Literature DB >> 24138813

CAFA and the open world of protein function predictions.

Christophe Dessimoz1, Nives Škunca, Paul D Thomas.   

Abstract

Entities:  

Keywords:  Open World assumption; community assessment; computational methods; gene ontology; protein databases; protein function prediction

Mesh：

Substances：

Year:  2013        PMID： 24138813     DOI： 10.1016/j.tig.2013.09.005

Source DB:  PubMed          Journal:  Trends Genet        ISSN： 0168-9525            Impact factor:   11.639


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  19 in total

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3.  Experimental Evidence for a Revision in the Annotation of Putative Pyridoxamine 5'-Phosphate Oxidases P(N/M)P from Fungi.

Authors:  Tatiana Domitrovic; Diana P Raymundo; Tiago Fernandes da Silva; Fernando L Palhano
Journal:  PLoS One       Date:  2015-09-01       Impact factor: 3.240

4.  Predicting protein function via downward random walks on a gene ontology.

Authors:  Guoxian Yu; Hailong Zhu; Carlotta Domeniconi; Jiming Liu
Journal:  BMC Bioinformatics       Date:  2015-08-27       Impact factor: 3.169

5.  Phylogenetic profiling: how much input data is enough?

Authors:  Nives Škunca; Christophe Dessimoz
Journal:  PLoS One       Date:  2015-02-13       Impact factor: 3.240

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

Authors:  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
Journal:  Genome Biol       Date:  2016-09-07       Impact factor: 13.583

7.  Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.

Authors:  Andrew F Neuwald; Stephen F Altschul
Journal:  PLoS Comput Biol       Date:  2016-12-21       Impact factor: 4.475

8.  The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective.

Authors:  Yuxiang Jiang; Wyatt T Clark; Iddo Friedberg; Predrag Radivojac
Journal:  Bioinformatics       Date:  2014-09-01       Impact factor: 6.937

9.  Inferring joint sequence-structural determinants of protein functional specificity.

Authors:  Andrew F Neuwald; L Aravind; Stephen F Altschul
Journal:  Elife       Date:  2018-01-16       Impact factor: 8.140

10.  Gene Function Prediction from Functional Association Networks Using Kernel Partial Least Squares Regression.

Authors:  Sonja Lehtinen; Jon Lees; Jürg Bähler; John Shawe-Taylor; Christine Orengo
Journal:  PLoS One       Date:  2015-08-19       Impact factor: 3.240
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