Literature DB >> 24590444

The automated function prediction SIG looks back at 2013 and prepares for 2014.

Mark N Wass1, Sean D Mooney1, Michal Linial1, Predrag Radivojac1, Iddo Friedberg2.   

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Year:  2014        PMID: 24590444      PMCID: PMC4080736          DOI: 10.1093/bioinformatics/btu117

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


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  6 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  A large-scale experiment to assess protein structure prediction methods.

Authors:  J Moult; J T Pedersen; R Judson; K Fidelis
Journal:  Proteins       Date:  1995-11

3.  The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.

Authors:  Peter N Robinson; Sebastian Köhler; Sebastian Bauer; Dominik Seelow; Denise Horn; Stefan Mundlos
Journal:  Am J Hum Genet       Date:  2008-10-23       Impact factor: 11.025

4.  Update on activities at the Universal Protein Resource (UniProt) in 2013.

Authors: 
Journal:  Nucleic Acids Res       Date:  2012-11-17       Impact factor: 16.971

5.  The Pfam protein families database.

Authors:  Marco Punta; Penny C Coggill; Ruth Y Eberhardt; Jaina Mistry; John Tate; Chris Boursnell; Ningze Pang; Kristoffer Forslund; Goran Ceric; Jody Clements; Andreas Heger; Liisa Holm; Erik L L Sonnhammer; Sean R Eddy; Alex Bateman; Robert D Finn
Journal:  Nucleic Acids Res       Date:  2011-11-29       Impact factor: 16.971

6.  A large-scale evaluation of computational protein function prediction.

Authors:  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; Julian Gough; Patrik Koskinen; Petri Törönen; 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 Hönigschmid; Thomas A Hopf; Stefanie Kaufmann; Michael Kiening; Denis Krompass; Cedric Landerer; Yannick Mahlich; Manfred Roos; Jari Björne; Tapio Salakoski; Andrew Wong; Hagit Shatkay; Fanny Gatzmann; Ingolf Sommer; Mark N Wass; Michael J E Sternberg; Nives Škunca; Fran Supek; Matko Bošnjak; Panče Panov; Sašo Džeroski; Tomislav Šmuc; 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
Journal:  Nat Methods       Date:  2013-01-27       Impact factor: 28.547

  6 in total
  5 in total

1.  Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure.

Authors:  Vasilis J Promponas; Ioannis Iliopoulos; Christos A Ouzounis
Journal:  Stand Genomic Sci       Date:  2015-11-19

2.  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

3.  Predicting protein functions using incomplete hierarchical labels.

Authors:  Guoxian Yu; Hailong Zhu; Carlotta Domeniconi
Journal:  BMC Bioinformatics       Date:  2015-01-16       Impact factor: 3.169

4.  The GOA database: gene Ontology annotation updates for 2015.

Authors:  Rachael P Huntley; Tony Sawford; Prudence Mutowo-Meullenet; Aleksandra Shypitsyna; Carlos Bonilla; Maria J Martin; Claire O'Donovan
Journal:  Nucleic Acids Res       Date:  2014-11-06       Impact factor: 19.160

5.  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

  5 in total

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