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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 Dalkıran
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 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 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 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 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
24
CAPSID - Computational Algorithms for Protein Structures and Interactions
Inria Nancy - Grand Est, LORIA - AIS - Department of Complex Systems, Artificial Intelligence & Robotics
Ehsaneddin Asgari
Author
Mohammad R.K. Mofrad
Author
Giuseppe Profiti 5
Author
Castrense Savojardo
Author
Indika Kahanda
Author
Natalie Thurlby
Author
Alice C Mchardy 7
Author
Alexandre Renaux 8 Site :
Author
Zheng Wang 12
Mail :
Author
Alfonso Romero 13
Mail :
Author
Alberto Paccanaro
Author
Haixuan Yang
Author
Mateo Torres
Author
Alex Warwick Vesztrocy
Author
Jose Manuel Rodriguez
Author
Michael Tress 20
Author
Matteo Re
Author
Giorgio Valentini 21
Mail :
Author
Marco Mesiti 22
Author
Daniel S. Roche 23
Author Employer institution : United States Naval Academy
Jonas Reeb
Author
David Ritchie
Mail :
Author IdHAL : david-ritchie ORCID : https://orcid.org/0000-0002-0906-7354
Sabeur Aridhi 24
Mail : Site :
Author IdHAL : sabeur-aridhi ORCID : https://orcid.org/0000-0002-3657-3762
Seyed Ziaeddin Alborzi 24
Mail : Site :
Author
Marie-Dominique Devignes 24
Mail :
Author
da Chen Emily Koo
Author
Richard Bonneau
Author
Vladimir Gligorijević
Author
Martti E.E. Tolvanen
Author
Tapio Salakoski 32
Mail :
Author
Daisuke Kihara 33
Author
Aashish Jain
Author
1
L2S - Laboratoire des signaux et systèmes (Plateau de Moulon 3 rue Joliot Curie 91192 GIF SUR YVETTE CEDEX - France)
- CNRS - Centre National de la Recherche Scientifique (France)
- CentraleSupélec (3, rue Joliot Curie, Plateau de Moulon, 91192 GIF-SUR-YVETTE Cedex - France)
- UP11 - Université Paris-Sud - Paris 11 (Bâtiment 300 - 91405 Orsay cedex - France)
2
European Bioinformatics Institute (France)
3
EPM - École Polytechnique de Montréal (Campus de l'Université de Montréal - 2500, chemin de Polytechnique - Montréal (Québec) H3T 1J4 - Canada)
4
Vinča Institute of Nuclear Sciences (12-14 Mike Petrovića Street, Belgrade - Serbia)
- University of Belgrade [Belgrade] (Studentski Trg 1, 11000 Belgrade - Serbia)
5
University of Bologna (Via Zamboni, 33 - 40126 Bologna - Italy)
6
MPIPZ - Max Planck Institute for Plant Breeding Research (Carl-von-Linné-Weg 10
50829 Köln - Germany)
7
European Virus Bioinformatics Center [Jena] (Leutragraben 1, 07743 Jena - Germany)
8
ULB - Université Libre de Bruxelles [Bruxelles] (Avenue Franklin Roosevelt 50 - 1050 Bruxelles - Belgium)
9
LIMOS - Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (Bât ISIMA Campus des Cézeaux BP 10025 63173 AUBIERE cedex - France)
- UBP - Université Blaise Pascal - Clermont-Ferrand 2 : UMR6158 (34, avenue Carnot - BP 185 / 63006 Clermont-Ferrand cedex - France)
- UdA - Université d'Auvergne - Clermont-Ferrand I (49, Boulevard François-Mitterrand / CS 60032 / 63001 Clermont-Ferrand Cedex 1 - France)
- Sigma CLERMONT - Sigma CLERMONT (Sigma CLERMONT Campus des Cézeaux CS 20265 63178 Aubière Cedex - France)
- CNRS - Centre National de la Recherche Scientifique : UMR6158 (France)
- Ecole Nationale Supérieure des Mines de St Etienne : UMR6158 (France)
10
Department of Computer Science (United Kingdom)
- University of Bristol [Bristol] (Senate House, Tyndall Avenue, Bristol BS8 1TH - United Kingdom)
11
Department of Computer Science [Columbia] (201 Naka Hall, Columbia, MO 65211, États-Unis - United States)
- University of Missouri [Columbia] (Columbia, MO 65211 - United States)
- University of Missouri System (Columbia Kansas City St. Louis Rolla, Missouri, U.S. - United States)
12
YSPH - Yale School of Public Health (60 College Street P.O. Box 208034 New Haven - United States)
13
Departamento de Geometría y Topología (18071;Granada - Spain)
- UGR - Universidad de Granada (Avda. del Hospicio, s/n C.P. 18010 Granada - Spain)
14
Tumor Biology Center (France)
15
Centre for Nephrology [London, UK] (Royal Free Hospital, London - United Kingdom)
- UCL - University College of London [London] (Gower Street, London WC1E 6BT - United Kingdom)
16
BCM - Baylor College of Medicine (One Baylor Plaza, Houston, Texas 77030 - United States)
- Baylor University (1301 S University Parks Dr, Waco, TX 76706, États-Unis - United States)
17
Department of Computer Science (Switzerland)
18
Department of Knowledge Technologies (Slovenia)
19
Structural and Molecular Biology Department, University College London (United Kingdom)
- QMUL - Queen Mary University of London (Mile End Road, London E1 4NS - United Kingdom)
20
CNIO - Spanish National Cancer Research Center (C/ Melchor Fernández Almagro, 3 E-28029 Madrid - Spain)
21
Dipartimento di Informatica (Sede di Crema, via Bramante, 65, I-26013 Crema (CR), Italia - Italy)
- Università degli studi di Milano [Milano] (Via Festa del Perdono 7 - 20122 Milano - Italy)
22
Dipartimento di Scienze dell'Informazione [Milano] (via Comelico 39/41, I-20135 Milano MI, Italia - Italy)
- Università degli studi di Milano [Milano] (Via Festa del Perdono 7 - 20122 Milano - Italy)
23
United States Naval Academy (Annapolis, Maryland - United States)
24
CAPSID - Computational Algorithms for Protein Structures and Interactions (France)
- Inria Nancy - Grand Est (615 rue du Jardin Botanique 54600 Villers-lès-Nancy - France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- LORIA - AIS - Department of Complex Systems, Artificial Intelligence & Robotics (France)
- LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications (Campus Scientifique BP 239 54506 Vandoeuvre-lès-Nancy Cedex - France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- UL - Université de Lorraine (34 cours Léopold - CS 25233 - 54052 Nancy cedex - France)
- CNRS - Centre National de la Recherche Scientifique : UMR7503 (France)
- LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications (Campus Scientifique BP 239 54506 Vandoeuvre-lès-Nancy Cedex - France)
25
Department of Molecular Medicine (Via 8 Febbraio 1848, 2, 35122 Padova - Italy)
- Universita degli Studi di Padova (Via 8 Febbraio 2, 35122 Padova - Italy)
26
Universita degli Studi di Padova (Via 8 Febbraio 2, 35122 Padova - Italy)
27
CRG - Centro de Regulación Genómica (Barcelone, Espagne - Spain)
- Universitat Pompeu Fabra [Barcelona] (Plaça de la Mercè, 10-12 08002 Barcelona - Spain)
28
Physics Department (National Tsing Hua University, Hsinchu 300 - Taiwan)
- NTHU - National Tsing Hua University [Hsinchu] (No. 101, Section 2, Guangfu Road, East District, Hsinchu City, Taïwan 300 - Taiwan)
29
DAUIN - Dipartimento di Automatica e Informatica [Torino] (Corso Duca degli Abruzzi, 24 10129 Torino - Italy)
- Polito - Politecnico di Torino [Torino] (Politecnico di Torino - Corso Duca degli Abruzzi, 24 10129 Torino - Italy)
30
Polito - Politecnico di Torino [Torino] (Politecnico di Torino - Corso Duca degli Abruzzi, 24 10129 Torino - Italy)
31
University of Turku (20014 Turun yliopisto, Finland - Finland)
32
Bioinformatics Laboratory (Datacity, 5th floor Lemminkäisenkatu 14 A Turku, Finland - Finland)
- University of Turku (20014 Turun yliopisto, Finland - Finland)
- Turku Center for Computer Science (Finland)
33
TTIC - Toyota Technological Institute at Chicago [Chicago] (6045 S. Kenwood Ave.
Chicago, Illinois 60637 - United States)
34
Swiss Institute of Bioinformatics (SIB) (Lausanne - Switzerland)
35
Department of Computer Science [Colorado State University] (United States)
- CSU - Colorado State University [Fort Collins] (Colorado State University, Fort Collins, Colorado 80523 USA - United States)
36
CPIB - Centre for Plant Integrative Biology [Nothingham] (Loughborough LE12 5RD - United Kingdom)
- UON - University of Nottingham, UK (University of Nottingham University Park Nottingham NG7 2RD - United Kingdom)
Complete list of metadatas
https://hal.inria.fr/hal-02393202
Contributor : Sabeur Aridhi <>
Submitted on : Wednesday, December 4, 2019 - 11:53:54 AM
Last modification on : Friday, March 6, 2020 - 3:29:24 PM
Contributor : Sabeur Aridhi <>
Submitted on : Wednesday, December 4, 2019 - 11:53:54 AM
Last modification on : Friday, March 6, 2020 - 3:29:24 PM
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Identifiers
- HAL Id : hal-02393202, version 1
- DOI : 10.1186/s13059-019-1835-8
Collections
LIMOS | UNIV-LORRAINE | SIGMA-CLERMONT | LORIA | LORIA-AIS | CENTRALESUPELEC | INRIA | L2S | SUP_LSS | CNRS | PRES_CLERMONT | UNIV-PARIS-SACLAY
Citation
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, BioMed Central, 2019, 20 (1), ⟨10.1186/s13059-019-1835-8⟩. ⟨hal-02393202⟩
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