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

Naihui Zhou; Yuxiang Jiang; Timothy R. Bergquist; Alexandra J. Lee; Balint Z. Kacsoh; Alex W. Crocker; Kimberley A. Lewis; George Georghiou; Huy N. Nguyen; Md Nafiz Hamid; Larry Davis; Tunca Dogan; Volkan Atalay; Ahmet S. Rifaioglu; Alperen Dalklran; Rengul Cetin Atalay; Chengxin Zhang; Rebecca L. Hurto; Peter L. Freddolino; Yang Zhang; Prajwal Bhat; Fran Supek; José M. Fernández; Branislava Gemovic; Vladimir R. Perovic; Radoslav S. 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 A. Freitas; Magdalena Antczak; Fabio Fabris; Mark N. Wass; Jie Hou; Jianlin Cheng; Zheng Wang; Alfonso E. 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 W. Rose; Christophe Dessimoz; Vedrana Vidulin; Saso Dzeroski; Ian Sillitoe; Sayoni Das; Jonathan Gill Lees; David T. Jones; Cen Wan; Domenico Cozzetto; Rui Fa; Mateo Torres; Alex Warwick Vesztrocy; Jose Manuel Rodriguez; Michael L. Tress; Marco Frasca; Marco Notaro; Giuliano Grossi; Alessandro Petrini; Matteo Re; Giorgio Valentini; Marco Mesiti; Daniel B. Roche; Jonas Reeb; David W. 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 S. Black; Dane Jo; Erica Suh; Jonathan B. Dayton; Dallas J. Larsen; Ashton R. Omdahl; Liam J. McGuffin; Danielle A. Brackenridge; Patricia C. Babbitt; Jeffrey M. 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 Altenhoff; Asa Ben-Hur; Burkhard Rost; Steven E. Brenner; Christine A. Orengo; Constance J. Jeffery; Giovanni Bosco; Deborah A. Hogan; Maria J. Martin; Claire O'Donovan; Sean D. Mooney; Casey S. Greene; Predrag Radivojac; Iddo Friedberg

doi:10.1186/s13059-019-1835-8

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

Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalklran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang ZhangPrajwal Bhat, Fran Supek, José M. Fernández, Branislava Gemovic, Vladimir R. Perovic, Radoslav S. 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 A. Freitas, Magdalena Antczak, Fabio Fabris, Mark N. Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E. 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 W. Rose, Christophe Dessimoz, Vedrana Vidulin, Saso Dzeroski, Ian Sillitoe, Sayoni Das, Jonathan Gill Lees, David T. Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, Jose Manuel Rodriguez, Michael L. Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini, Marco Mesiti, Daniel B. Roche, Jonas Reeb, David W. 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 S. Black, Dane Jo, Erica Suh, Jonathan B. Dayton, Dallas J. Larsen, Ashton R. Omdahl, Liam J. McGuffin, Danielle A. Brackenridge, Patricia C. Babbitt, Jeffrey M. 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 Altenhoff, Asa Ben-Hur, Burkhard Rost, Steven E. Brenner, Christine A. Orengo, Constance J. Jeffery, Giovanni Bosco, Deborah A. Hogan, Maria J. Martin, Claire O'Donovan, Sean D. Mooney, Casey S. Greene, Predrag Radivojac, Iddo Friedberg

Research output: Contribution to journal › Article › peer-review

Original language	English
Article number	244
Journal	Genome Biology
Volume	20
Issue number	1
DOIs	https://doi.org/10.1186/s13059-019-1835-8
State	Published - Nov 19 2019
Externally published	Yes

ASJC Scopus Subject Areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

Keywords

Biofilm
Community challenge
Critical assessment
Long-Term memory
Protein function prediction

Access to Document

10.1186/s13059-019-1835-8

Cite this

Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., Lewis, K. A., Georghiou, G., Nguyen, H. N., Hamid, M. N., Davis, L., Dogan, T., Atalay, V., Rifaioglu, A. S., Dalklran, A., Cetin Atalay, R., Zhang, C., Hurto, R. L., Freddolino, P. L., ... Friedberg, I. (2019). The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology, 20(1), Article 244. https://doi.org/10.1186/s13059-019-1835-8

Zhou, N, Jiang, Y, Bergquist, TR, Lee, AJ, Kacsoh, BZ, Crocker, AW, Lewis, KA, Georghiou, G, Nguyen, HN, Hamid, MN, Davis, L, Dogan, T, Atalay, V, Rifaioglu, AS, Dalklran, A, Cetin Atalay, R, Zhang, C, Hurto, RL, Freddolino, PL, Zhang, Y, Bhat, P, Supek, F, Fernández, JM, Gemovic, B, Perovic, VR, Davidović, RS, Sumonja, N, Veljkovic, N, Asgari, E, Mofrad, MRK, Profiti, G, Savojardo, C, Martelli, PL, Casadio, R, Boecker, F, Schoof, H, Kahanda, I, Thurlby, N, McHardy, AC, Renaux, A, Saidi, R, Gough, J, Freitas, AA, Antczak, M, Fabris, F, Wass, MN, Hou, J, Cheng, J, Wang, Z, Romero, AE, Paccanaro, A, Yang, H, Goldberg, T, Zhao, C, Holm, L, Törönen, P, Medlar, AJ, Zosa, E, Borukhov, I, Novikov, I, Wilkins, A, Lichtarge, O, Chi, PH, Tseng, WC, Linial, M, Rose, PW, Dessimoz, C, Vidulin, V, Dzeroski, S, Sillitoe, I, Das, S, Lees, JG, Jones, DT, Wan, C, Cozzetto, D, Fa, R, Torres, M, Warwick Vesztrocy, A, Rodriguez, JM, Tress, ML, Frasca, M, Notaro, M, Grossi, G, Petrini, A, Re, M, Valentini, G, Mesiti, M, Roche, DB, Reeb, J, Ritchie, DW, Aridhi, S, Alborzi, SZ, Devignes, MD, Koo, DCE, Bonneau, R, Gligorijević, V, Barot, M, Fang, H, Toppo, S, Lavezzo, E, Falda, M, Berselli, M, Tosatto, SCE, Carraro, M, Piovesan, D, Ur Rehman, H, Mao, Q, Zhang, S, Vucetic, S, Black, GS, Jo, D, Suh, E, Dayton, JB, Larsen, DJ, Omdahl, AR, McGuffin, LJ, Brackenridge, DA, Babbitt, PC, Yunes, JM, Fontana, P, Zhang, F, Zhu, S, You, R, Zhang, Z, Dai, S, Yao, S, Tian, W, Cao, R, Chandler, C, Amezola, M, Johnson, D, Chang, JM, Liao, WH, Liu, YW, Pascarelli, S, Frank, Y, Hoehndorf, R, Kulmanov, M, Boudellioua, I, Politano, G, Di Carlo, S, Benso, A, Hakala, K, Ginter, F, Mehryary, F, Kaewphan, S, Björne, J, Moen, H, Tolvanen, MEE, Salakoski, T, Kihara, D, Jain, A, Šmuc, T, Altenhoff, A, Ben-Hur, A, Rost, B, Brenner, SE, Orengo, CA, Jeffery, CJ, Bosco, G, Hogan, DA, Martin, MJ, O'Donovan, C, Mooney, SD, Greene, CS, Radivojac, P & Friedberg, I 2019, 'The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens', Genome Biology, vol. 20, no. 1, 244. https://doi.org/10.1186/s13059-019-1835-8

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

keywords = "Biofilm, Community challenge, Critical assessment, Long-Term memory, Protein function prediction",

author = "Naihui Zhou and Yuxiang Jiang and Bergquist, {Timothy R.} and Lee, {Alexandra J.} and Kacsoh, {Balint Z.} and Crocker, {Alex W.} and Lewis, {Kimberley A.} and George Georghiou and Nguyen, {Huy N.} and Hamid, {Md Nafiz} and Larry Davis and Tunca Dogan and Volkan Atalay and Rifaioglu, {Ahmet S.} and Alperen Dalklran and {Cetin Atalay}, Rengul and Chengxin Zhang and Hurto, {Rebecca L.} and Freddolino, {Peter L.} and Yang Zhang and Prajwal Bhat and Fran Supek and Fern{\'a}ndez, {Jos{\'e} M.} and Branislava Gemovic and Perovic, {Vladimir R.} and Davidovi{\'c}, {Radoslav S.} and Neven Sumonja and Nevena Veljkovic and Ehsaneddin Asgari and Mofrad, {Mohammad R.K.} and Giuseppe Profiti and Castrense Savojardo and Martelli, {Pier Luigi} and Rita Casadio and Florian Boecker and Heiko Schoof and Indika Kahanda and Natalie Thurlby and McHardy, {Alice C.} and Alexandre Renaux and Rabie Saidi and Julian Gough and Freitas, {Alex A.} and Magdalena Antczak and Fabio Fabris and Wass, {Mark N.} and Jie Hou and Jianlin Cheng and Zheng Wang and Romero, {Alfonso E.} and Alberto Paccanaro and Haixuan Yang and Tatyana Goldberg and Chenguang Zhao and Liisa Holm and Petri T{\"o}r{\"o}nen and Medlar, {Alan J.} and Elaine Zosa and Itamar Borukhov and Ilya Novikov and Angela Wilkins and Olivier Lichtarge and Chi, {Po Han} and Tseng, {Wei Cheng} and Michal Linial and Rose, {Peter W.} and Christophe Dessimoz and Vedrana Vidulin and Saso Dzeroski and Ian Sillitoe and Sayoni Das and Lees, {Jonathan Gill} and Jones, {David T.} and Cen Wan and Domenico Cozzetto and Rui Fa and Mateo Torres and {Warwick Vesztrocy}, Alex and Rodriguez, {Jose Manuel} and Tress, {Michael L.} and Marco Frasca and Marco Notaro and Giuliano Grossi and Alessandro Petrini and Matteo Re and Giorgio Valentini and Marco Mesiti and Roche, {Daniel B.} and Jonas Reeb and Ritchie, {David W.} and Sabeur Aridhi and Alborzi, {Seyed Ziaeddin} and Devignes, {Marie Dominique} and Koo, {Da Chen Emily} and Richard Bonneau and Vladimir Gligorijevi{\'c} and Meet Barot and Hai Fang and Stefano Toppo and Enrico Lavezzo and Marco Falda and Michele Berselli and Tosatto, {Silvio C.E.} and Marco Carraro and Damiano Piovesan and {Ur Rehman}, Hafeez and Qizhong Mao and Shanshan Zhang and Slobodan Vucetic and Black, {Gage S.} and Dane Jo and Erica Suh and Dayton, {Jonathan B.} and Larsen, {Dallas J.} and Omdahl, {Ashton R.} and McGuffin, {Liam J.} and Brackenridge, {Danielle A.} and Babbitt, {Patricia C.} and Yunes, {Jeffrey M.} and Paolo Fontana and Feng Zhang and Shanfeng Zhu and Ronghui You and Zihan Zhang and Suyang Dai and Shuwei Yao and Weidong Tian and Renzhi Cao and Caleb Chandler and Miguel Amezola and Devon Johnson and Chang, {Jia Ming} and Liao, {Wen Hung} and Liu, {Yi Wei} and Stefano Pascarelli and Yotam Frank and Robert Hoehndorf and Maxat Kulmanov and Imane Boudellioua and Gianfranco Politano and {Di Carlo}, Stefano and Alfredo Benso and Kai Hakala and Filip Ginter and Farrokh Mehryary and Suwisa Kaewphan and Jari Bj{\"o}rne and Hans Moen and Tolvanen, {Martti E.E.} and Tapio Salakoski and Daisuke Kihara and Aashish Jain and Tomislav {\v S}muc and Adrian Altenhoff and Asa Ben-Hur and Burkhard Rost and Brenner, {Steven E.} and Orengo, {Christine A.} and Jeffery, {Constance J.} and Giovanni Bosco and Hogan, {Deborah A.} and Martin, {Maria J.} and Claire O'Donovan and Mooney, {Sean D.} and Greene, {Casey S.} and Predrag Radivojac and Iddo Friedberg",

note = "Publisher Copyright: {\textcopyright} 2019 The Author(s).",

year = "2019",

month = nov,

day = "19",

doi = "10.1186/s13059-019-1835-8",

language = "English",

volume = "20",

number = "1",

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TY - JOUR

T1 - The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

AU - Zhou, Naihui

AU - Jiang, Yuxiang

AU - Bergquist, Timothy R.

AU - Lee, Alexandra J.

AU - Kacsoh, Balint Z.

AU - Crocker, Alex W.

AU - Lewis, Kimberley A.

AU - Georghiou, George

AU - Nguyen, Huy N.

AU - Hamid, Md Nafiz

AU - Davis, Larry

AU - Dogan, Tunca

AU - Atalay, Volkan

AU - Rifaioglu, Ahmet S.

AU - Dalklran, Alperen

AU - Cetin Atalay, Rengul

AU - Zhang, Chengxin

AU - Hurto, Rebecca L.

AU - Freddolino, Peter L.

AU - Zhang, Yang

AU - Bhat, Prajwal

AU - Supek, Fran

AU - Fernández, José M.

AU - Gemovic, Branislava

AU - Perovic, Vladimir R.

AU - Davidović, Radoslav S.

AU - Sumonja, Neven

AU - Veljkovic, Nevena

AU - Asgari, Ehsaneddin

AU - Mofrad, Mohammad R.K.

AU - Profiti, Giuseppe

AU - Savojardo, Castrense

AU - Martelli, Pier Luigi

AU - Casadio, Rita

AU - Boecker, Florian

AU - Schoof, Heiko

AU - Kahanda, Indika

AU - Thurlby, Natalie

AU - McHardy, Alice C.

AU - Renaux, Alexandre

AU - Saidi, Rabie

AU - Gough, Julian

AU - Freitas, Alex A.

AU - Antczak, Magdalena

AU - Fabris, Fabio

AU - Wass, Mark N.

AU - Hou, Jie

AU - Cheng, Jianlin

AU - Wang, Zheng

AU - Romero, Alfonso E.

AU - Paccanaro, Alberto

AU - Yang, Haixuan

AU - Goldberg, Tatyana

AU - Zhao, Chenguang

AU - Holm, Liisa

AU - Törönen, Petri

AU - Medlar, Alan J.

AU - Zosa, Elaine

AU - Borukhov, Itamar

AU - Novikov, Ilya

AU - Wilkins, Angela

AU - Lichtarge, Olivier

AU - Chi, Po Han

AU - Tseng, Wei Cheng

AU - Linial, Michal

AU - Rose, Peter W.

AU - Dessimoz, Christophe

AU - Vidulin, Vedrana

AU - Dzeroski, Saso

AU - Sillitoe, Ian

AU - Das, Sayoni

AU - Lees, Jonathan Gill

AU - Jones, David T.

AU - Wan, Cen

AU - Cozzetto, Domenico

AU - Fa, Rui

AU - Torres, Mateo

AU - Warwick Vesztrocy, Alex

AU - Rodriguez, Jose Manuel

AU - Tress, Michael L.

AU - Frasca, Marco

AU - Notaro, Marco

AU - Grossi, Giuliano

AU - Petrini, Alessandro

AU - Re, Matteo

AU - Valentini, Giorgio

AU - Mesiti, Marco

AU - Roche, Daniel B.

AU - Reeb, Jonas

AU - Ritchie, David W.

AU - Aridhi, Sabeur

AU - Alborzi, Seyed Ziaeddin

AU - Devignes, Marie Dominique

AU - Koo, Da Chen Emily

AU - Bonneau, Richard

AU - Gligorijević, Vladimir

AU - Barot, Meet

AU - Fang, Hai

AU - Toppo, Stefano

AU - Lavezzo, Enrico

AU - Falda, Marco

AU - Berselli, Michele

AU - Tosatto, Silvio C.E.

AU - Carraro, Marco

AU - Piovesan, Damiano

AU - Ur Rehman, Hafeez

AU - Mao, Qizhong

AU - Zhang, Shanshan

AU - Vucetic, Slobodan

AU - Black, Gage S.

AU - Jo, Dane

AU - Suh, Erica

AU - Dayton, Jonathan B.

AU - Larsen, Dallas J.

AU - Omdahl, Ashton R.

AU - McGuffin, Liam J.

AU - Brackenridge, Danielle A.

AU - Babbitt, Patricia C.

AU - Yunes, Jeffrey M.

AU - Fontana, Paolo

AU - Zhang, Feng

AU - Zhu, Shanfeng

AU - You, Ronghui

AU - Zhang, Zihan

AU - Dai, Suyang

AU - Yao, Shuwei

AU - Tian, Weidong

AU - Cao, Renzhi

AU - Chandler, Caleb

AU - Amezola, Miguel

AU - Johnson, Devon

AU - Chang, Jia Ming

AU - Liao, Wen Hung

AU - Liu, Yi Wei

AU - Pascarelli, Stefano

AU - Frank, Yotam

AU - Hoehndorf, Robert

AU - Kulmanov, Maxat

AU - Boudellioua, Imane

AU - Politano, Gianfranco

AU - Di Carlo, Stefano

AU - Benso, Alfredo

AU - Hakala, Kai

AU - Ginter, Filip

AU - Mehryary, Farrokh

AU - Kaewphan, Suwisa

AU - Björne, Jari

AU - Moen, Hans

AU - Tolvanen, Martti E.E.

AU - Salakoski, Tapio

AU - Kihara, Daisuke

AU - Jain, Aashish

AU - Šmuc, Tomislav

AU - Altenhoff, Adrian

AU - Ben-Hur, Asa

AU - Rost, Burkhard

AU - Brenner, Steven E.

AU - Orengo, Christine A.

AU - Jeffery, Constance J.

AU - Bosco, Giovanni

AU - Hogan, Deborah A.

AU - Martin, Maria J.

AU - O'Donovan, Claire

AU - Mooney, Sean D.

AU - Greene, Casey S.

AU - Radivojac, Predrag

AU - Friedberg, Iddo

PY - 2019/11/19

Y1 - 2019/11/19

KW - Biofilm

KW - Community challenge

KW - Critical assessment

KW - Long-Term memory

KW - Protein function prediction

UR - http://www.scopus.com/inward/record.url?scp=85075272104&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85075272104&partnerID=8YFLogxK

U2 - 10.1186/s13059-019-1835-8

DO - 10.1186/s13059-019-1835-8

M3 - Article

C2 - 31744546

AN - SCOPUS:85075272104

SN - 1474-7596

VL - 20

JO - Genome Biology

JF - Genome Biology

IS - 1

M1 - 244

ER -

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

ASJC Scopus Subject Areas

Keywords

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