{"id":257,"date":"2019-06-26T16:22:35","date_gmt":"2019-06-26T16:22:35","guid":{"rendered":"http:\/\/www.ebi.ac.uk\/about\/teams\/protein-function-development\/publications\/"},"modified":"2022-01-17T12:40:47","modified_gmt":"2022-01-17T12:40:47","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/about\/teams\/protein-function-development\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"
\n \n
\n

\n \n The Gene Ontology knowledgebase in 2026.\n <\/a>\n <\/h3>\n

\n Gene Ontology Consortium\n.\n <\/p>\n

\n Nucleic acids research, \n 2026<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkaf1292.\n <\/p>\n <\/article>\n

\n

\n \n From use cases to infrastructure: a cross-institutional survey of priorities in data-driven biomedical research.\n <\/a>\n <\/h3>\n

\n Mazumder R, Keeney J, Johnson L, Krammer L, McNeely P, Sepulveda J, Hangen D, Martin M, Jyothi D, De Almeida J, McGarvey P, Alaoui A, Cha S, Sedrakyan A, Shoelle E, Matheny M, LeNoue-Newton M, Winter R, Deppen S, Simonyan V, Horvath A.\n <\/p>\n

\n Journal of the American Medical Informatics Association : JAMIA, \n 2026<\/span>\n <\/p>\n\n

\n doi:10.1093\/jamia\/ocag001.\n <\/p>\n <\/article>\n

\n

\n \n Early terminated transcripts and missing proteins reflect artifacts in bacterial proteomes\n <\/a>\n <\/h3>\n

\n Insana G, Martin MJ, Pearson WR.\n <\/p>\n

\n Preprint, \n 2026<\/span>\n <\/p>\n\n

\n doi:10.64898\/2026.05.19.725897.\n <\/p>\n <\/article>\n

\n

\n \n EMBL's European Bioinformatics Institute (EMBL-EBI) in 2025.\n <\/a>\n <\/h3>\n

\n 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, Vizca\u00edno JA, Zdrazil B, McEntyre J.\n <\/p>\n

\n Nucleic acids research, \n 2026<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkaf1078.\n <\/p>\n <\/article>\n

\n

\n \n Expanding the human proteome with microproteins and peptideins.\n <\/a>\n <\/h3>\n

\n Deutsch EW, Kok LW, Mudge JM, Valls CF, Jungreis I, Ruiz-Orera J, Sun Z, Kusebauch U, Fierro-Monti I, Abelin JG, Alba MM, Aspden JL, Bandyopadhyay S, Banerjee K, Baranov PV, Bazzini AA, Bourassa F, Bruford EA, Calviello L, Carr SA, Carvunis AR, Chothani S, Clauwaert J, Dean K, Faridi P, Frankish A, Goodale A, Green T, Hubner N, Ingolia NT, Kellis M, Magrane M, Martin MJ, Martinez TF, Menschaert G, Ohler U, Orchard S, Potter A, Rackham OJL, Rees MG, Root DE, Roth JA, Roucou X, Sialana FJ, Slavoff SA, \u015awirski MI, Tierney JAS, Trifiro FA, Valen E, Vasylieva V, Wacholder A, Wang S, Wang L, Weissman JS, Wu W, Xie Z, Choudhary JS, Bassani-Sternberg M, Vizca\u00edno JA, Ternette N, Brunet MA, Moritz RL, Prensner JR, van Heesch S.\n <\/p>\n

\n Nature, \n 2026<\/span>\n <\/p>\n\n

\n doi:10.1038\/s41586-026-10459-x.\n <\/p>\n <\/article>\n

\n

\n \n The PanOryza pangene catalog of Asian cultivated rice.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Genome research, \n 2026<\/span>\n <\/p>\n\n

\n doi:10.1101\/gr.280790.125.\n <\/p>\n <\/article>\n

\n

\n \n What\u2019s new on the UniProt website: features and improvements for 2026\n <\/a>\n <\/h3>\n

\n Kandasaamy S, Kim M, Lock A.\n <\/p>\n

\n \n 2026<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.uniprot-website-updates-w.2026.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n Navigating UniProt: a brief overview and recent updates\n <\/a>\n <\/h3>\n

\n Kandasaamy S, Bowler-Barnett E, Kim M.\n <\/p>\n

\n \n 2026<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.uniprotwebsite-w.2025.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n SELFormerMM: multimodal molecular representation learning via SELFIES, structure, text, and knowledge graph integration\n <\/a>\n <\/h3>\n

\n Ulusoy E, Bostanc\u0131 \u015e, Deniz BE, Do\u011fan T.\n <\/p>\n

\n Preprint, \n 2026<\/span>\n <\/p>\n\n

\n doi:10.64898\/2026.03.17.712340.\n <\/p>\n <\/article>\n

\n

\n \n CROssBARv2: A Unified Computational Framework for Heterogeneous Biomedical Data Representation and LLM-Driven Exploration\n <\/a>\n <\/h3>\n

\n \u015een B, Ulusoy E, Darcan M, Erg\u00fcn M, Lobentanzer S, Rifaioglu AS, T\u00fcrei D, Saez-Rodriguez J, Do\u011fan T.\n <\/p>\n

\n Preprint, \n 2026<\/span>\n <\/p>\n\n

\n doi:10.64898\/2026.04.12.718028.\n <\/p>\n <\/article>\n

\n

\n \n OmniPath: integrated knowledgebase for multi-omics analysis.\n <\/a>\n <\/h3>\n

\n T\u00fcrei D, Schaul J, Palacio-Escat N, Boh\u00e1r B, Bai Y, Ceccarelli F, \u00c7evrim E, Daley M, Darcan M, Dimitrov D, Do\u011fan T, Domingo-Fern\u00e1ndez D, Dugourd A, G\u00e1bor A, Gul L, Hall BA, Hoyt CT, Ivanova O, Klein M, Lawrence T, Lawrence T, Ma\u00f1anes D, M\u00f3dos D, M\u00fcller-Dott S, \u00d6lbei M, Schmidt C, \u015een B, Theis FJ, \u00dcnl\u00fc A, Ulusoy E, Valdeolivas A, Korcsm\u00e1ros T, Saez-Rodriguez J.\n <\/p>\n

\n Nucleic acids research, \n 2026<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkaf1126.\n <\/p>\n <\/article>\n

\n

\n \n The UniProt website API: facilitating programmatic access to protein knowledge.\n <\/a>\n <\/h3>\n

\n Ahmad S, Jose da Costa Gonzales L, Bowler-Barnett EH, Rice DL, Kim M, Wijerathne S, Luciani A, Kandasaamy S, Luo J, Watkins X, Turner E, Martin MJ, UniProt Consortium\n.\n <\/p>\n

\n Nucleic acids research, \n 2025<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkaf394.\n <\/p>\n <\/article>\n

\n

\n \n UniProt: the Universal Protein Knowledgebase in 2025.\n <\/a>\n <\/h3>\n

\n UniProt Consortium\n.\n <\/p>\n

\n Nucleic acids research, \n 2025<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkae1010.\n <\/p>\n <\/article>\n

\n

\n \n REDIportal: toward\u00a0an integrated view of the A-to-I editing.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Nucleic acids research, \n 2025<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkae1083.\n <\/p>\n <\/article>\n

\n

\n \n ECLIPSE: Exploration of Complex Ligand-Protein Interactions through Learning from Systems-level Heterogeneous Biomedical Knowledge Graphs\n <\/a>\n <\/h3>\n

\n Atas Guvenilir H, Do\u011fan T.\n <\/p>\n

\n Preprint, \n 2025<\/span>\n <\/p>\n\n

\n doi:10.1101\/2025.11.05.686382.\n <\/p>\n <\/article>\n

\n

\n \n Molecular Contrastive Learning with Graph Attention Network (MoCL-GAT) for Enhanced Molecular Representation\n <\/a>\n <\/h3>\n

\n Dalk\u0131ran A, Rifaio\u011flu AS, Cetin-Atalay R, Acar AC, Do\u011fan T, Atalay MV.\n <\/p>\n

\n Preprint, \n 2025<\/span>\n <\/p>\n\n

\n doi:10.1101\/2025.09.17.676724.\n <\/p>\n <\/article>\n

\n

\n \n ProtHGT: Heterogeneous Graph Transformers for Automated Protein Function Prediction Using Biological Knowledge Graphs and Language Models\n <\/a>\n <\/h3>\n

\n Ulusoy E, Do\u011fan T.\n <\/p>\n

\n Preprint, \n 2025<\/span>\n <\/p>\n\n

\n doi:10.1101\/2025.04.19.649272.\n <\/p>\n <\/article>\n

\n

\n \n A Benchmarking Platform for Assessing Protein Language Models on Function-related Prediction Tasks\n <\/a>\n <\/h3>\n

\n \u00c7evrim E, Yi\u011fit MG, Ulusoy E, Y\u0131lmaz A, Do\u011fan T.\n <\/p>\n

\n Preprint, \n 2025<\/span>\n <\/p>\n\n

\n doi:10.1101\/2025.04.10.648084.\n <\/p>\n <\/article>\n

\n

\n \n Perspectives on tracking data reuse across biodata resources.\n <\/a>\n <\/h3>\n

\n 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 .\n <\/p>\n

\n Bioinformatics advances, \n 2024<\/span>\n <\/p>\n\n

\n doi:10.1093\/bioadv\/vbae057.\n <\/p>\n <\/article>\n

\n

\n \n Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.\n <\/a>\n <\/h3>\n

\n Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie ME, Sevilla C, Tiwari K, Ragueneau E, Gong C, Stephan R, May B, Haw R, Weiser J, Beavers D, Conley P, Hermjakob H, Stein LD, D'Eustachio P, Wu G.\n <\/p>\n

\n Database : the journal of biological databases and curation, \n 2024<\/span>\n <\/p>\n\n

\n doi:10.1093\/database\/baae031.\n <\/p>\n <\/article>\n

\n

\n \n New developments for the Quest for Orthologs benchmark service.\n <\/a>\n <\/h3>\n

\n 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, Gabald\u00f3n T, Kelly S, Hu Y, Iwasaki W, Capella-Gutierrez S, Dessimoz C, Thomas PD, Ebersberger I, Sonnhammer E.\n <\/p>\n

\n NAR genomics and bioinformatics, \n 2024<\/span>\n <\/p>\n\n

\n doi:10.1093\/nargab\/lqae167.\n <\/p>\n <\/article>\n

\n

\n \n Improved selection of canonical proteins for reference proteomes.\n <\/a>\n <\/h3>\n

\n Insana G, Martin MJ, Pearson WR.\n <\/p>\n

\n NAR genomics and bioinformatics, \n 2024<\/span>\n <\/p>\n\n

\n doi:10.1093\/nargab\/lqae066.\n <\/p>\n <\/article>\n

\n

\n \n Improved selection of canonical proteins for reference proteomes\n <\/a>\n <\/h3>\n

\n Insana G, Martin MJ, Pearson WR.\n <\/p>\n

\n Preprint, \n 2024<\/span>\n <\/p>\n\n

\n doi:10.1101\/2024.03.04.583387.\n <\/p>\n <\/article>\n

\n

\n \n ProtVar: mapping and contextualizing human missense variation.\n <\/a>\n <\/h3>\n

\n Stephenson JD, Totoo P, Burke DF, J\u00e4nes J, Beltrao P, Martin MJ.\n <\/p>\n

\n Nucleic acids research, \n 2024<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkae413.\n <\/p>\n <\/article>\n

\n

\n \n EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Nucleic acids research, \n 2024<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkad1088.\n <\/p>\n <\/article>\n

\n

\n \n Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.\n <\/a>\n <\/h3>\n

\n 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, L\u00fctteke 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.\n <\/p>\n

\n Database : the journal of biological databases and curation, \n 2024<\/span>\n <\/p>\n\n

\n doi:10.1093\/database\/baae073.\n <\/p>\n <\/article>\n

\n

\n \n Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.\n <\/a>\n <\/h3>\n

\n Ramsbottom KA, Prakash A, Perez-Riverol Y, Camacho OM, Sun Z, Kundu DJ, Bowler-Barnett E, Martin M, Fan J, Chebotarov D, McNally KL, Deutsch EW, Vizca\u00edno JA, Jones AR.\n <\/p>\n

\n Journal of proteome research, \n 2024<\/span>\n <\/p>\n\n

\n doi:10.1021\/acs.jproteome.4c00187.\n <\/p>\n <\/article>\n

\n

\n \n MBDBMetrics: an online metrics tool to measure the impact of biological data resources.\n <\/a>\n <\/h3>\n

\n Insana G, Ignatchenko A, Martin M, Bateman A, UniProt Consortium .\n <\/p>\n

\n Bioinformatics advances, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.1093\/bioadv\/vbad180.\n <\/p>\n <\/article>\n

\n

\n \n The Gene Ontology knowledgebase in 2023.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Genetics, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.1093\/genetics\/iyad031.\n <\/p>\n <\/article>\n

\n

\n \n UniProt: the Universal Protein Knowledgebase in 2023.\n <\/a>\n <\/h3>\n

\n UniProt Consortium.\n <\/p>\n

\n Nucleic acids research, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkac1052.\n <\/p>\n <\/article>\n

\n

\n \n Nightingale: web components for protein feature visualization.\n <\/a>\n <\/h3>\n

\n Salazar GA, Luciani A, Watkins X, Kandasaamy S, Rice DL, Blum M, Bateman A, Martin M.\n <\/p>\n

\n Bioinformatics advances, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.1093\/bioadv\/vbad064.\n <\/p>\n <\/article>\n

\n

\n \n The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140\u2009214 UK Biobank participants.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Blood, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.1182\/blood.2023020118.\n <\/p>\n <\/article>\n

\n

\n \n UniProt and Mass Spectrometry-Based Proteomics-A 2-Way Working Relationship.\n <\/a>\n <\/h3>\n

\n Bowler-Barnett EH, Fan J, Luo J, Magrane M, Martin MJ, Orchard S, UniProt Consortium.\n <\/p>\n

\n Molecular & cellular proteomics : MCP, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.1016\/j.mcpro.2023.100591.\n <\/p>\n <\/article>\n

\n

\n \n Phosphorylation in the <i>Plasmodium falciparum<\/i> proteome: A meta-analysis of publicly available data sets\n <\/a>\n <\/h3>\n

\n Camacho OJM, Ramsbottom KA, Prakash A, Sun Z, Riverol YP, Bowler-Barnett E, Martin M, Fan J, Deutsch EW, Vizca\u00edno JA, Jones AR.\n <\/p>\n

\n Preprint, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.1101\/2023.11.20.567785.\n <\/p>\n <\/article>\n

\n

\n \n <strong>Nightingale<\/strong>: Web components for protein feature visualization\n <\/a>\n <\/h3>\n

\n Salazar GA, Luciani A, Watkins X, Kandasaamy S, Rice DL, Blum M, Bateman A, Martin M.\n <\/p>\n

\n Preprint, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.20944\/preprints202305.1797.v1.\n <\/p>\n <\/article>\n

\n

\n \n UniProt Tools: BLAST, Align, Peptide Search, and ID Mapping.\n <\/a>\n <\/h3>\n

\n Zaru R, Orchard S, UniProt Consortium.\n <\/p>\n

\n Current protocols, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.1002\/cpz1.697.\n <\/p>\n <\/article>\n

\n

\n \n Searching and Navigating UniProt Databases.\n <\/a>\n <\/h3>\n

\n Lussi YC, Magrane M, Martin MJ, Orchard S, UniProt Consortium.\n <\/p>\n

\n Current protocols, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.1002\/cpz1.700.\n <\/p>\n <\/article>\n

\n

\n \n Contextualising human missense variation with ProtVar\n <\/a>\n <\/h3>\n

\n Stephenson J, Totoo P.\n <\/p>\n

\n \n 2023<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.protvar-w.2023.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n Transfer learning for drug-target interaction prediction.\n <\/a>\n <\/h3>\n

\n Dalk\u0131ran A, Atakan A, Rifaio\u011flu AS, Martin MJ, Atalay R\u00c7, Acar AC, Do\u011fan T, Atalay V.\n <\/p>\n

\n Bioinformatics (Oxford, England), \n 2023<\/span>\n <\/p>\n\n

\n doi:10.1093\/bioinformatics\/btad234.\n <\/p>\n <\/article>\n

\n

\n \n Democratizing knowledge representation with BioCypher.\n <\/a>\n <\/h3>\n

\n Lobentanzer S, Aloy P, Baumbach J, Bohar B, Carey VJ, Charoentong P, Danhauser K, Do\u011fan 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.\n <\/p>\n

\n Nature biotechnology, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.1038\/s41587-023-01848-y.\n <\/p>\n <\/article>\n

\n

\n \n Rhea, the reaction knowledgebase in 2022.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Nucleic acids research, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkab1016.\n <\/p>\n <\/article>\n

\n

\n \n The reactome pathway knowledgebase 2022.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Nucleic acids research, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkab1028.\n <\/p>\n <\/article>\n

\n

\n \n The Quest for Orthologs orthology benchmark service in 2022.\n <\/a>\n <\/h3>\n

\n 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, Pili\u017eota I, Guijarro-Clarke C, OpenEBench team the Quest for Orthologs Consortium, Iwasaki W, Lecompte O, Sonnhammer E, Roos DS, Gabald\u00f3n T, Thybert D, Thomas PD, Hu Y, Emms DM, Bruford E, Capella-Gutierrez S, Martin MJ, Dessimoz C, Altenhoff A.\n <\/p>\n

\n Nucleic acids research, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkac330.\n <\/p>\n <\/article>\n

\n

\n \n Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins.\n <\/a>\n <\/h3>\n

\n Hasenahuer MA, Sanchis-Juan A, Laskowski RA, Baker JA, Stephenson JD, Orengo CA, Raymond FL, Thornton JM.\n <\/p>\n

\n Journal of molecular biology, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1016\/j.jmb.2022.167892.\n <\/p>\n <\/article>\n

\n

\n \n Saturation genome editing of DDX3X clarifies pathogenicity of germline and somatic variation\n <\/a>\n <\/h3>\n

\n Radford E, Tan H, Andersson M, Stephenson J, Gardner E, Ironfield H, Waters A, Gitterman D, Lindsay S, Abascal F, Martincorena I, Kolesnik A, Ng-Cordell E, Firth H, Baker K, Perry J, Adams D, Gerety S, Hurles M.\n <\/p>\n

\n Preprint, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1101\/2022.06.10.22276179.\n <\/p>\n <\/article>\n

\n

\n \n A roadmap for the functional annotation of protein families: a community perspective.\n <\/a>\n <\/h3>\n

\n de Cr\u00e9cy-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.\n <\/p>\n

\n Database : the journal of biological databases and curation, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1093\/database\/baac062.\n <\/p>\n <\/article>\n

\n

\n \n Hierarchical deep learning for predicting GO annotations by integrating protein knowledge.\n <\/a>\n <\/h3>\n

\n Merino GA, Saidi R, Milone DH, Stegmayer G, Martin MJ.\n <\/p>\n

\n Bioinformatics (Oxford, England), \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1093\/bioinformatics\/btac536.\n <\/p>\n <\/article>\n

\n

\n \n Standardized annotation of translated open reading frames.\n <\/a>\n <\/h3>\n

\n Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Alb\u00e0 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.\n <\/p>\n

\n Nature biotechnology, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1038\/s41587-022-01369-0.\n <\/p>\n <\/article>\n

\n

\n \n SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins.\n <\/a>\n <\/h3>\n

\n \u00d6zsar\u0131 G, Rifaioglu AS, Atakan A, Do\u011fan T, Martin MJ, \u00c7etin Atalay R, Atalay V.\n <\/p>\n

\n Bioinformatics (Oxford, England), \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1093\/bioinformatics\/btac458.\n <\/p>\n <\/article>\n

\n

\n \n Method for Independent Estimation of the False Localization Rate for Phosphoproteomics.\n <\/a>\n <\/h3>\n

\n Ramsbottom KA, Prakash A, Riverol YP, Camacho OM, Martin MJ, Vizca\u00edno JA, Deutsch EW, Jones AR.\n <\/p>\n

\n Journal of proteome research, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1021\/acs.jproteome.1c00827.\n <\/p>\n <\/article>\n

\n

\n \n Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation.\n <\/a>\n <\/h3>\n

\n Kalyuzhnyy A, Eyers PA, Eyers CE, Bowler-Barnett E, Martin MJ, Sun Z, Deutsch EW, Jones AR.\n <\/p>\n

\n Journal of proteome research, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1021\/acs.jproteome.2c00131.\n <\/p>\n <\/article>\n

\n

\n \n The IntAct database: efficient access to fine-grained molecular interaction data.\n <\/a>\n <\/h3>\n

\n Del Toro N, Shrivastava A, Ragueneau E, Meldal B, Combe C, Barrera E, Perfetto L, How K, Ratan P, Shirodkar G, Lu O, M\u00e9sz\u00e1ros 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.\n <\/p>\n

\n Nucleic acids research, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkab1006.\n <\/p>\n <\/article>\n

\n

\n \n The European Nucleotide Archive in 2021.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Nucleic acids research, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkab1051.\n <\/p>\n <\/article>\n

\n

\n \n Mutual Annotation-Based Prediction of Protein Domain Functions with Domain2GO\n <\/a>\n <\/h3>\n

\n Ulusoy E, Do\u011fan T.\n <\/p>\n

\n Preprint, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1101\/2022.11.03.514980.\n <\/p>\n <\/article>\n

\n

\n \n How to Best Represent Proteins in Machine Learning-based Prediction of Drug\/Compound-Target Interactions\n <\/a>\n <\/h3>\n

\n Atas H, Do\u011fan T.\n <\/p>\n

\n Preprint, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1101\/2022.05.01.490207.\n <\/p>\n <\/article>\n

\n

\n \n UniProt: the universal protein knowledgebase in 2021.\n <\/a>\n <\/h3>\n

\n UniProt Consortium.\n <\/p>\n

\n Nucleic acids research, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkaa1100.\n <\/p>\n <\/article>\n

\n

\n \n A GO catalogue of human DNA-binding transcription factors.\n <\/a>\n <\/h3>\n

\n Lovering RC, Gaudet P, Acencio ML, Ignatchenko A, Jolma A, Fornes O, Kuiper M, Kulakovskiy IV, L\u00e6greid A, Martin MJ, Logie C.\n <\/p>\n

\n Biochimica et biophysica acta. Gene regulatory mechanisms, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1016\/j.bbagrm.2021.194765.\n <\/p>\n <\/article>\n

\n

\n \n The Gene Ontology resource: enriching a GOld mine.\n <\/a>\n <\/h3>\n

\n Gene Ontology Consortium.\n <\/p>\n

\n Nucleic acids research, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkaa1113.\n <\/p>\n <\/article>\n

\n

\n \n An open dataset of &lt;i&gt;Plasmodium falciparum&lt;\/i&gt; genome variation in 7,000 worldwide samples.\n <\/a>\n <\/h3>\n

\n 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, Djimd\u00e9 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, Konat\u00e9 A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Ma\u00efga-Ascofar\u00e9 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.\n <\/p>\n

\n Wellcome open research, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.12688\/wellcomeopenres.16168.2.\n <\/p>\n <\/article>\n

\n

\n \n Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB.\n <\/a>\n <\/h3>\n

\n Feuermann M, Boutet E, Morgat A, Axelsen KB, Bansal P, Bolleman J, de Castro E, Coudert E, Gasteiger E, G\u00e9hant S, Lieberherr D, Lombardot T, Neto TB, Pedruzzi I, Poux S, Pozzato M, Redaschi N, Bridge A, On Behalf Of The UniProt Consortium.\n <\/p>\n

\n Metabolites, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.3390\/metabo11010048.\n <\/p>\n <\/article>\n

\n

\n \n The Enzyme Portal: an integrative tool for enzyme information and analysis.\n <\/a>\n <\/h3>\n

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

\n The FEBS journal, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1111\/febs.16168.\n <\/p>\n <\/article>\n

\n

\n \n Protein domain-based prediction of drug\/compound-target interactions and experimental validation on LIM kinases.\n <\/a>\n <\/h3>\n

\n Do\u011fan T, Akhan G\u00fczelcan E, Baumann M, Koyas A, Atas H, Baxendale IR, Martin M, Cetin-Atalay R.\n <\/p>\n

\n PLoS computational biology, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1371\/journal.pcbi.1009171.\n <\/p>\n <\/article>\n

\n

\n \n Enhancing the interoperability of glycan data flow between ChEBI, PubChem and GlyGen.\n <\/a>\n <\/h3>\n

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

\n Glycobiology, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1093\/glycob\/cwab078.\n <\/p>\n <\/article>\n

\n

\n \n CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations.\n <\/a>\n <\/h3>\n

\n Do\u011fan T, Atas H, Joshi V, Atakan A, Rifaioglu AS, Nalbat E, Nightingale A, Saidi R, Volynkin V, Zellner H, Cetin-Atalay R, Martin M, Atalay V.\n <\/p>\n

\n Nucleic acids research, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkab543.\n <\/p>\n <\/article>\n

\n

\n \n Enhancing the interoperability of glycan data flow between ChEBI, PubChem, and GlyGen.\n <\/a>\n <\/h3>\n

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

\n Preprint, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1101\/2021.06.17.448729.\n <\/p>\n <\/article>\n

\n

\n \n Protein Domain-Based Prediction of Compound\u2013Target Interactions and Experimental Validation on LIM Kinases\n <\/a>\n <\/h3>\n

\n Do\u011fan T, Akhan G\u00fczelcan E, Baumann M, Koyas A, Atas H, Baxendale I, Martin M, Cetin-Atalay R.\n <\/p>\n

\n Preprint, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1101\/2021.06.14.448307.\n <\/p>\n <\/article>\n

\n

\n \n A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq\n <\/a>\n <\/h3>\n

\n Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Gonzalez JM, Magrane M, Martinez T, Schulz JF, Yang YT, Alb\u00e0 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.\n <\/p>\n

\n Preprint, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1101\/2021.06.10.447896.\n <\/p>\n <\/article>\n

\n

\n \n Ten Years of Collaborative Progress in the Quest for Orthologs.\n <\/a>\n <\/h3>\n

\n Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Thomas PD, Gabald\u00f3n T, Sonnhammer E, Dessimoz C, Uchiyama I, QFO Consortium.\n <\/p>\n

\n Molecular biology and evolution, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1093\/molbev\/msab098.\n <\/p>\n <\/article>\n

\n

\n \n UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Bioinformatics (Oxford, England), \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1093\/bioinformatics\/btaa663.\n <\/p>\n <\/article>\n

\n

\n \n Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.\n <\/a>\n <\/h3>\n

\n 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, H\u00f6lzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, K\u00fchnert D, Lasso G, Libin P, List M, L\u00f6chel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki EP, O'Toole \u00c1N, 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.\n <\/p>\n

\n Briefings in bioinformatics, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1093\/bib\/bbaa232.\n <\/p>\n <\/article>\n

\n

\n \n MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery.\n <\/a>\n <\/h3>\n

\n Rifaioglu AS, Cetin Atalay R, Cansen Kahraman D, Do\u011fan T, Martin M, Atalay V.\n <\/p>\n

\n Bioinformatics (Oxford, England), \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1093\/bioinformatics\/btaa858.\n <\/p>\n <\/article>\n

\n

\n \n The InterPro protein families and domains database: 20 years on.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Nucleic acids research, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkaa977.\n <\/p>\n <\/article>\n

\n

\n \n The European Nucleotide Archive in 2019.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Nucleic acids research, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkz1063.\n <\/p>\n <\/article>\n

\n

\n \n A GO catalogue of human DNA-binding transcription factors\n <\/a>\n <\/h3>\n

\n Lovering RC, Gaudet P, Acencio ML, Ignatchenko A, Jolma A, Fornes O, Kuiper M, Kulakovskiy IV, L\u00e6greid A, Martin MJ, Logie C.\n <\/p>\n

\n Preprint, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1101\/2020.10.28.359232.\n <\/p>\n <\/article>\n

\n

\n \n UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Bioinformatics (Oxford, England), \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1093\/bioinformatics\/btaa485.\n <\/p>\n <\/article>\n

\n

\n \n The reactome pathway knowledgebase.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Nucleic acids research, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkz1031.\n <\/p>\n <\/article>\n

\n

\n \n Genome variation and population structure among 1142 mosquitoes of the African malaria vector species &lt;i&gt;Anopheles gambiae&lt;\/i&gt; and &lt;i&gt;Anopheles coluzzii&lt;\/i&gt;.\n <\/a>\n <\/h3>\n

\n Anopheles gambiae 1000 Genomes Consortium.\n <\/p>\n

\n Genome research, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1101\/gr.262790.120.\n <\/p>\n <\/article>\n

\n

\n \n Caenorhabditis elegans phosphatase complexes in UniProtKB and Complex Portal.\n <\/a>\n <\/h3>\n

\n Bye-A-Jee H, Zaru R, Magrane M, Orchard S, UniProt Consortium.\n <\/p>\n

\n The FEBS journal, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1111\/febs.15213.\n <\/p>\n <\/article>\n

\n

\n \n The DNA polymerases of &lt;i&gt;Drosophila melanogaster&lt;\/i&gt;.\n <\/a>\n <\/h3>\n

\n Marygold SJ, Attrill H, Speretta E, Warner K, Magrane M, Berloco M, Cotterill S, McVey M, Rong Y, Yamaguchi M.\n <\/p>\n

\n Fly, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1080\/19336934.2019.1710076.\n <\/p>\n <\/article>\n

\n

\n \n DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations.\n <\/a>\n <\/h3>\n

\n Rifaioglu AS, Nalbat E, Atalay V, Martin MJ, Cetin-Atalay R, Do\u011fan T.\n <\/p>\n

\n Chemical science, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1039\/c9sc03414e.\n <\/p>\n <\/article>\n

\n

\n \n CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations\n <\/a>\n <\/h3>\n

\n Do\u011fan T, Atas H, Joshi V, Atakan A, Rifaioglu AS, Nalbat E, Nightingale A, Saidi R, Volynkin V, Zellner H, Cetin-Atalay R, Martin M, Atalay V.\n <\/p>\n

\n Preprint, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1101\/2020.09.14.296889.\n <\/p>\n <\/article>\n

\n

\n \n Effect of sequence padding on the performance of deep learning models in archaeal protein functional prediction.\n <\/a>\n <\/h3>\n

\n Lopez-Del Rio A, Martin M, Perera-Lluna A, Saidi R.\n <\/p>\n

\n Scientific reports, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1038\/s41598-020-71450-8.\n <\/p>\n <\/article>\n

\n

\n \n A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Journal of Alzheimer's disease : JAD, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.3233\/jad-200206.\n <\/p>\n <\/article>\n

\n

\n \n Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research\n <\/a>\n <\/h3>\n

\n 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, H\u00f6lzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, K\u00fchnert D, Lasso G, Libin P, List M, L\u00f6chel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki E, O'Toole \u00c1N, Palacios-Ontiveros N, Petrov AI, Rangel-Pi\u00f1eros 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.\n <\/p>\n

\n Preprint, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.20944\/preprints202005.0376.v1.\n <\/p>\n <\/article>\n

\n

\n \n Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data.\n <\/a>\n <\/h3>\n

\n Kramarz B, Huntley RP, Rodr\u00edguez-L\u00f3pez M, Roncaglia P, Saverimuttu SCC, Parkinson H, Bandopadhyay R, Martin MJ, Orchard S, Hooper NM, Brough D, Lovering RC.\n <\/p>\n

\n Journal of Alzheimer's disease : JAD, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.3233\/jad-200207.\n <\/p>\n <\/article>\n

\n

\n \n The Quest for Orthologs benchmark service and consensus calls in 2020.\n <\/a>\n <\/h3>\n

\n Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hern\u00e1ndez-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fern\u00e1ndez JM, Cod\u00f3 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.\n <\/p>\n

\n Nucleic acids research, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkaa308.\n <\/p>\n <\/article>\n

\n

\n \n GlyGen data model and processing workflow.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Bioinformatics (Oxford, England), \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1093\/bioinformatics\/btaa238.\n <\/p>\n <\/article>\n

\n

\n \n Effect of Sequence Padding on the Performance of Protein-Based Deep Learning Models\n <\/a>\n <\/h3>\n

\n Rio AL, Martin M, Perera-Lluna A, Saidi R.\n <\/p>\n

\n Preprint, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.21203\/rs.2.21336\/v1.\n <\/p>\n <\/article>\n

\n

\n \n GlyGen: Computational and Informatics Resources for Glycoscience.\n <\/a>\n <\/h3>\n

\n 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.\n <\/p>\n

\n Glycobiology, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1093\/glycob\/cwz080.\n <\/p>\n <\/article>\n

\n

\n \n Evaluation of Methods for Protein Representation Learning: A Quantitative Analysis\n <\/a>\n <\/h3>\n

\n Unsal S, Ata\u015f H, Albayrak M, Turhan K, Acar AC, Do\u011fan T.\n <\/p>\n

\n Preprint, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1101\/2020.10.28.359828.\n <\/p>\n <\/article>\n

\n

\n \n The COMPARE Data Hubs.\n <\/a>\n <\/h3>\n

\n Amid C, Pakseresht N, Silvester N, Jayathilaka S, Lund O, Dynovski LD, Pataki B\u00c1, Visontai D, Xavier BB, Alako BTF, Belka A, Cisneros JLB, Cotten M, Haringhuizen GB, Harrison PW, H\u00f6per 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, St\u00e9ger J, Szalai-Gindl JM, Thomsen MCF, Cacci\u00f2 SM, Csabai I, Kroneman A, Koopmans M, Aarestrup F, Cochrane G.\n <\/p>\n

\n Database : the journal of biological databases and curation, \n 2019<\/span>\n <\/p>\n\n

\n doi:10.1093\/database\/baz136.\n <\/p>\n <\/article>\n

\n

\n \n The COMPARE Data Hubs\n <\/a>\n <\/h3>\n

\n Amid C, Pakseresht N, Silvester N, Jayathilaka S, Lund O, Dynovski LD, Pataki B\u00c1, Visontai D, Cotten M, Xavier BB, Alako B, Belka A, Cisneros JJL, Haringhuizen GB, Harrison PW, H\u00f6per D, Holt S, Hundahl C, Hussein A, Kaas RS, Malhotra-Kumar S, Leinonen R, Nieuwenhuijse DF, Rahman N, Ribeiro CdS, Skiby JE, St\u00e9ger J, Szalai-Gindl JM, Thomsen MCF, Csabai I, Koopmans M, Aarestrup F, Cochrane G.\n <\/p>\n

\n Preprint, \n 2019<\/span>\n <\/p>\n\n

\n doi:10.1101\/555938.\n <\/p>\n <\/article>\n

\n

\n \n The European Nucleotide Archive in 2018.\n <\/a>\n <\/h3>\n

\n Harrison PW, Alako B, Amid C, Cerde\u00f1o-T\u00e1rraga A, Cleland I, Holt S, Hussein A, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Mart\u00ednez-Villacorta J, Milano A, Pakseresht N, Rajan J, Reddy K, Richards E, Rosello M, Silvester N, Smirnov D, Toribio AL, Vijayaraja S, Cochrane G.\n <\/p>\n

\n Nucleic acids research, \n 2019<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gky1078.\n <\/p>\n <\/article>\n

\n

\n \n FAIR adoption, assessment and challenges at UniProt.\n <\/a>\n <\/h3>\n

\n Garcia L, Bolleman J, Gehant S, Redaschi N, Martin M, UniProt Consortium.\n <\/p>\n

\n Scientific data, \n 2019<\/span>\n <\/p>\n\n

\n doi:10.1038\/s41597-019-0180-9.\n <\/p>\n <\/article>\n

\n

\n \n The Gene Ontology Resource: 20 years and still GOing strong.\n <\/a>\n <\/h3>\n

\n The\u00a0Gene\u00a0Ontology\u00a0Consortium.\n <\/p>\n

\n Nucleic acids research, \n 2019<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gky1055.\n <\/p>\n <\/article>\n

\n

\n \n UniProt: a worldwide hub of protein knowledge.\n <\/a>\n <\/h3>\n

\n UniProt Consortium.\n <\/p>\n

\n Nucleic acids research, \n 2019<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gky1049.\n <\/p>\n <\/article>\n

\n

\n \n Updates in Rhea: SPARQLing biochemical reaction data.\n <\/a>\n <\/h3>\n

\n Lombardot T, Morgat A, Axelsen KB, Aimo L, Hyka-Nouspikel N, Niknejad A, Ignatchenko A, Xenarios I, Coudert E, Redaschi N, Bridge A.\n <\/p>\n

\n Nucleic acids research, \n 2019<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gky876.\n <\/p>\n <\/article>\n

\n

\n \n Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species <i>Anopheles gambiae<\/i> and <i>Anopheles coluzzii<\/i>\n <\/a>\n <\/h3>\n

\n 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\u2019Loughlin S, Pinto J, Riehle MM, Sharakhov I, Schrider DR, Vernick KD, White BJ, Donnelly MJ, Kwiatkowski DP.\n <\/p>\n

\n Preprint, \n 2019<\/span>\n <\/p>\n\n

\n doi:10.1101\/864314.\n <\/p>\n <\/article>\n

\n

\n \n Challenges in the annotation of pseudoenzymes in databases: the UniProtKB approach.\n <\/a>\n <\/h3>\n

\n Zaru R, Magrane M, Orchard S, UniProt Consortium.\n <\/p>\n

\n The FEBS journal, \n 2019<\/span>\n <\/p>\n\n

\n doi:10.1111\/febs.15100.\n <\/p>\n <\/article>\n

\n

\n \n VarSite: Disease variants and protein structure.\n <\/a>\n <\/h3>\n

\n Laskowski RA, Stephenson JD, Sillitoe I, Orengo CA, Thornton JM.\n <\/p>\n

\n Protein science : a publication of the Protein Society, \n 2019<\/span>\n <\/p>\n\n

\n doi:10.1002\/pro.3746.\n <\/p>\n <\/article>\n <\/div>","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-publications.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-257","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/protein-function-development\/wp-json\/wp\/v2\/pages\/257","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/protein-function-development\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/protein-function-development\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/protein-function-development\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/protein-function-development\/wp-json\/wp\/v2\/comments?post=257"}],"version-history":[{"count":3,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/protein-function-development\/wp-json\/wp\/v2\/pages\/257\/revisions"}],"predecessor-version":[{"id":880,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/protein-function-development\/wp-json\/wp\/v2\/pages\/257\/revisions\/880"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/protein-function-development\/wp-json\/wp\/v2\/media?parent=257"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/protein-function-development\/wp-json\/wp\/v2\/embl_taxonomy?post=257"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}