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

Naihui Zhou , Yuxiang Jiang , Timothy Bergquist , Alexandra Lee , Balint Kacsoh , Alex Crocker , Kimberley Lewis , George Georghiou , Huy Nguyen (1) , Md Nafiz Hamid , Larry Davis , Tunca Dogan (2) , Volkan Atalay , Ahmet Rifaioglu , Alperen Dalkiran , Rengul Cetin Atalay , Chengxin Zhang , Rebecca Hurto , Peter Freddolino , Yang Zhang , Prajwal Bhat , Fran Supek , Jose Fernandez (3) , Branislava Gemovic , Vladimir Perovic , Radoslav Davidović (4) , Neven Sumonja , Nevena Veljkovic , Ehsaneddin Asgari , Mohammad R.K. Mofrad , Giuseppe Profiti (5) , Castrense Savojardo , Pier Luigi Martelli , Rita Casadio (5) , Florian Boecker , Heiko Schoof (6) , Indika Kahanda , Natalie Thurlby , Alice C Mchardy (7) , Alexandre Renaux (8) , Rabie Saidi (9) , Julian Gough (10) , Alex Freitas , Magdalena Antczak , Fabio Fabris , Mark Wass , Jie Hou , Jianlin Cheng (11) , Zheng Wang (12) , Alfonso Romero (13) , Alberto Paccanaro , Haixuan Yang , Tatyana Goldberg (14) , Chenguang Zhao , Liisa Holm , Petri Törönen , Alan J. Medlar (15) , Elaine Zosa , Itamar Borukhov , Ilya Novikov , Angela Wilkins , Olivier Lichtarge (16) , Po-Han Chi , Wei-Cheng Tseng , Michal Linial , Peter Rose , Christophe Dessimoz (17) , Vedrana Vidulin , Saso Dzeroski (18) , Ian Sillitoe (19) , Sayoni Das , Jonathan Gill Lees , David Jones , Cen Wan , Domenico Cozzetto , Rui Fa , Mateo Torres , Alex Warwick Vesztrocy , Jose Manuel Rodriguez , Michael Tress (20) , Marco Frasca , Marco Notaro , Giuliano Grossi , Alessandro Petrini (21) , Matteo Re , Giorgio Valentini (21) , Marco Mesiti (22) , Daniel S. Roche (23) , Jonas Reeb , David Ritchie , Sabeur Aridhi (24) , Seyed Ziaeddin Alborzi (24) , Marie-Dominique Devignes (24) , da Chen Emily Koo , Richard Bonneau , Vladimir Gligorijević , Meet Barot , Hai Fang , Stefano Toppo , Enrico Lavezzo (25) , Marco Falda , Michele Berselli , Silvio C.E. Tosatto (26) , Marco Carraro , Damiano Piovesan (26) , Hafeez Ur Rehman , Qizhong Mao , Shanshan Zhang , Slobodan Vucetic , Gage Black , Dane Jo , Erica Suh , Jonathan Dayton , Dallas Larsen , Ashton Omdahl , Liam Mcguffin , Danielle Brackenridge , Patricia Babbitt , Jeffrey Yunes , Paolo Fontana , Feng Zhang , Shanfeng Zhu , Ronghui You , Zihan Zhang , Suyang Dai , Shuwei Yao , Weidong Tian , Renzhi Cao , Caleb Chandler , Miguel Amezola , Devon Johnson , Jia-Ming Chang (27) , Wen-Hung Liao , Yi-Wei Liu (28) , Stefano Pascarelli , Yotam Frank , Robert Hoehndorf , Maxat Kulmanov , Imane Boudellioua , Gianfranco Politano , Stefano Di Carlo (29) , Alfredo Benso (30) , Kai Hakala , Filip Ginter (31) , Farrokh Mehryary , Suwisa Kaewphan , Jari Björne , Hans Moen , Martti E.E. Tolvanen , Tapio Salakoski (32) , Daisuke Kihara (33) , Aashish Jain , Tomislav Šmuc , Adrian M Altenhoff (34) , Asa Ben-Hur (35) , Burkhard Rost (14) , Steven Brenner , Christine Orengo (19) , Constance Jeffery , Giovanni Bosco , Deborah Hogan , Maria Martin , Claire O’donovan , Sean Mooney (36) , Casey Greene , Predrag Radivojac , Iddo Friedberg

1 ISU - Iowa State University
2 European Bioinformatics Institute
3 EPM - École Polytechnique de Montréal
4 Vinča Institute of Nuclear Sciences
5 UNIBO - Alma Mater Studiorum Università di Bologna = University of Bologna
6 MPIPZ - Max Planck Institute for Plant Breeding Research
7 European Virus Bioinformatics Center [Jena]
8 ULB - Université libre de Bruxelles
9 LIMOS - Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes
10 Department of Computer Science
11 Department of Computer Science [Columbia]
12 YSPH - Yale School of Public Health
13 Departamento de Geometría y Topología
14 Tumor Biology Center
15 Centre for Nephrology [London, UK]
16 BCM - Baylor College of Medicine
17 Department of Computer Science
18 Department of Knowledge Technologies
19 UCL - University College of London [London]
20 CNIO - Spanish National Cancer Research Center
21 Dipartimento di Informatica
22 Dipartimento di Scienze dell'Informazione [Milano]
23 United States Naval Academy
24 CAPSID - Computational Algorithms for Protein Structures and Interactions
25 Department of Molecular Medicine
26 Unipd - Università degli Studi di Padova = University of Padua
27 CRG - Centro de Regulación Genómica
28 Physics Department
29 DAUIN - Dipartimento di Automatica e Informatica [Torino]
30 Polito - Politecnico di Torino = Polytechnic of Turin
31 University of Turku
32 Bioinformatics Laboratory
33 TTIC - Toyota Technological Institute at Chicago [Chicago]
34 SIB - Swiss Institute of Bioinformatics [Lausanne]
35 Department of Computer Science [Colorado State University]
36 CPIB - Centre for Plant Integrative Biology [Nothingham]

Domaines: Base de données [cs.DB]; Bio-informatique [q-bio.QM]; Intelligence artificielle [cs.AI]; Apprentissage [cs.LG]; Calcul parallèle, distribué et partagé [cs.DC]

Naihui Zhou, Yuxiang Jiang, Timothy Bergquist, Alexandra Lee, Balint Kacsoh, et al.. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology, 2019, 20 (1), ⟨10.1186/s13059-019-1835-8⟩. ⟨hal-02393202⟩