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Protein Function Development

Services for protein sequences and their function

Publications

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Publication year

Team publications

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2025.

Thakur M, Bosc N, Brooksbank C, Ernst C, Freeberg MA, Gurwitz KT, Hermjakob H, Hulcoop DG, Martin MJ, McDonagh EM, Mithani A, O'Boyle NM, Ochoa D, Payne T, Perez-Riverol Y, Sarkans U, Sokolov A, Staudt N, Stephenson JD, Tzampatzopoulou E, Vizcaíno JA, Zdrazil B, McEntyre J.

Nucleic acids research, 2026

doi:10.1093/nar/gkaf1078.

The PanOryza pangene catalog of Asian cultivated rice.

Contreras-Moreira B, Sharma E, Saraf S, Naamati G, Gupta P, Elser J, Chebotarov D, Chougule K, Lu Z, Wei S, Olson A, Tsang I, Lodha D, Zhou Y, Yu Z, Zhao W, Zhang J, Amberkar S, Sue-Ob K, Sun Z, Martin M, McNally KL, Ware D, Deutsch EW, Copetti D, Wing RA, Jaiswal P, Dyer S, Jones AR.

Genome research, 2026

doi:10.1101/gr.280790.125.

OmniPath: integrated knowledgebase for multi-omics analysis.

Türei D, Schaul J, Palacio-Escat N, Bohár B, Bai Y, Ceccarelli F, Çevrim E, Daley M, Darcan M, Dimitrov D, Doğan T, Domingo-Fernández D, Dugourd A, Gábor A, Gul L, Hall BA, Hoyt CT, Ivanova O, Klein M, Lawrence T, Mañanes D, Módos D, Müller-Dott S, Ölbei M, Schmidt C, Şen B, Theis FJ, Ünlü A, Ulusoy E, Valdeolivas A, Korcsmáros T, Saez-Rodriguez J.

Nucleic acids research, 2026

doi:10.1093/nar/gkaf1126.

REDIportal: toward an integrated view of the A-to-I editing.

D'Addabbo P, Cohen-Fultheim R, Twersky I, Fonzino A, Silvestris DA, Prakash A, Mazzacuva PL, Vizcaino JA, Green A, Sweeney B, Yates A, Lussi Y, Luo J, Martin MJ, Eisenberg E, Levanon EY, Pesole G, Picardi E.

Nucleic acids research, 2025

doi:10.1093/nar/gkae1083.

New developments for the Quest for Orthologs benchmark service.

Altenhoff A, Nevers Y, Tran V, Jyothi D, Martin M, Cosentino S, Majidian S, Marcet-Houben M, Fuentes-Palacios D, Persson E, Walsh T, Lecompte O, Gabaldón T, Kelly S, Hu Y, Iwasaki W, Capella-Gutierrez S, Dessimoz C, Thomas PD, Ebersberger I, Sonnhammer E.

NAR genomics and bioinformatics, 2024

doi:10.1093/nargab/lqae167.

Perspectives on tracking data reuse across biodata resources.

Ross KE, Bastian FB, Buys M, Cook CE, D'Eustachio P, Harrison M, Hermjakob H, Li D, Lord P, Natale DA, Peters B, Sternberg PW, Su AI, Thakur M, Thomas PD, Bateman A, and the UniProt Consortium .

Bioinformatics advances, 2024

doi:10.1093/bioadv/vbae057.

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.

Thakur M, Buniello A, Brooksbank C, Gurwitz KT, Hall M, Hartley M, Hulcoop DG, Leach AR, Marques D, Martin M, Mithani A, McDonagh EM, Mutasa-Gottgens E, Ochoa D, Perez-Riverol Y, Stephenson J, Varadi M, Velankar S, Vizcaino JA, Witham R, McEntyre J.

Nucleic acids research, 2024

doi:10.1093/nar/gkad1088.

Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.

Martinez K, Agirre J, Akune Y, Aoki-Kinoshita KF, Arighi C, Axelsen KB, Bolton E, Bordeleau E, Edwards NJ, Fadda E, Feizi T, Hayes C, Ives CM, Joshi HJ, Krishna Prasad K, Kossida S, Lisacek F, Liu Y, Lütteke T, Ma J, Malik A, Martin M, Mehta AY, Neelamegham S, Panneerselvam K, Ranzinger R, Ricard-Blum S, Sanou G, Shanker V, Thomas PD, Tiemeyer M, Urban J, Vita R, Vora J, Yamamoto Y, Mazumder R.

Database : the journal of biological databases and curation, 2024

doi:10.1093/database/baae073.

The Gene Ontology knowledgebase in 2023.

Gene Ontology Consortium, Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL, Hill DP, Lee R, Mi H, Moxon S, Mungall CJ, Muruganugan A, Mushayahama T, Sternberg PW, Thomas PD, Van Auken K, Ramsey J, Siegele DA, Chisholm RL, Fey P, Aspromonte MC, Nugnes MV, Quaglia F, Tosatto S, Giglio M, Nadendla S, Antonazzo G, Attrill H, Dos Santos G, Marygold S, Strelets V, Tabone CJ, Thurmond J, Zhou P, Ahmed SH, Asanitthong P, Luna Buitrago D, Erdol MN, Gage MC, Ali Kadhum M, Li KYC, Long M, Michalak A, Pesala A, Pritazahra A, Saverimuttu SCC, Su R, Thurlow KE, Lovering RC, Logie C, Oliferenko S, Blake J, Christie K, Corbani L, Dolan ME, Drabkin HJ, Hill DP, Ni L, Sitnikov D, Smith C, Cuzick A, Seager J, Cooper L, Elser J, Jaiswal P, Gupta P, Jaiswal P, Naithani S, Lera-Ramirez M, Rutherford K, Wood V, De Pons JL, Dwinell MR, Hayman GT, Kaldunski ML, Kwitek AE, Laulederkind SJF, Tutaj MA, Vedi M, Wang SJ, D'Eustachio P, Aimo L, Axelsen K, Bridge A, Hyka-Nouspikel N, Morgat A, Aleksander SA, Cherry JM, Engel SR, Karra K, Miyasato SR, Nash RS, Skrzypek MS, Weng S, Wong ED, Bakker E, Berardini TZ, Reiser L, Auchincloss A, Axelsen K, Argoud-Puy G, Blatter MC, Boutet E, Breuza L, Bridge A, Casals-Casas C, Coudert E, Estreicher A, Livia Famiglietti M, Feuermann M, Gos A, Gruaz-Gumowski N, Hulo C, Hyka-Nouspikel N, Jungo F, Le Mercier P, Lieberherr D, Masson P, Morgat A, Pedruzzi I, Pourcel L, Poux S, Rivoire C, Sundaram S, Bateman A, Bowler-Barnett E, Bye-A-Jee H, Denny P, Ignatchenko A, Ishtiaq R, Lock A, Lussi Y, Magrane M, Martin MJ, Orchard S, Raposo P, Speretta E, Tyagi N, Warner K, Zaru R, Diehl AD, Lee R, Chan J, Diamantakis S, Raciti D, Zarowiecki M, Fisher M, James-Zorn C, Ponferrada V, Zorn A, Ramachandran S, Ruzicka L, Westerfield M.

Genetics, 2023

doi:10.1093/genetics/iyad031.

The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants.

Stefanucci L, Collins J, Sims MC, Barrio-Hernandez I, Sun L, Burren OS, Perfetto L, Bender I, Callahan TJ, Fleming K, Guerrero JA, Hermjakob H, Martin MJ, Stephenson J, Paneerselvam K, Petrovski S, Porras P, Robinson PN, Wang Q, Watkins X, Frontini M, Laskowski RA, Beltrao P, Di Angelantonio E, Gomez K, Laffan M, Ouwehand WH, Mumford AD, Freson K, Carss K, Downes K, Gleadall N, Megy K, Bruford E, Vuckovic D.

Blood, 2023

doi:10.1182/blood.2023020118.

Democratizing knowledge representation with BioCypher.

Lobentanzer S, Aloy P, Baumbach J, Bohar B, Carey VJ, Charoentong P, Danhauser K, Doğan T, Dreo J, Dunham I, Farr E, Fernandez-Torras A, Gyori BM, Hartung M, Hoyt CT, Klein C, Korcsmaros T, Maier A, Mann M, Ochoa D, Pareja-Lorente E, Popp F, Preusse M, Probul N, Schwikowski B, Sen B, Strauss MT, Turei D, Ulusoy E, Waltemath D, Wodke JAH, Saez-Rodriguez J.

Nature biotechnology, 2023

doi:10.1038/s41587-023-01848-y.

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.

Nucleic acids research, 2022

doi:10.1093/nar/gkab1016.

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.

Nucleic acids research, 2022

doi:10.1093/nar/gkab1028.

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.

Nucleic acids research, 2022

doi:10.1093/nar/gkac330.

A roadmap for the functional annotation of protein families: a community perspective.

de Crécy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O'Donoghue S, Orengo C, O'Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J.

Database : the journal of biological databases and curation, 2022

doi:10.1093/database/baac062.

Standardized annotation of translated open reading frames.

Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S.

Nature biotechnology, 2022

doi:10.1038/s41587-022-01369-0.

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.

Nucleic acids research, 2022

doi:10.1093/nar/gkab1006.

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.

Nucleic acids research, 2022

doi:10.1093/nar/gkab1051.

An open dataset of <i>Plasmodium falciparum</i> genome variation in 7,000 worldwide samples.

MalariaGEN, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NP, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H.

Wellcome open research, 2021

doi:10.12688/wellcomeopenres.16168.2.

The European Nucleotide Archive in 2020.

Harrison PW, Ahamed A, Aslam R, Alako BTF, Burgin J, Buso N, Courtot M, Fan J, Gupta D, Haseeb M, Holt S, Ibrahim T, Ivanov E, Jayathilaka S, Balavenkataraman Kadhirvelu V, Kumar M, Lopez R, Kay S, Leinonen R, Liu X, O'Cathail C, Pakseresht A, Park Y, Pesant S, Rahman N, Rajan J, Sokolov A, Vijayaraja S, Waheed Z, Zyoud A, Burdett T, Cochrane G.

Nucleic acids research, 2021

doi:10.1093/nar/gkaa1028.

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

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

Bioinformatics (Oxford, England), 2021

doi:10.1093/bioinformatics/btaa663.

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

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

Briefings in bioinformatics, 2021

doi:10.1093/bib/bbaa232.

The InterPro protein families and domains database: 20 years on.

Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD.

Nucleic acids research, 2021

doi:10.1093/nar/gkaa977.

The European Nucleotide Archive in 2019.

Amid C, Alako BTF, Balavenkataraman Kadhirvelu V, Burdett T, Burgin J, Fan J, Harrison PW, Holt S, Hussein A, Ivanov E, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martinez-Villacorta J, Milano A, Pakseresht A, Rahman N, Rajan J, Reddy K, Richards E, Smirnov D, Sokolov A, Vijayaraja S, Cochrane G.

Nucleic acids research, 2020

doi:10.1093/nar/gkz1063.

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

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

Bioinformatics (Oxford, England), 2020

doi:10.1093/bioinformatics/btaa485.

The reactome pathway knowledgebase.

Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P.

Nucleic acids research, 2020

doi:10.1093/nar/gkz1031.

A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets.

Breuza L, Arighi CN, Argoud-Puy G, Casals-Casas C, Estreicher A, Famiglietti ML, Georghiou G, Gos A, Gruaz-Gumowski N, Hinz U, Hyka-Nouspikel N, Kramarz B, Lovering RC, Lussi Y, Magrane M, Masson P, Perfetto L, Poux S, Rodriguez-Lopez M, Stoeckert C, Sundaram S, Wang LS, Wu E, Orchard S, IMEx Consortium, UniProt Consortium.

Journal of Alzheimer's disease : JAD, 2020

doi:10.3233/jad-200206.

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

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

Preprint, 2020

doi:10.20944/preprints202005.0376.v1.

The Quest for Orthologs benchmark service and consensus calls in 2020.

Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernández-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernández JM, Codó L, For Orthologs Consortium TQ, Gelpi JL, Huerta-Cepas J, Iwasaki W, Kelly S, Lecompte O, Muffato M, Martin MJ, Capella-Gutierrez S, Thomas PD, Sonnhammer E, Dessimoz C.

Nucleic acids research, 2020

doi:10.1093/nar/gkaa308.

GlyGen data model and processing workflow.

Kahsay R, Vora J, Navelkar R, Mousavi R, Fochtman BC, Holmes X, Pattabiraman N, Ranzinger R, Mahadik R, Williamson T, Kulkarni S, Agarwal G, Martin M, Vasudev P, Garcia L, Edwards N, Zhang W, Natale DA, Ross K, Aoki-Kinoshita KF, Campbell MP, York WS, Mazumder R.

Bioinformatics (Oxford, England), 2020

doi:10.1093/bioinformatics/btaa238.

GlyGen: Computational and Informatics Resources for Glycoscience.

York WS, Mazumder R, Ranzinger R, Edwards N, Kahsay R, Aoki-Kinoshita KF, Campbell MP, Cummings RD, Feizi T, Martin M, Natale DA, Packer NH, Woods RJ, Agarwal G, Arpinar S, Bhat S, Blake J, Castro LJG, Fochtman B, Gildersleeve J, Goldman R, Holmes X, Jain V, Kulkarni S, Mahadik R, Mehta A, Mousavi R, Nakarakommula S, Navelkar R, Pattabiraman N, Pierce MJ, Ross K, Vasudev P, Vora J, Williamson T, Zhang W.

Glycobiology, 2020

doi:10.1093/glycob/cwz080.

The COMPARE Data Hubs.

Amid C, Pakseresht N, Silvester N, Jayathilaka S, Lund O, Dynovski LD, Pataki BÁ, Visontai D, Xavier BB, Alako BTF, Belka A, Cisneros JLB, Cotten M, Haringhuizen GB, Harrison PW, Höper D, Holt S, Hundahl C, Hussein A, Kaas RS, Liu X, Leinonen R, Malhotra-Kumar S, Nieuwenhuijse DF, Rahman N, Dos S Ribeiro C, Skiby JE, Schmitz D, Stéger J, Szalai-Gindl JM, Thomsen MCF, Cacciò SM, Csabai I, Kroneman A, Koopmans M, Aarestrup F, Cochrane G.

Database : the journal of biological databases and curation, 2019

doi:10.1093/database/baz136.

The COMPARE Data Hubs

Amid C, Pakseresht N, Silvester N, Jayathilaka S, Lund O, Dynovski LD, Pataki BÁ, Visontai D, Cotten M, Xavier BB, Alako B, Belka A, Cisneros JJL, Haringhuizen GB, Harrison PW, Höper D, Holt S, Hundahl C, Hussein A, Kaas RS, Malhotra-Kumar S, Leinonen R, Nieuwenhuijse DF, Rahman N, Ribeiro CdS, Skiby JE, Stéger J, Szalai-Gindl JM, Thomsen MCF, Csabai I, Koopmans M, Aarestrup F, Cochrane G.

Preprint, 2019

doi:10.1101/555938.

The European Nucleotide Archive in 2018.

Harrison PW, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Holt S, Hussein A, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Milano A, Pakseresht N, Rajan J, Reddy K, Richards E, Rosello M, Silvester N, Smirnov D, Toribio AL, Vijayaraja S, Cochrane G.

Nucleic acids research, 2019

doi:10.1093/nar/gky1078.

InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD.

Nucleic acids research, 2019

doi:10.1093/nar/gky1100.

The Pfam protein families database in 2019.

El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer ELL, Hirsh L, Paladin L, Piovesan D, Tosatto SCE, Finn RD.

Nucleic acids research, 2019

doi:10.1093/nar/gky995.

Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species <i>Anopheles gambiae</i> and <i>Anopheles coluzzii</i>

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Genome biology, 2019

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Molecular biology and evolution, 2019

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Nucleic acids research, 2018

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Science (New York, N.Y.), 2018

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Journal of proteome research, 2018

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Bioinformatics (Oxford, England), 2018

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Nature, 2017

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PLoS biology, 2017

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Nucleic acids research, 2016

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Genome biology, 2016

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Nature methods, 2016

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Current protocols in bioinformatics, 2016

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Database : the journal of biological databases and curation, 2016

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Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association, 2015

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Bioinformatics (Oxford, England), 2014

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Nucleic acids research, 2011

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Dasty3, a WEB framework for DAS.

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Bioinformatics (Oxford, England), 2011

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UniProt: the Universal Protein knowledgebase.

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Nucleic acids research, 2004

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Nucleic acids research, 2026

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The PanOryza pangene catalog of Asian cultivated rice.

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Genome research, 2026

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OmniPath: integrated knowledgebase for multi-omics analysis.

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Nucleic acids research, 2026

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REDIportal: toward an integrated view of the A-to-I editing.

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Nucleic acids research, 2025

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New developments for the Quest for Orthologs benchmark service.

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NAR genomics and bioinformatics, 2024

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Perspectives on tracking data reuse across biodata resources.

Ross KE, Bastian FB, Buys M, Cook CE, D'Eustachio P, Harrison M, Hermjakob H, Li D, Lord P, Natale DA, Peters B, Sternberg PW, Su AI, Thakur M, Thomas PD, Bateman A, and the UniProt Consortium .

Bioinformatics advances, 2024

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EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.

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Nucleic acids research, 2024

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Database : the journal of biological databases and curation, 2024

doi:10.1093/database/baae073.

The Gene Ontology knowledgebase in 2023.

Gene Ontology Consortium, Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL, Hill DP, Lee R, Mi H, Moxon S, Mungall CJ, Muruganugan A, Mushayahama T, Sternberg PW, Thomas PD, Van Auken K, Ramsey J, Siegele DA, Chisholm RL, Fey P, Aspromonte MC, Nugnes MV, Quaglia F, Tosatto S, Giglio M, Nadendla S, Antonazzo G, Attrill H, Dos Santos G, Marygold S, Strelets V, Tabone CJ, Thurmond J, Zhou P, Ahmed SH, Asanitthong P, Luna Buitrago D, Erdol MN, Gage MC, Ali Kadhum M, Li KYC, Long M, Michalak A, Pesala A, Pritazahra A, Saverimuttu SCC, Su R, Thurlow KE, Lovering RC, Logie C, Oliferenko S, Blake J, Christie K, Corbani L, Dolan ME, Drabkin HJ, Hill DP, Ni L, Sitnikov D, Smith C, Cuzick A, Seager J, Cooper L, Elser J, Jaiswal P, Gupta P, Jaiswal P, Naithani S, Lera-Ramirez M, Rutherford K, Wood V, De Pons JL, Dwinell MR, Hayman GT, Kaldunski ML, Kwitek AE, Laulederkind SJF, Tutaj MA, Vedi M, Wang SJ, D'Eustachio P, Aimo L, Axelsen K, Bridge A, Hyka-Nouspikel N, Morgat A, Aleksander SA, Cherry JM, Engel SR, Karra K, Miyasato SR, Nash RS, Skrzypek MS, Weng S, Wong ED, Bakker E, Berardini TZ, Reiser L, Auchincloss A, Axelsen K, Argoud-Puy G, Blatter MC, Boutet E, Breuza L, Bridge A, Casals-Casas C, Coudert E, Estreicher A, Livia Famiglietti M, Feuermann M, Gos A, Gruaz-Gumowski N, Hulo C, Hyka-Nouspikel N, Jungo F, Le Mercier P, Lieberherr D, Masson P, Morgat A, Pedruzzi I, Pourcel L, Poux S, Rivoire C, Sundaram S, Bateman A, Bowler-Barnett E, Bye-A-Jee H, Denny P, Ignatchenko A, Ishtiaq R, Lock A, Lussi Y, Magrane M, Martin MJ, Orchard S, Raposo P, Speretta E, Tyagi N, Warner K, Zaru R, Diehl AD, Lee R, Chan J, Diamantakis S, Raciti D, Zarowiecki M, Fisher M, James-Zorn C, Ponferrada V, Zorn A, Ramachandran S, Ruzicka L, Westerfield M.

Genetics, 2023

doi:10.1093/genetics/iyad031.

The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants.

Stefanucci L, Collins J, Sims MC, Barrio-Hernandez I, Sun L, Burren OS, Perfetto L, Bender I, Callahan TJ, Fleming K, Guerrero JA, Hermjakob H, Martin MJ, Stephenson J, Paneerselvam K, Petrovski S, Porras P, Robinson PN, Wang Q, Watkins X, Frontini M, Laskowski RA, Beltrao P, Di Angelantonio E, Gomez K, Laffan M, Ouwehand WH, Mumford AD, Freson K, Carss K, Downes K, Gleadall N, Megy K, Bruford E, Vuckovic D.

Blood, 2023

doi:10.1182/blood.2023020118.

Democratizing knowledge representation with BioCypher.

Lobentanzer S, Aloy P, Baumbach J, Bohar B, Carey VJ, Charoentong P, Danhauser K, Doğan T, Dreo J, Dunham I, Farr E, Fernandez-Torras A, Gyori BM, Hartung M, Hoyt CT, Klein C, Korcsmaros T, Maier A, Mann M, Ochoa D, Pareja-Lorente E, Popp F, Preusse M, Probul N, Schwikowski B, Sen B, Strauss MT, Turei D, Ulusoy E, Waltemath D, Wodke JAH, Saez-Rodriguez J.

Nature biotechnology, 2023

doi:10.1038/s41587-023-01848-y.

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.

Nucleic acids research, 2022

doi:10.1093/nar/gkab1016.

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.

Nucleic acids research, 2022

doi:10.1093/nar/gkab1028.

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.

Nucleic acids research, 2022

doi:10.1093/nar/gkac330.

A roadmap for the functional annotation of protein families: a community perspective.

de Crécy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O'Donoghue S, Orengo C, O'Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J.

Database : the journal of biological databases and curation, 2022

doi:10.1093/database/baac062.

Standardized annotation of translated open reading frames.

Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S.

Nature biotechnology, 2022

doi:10.1038/s41587-022-01369-0.

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.

Nucleic acids research, 2022

doi:10.1093/nar/gkab1006.

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.

Nucleic acids research, 2022

doi:10.1093/nar/gkab1051.

An open dataset of &lt;i&gt;Plasmodium falciparum&lt;/i&gt; genome variation in 7,000 worldwide samples.

MalariaGEN, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NP, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H.

Wellcome open research, 2021

doi:10.12688/wellcomeopenres.16168.2.

The European Nucleotide Archive in 2020.

Harrison PW, Ahamed A, Aslam R, Alako BTF, Burgin J, Buso N, Courtot M, Fan J, Gupta D, Haseeb M, Holt S, Ibrahim T, Ivanov E, Jayathilaka S, Balavenkataraman Kadhirvelu V, Kumar M, Lopez R, Kay S, Leinonen R, Liu X, O'Cathail C, Pakseresht A, Park Y, Pesant S, Rahman N, Rajan J, Sokolov A, Vijayaraja S, Waheed Z, Zyoud A, Burdett T, Cochrane G.

Nucleic acids research, 2021

doi:10.1093/nar/gkaa1028.

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

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

Bioinformatics (Oxford, England), 2021

doi:10.1093/bioinformatics/btaa663.

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

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

Briefings in bioinformatics, 2021

doi:10.1093/bib/bbaa232.

The InterPro protein families and domains database: 20 years on.

Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD.

Nucleic acids research, 2021

doi:10.1093/nar/gkaa977.

The European Nucleotide Archive in 2019.

Amid C, Alako BTF, Balavenkataraman Kadhirvelu V, Burdett T, Burgin J, Fan J, Harrison PW, Holt S, Hussein A, Ivanov E, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martinez-Villacorta J, Milano A, Pakseresht A, Rahman N, Rajan J, Reddy K, Richards E, Smirnov D, Sokolov A, Vijayaraja S, Cochrane G.

Nucleic acids research, 2020

doi:10.1093/nar/gkz1063.

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

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

Bioinformatics (Oxford, England), 2020

doi:10.1093/bioinformatics/btaa485.

The reactome pathway knowledgebase.

Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P.

Nucleic acids research, 2020

doi:10.1093/nar/gkz1031.

A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets.

Breuza L, Arighi CN, Argoud-Puy G, Casals-Casas C, Estreicher A, Famiglietti ML, Georghiou G, Gos A, Gruaz-Gumowski N, Hinz U, Hyka-Nouspikel N, Kramarz B, Lovering RC, Lussi Y, Magrane M, Masson P, Perfetto L, Poux S, Rodriguez-Lopez M, Stoeckert C, Sundaram S, Wang LS, Wu E, Orchard S, IMEx Consortium, UniProt Consortium.

Journal of Alzheimer's disease : JAD, 2020

doi:10.3233/jad-200206.

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

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

Preprint, 2020

doi:10.20944/preprints202005.0376.v1.

The Quest for Orthologs benchmark service and consensus calls in 2020.

Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernández-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernández JM, Codó L, For Orthologs Consortium TQ, Gelpi JL, Huerta-Cepas J, Iwasaki W, Kelly S, Lecompte O, Muffato M, Martin MJ, Capella-Gutierrez S, Thomas PD, Sonnhammer E, Dessimoz C.

Nucleic acids research, 2020

doi:10.1093/nar/gkaa308.

GlyGen data model and processing workflow.

Kahsay R, Vora J, Navelkar R, Mousavi R, Fochtman BC, Holmes X, Pattabiraman N, Ranzinger R, Mahadik R, Williamson T, Kulkarni S, Agarwal G, Martin M, Vasudev P, Garcia L, Edwards N, Zhang W, Natale DA, Ross K, Aoki-Kinoshita KF, Campbell MP, York WS, Mazumder R.

Bioinformatics (Oxford, England), 2020

doi:10.1093/bioinformatics/btaa238.

GlyGen: Computational and Informatics Resources for Glycoscience.

York WS, Mazumder R, Ranzinger R, Edwards N, Kahsay R, Aoki-Kinoshita KF, Campbell MP, Cummings RD, Feizi T, Martin M, Natale DA, Packer NH, Woods RJ, Agarwal G, Arpinar S, Bhat S, Blake J, Castro LJG, Fochtman B, Gildersleeve J, Goldman R, Holmes X, Jain V, Kulkarni S, Mahadik R, Mehta A, Mousavi R, Nakarakommula S, Navelkar R, Pattabiraman N, Pierce MJ, Ross K, Vasudev P, Vora J, Williamson T, Zhang W.

Glycobiology, 2020

doi:10.1093/glycob/cwz080.

The COMPARE Data Hubs.

Amid C, Pakseresht N, Silvester N, Jayathilaka S, Lund O, Dynovski LD, Pataki BÁ, Visontai D, Xavier BB, Alako BTF, Belka A, Cisneros JLB, Cotten M, Haringhuizen GB, Harrison PW, Höper D, Holt S, Hundahl C, Hussein A, Kaas RS, Liu X, Leinonen R, Malhotra-Kumar S, Nieuwenhuijse DF, Rahman N, Dos S Ribeiro C, Skiby JE, Schmitz D, Stéger J, Szalai-Gindl JM, Thomsen MCF, Cacciò SM, Csabai I, Kroneman A, Koopmans M, Aarestrup F, Cochrane G.

Database : the journal of biological databases and curation, 2019

doi:10.1093/database/baz136.

The COMPARE Data Hubs

Amid C, Pakseresht N, Silvester N, Jayathilaka S, Lund O, Dynovski LD, Pataki BÁ, Visontai D, Cotten M, Xavier BB, Alako B, Belka A, Cisneros JJL, Haringhuizen GB, Harrison PW, Höper D, Holt S, Hundahl C, Hussein A, Kaas RS, Malhotra-Kumar S, Leinonen R, Nieuwenhuijse DF, Rahman N, Ribeiro CdS, Skiby JE, Stéger J, Szalai-Gindl JM, Thomsen MCF, Csabai I, Koopmans M, Aarestrup F, Cochrane G.

Preprint, 2019

doi:10.1101/555938.

The European Nucleotide Archive in 2018.

Harrison PW, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Holt S, Hussein A, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Milano A, Pakseresht N, Rajan J, Reddy K, Richards E, Rosello M, Silvester N, Smirnov D, Toribio AL, Vijayaraja S, Cochrane G.

Nucleic acids research, 2019

doi:10.1093/nar/gky1078.

InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD.

Nucleic acids research, 2019

doi:10.1093/nar/gky1100.

The Pfam protein families database in 2019.

El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer ELL, Hirsh L, Paladin L, Piovesan D, Tosatto SCE, Finn RD.

Nucleic acids research, 2019

doi:10.1093/nar/gky995.

Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species <i>Anopheles gambiae</i> and <i>Anopheles coluzzii</i>

The Anopheles gambiae 1000 Genomes Consortium, Clarkson CS, Miles A, Harding NJ, Lucas ER, Battey CJ, Amaya-Romero JE, Cano J, Diabate A, Constant E, Nwakanma DC, Jawara M, Essandoh J, Dinis J, Le Goff G, Robert V, Troco AD, Costantini C, Rohatgi KR, Elissa N, Coulibaly B, Midega J, Mbogo C, Mawejje HD, Stalker J, Rockett KA, Drury E, Mead D, Jeffreys AE, Hubbart C, Rowlands K, Isaacs AT, Jyothi D, Malangone C, Kamali M, Henrichs C, Simpson V, Ayala D, Besansky NJ, Burt A, Caputo B, della Torre A, Fontaine M, Godfray HCJ, Hahn MW, Kern AD, Lawniczak MKN, O’Loughlin S, Pinto J, Riehle MM, Sharakhov I, Schrider DR, Vernick KD, White BJ, Donnelly MJ, Kwiatkowski DP.

Preprint, 2019

doi:10.1101/864314.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I.

Genome biology, 2019

doi:10.1186/s13059-019-1835-8.

Advances and Applications in the Quest for Orthologs.

Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, da Silva AS, Wang Y, Sonnhammer E, Thomas PD.

Molecular biology and evolution, 2019

doi:10.1093/molbev/msz150.

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