A large-scale evaluation of computational protein function prediction

Predrag Radivojac, Wyatt T. Clark, Tal Ronnen Oron, Alexandra M. Schnoes, Tobias Wittkop, Artem Sokolov, Kiley Graim, Christopher Funk, Karin Verspoor, Asa Ben-Hur, Gaurav Pandey, Jeffrey M. Yunes, Ameet S. Talwalkar, Susanna Repo, Michael L. Souza, Damiano Piovesan, Rita Casadio, Zheng Wang, Jianlin Cheng, Hai Fang & 82 others Julian Goughl, Patrik Koskinen, Petri Toronen, Jussi Nokso-Koivisto, Liisa Holm, Domenico Cozzetto, Daniel W. A. Buchan, Kevin Bryson, David T. Jones, Bhakti Limaye, Harshal Inamdar, Avik Datta, Sunitha K. Manjari, Rajendra Joshi, Meghana Chitale, Daisuke Kihara, Andreas M. Lisewski, Serkan Erdin, Eric Venner, Olivier Lichtarge, Robert Rentzsch, Haixuan Yang, Alfonso E. Romero, Prajwal Bhat, Alberto Paccanaro, Tobias Hamp, Rebecca Kassner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, Ariane Boehm, Tatjana Braun, Maximilian Hecht, Mark Heron, Peter Hoenigschmid, Thomas A. Hopf, Stefanie Kaufmann, Michael Kiening, Denis Krompass, Cedric Landerer, Yannick Mahlich, Manfred Roos, Jari Bjorne, Tapio Salakoski, Andrew Wong, Hagit Shatkay, Fanny Gatzmann, Ingolf Sommer, Mark N. Wass, Michael J. E. Sternberg, Nives Skunca, Fran Supek, Matko Bosnjak, Pance Panov, Saso Dzeroski, Tomislav Smuc, Yiannis A. I. Kourmpetis, Aalt D. J. van Dijk, Cajo J. F. ter Braak, Yuanpeng Zhou, Qingtian Gong, Xinran Dong, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Barbara Di Camillo, Stefano Toppo, Liang Lan, Nemanja Djuric, Yuhong Guo, Slobodan Vucetic, Amos Bairoch, Michal Linial, Patricia C. Babbitt, Steven E. Brenner, Christine Orengo, Burkhard Rost, Sean D. Mooney, Iddo Friedberg

Research output: Contribution to journalArticleScientificpeer-review

Original languageEnglish
JournalNature methods
Volume10
Issue number3
Pages (from-to)221-227
Number of pages7
ISSN1548-7091
DOIs
Publication statusPublished - Mar 2013
MoE publication typeA1 Journal article-refereed

Fields of Science

  • GENE ONTOLOGY
  • SEQUENCE
  • RNA
  • ANNOTATION
  • DATABASE
  • NETWORK
  • GENOMES
  • GOLD
  • 1184 Genetics, developmental biology, physiology

Cite this

Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., ... Friedberg, I. (2013). A large-scale evaluation of computational protein function prediction. Nature methods, 10(3), 221-227. https://doi.org/10.1038/NMETH.2340
Radivojac, Predrag ; Clark, Wyatt T. ; Oron, Tal Ronnen ; Schnoes, Alexandra M. ; Wittkop, Tobias ; Sokolov, Artem ; Graim, Kiley ; Funk, Christopher ; Verspoor, Karin ; Ben-Hur, Asa ; Pandey, Gaurav ; Yunes, Jeffrey M. ; Talwalkar, Ameet S. ; Repo, Susanna ; Souza, Michael L. ; Piovesan, Damiano ; Casadio, Rita ; Wang, Zheng ; Cheng, Jianlin ; Fang, Hai ; Goughl, Julian ; Koskinen, Patrik ; Toronen, Petri ; Nokso-Koivisto, Jussi ; Holm, Liisa ; Cozzetto, Domenico ; Buchan, Daniel W. A. ; Bryson, Kevin ; Jones, David T. ; Limaye, Bhakti ; Inamdar, Harshal ; Datta, Avik ; Manjari, Sunitha K. ; Joshi, Rajendra ; Chitale, Meghana ; Kihara, Daisuke ; Lisewski, Andreas M. ; Erdin, Serkan ; Venner, Eric ; Lichtarge, Olivier ; Rentzsch, Robert ; Yang, Haixuan ; Romero, Alfonso E. ; Bhat, Prajwal ; Paccanaro, Alberto ; Hamp, Tobias ; Kassner, Rebecca ; Seemayer, Stefan ; Vicedo, Esmeralda ; Schaefer, Christian ; Achten, Dominik ; Auer, Florian ; Boehm, Ariane ; Braun, Tatjana ; Hecht, Maximilian ; Heron, Mark ; Hoenigschmid, Peter ; Hopf, Thomas A. ; Kaufmann, Stefanie ; Kiening, Michael ; Krompass, Denis ; Landerer, Cedric ; Mahlich, Yannick ; Roos, Manfred ; Bjorne, Jari ; Salakoski, Tapio ; Wong, Andrew ; Shatkay, Hagit ; Gatzmann, Fanny ; Sommer, Ingolf ; Wass, Mark N. ; Sternberg, Michael J. E. ; Skunca, Nives ; Supek, Fran ; Bosnjak, Matko ; Panov, Pance ; Dzeroski, Saso ; Smuc, Tomislav ; Kourmpetis, Yiannis A. I. ; van Dijk, Aalt D. J. ; ter Braak, Cajo J. F. ; Zhou, Yuanpeng ; Gong, Qingtian ; Dong, Xinran ; Tian, Weidong ; Falda, Marco ; Fontana, Paolo ; Lavezzo, Enrico ; Di Camillo, Barbara ; Toppo, Stefano ; Lan, Liang ; Djuric, Nemanja ; Guo, Yuhong ; Vucetic, Slobodan ; Bairoch, Amos ; Linial, Michal ; Babbitt, Patricia C. ; Brenner, Steven E. ; Orengo, Christine ; Rost, Burkhard ; Mooney, Sean D. ; Friedberg, Iddo. / A large-scale evaluation of computational protein function prediction. In: Nature methods. 2013 ; Vol. 10, No. 3. pp. 221-227.
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title = "A large-scale evaluation of computational protein function prediction",
keywords = "GENE ONTOLOGY, SEQUENCE, RNA, ANNOTATION, DATABASE, NETWORK, GENOMES, GOLD, 1184 Genetics, developmental biology, physiology",
author = "Predrag Radivojac and Clark, {Wyatt T.} and Oron, {Tal Ronnen} and Schnoes, {Alexandra M.} and Tobias Wittkop and Artem Sokolov and Kiley Graim and Christopher Funk and Karin Verspoor and Asa Ben-Hur and Gaurav Pandey and Yunes, {Jeffrey M.} and Talwalkar, {Ameet S.} and Susanna Repo and Souza, {Michael L.} and Damiano Piovesan and Rita Casadio and Zheng Wang and Jianlin Cheng and Hai Fang and Julian Goughl and Patrik Koskinen and Petri Toronen and Jussi Nokso-Koivisto and Liisa Holm and Domenico Cozzetto and Buchan, {Daniel W. A.} and Kevin Bryson and Jones, {David T.} and Bhakti Limaye and Harshal Inamdar and Avik Datta and Manjari, {Sunitha K.} and Rajendra Joshi and Meghana Chitale and Daisuke Kihara and Lisewski, {Andreas M.} and Serkan Erdin and Eric Venner and Olivier Lichtarge and Robert Rentzsch and Haixuan Yang and Romero, {Alfonso E.} and Prajwal Bhat and Alberto Paccanaro and Tobias Hamp and Rebecca Kassner and Stefan Seemayer and Esmeralda Vicedo and Christian Schaefer and Dominik Achten and Florian Auer and Ariane Boehm and Tatjana Braun and Maximilian Hecht and Mark Heron and Peter Hoenigschmid and Hopf, {Thomas A.} and Stefanie Kaufmann and Michael Kiening and Denis Krompass and Cedric Landerer and Yannick Mahlich and Manfred Roos and Jari Bjorne and Tapio Salakoski and Andrew Wong and Hagit Shatkay and Fanny Gatzmann and Ingolf Sommer and Wass, {Mark N.} and Sternberg, {Michael J. E.} and Nives Skunca and Fran Supek and Matko Bosnjak and Pance Panov and Saso Dzeroski and Tomislav Smuc and Kourmpetis, {Yiannis A. I.} and {van Dijk}, {Aalt D. J.} and {ter Braak}, {Cajo J. F.} and Yuanpeng Zhou and Qingtian Gong and Xinran Dong and Weidong Tian and Marco Falda and Paolo Fontana and Enrico Lavezzo and {Di Camillo}, Barbara and Stefano Toppo and Liang Lan and Nemanja Djuric and Yuhong Guo and Slobodan Vucetic and Amos Bairoch and Michal Linial and Babbitt, {Patricia C.} and Brenner, {Steven E.} and Christine Orengo and Burkhard Rost and Mooney, {Sean D.} and Iddo Friedberg",
year = "2013",
month = "3",
doi = "10.1038/NMETH.2340",
language = "English",
volume = "10",
pages = "221--227",
journal = "Nature methods",
issn = "1548-7091",
publisher = "Macmillan Publishers",
number = "3",

}

Radivojac, P, Clark, WT, Oron, TR, Schnoes, AM, Wittkop, T, Sokolov, A, Graim, K, Funk, C, Verspoor, K, Ben-Hur, A, Pandey, G, Yunes, JM, Talwalkar, AS, Repo, S, Souza, ML, Piovesan, D, Casadio, R, Wang, Z, Cheng, J, Fang, H, Goughl, J, Koskinen, P, Toronen, P, Nokso-Koivisto, J, Holm, L, Cozzetto, D, Buchan, DWA, Bryson, K, Jones, DT, Limaye, B, Inamdar, H, Datta, A, Manjari, SK, Joshi, R, Chitale, M, Kihara, D, Lisewski, AM, Erdin, S, Venner, E, Lichtarge, O, Rentzsch, R, Yang, H, Romero, AE, Bhat, P, Paccanaro, A, Hamp, T, Kassner, R, Seemayer, S, Vicedo, E, Schaefer, C, Achten, D, Auer, F, Boehm, A, Braun, T, Hecht, M, Heron, M, Hoenigschmid, P, Hopf, TA, Kaufmann, S, Kiening, M, Krompass, D, Landerer, C, Mahlich, Y, Roos, M, Bjorne, J, Salakoski, T, Wong, A, Shatkay, H, Gatzmann, F, Sommer, I, Wass, MN, Sternberg, MJE, Skunca, N, Supek, F, Bosnjak, M, Panov, P, Dzeroski, S, Smuc, T, Kourmpetis, YAI, van Dijk, ADJ, ter Braak, CJF, Zhou, Y, Gong, Q, Dong, X, Tian, W, Falda, M, Fontana, P, Lavezzo, E, Di Camillo, B, Toppo, S, Lan, L, Djuric, N, Guo, Y, Vucetic, S, Bairoch, A, Linial, M, Babbitt, PC, Brenner, SE, Orengo, C, Rost, B, Mooney, SD & Friedberg, I 2013, 'A large-scale evaluation of computational protein function prediction', Nature methods, vol. 10, no. 3, pp. 221-227. https://doi.org/10.1038/NMETH.2340

A large-scale evaluation of computational protein function prediction. / Radivojac, Predrag; Clark, Wyatt T.; Oron, Tal Ronnen; Schnoes, Alexandra M.; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M.; Talwalkar, Ameet S.; Repo, Susanna; Souza, Michael L.; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Goughl, Julian; Koskinen, Patrik; Toronen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W. A.; Bryson, Kevin; Jones, David T.; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K.; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M.; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E.; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kassner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Boehm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hoenigschmid, Peter; Hopf, Thomas A.; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Bjorne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N.; Sternberg, Michael J. E.; Skunca, Nives; Supek, Fran; Bosnjak, Matko; Panov, Pance; Dzeroski, Saso; Smuc, Tomislav; Kourmpetis, Yiannis A. I.; van Dijk, Aalt D. J.; ter Braak, Cajo J. F.; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C.; Brenner, Steven E.; Orengo, Christine; Rost, Burkhard; Mooney, Sean D.; Friedberg, Iddo.

In: Nature methods, Vol. 10, No. 3, 03.2013, p. 221-227.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - A large-scale evaluation of computational protein function prediction

AU - Radivojac, Predrag

AU - Clark, Wyatt T.

AU - Oron, Tal Ronnen

AU - Schnoes, Alexandra M.

AU - Wittkop, Tobias

AU - Sokolov, Artem

AU - Graim, Kiley

AU - Funk, Christopher

AU - Verspoor, Karin

AU - Ben-Hur, Asa

AU - Pandey, Gaurav

AU - Yunes, Jeffrey M.

AU - Talwalkar, Ameet S.

AU - Repo, Susanna

AU - Souza, Michael L.

AU - Piovesan, Damiano

AU - Casadio, Rita

AU - Wang, Zheng

AU - Cheng, Jianlin

AU - Fang, Hai

AU - Goughl, Julian

AU - Koskinen, Patrik

AU - Toronen, Petri

AU - Nokso-Koivisto, Jussi

AU - Holm, Liisa

AU - Cozzetto, Domenico

AU - Buchan, Daniel W. A.

AU - Bryson, Kevin

AU - Jones, David T.

AU - Limaye, Bhakti

AU - Inamdar, Harshal

AU - Datta, Avik

AU - Manjari, Sunitha K.

AU - Joshi, Rajendra

AU - Chitale, Meghana

AU - Kihara, Daisuke

AU - Lisewski, Andreas M.

AU - Erdin, Serkan

AU - Venner, Eric

AU - Lichtarge, Olivier

AU - Rentzsch, Robert

AU - Yang, Haixuan

AU - Romero, Alfonso E.

AU - Bhat, Prajwal

AU - Paccanaro, Alberto

AU - Hamp, Tobias

AU - Kassner, Rebecca

AU - Seemayer, Stefan

AU - Vicedo, Esmeralda

AU - Schaefer, Christian

AU - Achten, Dominik

AU - Auer, Florian

AU - Boehm, Ariane

AU - Braun, Tatjana

AU - Hecht, Maximilian

AU - Heron, Mark

AU - Hoenigschmid, Peter

AU - Hopf, Thomas A.

AU - Kaufmann, Stefanie

AU - Kiening, Michael

AU - Krompass, Denis

AU - Landerer, Cedric

AU - Mahlich, Yannick

AU - Roos, Manfred

AU - Bjorne, Jari

AU - Salakoski, Tapio

AU - Wong, Andrew

AU - Shatkay, Hagit

AU - Gatzmann, Fanny

AU - Sommer, Ingolf

AU - Wass, Mark N.

AU - Sternberg, Michael J. E.

AU - Skunca, Nives

AU - Supek, Fran

AU - Bosnjak, Matko

AU - Panov, Pance

AU - Dzeroski, Saso

AU - Smuc, Tomislav

AU - Kourmpetis, Yiannis A. I.

AU - van Dijk, Aalt D. J.

AU - ter Braak, Cajo J. F.

AU - Zhou, Yuanpeng

AU - Gong, Qingtian

AU - Dong, Xinran

AU - Tian, Weidong

AU - Falda, Marco

AU - Fontana, Paolo

AU - Lavezzo, Enrico

AU - Di Camillo, Barbara

AU - Toppo, Stefano

AU - Lan, Liang

AU - Djuric, Nemanja

AU - Guo, Yuhong

AU - Vucetic, Slobodan

AU - Bairoch, Amos

AU - Linial, Michal

AU - Babbitt, Patricia C.

AU - Brenner, Steven E.

AU - Orengo, Christine

AU - Rost, Burkhard

AU - Mooney, Sean D.

AU - Friedberg, Iddo

PY - 2013/3

Y1 - 2013/3

KW - GENE ONTOLOGY

KW - SEQUENCE

KW - RNA

KW - ANNOTATION

KW - DATABASE

KW - NETWORK

KW - GENOMES

KW - GOLD

KW - 1184 Genetics, developmental biology, physiology

U2 - 10.1038/NMETH.2340

DO - 10.1038/NMETH.2340

M3 - Article

VL - 10

SP - 221

EP - 227

JO - Nature methods

JF - Nature methods

SN - 1548-7091

IS - 3

ER -

Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A et al. A large-scale evaluation of computational protein function prediction. Nature methods. 2013 Mar;10(3):221-227. https://doi.org/10.1038/NMETH.2340