An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Yuxiang Jiang; Tal Ronnen Oron; Wyatt T. Clark; Asma R. Bankapur; Daniel D'Andrea; Rosalba Lepore; Christopher S. Funk; Indika Kahanda; Karin M. Verspoor; Asa Ben-Hur; Da Chen Emily Koo; Duncan Penfold-Brown; Dennis Shasha; Noah Youngs; Richard Bonneau; Alexandra Lin; Sayed M.E. Sahraeian; Pier Luigi Martelli; Giuseppe Profiti; Rita Casadio; Renzhi Cao; Zhaolong Zhong; Jianlin Cheng; Adrian Altenhoff; Nives Skunca; Christophe Dessimoz; Tunca Dogan; Kai Hakala; Suwisa Kaewphan; Farrokh Mehryary; Tapio Salakoski; Filip Ginter; Hai Fang; Ben Smithers; Matt Oates; Julian Gough; Petri Törönen; Patrik Koskinen; Liisa Holm; Ching Tai Chen; Wen Lian Hsu; Kevin Bryson; Domenico Cozzetto; Federico Minneci; David T. Jones; Samuel Chapman; Dukka Bkc; Ishita K. Khan; Daisuke Kihara; Dan Ofer; Nadav Rappoport; Amos Stern; Elena Cibrian-Uhalte; Paul Denny; Rebecca E. Foulger; Reija Hieta; Duncan Legge; Ruth C. Lovering; Michele Magrane; Anna N. Melidoni; Prudence Mutowo-Meullenet; Klemens Pichler; Aleksandra Shypitsyna; Biao Li; Pooya Zakeri; Sarah ElShal; Léon Charles Tranchevent; Sayoni Das; Natalie L. Dawson; David Lee; Jonathan G. Lees; Ian Sillitoe; Prajwal Bhat; Tamás Nepusz; Alfonso E. Romero; Rajkumar Sasidharan; Haixuan Yang; Alberto Paccanaro; Jesse Gillis; Adriana E. Sedeño-Cortés; Paul Pavlidis; Shou Feng; Juan M. Cejuela; Tatyana Goldberg; Tobias Hamp; Lothar Richter; Asaf Salamov; Toni Gabaldon; Marina Marcet-Houben; Fran Supek; Qingtian Gong; Wei Ning; Yuanpeng Zhou; Weidong Tian; Marco Falda; Paolo Fontana; Enrico Lavezzo; Stefano Toppo; Carlo Ferrari; Manuel Giollo; Damiano Piovesan; Silvio C.E. Tosatto; Angela del Pozo; José M. Fernández; Paolo Maietta; Alfonso Valencia; Michael L. Tress; Alfredo Benso; Stefano Di Carlo; Gianfranco Politano; Alessandro Savino; Hafeez Ur Rehman; Matteo Re; Marco Mesiti; Giorgio Valentini; Joachim W. Bargsten; Aalt D.J. van Dijk; Branislava Gemovic; Sanja Glisic; Vladmir Perovic; Veljko Veljkovic; Nevena Veljkovic; Danillo C. Almeida-e-Silva; Ricardo Z.N. Vencio; Malvika Sharan; Jörg Vogel; Lakesh Kansakar; Shanshan Zhang; Slobodan Vucetic; Zheng Wang; Michael J.E. Sternberg; Mark N. Wass; Rachael P. Huntley; Maria J. Martin; Claire O'Donovan; Peter N. Robinson; Yves Moreau; Anna Tramontano; Patricia C. Babbitt; Steven E. Brenner; Michal Linial; Christine A. Orengo; Burkhard Rost; Casey S. Greene; Sean D. Mooney; Iddo Friedberg; Predrag Radivojac

doi:10.1186/s13059-016-1037-6

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Yuxiang Jiang, Tal Ronnen Oron, Wyatt T. Clark, Asma R. Bankapur, Daniel D'Andrea, Rosalba Lepore, Christopher S. Funk, Indika Kahanda, Karin M. Verspoor, Asa Ben-Hur, Da Chen Emily Koo, Duncan Penfold-Brown, Dennis Shasha, Noah Youngs, Richard Bonneau, Alexandra Lin, Sayed M.E. Sahraeian, Pier Luigi Martelli, Giuseppe Profiti, Rita CasadioRenzhi Cao, Zhaolong Zhong, Jianlin Cheng, Adrian Altenhoff, Nives Skunca, Christophe Dessimoz, Tunca Dogan, Kai Hakala, Suwisa Kaewphan, Farrokh Mehryary, Tapio Salakoski, Filip Ginter, Hai Fang, Ben Smithers, Matt Oates, Julian Gough, Petri Törönen, Patrik Koskinen, Liisa Holm, Ching Tai Chen, Wen Lian Hsu, Kevin Bryson, Domenico Cozzetto, Federico Minneci, David T. Jones, Samuel Chapman, Dukka Bkc, Ishita K. Khan, Daisuke Kihara, Dan Ofer, Nadav Rappoport, Amos Stern, Elena Cibrian-Uhalte, Paul Denny, Rebecca E. Foulger, Reija Hieta, Duncan Legge, Ruth C. Lovering, Michele Magrane, Anna N. Melidoni, Prudence Mutowo-Meullenet, Klemens Pichler, Aleksandra Shypitsyna, Biao Li, Pooya Zakeri, Sarah ElShal, Léon Charles Tranchevent, Sayoni Das, Natalie L. Dawson, David Lee, Jonathan G. Lees, Ian Sillitoe, Prajwal Bhat, Tamás Nepusz, Alfonso E. Romero, Rajkumar Sasidharan, Haixuan Yang, Alberto Paccanaro, Jesse Gillis, Adriana E. Sedeño-Cortés, Paul Pavlidis, Shou Feng, Juan M. Cejuela, Tatyana Goldberg, Tobias Hamp, Lothar Richter, Asaf Salamov, Toni Gabaldon, Marina Marcet-Houben, Fran Supek, Qingtian Gong, Wei Ning, Yuanpeng Zhou, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Stefano Toppo, Carlo Ferrari, Manuel Giollo, Damiano Piovesan, Silvio C.E. Tosatto, Angela del Pozo, José M. Fernández, Paolo Maietta, Alfonso Valencia, Michael L. Tress, Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino, Hafeez Ur Rehman, Matteo Re, Marco Mesiti, Giorgio Valentini, Joachim W. Bargsten, Aalt D.J. van Dijk, Branislava Gemovic, Sanja Glisic, Vladmir Perovic, Veljko Veljkovic, Nevena Veljkovic, Danillo C. Almeida-e-Silva, Ricardo Z.N. Vencio, Malvika Sharan, Jörg Vogel, Lakesh Kansakar, Shanshan Zhang, Slobodan Vucetic, Zheng Wang, Michael J.E. Sternberg, Mark N. Wass, Rachael P. Huntley, Maria J. Martin, Claire O'Donovan, Peter N. Robinson, Yves Moreau, Anna Tramontano, Patricia C. Babbitt, Steven E. Brenner, Michal Linial, Christine A. Orengo, Burkhard Rost, Casey S. Greene, Sean D. Mooney, Iddo Friedberg, Predrag Radivojac

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

Original language	English
Article number	184
Journal	Genome Biology
Volume	17
Issue number	1
DOIs	https://doi.org/10.1186/s13059-016-1037-6
State	Published - Sep 7 2016
Externally published	Yes

ASJC Scopus Subject Areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

Keywords

Disease gene prioritization
Protein function prediction

Access to Document

10.1186/s13059-016-1037-6

Cite this

Jiang, Y., Oron, T. R., Clark, W. T., Bankapur, A. R., D'Andrea, D., Lepore, R., Funk, C. S., Kahanda, I., Verspoor, K. M., Ben-Hur, A., Koo, D. C. E., Penfold-Brown, D., Shasha, D., Youngs, N., Bonneau, R., Lin, A., Sahraeian, S. M. E., Martelli, P. L., Profiti, G., ... Radivojac, P. (2016). An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology, 17(1), Article 184. https://doi.org/10.1186/s13059-016-1037-6

Jiang, Y, Oron, TR, Clark, WT, Bankapur, AR, D'Andrea, D, Lepore, R, Funk, CS, Kahanda, I, Verspoor, KM, Ben-Hur, A, Koo, DCE, Penfold-Brown, D, Shasha, D, Youngs, N, Bonneau, R, Lin, A, Sahraeian, SME, Martelli, PL, Profiti, G, Casadio, R, Cao, R, Zhong, Z, Cheng, J, Altenhoff, A, Skunca, N, Dessimoz, C, Dogan, T, Hakala, K, Kaewphan, S, Mehryary, F, Salakoski, T, Ginter, F, Fang, H, Smithers, B, Oates, M, Gough, J, Törönen, P, Koskinen, P, Holm, L, Chen, CT, Hsu, WL, Bryson, K, Cozzetto, D, Minneci, F, Jones, DT, Chapman, S, Bkc, D, Khan, IK, Kihara, D, Ofer, D, Rappoport, N, Stern, A, Cibrian-Uhalte, E, Denny, P, Foulger, RE, Hieta, R, Legge, D, Lovering, RC, Magrane, M, Melidoni, AN, Mutowo-Meullenet, P, Pichler, K, Shypitsyna, A, Li, B, Zakeri, P, ElShal, S, Tranchevent, LC, Das, S, Dawson, NL, Lee, D, Lees, JG, Sillitoe, I, Bhat, P, Nepusz, T, Romero, AE, Sasidharan, R, Yang, H, Paccanaro, A, Gillis, J, Sedeño-Cortés, AE, Pavlidis, P, Feng, S, Cejuela, JM, Goldberg, T, Hamp, T, Richter, L, Salamov, A, Gabaldon, T, Marcet-Houben, M, Supek, F, Gong, Q, Ning, W, Zhou, Y, Tian, W, Falda, M, Fontana, P, Lavezzo, E, Toppo, S, Ferrari, C, Giollo, M, Piovesan, D, Tosatto, SCE, del Pozo, A, Fernández, JM, Maietta, P, Valencia, A, Tress, ML, Benso, A, Di Carlo, S, Politano, G, Savino, A, Rehman, HU, Re, M, Mesiti, M, Valentini, G, Bargsten, JW, van Dijk, ADJ, Gemovic, B, Glisic, S, Perovic, V, Veljkovic, V, Veljkovic, N, Almeida-e-Silva, DC, Vencio, RZN, Sharan, M, Vogel, J, Kansakar, L, Zhang, S, Vucetic, S, Wang, Z, Sternberg, MJE, Wass, MN, Huntley, RP, Martin, MJ, O'Donovan, C, Robinson, PN, Moreau, Y, Tramontano, A, Babbitt, PC, Brenner, SE, Linial, M, Orengo, CA, Rost, B, Greene, CS, Mooney, SD, Friedberg, I & Radivojac, P 2016, 'An expanded evaluation of protein function prediction methods shows an improvement in accuracy', Genome Biology, vol. 17, no. 1, 184. https://doi.org/10.1186/s13059-016-1037-6

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T1 - An expanded evaluation of protein function prediction methods shows an improvement in accuracy

AU - Jiang, Yuxiang

AU - Oron, Tal Ronnen

AU - Clark, Wyatt T.

AU - Bankapur, Asma R.

AU - D'Andrea, Daniel

AU - Lepore, Rosalba

AU - Funk, Christopher S.

AU - Kahanda, Indika

AU - Verspoor, Karin M.

AU - Ben-Hur, Asa

AU - Koo, Da Chen Emily

AU - Penfold-Brown, Duncan

AU - Shasha, Dennis

AU - Youngs, Noah

AU - Bonneau, Richard

AU - Lin, Alexandra

AU - Sahraeian, Sayed M.E.

AU - Martelli, Pier Luigi

AU - Profiti, Giuseppe

AU - Casadio, Rita

AU - Cao, Renzhi

AU - Zhong, Zhaolong

AU - Cheng, Jianlin

AU - Altenhoff, Adrian

AU - Skunca, Nives

AU - Dessimoz, Christophe

AU - Dogan, Tunca

AU - Hakala, Kai

AU - Kaewphan, Suwisa

AU - Mehryary, Farrokh

AU - Salakoski, Tapio

AU - Ginter, Filip

AU - Fang, Hai

AU - Smithers, Ben

AU - Oates, Matt

AU - Gough, Julian

AU - Törönen, Petri

AU - Koskinen, Patrik

AU - Holm, Liisa

AU - Chen, Ching Tai

AU - Hsu, Wen Lian

AU - Bryson, Kevin

AU - Cozzetto, Domenico

AU - Minneci, Federico

AU - Jones, David T.

AU - Chapman, Samuel

AU - Bkc, Dukka

AU - Khan, Ishita K.

AU - Kihara, Daisuke

AU - Ofer, Dan

AU - Rappoport, Nadav

AU - Stern, Amos

AU - Cibrian-Uhalte, Elena

AU - Denny, Paul

AU - Foulger, Rebecca E.

AU - Hieta, Reija

AU - Legge, Duncan

AU - Lovering, Ruth C.

AU - Magrane, Michele

AU - Melidoni, Anna N.

AU - Mutowo-Meullenet, Prudence

AU - Pichler, Klemens

AU - Shypitsyna, Aleksandra

AU - Li, Biao

AU - Zakeri, Pooya

AU - ElShal, Sarah

AU - Tranchevent, Léon Charles

AU - Das, Sayoni

AU - Dawson, Natalie L.

AU - Lee, David

AU - Lees, Jonathan G.

AU - Sillitoe, Ian

AU - Bhat, Prajwal

AU - Nepusz, Tamás

AU - Romero, Alfonso E.

AU - Sasidharan, Rajkumar

AU - Yang, Haixuan

AU - Paccanaro, Alberto

AU - Gillis, Jesse

AU - Sedeño-Cortés, Adriana E.

AU - Pavlidis, Paul

AU - Feng, Shou

AU - Cejuela, Juan M.

AU - Goldberg, Tatyana

AU - Hamp, Tobias

AU - Richter, Lothar

AU - Salamov, Asaf

AU - Gabaldon, Toni

AU - Marcet-Houben, Marina

AU - Supek, Fran

AU - Gong, Qingtian

AU - Ning, Wei

AU - Zhou, Yuanpeng

AU - Tian, Weidong

AU - Falda, Marco

AU - Fontana, Paolo

AU - Lavezzo, Enrico

AU - Toppo, Stefano

AU - Ferrari, Carlo

AU - Giollo, Manuel

AU - Piovesan, Damiano

AU - Tosatto, Silvio C.E.

AU - del Pozo, Angela

AU - Fernández, José M.

AU - Maietta, Paolo

AU - Valencia, Alfonso

AU - Tress, Michael L.

AU - Benso, Alfredo

AU - Di Carlo, Stefano

AU - Politano, Gianfranco

AU - Savino, Alessandro

AU - Rehman, Hafeez Ur

AU - Re, Matteo

AU - Mesiti, Marco

AU - Valentini, Giorgio

AU - Bargsten, Joachim W.

AU - van Dijk, Aalt D.J.

AU - Gemovic, Branislava

AU - Glisic, Sanja

AU - Perovic, Vladmir

AU - Veljkovic, Veljko

AU - Veljkovic, Nevena

AU - Almeida-e-Silva, Danillo C.

AU - Vencio, Ricardo Z.N.

AU - Sharan, Malvika

AU - Vogel, Jörg

AU - Kansakar, Lakesh

AU - Zhang, Shanshan

AU - Vucetic, Slobodan

AU - Wang, Zheng

AU - Sternberg, Michael J.E.

AU - Wass, Mark N.

AU - Huntley, Rachael P.

AU - Martin, Maria J.

AU - O'Donovan, Claire

AU - Robinson, Peter N.

AU - Moreau, Yves

AU - Tramontano, Anna

AU - Babbitt, Patricia C.

AU - Brenner, Steven E.

AU - Linial, Michal

AU - Orengo, Christine A.

AU - Rost, Burkhard

AU - Greene, Casey S.

AU - Mooney, Sean D.

AU - Friedberg, Iddo

AU - Radivojac, Predrag

PY - 2016/9/7

Y1 - 2016/9/7

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KW - Protein function prediction

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SN - 1474-7596

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JO - Genome Biology

JF - Genome Biology

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ER -

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

ASJC Scopus Subject Areas

Keywords

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