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; Md Nafiz Hamid; Larry Davis; Tunca Dogan; Volkan Atalay; Ahmet Rifaioglu; Alperen Dalkiran; Rengul Cetin Atalay; Chengxin Zhang; Rebecca Hurto; Peter Freddolino; Yang Zhang; Prajwal Bhat; Fran Supek; Jose Fernandez; Branislava Gemovic; Vladimir Perovic; Radoslav Davidović; Neven Sumonja; Nevena Veljkovic; Ehsaneddin Asgari; Mohammad R.K. Mofrad; Giuseppe Profiti; Castrense Savojardo; Pier Luigi Martelli; Rita Casadio; Florian Boecker; Heiko Schoof; Indika Kahanda; Natalie Thurlby; Alice C Mchardy; Alexandre Renaux; Rabie Saidi; Julian Gough; Alex Freitas; Magdalena Antczak; Fabio Fabris; Mark Wass; Jie Hou; Jianlin Cheng; Zheng Wang; Alfonso Romero; Alberto Paccanaro; Haixuan Yang; Tatyana Goldberg; Chenguang Zhao; Liisa Holm; Petri Törönen; Alan J. Medlar; Elaine Zosa; Itamar Borukhov; Ilya Novikov; Angela Wilkins; Olivier Lichtarge; Po-Han Chi; Wei-Cheng Tseng; Michal Linial; Peter Rose; Christophe Dessimoz; Vedrana Vidulin; Saso Dzeroski; Ian Sillitoe; Sayoni Das; Jonathan Gill Lees; David Jones; Cen Wan; Domenico Cozzetto; Rui Fa; Mateo Torres; Alex Warwick Vesztrocy; Jose Manuel Rodriguez; Michael Tress; Marco Frasca; Marco Notaro; Giuliano Grossi; Alessandro Petrini; Matteo Re; Giorgio Valentini; Marco Mesiti; Daniel S. Roche; Jonas Reeb; David Ritchie; Sabeur Aridhi; Seyed Ziaeddin Alborzi; Marie-Dominique Devignes; da Chen Emily Koo; Richard Bonneau; Vladimir Gligorijević; Meet Barot; Hai Fang; Stefano Toppo; Enrico Lavezzo; Marco Falda; Michele Berselli; Silvio C.E. Tosatto; Marco Carraro; Damiano Piovesan; 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; Wen-Hung Liao; Yi-Wei Liu; Stefano Pascarelli; Yotam Frank; Robert Hoehndorf; Maxat Kulmanov; Imane Boudellioua; Gianfranco Politano; Stefano Di Carlo; Alfredo Benso; Kai Hakala; Filip Ginter; Farrokh Mehryary; Suwisa Kaewphan; Jari Björne; Hans Moen; Martti E.E. Tolvanen; Tapio Salakoski; Daisuke Kihara; Aashish Jain; Tomislav Šmuc; Adrian M Altenhoff; Asa Ben-Hur; Burkhard Rost; Steven Brenner; Christine Orengo; Constance Jeffery; Giovanni Bosco; Deborah Hogan; Maria Martin; Claire O’donovan; Sean Mooney; Casey Greene; Predrag Radivojac; Iddo Friedberg

doi:10.1186/s13059-019-1835-8

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

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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

Iowa State University

Md Nafiz Hamid

Function : Author

Larry Davis

Function : Author

Tunca Dogan

Function : Author

European Bioinformatics Institute

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

Function : Author
PersonId : 757354
ORCID : 0000-0003-4102-2671

Prajwal Bhat

Function : Author

Fran Supek

Function : Author

Jose Fernandez

Function : Author

École Polytechnique de Montréal

Branislava Gemovic

Function : Author

Vladimir Perovic

Function : Author

Radoslav Davidović

Function : Author
PersonId : 792609
ORCID : 0000-0002-6097-6203

Vinča Institute of Nuclear Sciences

Neven Sumonja

Function : Author

Nevena Veljkovic

Function : Author
PersonId : 798803
ORCID : 0000-0001-6562-5800

Ehsaneddin Asgari

Function : Author

Mohammad R.K. Mofrad

Function : Author

Giuseppe Profiti

Function : Author

University of Bologna/Università di Bologna

Castrense Savojardo

Function : Author

Pier Luigi Martelli

Function : Author

Rita Casadio

Function : Author

University of Bologna/Università di Bologna

Florian Boecker

Function : Author

Heiko Schoof

Function : Author

Max Planck Institute for Plant Breeding Research

Indika Kahanda

Function : Author

Natalie Thurlby

Function : Author

Alice C Mchardy

Function : Author

European Virus Bioinformatics Center [Jena]

Alexandre Renaux

Function : Author

Université libre de Bruxelles

Rabie Saidi

Function : Author
PersonId : 867520

Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes

Julian Gough

Function : Author

Department of Computer Science

Alex Freitas

Function : Author

Magdalena Antczak

Function : Author

Fabio Fabris

Function : Author

Mark Wass

Function : Author

Jie Hou

Function : Author

Jianlin Cheng

Function : Author

Department of Computer Science [Columbia]

Zheng Wang

Function : Author
PersonId : 922364

Yale School of Public Health

Alfonso Romero

Function : Author
PersonId : 928059

Departamento de Geometría y Topología

Alberto Paccanaro

Function : Author

Haixuan Yang

Function : Author

Tatyana Goldberg

Function : Author

Tumor Biology Center

Chenguang Zhao

Function : Author

Liisa Holm

Function : Author

Petri Törönen

Function : Author

Alan J. Medlar

Function : Author

Centre for Nephrology [London, UK]

Elaine Zosa

Function : Author
PersonId : 798804
ORCID : 0000-0003-2482-0663

Itamar Borukhov

Function : Author

Ilya Novikov

Function : Author

Angela Wilkins

Function : Author

Olivier Lichtarge

Function : Author

Baylor College of Medicine

Po-Han Chi

Function : Author

Wei-Cheng Tseng

Function : Author

Michal Linial

Function : Author

Peter Rose

Function : Author

Christophe Dessimoz

Function : Author

Department of Computer Science

Vedrana Vidulin

Function : Author

Saso Dzeroski

Function : Author

Department of Knowledge Technologies

Ian Sillitoe

Function : Author

University College of London [London]

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

Michael Tress

Function : Author

Spanish National Cancer Research Center

Marco Frasca

Function : Author

Marco Notaro

Function : Author

Giuliano Grossi

Function : Author

Alessandro Petrini

Function : Author
PersonId : 1054038

Dipartimento di Informatica

Matteo Re

Function : Author

Giorgio Valentini

Function : Author
PersonId : 1008215

Dipartimento di Informatica

Marco Mesiti

Function : Author

Dipartimento di Scienze dell'Informazione [Milano]

Daniel S. Roche

Function : Author

United States Naval Academy

Jonas Reeb

Function : Author

David Ritchie

Function : Author
PersonId : 1609
IdHAL : david-ritchie
ORCID : 0000-0002-0906-7354
IdRef : 172270383

Sabeur Aridhi

Function : Author
PersonId : 16269
IdHAL : sabeur-aridhi
ORCID : 0000-0002-3657-3762
IdRef : 17650513X

Computational Algorithms for Protein Structures and Interactions

Seyed Ziaeddin Alborzi

Function : Author
PersonId : 971733

Computational Algorithms for Protein Structures and Interactions

Marie-Dominique Devignes

Function : Author
PersonId : 742369
IdHAL : mddevignes
ORCID : 0000-0002-0399-8713
IdRef : 134215001

Computational Algorithms for Protein Structures and Interactions

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

Enrico Lavezzo

Function : Author

Department of Molecular Medicine

Marco Falda

Function : Author

Michele Berselli

Function : Author

Silvio C.E. Tosatto

Function : Author

Università degli Studi di Padova = University of Padua

Marco Carraro

Function : Author

Damiano Piovesan

Function : Author
PersonId : 791665
ORCID : 0000-0001-8210-2390

Università degli Studi di Padova = University of Padua

Hafeez Ur Rehman

Function : Author

Qizhong Mao

Function : Author

Shanshan Zhang

Function : Author
PersonId : 798805
ORCID : 0000-0002-9033-3786

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

Jia-Ming Chang

Function : Author

Centro de Regulación Genómica

Wen-Hung Liao

Function : Author

Yi-Wei Liu

Function : Author

Physics Department

Stefano Pascarelli

Function : Author

Yotam Frank

Function : Author

Robert Hoehndorf

Function : Author

Maxat Kulmanov

Function : Author

Imane Boudellioua

Function : Author

Gianfranco Politano

Function : Author

Stefano Di Carlo

Function : Author

Dipartimento di Automatica e Informatica [Torino]

Alfredo Benso

Function : Author

Politecnico di Torino = Polytechnic of Turin

Kai Hakala

Function : Author

Filip Ginter

Function : Author

University of Turku

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

Bioinformatics Laboratory

Daisuke Kihara

Function : Author
PersonId : 765070
ORCID : 0000-0003-4091-6614
IdRef : 155148435

Toyota Technological Institute at Chicago [Chicago]

Aashish Jain

Function : Author

Tomislav Šmuc

Function : Author

Adrian M Altenhoff

Function : Author

Swiss Institute of Bioinformatics [Lausanne]

Asa Ben-Hur

Function : Author

Department of Computer Science [Colorado State University]

Burkhard Rost

Function : Author

Tumor Biology Center

Steven Brenner

Function : Author

Christine Orengo

Function : Author

University College of London [London]

Constance Jeffery

Function : Author

Giovanni Bosco

Function : Author

Deborah Hogan

Function : Author

Maria Martin

Function : Author

Claire O’donovan

Function : Author

Sean Mooney

Function : Author

Centre for Plant Integrative Biology [Nothingham]

Casey Greene

Function : Author

Predrag Radivojac

Function : Author

Iddo Friedberg

Function : Author

Domains

Computer Science [cs] Databases [cs.DB] Computer Science [cs] Bioinformatics [q-bio.QM] Computer Science [cs] Artificial Intelligence [cs.AI] Computer Science [cs] Machine Learning [cs.LG] Computer Science [cs] Distributed, Parallel, and Cluster Computing [cs.DC]

Sabeur Aridhi : Connect in order to contact the contributor

https://hal.inria.fr/hal-02393202

Submitted on : Wednesday, December 4, 2019-11:53:54 AM

Last modification on : Tuesday, January 10, 2023-10:30:11 AM

Dates and versions

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

Identifiers

HAL Id : hal-02393202 , version 1
DOI : 10.1186/s13059-019-1835-8
PUBMEDCENTRAL : PMC6864930

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

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