reveals germinal center-associated epigenetic dysregulation in B cell responses

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

2021 CTX-AGR-MED The future of preprint peer review

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

2021 PPR LY6S, a New Interferon-Inducible Human Member of the Ly6a-Subfamily Expressed by Spleen Cells and Associated with Inflammation and Viral Resistance

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

2021 PPR Towards a structurally resolved human protein interaction network

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

2021 CTX-AGR-MED Transcriptional differences between JAK2-V617F and wild-type bone marrow cells in patients with myeloproliferative neoplasms.

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

2021 PPR Genetic, parental and lifestyle factors influence telomere length

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

2021 CTX-AGR-MED RNA modifications detection by comparative Nanopore direct RNA sequencing.

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

2021 CTX-AGR-MED Target 2035 - update on the quest for a probe for every protein.

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

2021 PPR 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

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

2021 CTX-AGR-MED COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

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

2021 CTX-AGR-MED REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.

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

2021 CTX-AGR-MED A global view of standards for open image data formats and repositories.

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

2021 PPR The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

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

2021 CTX-AGR-MED What makes a megaplasmid?

What makes a megaplasmid?

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

2021

10.1098/rstb.2020.0472

2021 PPR Nanopore ReCappable Sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs

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

2021 PPR Multiple adaptive solutions to face climatic constraints: novel insights in the debate over the role of convergence in local adaptation

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

2021 CTX-AGR-MED Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean.

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

2021 CTX-AGR-MED The Data Use Ontology to streamline responsible access to human biomedical datasets.

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

2021 PPR Towards a structurally resolved human protein interaction network

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

2021 CTX-AGR-MED Anatomical structures, cell types and biomarkers of the Human Reference Atlas.

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

2021 CTX-AGR-MED 100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care - Preliminary Report.

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

2021 CTX-AGR-MED GA4GH: International policies and standards for data sharing across genomic research and healthcare

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

2021 CTX-AGR-MED Author Correction: Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development.

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

2021 CTX-AGR-MED The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification.

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

2021 CTX-AGR-MED GA4GH: International policies and standards for data sharing across genomic research and healthcare.

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

2021 CTX-AGR-MED The gene regulation knowledge commons: the action area of GREEKC.

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

2021 CTX-AGR-MED High-throughput functional characterization of protein phosphorylation sites in yeast.

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

2021 CTX-AGR-MED Correction: Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images.

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

2021 CTX-AGR-MED Genomic reconstruction of the SARS-CoV-2 epidemic in England.

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

2021 CTX-AGR-MED Author Correction: Macroscale patterns of oceanic zooplankton composition and size structure.

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

2021 CTX-AGR-MED A proteomics sample metadata representation for multiomics integration and big data analysis.

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

2021 PPR The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life

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

2021 PPR The production of 4,182 mouse lines identifies experimental and biological variables impacting Cas9-mediated mutant mouse line production

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

2021 CTX-AGR-MED COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

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

2021 CTX-AGR-MED Cell type-specific novel long non-coding RNA and circular RNA in the BLUEPRINT hematopoietic transcriptomes atlas.

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

2021 CTX-AGR-MED OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.

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

2021 PPR A structural biology community assessment of AlphaFold 2 applications

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

2021 CTX-AGR-MED Correction: Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease.

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

2021 PPR Breast cancer risks associated with missense variants in breast cancer susceptibility genes

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

2021 CTX-AGR-MED Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.

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

2021 CTX-AGR-MED Identifying genetic determinants of inflammatory pain in mice using a large-scale gene-targeted screen.

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

2021 CTX-AGR-MED Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis.

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

2021 CTX-AGR-MED Correction to: Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases.

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

2021 CTX-AGR-MED Correction to: Solving patients with rare diseases through programmatic reanalysis of genome-phenome data.

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

2021 CTX-AGR-MED Correction: Solving unsolved rare neurological diseases-a Solve-RD viewpoint.

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

2021 CTX-AGR-MED ISA API: An open platform for interoperable life science experimental metadata.

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

2021 PPR Genetic variants associated with cross-disorder and disorder-specific risk for psychiatric disorders are enriched at epigenetically active sites in peripheral lymphoid cells

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

2021 PPR Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

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

2021 CTX-AGR-MED Macroscale patterns of oceanic zooplankton composition and size structure.

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

2021 CTX-AGR-MED Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology.

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

2021 CTX-AGR-MED Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease.

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

2021 CTX-AGR-MED Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution.

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

2021 PPR Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lung cancer

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

2021 CTX-AGR-MED Highly accurate protein structure prediction for the human proteome.

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

2021 PPR 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

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

2021 CTX-AGR-MED The PROTACtable genome.

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

2021 CTX-AGR-MED Refget: standardised access to reference sequences.

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

2021 CTX-AGR-MED Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity.

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

2021 CTX-AGR-MED UCSC Cell Browser: Visualize Your Single-Cell Data.

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

2021 CTX-AGR-MED MaxDIA enables library-based and library-free data-independent acquisition proteomics.

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

2021 CTX-AGR-MED Dense optical flow software to quantify cellular contractility.

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

2021 CTX-AGR-MED 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.

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

2021 PPR Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly

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

2021 CTX-AGR-MED The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.

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

2021 CTX-AGR-MED Ten Years of Collaborative Progress in the Quest for Orthologs.

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

2021 CTX-AGR-MED Universal Spectrum Identifier for mass spectra.

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

2021 PPR Transferability of genetic loci and polygenic scores for cardiometabolic traits in British Pakistanis and Bangladeshis

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

2021 CTX-AGR-MED Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.

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

2021 PPR Big Data Analysis of Electronic Health Records: Clinically interpretable representations of older adult inpatient trajectories using time-series numerical data and Hidden Markov Models

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

2021 PPR A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

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

2021 CTX-AGR-MED A map of transcriptional heterogeneity and regulatory variation in human microglia.

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

2021 CTX-AGR-MED Crowdsourced mapping of unexplored target space of kinase inhibitors.

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

2021 PPR Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas

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

2021 CTX-AGR-MED Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases.

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

2021 CTX-AGR-MED Solving patients with rare diseases through programmatic reanalysis of genome-phenome data.

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

2021 PPR Genomic reconstruction of the SARS-CoV-2 epidemic in England

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

2021 CTX-AGR-MED Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries.

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

2021 PPR A proteomics sample metadata representation for multiomics integration, and big data analysis

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

2021 CTX-AGR-MED An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities.

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

2021 CTX-AGR-MED Mapping Rora expression in resting and activated CD4+ T cells.

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

2021 PPR Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

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

2021 CTX-AGR-MED Diagnostic accuracy of non-invasive tests for advanced fibrosis in patients with NAFLD: an individual patient data meta-analysis.

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

2021 PPR The Medaka Inbred Kiyosu-Karlsruhe (MIKK) Panel

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

2021 CTX-AGR-MED Diagnostic accuracy of elastography and magnetic resonance imaging in patients with NAFLD: A systematic review and meta-analysis.

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

2021 CTX-AGR-MED The genome sequence of the brown trout, Salmo trutta Linnaeus 1758.

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

2021 CTX-AGR-MED Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images.

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

2021 CTX-AGR-MED Solving unsolved rare neurological diseases-a Solve-RD viewpoint.

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

2021 CTX-AGR-MED Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities".

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

2021 CTX-AGR-MED Author Correction: Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts.

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

2021 CTX-AGR-MED Towards complete and error-free genome assemblies of all vertebrate species.

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

2021 CTX-AGR-MED A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage.

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

2021 CTX-AGR-MED Single-cell multi-omics analysis of the immune response in COVID-19.

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

2021 CTX-AGR-MED Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease.

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

2021 CTX-AGR-MED Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19.

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

2021 PPR Cells of the human intestinal tract mapped across space and time

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

2021 CTX-AGR-MED A resource of targeted mutant mouse lines for 5,061 genes.

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

2021 CTX-AGR-MED User-friendly, scalable tools and workflows for single-cell RNA-seq analysis.

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

2021 CTX-AGR-MED Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine.

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

2021 CTX-AGR-MED The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).

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

2021 CTX-AGR-MED UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.

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

2021 CTX-AGR-MED Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research.

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

2021 CTX-AGR-MED Suppression of insulin-induced gene 1 (INSIG1) function promotes hepatic lipid remodelling and restrains NASH progression.

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

2021 CTX-AGR-MED The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.

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

2021 CTX-AGR-MED Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics.

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

2021 CTX-AGR-MED Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.

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

2021 CTX-AGR-MED Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.

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

2021 CTX-AGR-MED 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.

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

2021 PPR Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis

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

2021 CTX-AGR-MED An ancestral 10-bp repeat expansion in VWA1 causes recessive hereditary motor neuropathy.

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

2021 CTX-AGR-MED Haplotype-resolved diverse human genomes and integrated analysis of structural variation.

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

2021 CTX-AGR-MED Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries.

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

2021 CTX-AGR-MED Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.

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

2021 CTX-AGR-MED MAIP: a web service for predicting blood-stage malaria inhibitors.

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

2021 CTX-AGR-MED Reconstructing the Lineage Histories and Differentiation Trajectories of Individual Cancer Cells in Myeloproliferative Neoplasms.

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

2021 CTX-AGR-MED Tumour gene expression signature in primary melanoma predicts long-term outcomes.

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

2021 CTX-AGR-MED Data Sharing Under the General Data Protection Regulation: Time to Harmonize Law and Research Ethics?

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

2021 PPR High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

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

2021 CTX-AGR-MED Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

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

2021 CTX-AGR-MED SARS-CoV-2 infection remodels the host protein thermal stability landscape.

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

2021 CTX-AGR-MED Twelve years of SAMtools and BCFtools.

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

2021 CTX-AGR-MED Reproducibility in systems biology modelling.

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

2021 CTX-AGR-MED Identifying causative mechanisms linking early-life stress to psycho-cardio-metabolic multi-morbidity: The EarlyCause project.

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

2021 CTX-AGR-MED A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain.

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

2021 CTX-AGR-MED Sustainable data analysis with Snakemake.

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

2021 PPR The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

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

2021 PPR Recognizing the value of software: a software citation guide

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

2021 CTX-AGR-MED Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts.

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

2021 CTX-AGR-MED The Protein Data Bank Archive.

The Protein Data Bank Archive.

Velankar S, Burley SK, Kurisu G, Hoch JC, Markley JL.

2021

10.1007/978-1-0716-1406-8_1

2021 CTX-AGR-MED Pfam: The protein families database in 2021.

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

2021 CTX-AGR-MED The InterPro protein families and domains database: 20 years on.

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

2021 CTX-AGR-MED Rfam 14: expanded coverage of metagenomic, viral and microRNA families.

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

2021 CTX-AGR-MED The European Nucleotide Archive in 2020.

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

2021 CTX-AGR-MED PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.

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

2021 CTX-AGR-MED From ArrayExpress to BioStudies.

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

2021 CTX-AGR-MED Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.

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

2021 CTX-AGR-MED Europe PMC in 2020.

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

2021 CTX-AGR-MED Ensembl 2021.

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

2021 CTX-AGR-MED Open Targets Platform: supporting systematic drug-target identification and prioritisation.

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

2021 CTX-AGR-MED GENCODE 2021.

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

2021 CTX-AGR-MED Opinion: Standardizing gene product nomenclature-a call to action.

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

2020 CTX-AGR-MED Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density.

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

2020 PPR The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data

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

2020 CTX-AGR-MED Metagenomics Bioinformatics

Metagenomics Bioinformatics

Mitchell A, Finn R, Kale V.

2020

10.6019/tol.metagenomics-t.2019.00001.1

2020 PPR De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

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

2020 CTX-AGR-MED Processes Underlying Glycemic Deterioration in Type 2 Diabetes: An IMI DIRECT Study.

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

2020 PPR A genomic epidemiology study of multidrug-resistant Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii in two intensive care units in Hanoi, Vietnam

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

2020 CTX-AGR-MED Urinary metabolic phenotyping for Alzheimer's disease.

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

2020 PPR Universal Spectrum Identifier for mass spectra

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

2020 CTX-AGR-MED Metabolomics: The Stethoscope for the Twenty-First Century.

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

2020 CTX-AGR-MED NCKAP1L defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammation.

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

2020 CTX-AGR-MED Guidelines for reporting single-cell RNA-seq experiments.

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

2020 CTX-AGR-MED Towards a unified open access dataset of molecular interactions.

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

2020 CTX-AGR-MED Author Correction: A dynamic COVID-19 immune signature includes associations with poor prognosis.

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

2020 CTX-AGR-MED Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

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

2020 CTX-AGR-MED Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis.

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

2020 CTX-AGR-MED Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community.

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

2020 PPR Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19

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

2020 PPR SARS-CoV-2 infection remodels the host protein thermal stability landscape

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

2020 CTX-AGR-MED Functional Characterization of the Lin28/let-7 Circuit During Forelimb Regeneration in Ambystoma mexicanum and Its Influence on Metabolic Reprogramming.

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

2020 CTX-AGR-MED Stability of SARS-CoV-2 phylogenies.

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

2020 PPR ISA API: An open platform for interoperable life science experimental metadata

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

2020 CTX-AGR-MED A reference map of potential determinants for the human serum metabolome.

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

2020 PPR Whole genome sequencing for diagnosis of neurological repeat expansion disorders

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

2020 CTX-AGR-MED UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.

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

2020 PPR UCSC Cell Browser: Visualize Your Single-Cell Data

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

2020 PPR COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

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

2020 CTX-AGR-MED A high-stringency blueprint of the human proteome.

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

2020 CTX-AGR-MED Using Deep Learning to Extrapolate Protein Expression Measurements.

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

2020 CTX-AGR-MED Network integration and modelling of dynamic drug responses at multi-omics levels.

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

2020 CTX-AGR-MED Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry.

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

2020 CTX-AGR-MED Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

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

2020 CTX-AGR-MED Transparency and reproducibility in artificial intelligence.

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

2020 CTX-AGR-MED Dissemination and analysis of the quality assurance (QA) and quality control (QC) practices of LC-MS based untargeted metabolomics practitioners.

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

2020 CTX-AGR-MED 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.

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

2020 CTX-AGR-MED Extensive heterogeneity in somatic mutation and selection in the human bladder.

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

2020 CTX-AGR-MED Author Correction: A dynamic COVID-19 immune signature includes associations with poor prognosis.

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

2020 CTX-AGR-MED A single-cell RNA-sequencing training and analysis suite using the Galaxy framework.

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

2020 CTX-AGR-MED Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

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

2020 CTX-AGR-MED Global Public Perceptions of Genomic Data Sharing: What Shapes the Willingness to Donate DNA and Health Data?

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

2020 PPR Open Targets Genetics: An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci

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

2020 PPR A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

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

2020 CTX-AGR-MED MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets.

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

2020 PPR COVID-19 and beyond: a call for action and audacious solidarity to all the citizens and nations, it is humanity’s fight

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

2020 CTX-AGR-MED LifeTime and improving European healthcare through cell-based interceptive medicine.

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.

2020

10.1038/s41586-020-2715-9

2020 CTX-AGR-MED Publisher Correction: The tuatara genome reveals ancient features of amniote evolution.

Publisher Correction: The tuatara genome reveals ancient features of amniote evolution.

Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, Martin FJ, Flicek P, Petersen B, Kang L, Michalak P, Buckley TR, Wilson M, Cheng Y, Miller H, Schott RK, Jordan MD, Newcomb RD, Arroyo JI, Valenzuela N, Hore TA, Renart J, Peona V, Peart CR, Warmuth VM, Zeng L, Kortschak RD, Raison JM, Zapata VV, Wu Z, Santesmasses D, Mariotti M, Guigó R, Rupp SM, Twort VG, Dussex N, Taylor H, Abe H, Bond DM, Paterson JM, Mulcahy DG, Gonzalez VL, Barbieri CG, DeMeo DP, Pabinger S, Van Stijn T, Clarke S, Ryder O, Edwards SV, Salzberg SL, Anderson L, Nelson N, Stone C, Ngatiwai Trust Board.

2020

10.1038/s41586-020-2661-6

2020 CTX-AGR-MED Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development.

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.

2020

10.1038/s41590-020-0772-8

2020 CTX-AGR-MED Sex differences in oncogenic mutational processes.

Sex differences in oncogenic mutational processes.

Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, PCAWG Tumour Subtypes and Clinical Translation, Boutros PC, PCAWG Consortium.

2020

10.1038/s41467-020-17359-2

2020 PPR Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development

Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development

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

2020

10.1101/2020.08.27.268730

2020 PPR Reconstructing the lineage histories and differentiation trajectories of individual cancer cells in JAK2-mutant myeloproliferative neoplasms

Reconstructing the lineage histories and differentiation trajectories of individual cancer cells in JAK2-mutant myeloproliferative neoplasms

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

2020

10.1101/2020.08.24.265058

2020 CTX-AGR-MED Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma.

Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma.

Ordoñez R, Kulis M, Russiñol N, Chapaprieta V, Carrasco-Leon A, García-Torre B, Charalampopoulou S, Clot G, Beekman R, Meydan C, Duran-Ferrer M, Verdaguer-Dot N, Vilarrasa-Blasi R, Soler-Vila P, Garate L, Miranda E, San José-Enériz E, Rodriguez-Madoz JR, Ezponda T, Martínez-Turrilas R, Vilas-Zornoza A, Lara-Astiaso D, Dupéré-Richer D, Martens JHA, El-Omri H, Taha RY, Calasanz MJ, Paiva B, San Miguel J, Flicek P, Gut I, Melnick A, Mitsiades CS, Licht JD, Campo E, Stunnenberg HG, Agirre X, Prosper F, Martin-Subero JI.

2020

10.1101/gr.265520.120

2020 CTX-AGR-MED Genetic and functional insights into the fractal structure of the heart.

Genetic and functional insights into the fractal structure of the heart.

Meyer HV, Dawes TJW, Serrani M, Bai W, Tokarczuk P, Cai J, de Marvao A, Henry A, Lumbers RT, Gierten J, Thumberger T, Wittbrodt J, Ware JS, Rueckert D, Matthews PM, Prasad SK, Costantino ML, Cook SA, Birney E, O'Regan DP.

2020

10.1038/s41586-020-2635-8

2020 CTX-AGR-MED A dynamic COVID-19 immune signature includes associations with poor prognosis.

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/s41591-020-1038-6

2020 PPR Reproducibility in systems biology modelling

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.

2020

10.1101/2020.08.07.239855

2020 CTX-AGR-MED Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci.

Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci.

Cavadas B, Camacho R, Ferreira JC, Ferreira RM, Figueiredo C, Brazma A, Fonseca NA, Pereira L.

2020

10.3390/microorganisms8081196

2020 CTX-AGR-MED The tuatara genome reveals ancient features of amniote evolution.

The tuatara genome reveals ancient features of amniote evolution.

Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, Martin FJ, Flicek P, Petersen B, Kang L, Michalak P, Buckley TR, Wilson M, Cheng Y, Miller H, Schott RK, Jordan MD, Newcomb RD, Arroyo JI, Valenzuela N, Hore TA, Renart J, Peona V, Peart CR, Warmuth VM, Zeng L, Kortschak RD, Raison JM, Zapata VV, Wu Z, Santesmasses D, Mariotti M, Guigó R, Rupp SM, Twort VG, Dussex N, Taylor H, Abe H, Bond DM, Paterson JM, Mulcahy DG, Gonzalez VL, Barbieri CG, DeMeo DP, Pabinger S, Van Stijn T, Clarke S, Ryder O, Edwards SV, Salzberg SL, Anderson L, Nelson N, Stone C, Ngatiwai Trust Board.

2020

10.1038/s41586-020-2561-9

2020 CTX-AGR-MED DYNC2H1 hypomorphic or retina-predominant variants cause nonsyndromic retinal degeneration.

DYNC2H1 hypomorphic or retina-predominant variants cause nonsyndromic retinal degeneration.

Vig A, Poulter JA, Ottaviani D, Tavares E, Toropova K, Tracewska AM, Mollica A, Kang J, Kehelwathugoda O, Paton T, Maynes JT, Wheway G, Arno G, Genomics England Research Consortium, Khan KN, McKibbin M, Toomes C, Ali M, Di Scipio M, Li S, Ellingford J, Black G, Webster A, Rydzanicz M, Stawiński P, Płoski R, Vincent A, Cheetham ME, Inglehearn CF, Roberts A, Heon E.

2020

10.1038/s41436-020-0915-1

2020