The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens - Inria - Institut national de recherche en sciences et technologies du numérique
Journal Articles Genome Biology Year : 2019

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]
Naihui Zhou
  • Function : Author
Yuxiang Jiang
  • Function : Author
Timothy Bergquist
  • Function : Author
Alexandra Lee
  • Function : Author
Balint Kacsoh
  • Function : Author
Alex Crocker
  • Function : Author
Kimberley Lewis
  • Function : Author
George Georghiou
  • Function : Author
Huy Nguyen
  • Function : Author
Md Nafiz Hamid
  • Function : Author
Larry Davis
  • Function : Author
Volkan Atalay
  • Function : Author
Ahmet Rifaioglu
  • Function : Author
Alperen Dalkiran
  • Function : Author
Rengul Cetin Atalay
  • Function : Author
Chengxin Zhang
  • Function : Author
Rebecca Hurto
  • Function : Author
Peter Freddolino
  • Function : Author
Yang Zhang
Prajwal Bhat
  • Function : Author
Fran Supek
  • Function : Author
Branislava Gemovic
  • Function : Author
Vladimir Perovic
  • Function : Author
Neven Sumonja
  • Function : Author
Nevena Veljkovic
Ehsaneddin Asgari
  • Function : Author
Mohammad R.K. Mofrad
  • Function : Author
Castrense Savojardo
  • Function : Author
Pier Luigi Martelli
  • Function : Author
Florian Boecker
  • Function : Author
Indika Kahanda
  • Function : Author
Natalie Thurlby
  • Function : Author
Alex Freitas
  • Function : Author
Magdalena Antczak
  • Function : Author
Fabio Fabris
  • Function : Author
Mark Wass
  • Function : Author
Jie Hou
  • Function : Author
Zheng Wang
  • Function : Author
  • PersonId : 922364
Alfonso Romero
  • Function : Author
  • PersonId : 928059
Alberto Paccanaro
  • Function : Author
Haixuan Yang
  • Function : Author
Chenguang Zhao
  • Function : Author
Liisa Holm
  • Function : Author
Petri Törönen
  • Function : Author
Elaine Zosa
Itamar Borukhov
  • Function : Author
Ilya Novikov
  • Function : Author
Angela Wilkins
  • Function : Author
Po-Han Chi
  • Function : Author
Wei-Cheng Tseng
  • Function : Author
Michal Linial
  • Function : Author
Peter Rose
  • Function : Author
Vedrana Vidulin
  • Function : Author
Sayoni Das
  • Function : Author
Jonathan Gill Lees
  • Function : Author
David Jones
  • Function : Author
Cen Wan
  • Function : Author
Domenico Cozzetto
  • Function : Author
Rui Fa
  • Function : Author
Mateo Torres
  • Function : Author
Alex Warwick Vesztrocy
  • Function : Author
Jose Manuel Rodriguez
  • Function : Author
Marco Frasca
  • Function : Author
Marco Notaro
  • Function : Author
Giuliano Grossi
  • Function : Author
Alessandro Petrini
  • Function : Author
  • PersonId : 1054038
Matteo Re
  • Function : Author
Giorgio Valentini
  • Function : Author
  • PersonId : 1008215
Jonas Reeb
  • Function : Author
David Ritchie
da Chen Emily Koo
  • Function : Author
Richard Bonneau
  • Function : Author
Vladimir Gligorijević
  • Function : Author
Meet Barot
  • Function : Author
Hai Fang
  • Function : Author
Stefano Toppo
  • Function : Author
Marco Falda
  • Function : Author
Michele Berselli
  • Function : Author
Marco Carraro
  • Function : Author
Hafeez Ur Rehman
  • Function : Author
Qizhong Mao
  • Function : Author
Shanshan Zhang
Slobodan Vucetic
  • Function : Author
Gage Black
  • Function : Author
Dane Jo
  • Function : Author
Erica Suh
  • Function : Author
Jonathan Dayton
  • Function : Author
Dallas Larsen
  • Function : Author
Ashton Omdahl
  • Function : Author
Liam Mcguffin
  • Function : Author
Danielle Brackenridge
  • Function : Author
Patricia Babbitt
  • Function : Author
Jeffrey Yunes
  • Function : Author
Paolo Fontana
  • Function : Author
Feng Zhang
  • Function : Author
  • PersonId : 936796
Shanfeng Zhu
  • Function : Author
Ronghui You
  • Function : Author
Zihan Zhang
  • Function : Author
Suyang Dai
  • Function : Author
Shuwei Yao
  • Function : Author
Weidong Tian
  • Function : Author
Renzhi Cao
  • Function : Author
Caleb Chandler
  • Function : Author
Miguel Amezola
  • Function : Author
Devon Johnson
  • Function : Author
Wen-Hung Liao
  • Function : Author
Yi-Wei Liu
  • Function : Author
Stefano Pascarelli
  • Function : Author
Yotam Frank
  • Function : Author
Robert Hoehndorf
  • Function : Author
Maxat Kulmanov
  • Function : Author
Imane Boudellioua
  • Function : Author
Gianfranco Politano
  • Function : Author
Kai Hakala
  • Function : Author
Filip Ginter
  • Function : Author
Farrokh Mehryary
  • Function : Author
Suwisa Kaewphan
  • Function : Author
Jari Björne
  • Function : Author
Hans Moen
  • Function : Author
Martti E.E. Tolvanen
  • Function : Author
Tapio Salakoski
  • Function : Author
  • PersonId : 834093
Aashish Jain
  • Function : Author
Tomislav Šmuc
  • Function : Author
Steven Brenner
  • Function : Author
Constance Jeffery
  • Function : Author
Giovanni Bosco
  • Function : Author
Deborah Hogan
  • Function : Author
Maria Martin
  • Function : Author
Claire O’donovan
  • Function : Author
Casey Greene
  • Function : Author
Predrag Radivojac
  • Function : Author
Iddo Friedberg
  • Function : Author

Dates and versions

hal-02393202 , version 1 (04-12-2019)

Identifiers

Cite

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⟩
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