An expanded evaluation of protein function prediction methods shows an improvement in accuracy
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Published:2016-09-07
Issue:1
Volume:17
Page:
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ISSN:1474-760X
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Container-title:Genome Biology
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language:en
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Short-container-title:Genome Biol
Author:
Jiang Yuxiang, Oron Tal Ronnen, Clark Wyatt T., Bankapur Asma R., D’Andrea Daniel, Lepore Rosalba, Funk Christopher S., Kahanda Indika, Verspoor Karin M., Ben-Hur Asa, Koo Da Chen Emily, Penfold-Brown Duncan, Shasha Dennis, Youngs Noah, Bonneau Richard, Lin Alexandra, Sahraeian Sayed M. E., Martelli Pier Luigi, Profiti Giuseppe, Casadio Rita, Cao Renzhi, Zhong Zhaolong, Cheng Jianlin, Altenhoff Adrian, Skunca Nives, Dessimoz Christophe, Dogan Tunca, Hakala Kai, Kaewphan Suwisa, Mehryary Farrokh, Salakoski Tapio, Ginter Filip, Fang Hai, Smithers Ben, Oates Matt, Gough Julian, Törönen Petri, Koskinen Patrik, Holm Liisa, Chen Ching-Tai, Hsu Wen-Lian, Bryson Kevin, Cozzetto Domenico, Minneci Federico, Jones David T., Chapman Samuel, BKC Dukka, Khan Ishita K., Kihara Daisuke, Ofer Dan, Rappoport Nadav, Stern Amos, Cibrian-Uhalte Elena, Denny Paul, Foulger Rebecca E., Hieta Reija, Legge Duncan, Lovering Ruth C., Magrane Michele, Melidoni Anna N., Mutowo-Meullenet Prudence, Pichler Klemens, Shypitsyna Aleksandra, Li Biao, Zakeri Pooya, ElShal Sarah, Tranchevent Léon-Charles, Das Sayoni, Dawson Natalie L., Lee David, Lees Jonathan G., Sillitoe Ian, Bhat Prajwal, Nepusz Tamás, Romero Alfonso E., Sasidharan Rajkumar, Yang Haixuan, Paccanaro Alberto, Gillis Jesse, Sedeño-Cortés Adriana E., Pavlidis Paul, Feng Shou, Cejuela Juan M., Goldberg Tatyana, Hamp Tobias, Richter Lothar, Salamov Asaf, Gabaldon Toni, Marcet-Houben Marina, Supek Fran, Gong Qingtian, Ning Wei, Zhou Yuanpeng, Tian Weidong, Falda Marco, Fontana Paolo, Lavezzo Enrico, Toppo Stefano, Ferrari Carlo, Giollo Manuel, Piovesan Damiano, Tosatto Silvio C.E., del Pozo Angela, Fernández José M., Maietta Paolo, Valencia Alfonso, Tress Michael L., Benso Alfredo, Di Carlo Stefano, Politano Gianfranco, Savino Alessandro, Rehman Hafeez Ur, Re Matteo, Mesiti Marco, Valentini Giorgio, Bargsten Joachim W., van Dijk Aalt D. J., Gemovic Branislava, Glisic Sanja, Perovic Vladmir, Veljkovic Veljko, Veljkovic Nevena, Almeida-e-Silva Danillo C., Vencio Ricardo Z. N., Sharan Malvika, Vogel Jörg, Kansakar Lakesh, Zhang Shanshan, Vucetic Slobodan, Wang Zheng, Sternberg Michael J. E., Wass Mark N., Huntley Rachael P., Martin Maria J., O’Donovan Claire, Robinson Peter N., Moreau Yves, Tramontano Anna, Babbitt Patricia C., Brenner Steven E., Linial Michal, Orengo Christine A., Rost Burkhard, Greene Casey S., Mooney Sean D., Friedberg IddoORCID, Radivojac Predrag
Funder
Directorate for Biological Sciences
Publisher
Springer Science and Business Media LLC
Reference19 articles.
1. Costello JC, Stolovitzky G. Seeking the wisdom of crowds through challenge-based competitions in biomedical research. Clin Pharmacol Ther. 2013; 93(5):396–8. 2. Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, et al. A large-scale evaluation of computational protein function prediction. Nat Methods. 2013; 10(3):221–7. 3. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000; 25(1):25–9. 4. Dessimoz C, Skunca N, Thomas PD. CAFA and the open world of protein function predictions. Trends Genet. 2013; 29(11):609–10. 5. Gillis J, Pavlidis P. Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA). BMC Bioinform. 2013; 14(Suppl 3):15.
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