Software  

PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries

Adriano Barbosa-Silva, Jean-Fred Fontaine, Elisa R Donnard, Fernanda Stussi, J Ortega, Miguel A Andrade-Navarro BMC Bioinformatics 2011, 12:435 (9 November 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Proceedings  

Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization)

Elina Tjioe, Michael W Berry, Ramin Homayouni BMC Bioinformatics 2010, 11(Suppl 6):S14 (7 October 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article  

Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model

Xin He, Moushumi Sarma, Xu Ling, Brant Chee, Chengxiang Zhai, Bruce Schatz BMC Bioinformatics 2010, 11:272 (20 May 2010)

Abstract | Full text | PDF | PubMed

Proceedings  

Large-scale directional relationship extraction and resolution

Cory B Giles, Jonathan D Wren BMC Bioinformatics 2008, 9(Suppl 9):S11 (12 August 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article  

Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection

Inkyung Jung, Jaehyung Lee, Soo-Young Lee, Dongsup Kim BMC Bioinformatics 2008, 9:298 (1 July 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article  

Improving protein function prediction methods with integrated literature data

Aaron P Gabow, Sonia M Leach, William A Baumgartner, Lawrence E Hunter, Debra S Goldberg BMC Bioinformatics 2008, 9:198 (15 April 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article  

Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation

Rob Jelier, Guido Jenster, Lambert CJ Dorssers, Bas J Wouters, Peter JM Hendriksen, Barend Mons, Ruud Delwel, Jan A Kors BMC Bioinformatics 2007, 8:14 (18 January 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Software  

bioNMF: a versatile tool for non-negative matrix factorization in biology

Alberto Pascual-Montano, Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, Jose M Carazo, Roberto D Pascual-Marqui BMC Bioinformatics 2006, 7:366 (28 July 2006)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Methodology article  

A literature-based similarity metric for biological processes

Monica Chagoyen, Pedro Carmona-Saez, Concha Gil, Jose M Carazo, Alberto Pascual-Montano BMC Bioinformatics 2006, 7:363 (26 July 2006)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Methodology article  

Biclustering of gene expression data by non-smooth non-negative matrix factorization

Pedro Carmona-Saez, Roberto D Pascual-Marqui, F Tirado, Jose M Carazo, Alberto Pascual-Montano BMC Bioinformatics 2006, 7:78 (17 February 2006)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central