2026-06-14T03:29:15Zhttps://repisalud.isciii.es/rest/oai/request
oai:repisalud.isciii.es:20.500.12105/89322024-09-27T10:13:14Zcom_20.500.12105_19604com_20.500.12105_2051col_20.500.12105_19607
Repisalud author Zhou, Naihui author Jiang, Yuxiang author Bergquist, Timothy R author Lee, Alexandra J author Kacsoh, Balint Z author Crocker, Alex W author Lewis, Kimberley A author Georghiou, George author Nguyen, Huy N author Hamid, Md Nafiz author Davis, Larry author Dogan, Tunca author Atalay, Volkan author Rifaioglu, Ahmet S author Dalkıran, Alperen author Cetin Atalay, Rengul author Zhang, Chengxin author Hurto, Rebecca L author Freddolino, Peter L author Zhang, Yang author Bhat, Prajwal author Supek, Fran author Fernández, José M author Gemovic, Branislava author Perovic, Vladimir R author Davidović, Radoslav S author Sumonja, Neven author Veljkovic, Nevena author Asgari, Ehsaneddin author Mofrad, Mohammad R K author Profiti, Giuseppe author Savojardo, Castrense author Martelli, Pier Luigi author Casadio, Rita author Boecker, Florian author Schoof, Heiko author Kahanda, Indika author Thurlby, Natalie author McHardy, Alice C author Renaux, Alexandre author Saidi, Rabie author Gough, Julian author Freitas, Alex A author Antczak, Magdalena author Fabris, Fabio author Wass, Mark N author Hou, Jie author Cheng, Jianlin author Wang, Zheng author Romero, Alfonso E author Paccanaro, Alberto author Yang, Haixuan author Goldberg, Tatyana author Zhao, Chenguang author Holm, Liisa author Törönen, Petri author Medlar, Alan J author Zosa, Elaine author Borukhov, Itamar author Novikov, Ilya author Wilkins, Angela author Lichtarge, Olivier author Chi, Po-Han author Tseng, Wei-Cheng author Linial, Michal author Rose, Peter W author Dessimoz, Christophe author Vidulin, Vedrana author Dzeroski, Saso author Sillitoe, Ian author Das, Sayoni author Lees, Jonathan Gill author Jones, David T author Wan, Cen author Cozzetto, Domenico author Fa, Rui author Torres, Mateo author Warwick Vesztrocy, Alex author Rodriguez, Jose Manuel author Tress, Michael L author Frasca, Marco author Notaro, Marco author Grossi, Giuliano author Petrini, Alessandro author Re, Matteo author Valentini, Giorgio author Mesiti, Marco author Roche, Daniel B author Reeb, Jonas author Ritchie, David W author Aridhi, Sabeur author Alborzi, Seyed Ziaeddin author Devignes, Marie-Dominique author Koo, Da Chen Emily author Bonneau, Richard author Gligorijević, Vladimir author Barot, Meet author Fang, Hai author Toppo, Stefano author Lavezzo, Enrico author Falda, Marco author Berselli, Michele author Tosatto, Silvio C E author Carraro, Marco author Piovesan, Damiano author Ur Rehman, Hafeez author Mao, Qizhong author Zhang, Shanshan author Vucetic, Slobodan author Black, Gage S author Jo, Dane author Suh, Erica author Dayton, Jonathan B author Larsen, Dallas J author Omdahl, Ashton R author McGuffin, Liam J author Brackenridge, Danielle A author Babbitt, Patricia C author Yunes, Jeffrey M author Fontana, Paolo author Zhang, Feng author Zhu, Shanfeng author You, Ronghui author Zhang, Zihan author Dai, Suyang author Yao, Shuwei author Tian, Weidong author Cao, Renzhi author Chandler, Caleb author Amezola, Miguel author Johnson, Devon author Chang, Jia-Ming author Liao, Wen-Hung author Liu, Yi-Wei author Pascarelli, Stefano author Frank, Yotam author Hoehndorf, Robert author Kulmanov, Maxat author Boudellioua, Imane author Politano, Gianfranco author Di Carlo, Stefano author Benso, Alfredo author Hakala, Kai author Ginter, Filip author Mehryary, Farrokh author Kaewphan, Suwisa author Björne, Jari author Moen, Hans author Tolvanen, Martti E E author Salakoski, Tapio author Kihara, Daisuke author Jain, Aashish author Šmuc, Tomislav author Altenhoff, Adrian author Ben-Hur, Asa author Rost, Burkhard author Brenner, Steven E author Orengo, Christine A author Jeffery, Constance J author Bosco, Giovanni author Hogan, Deborah A author Martin, Maria J author O'Donovan, Claire author Mooney, Sean D author Greene, Casey S author Radivojac, Predrag author Friedberg, Iddo 2020-01-29T09:56:34Z 2020-01-29T09:56:34Z 2019-11 Genome Biol. 2019; 20(1):244 10.1186/s13059-019-1835-8 1474-760X 1474-760X Genome biology 31744546 http://hdl.handle.net/20.500.12105/8932 BACKGROUND: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. RESULTS: Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. CONCLUSION: We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens. eng Biofilm Community challenge Critical assessment Long-term memory Protein function prediction The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens journal article 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 URL https://repisalud.isciii.es/bitstreams/d69e51fa-e024-4838-85e8-400c56600d3d/download File MD5 55ab9e637bcb6d0cffc89ebcbe0b034e 8539006 application/pdf CAFAChallengeReportsImproved_2019.pdf URL https://repisalud.isciii.es/bitstreams/6452958e-fc5e-407e-9e3e-ca0d0f6cf3fd/download File MD5 7a3c609d05c885d02af622d56b08c73c 5962307 application/pdf CAFAChallengeReportsImproved_2019_SUPPLMAT.pdf URL https://repisalud.isciii.es/bitstreams/eaab7b76-8198-45c5-b62e-dbf8a3ae40a8/download File MD5 d218ece0cd8f32f9973b32f6ef5e0516 89952 text/plain CAFAChallengeReportsImproved_2019.pdf.txt URL https://repisalud.isciii.es/bitstreams/6becb3b1-9510-4a49-beca-c71cfd554471/download File MD5 fcb408616d553cddb9e34041788fd41e 11701 text/plain CAFAChallengeReportsImproved_2019_SUPPLMAT.pdf.txt