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TXTGate: profiling gene groups with text-based information
Patrick Glenisson, Bert Coessens, Steven Van Vooren, Janick Mathys, Yves Moreau, Bart De Moor
Genome Biol. 2004; 5(6): R43. Published online 2004 May 28. doi: 10.1186/gb-2004-5-6-r43
PMCID:
PMC463076
Abstract Full Text PDF–356K Supplementary Material
 Is Cited by the Following 22 Articles in this Archive:
The Text-mining based PubChem Bioassay neighboring analysis
Lianyi Han, Tugba O Suzek, Yanli Wang, Steve H Bryant
BMC Bioinformatics. 2010; 11: 549. Published online 2010 November 8. doi: 10.1186/1471-2105-11-549
PMCID:
PMC3098095
Abstract Full Text PDF–331K
Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model
Xin He, Moushumi Sen Sarma, Xu Ling, Brant Chee, Chengxiang Zhai, Bruce Schatz
BMC Bioinformatics. 2010; 11: 272. Published online 2010 May 20. doi: 10.1186/1471-2105-11-272
PMCID:
PMC2885378
Abstract Full Text PDF–1.6M Supplementary Material
Rewriting and suppressing UMLS terms for improved biomedical term identification
Kristina M Hettne, Erik M van Mulligen, Martijn J Schuemie, Bob JA Schijvenaars, Jan A Kors
J Biomed Semantics. 2010; 1: 5. Published online 2010 March 31. doi: 10.1186/2041-1480-1-5
PMCID:
PMC2895736
Abstract Full Text PDF–291K Supplementary Material
Gene prioritization and clustering by multi-view text mining
Shi Yu, Leon-Charles Tranchevent, Bart De Moor, Yves Moreau
BMC Bioinformatics. 2010; 11: 28. Published online 2010 January 14. doi: 10.1186/1471-2105-11-28
PMCID:
PMC3098068
Abstract Full Text PDF–1.6M Supplementary Material
Martini: using literature keywords to compare gene sets
Theodoros G. Soldatos, Seán I. O’Donoghue, Venkata P. Satagopam, Lars J. Jensen, Nigel P. Brown, Adriano Barbosa-Silva, Reinhard Schneider
Nucleic Acids Res. 2010 January; 38(1): 26–38. Published online 2010 January. doi: 10.1093/nar/gkp876
PMCID:
PMC2800231
Abstract Full Text PDF–4.3M
Biomedical Text Mining and Its Applications
Raul Rodriguez-Esteban
PLoS Comput Biol. 2009 December; 5(12): e1000597. Published online 2009 December 24. doi: 10.1371/journal.pcbi.1000597
PMCID:
PMC2791166
Full Text PDF–542K
Protein comparison at the domain architecture level
Byungwook Lee, Doheon Lee
BMC Bioinformatics. 2009; 10(Suppl 15): S5. Published online 2009 December 3. doi: 10.1186/1471-2105-10-S15-S5
PMCID:
PMC2788356
Abstract Full Text PDF–804K
Text-based over-representation analysis of microarray gene lists with annotation bias
Hui Sun Leong, David Kipling
Nucleic Acids Res. 2009 June; 37(11): e79. Published online 2009 June. doi: 10.1093/nar/gkp310
PMCID:
PMC2699530
Abstract Full Text PDF–889K Supplementary Material
Endeavour update: a web resource for gene prioritization in multiple species
Léon-Charles Tranchevent, Roland Barriot, Shi Yu, Steven Van Vooren, Peter Van Loo, Bert Coessens, Bart De Moor, Stein Aerts, Yves Moreau
Nucleic Acids Res. 2008 July 1; 36(Web Server issue): W377–W384. Published online 2008 July 1. doi: 10.1093/nar/gkn325
PMCID:
PMC2447805
Abstract Full Text PDF–2.2M Supplementary Material
DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture
Byungwook Lee, Doheon Lee
Nucleic Acids Res. 2008 July 1; 36(Web Server issue): W60–W64. Published online 2008 July 1. doi: 10.1093/nar/gkn172
PMCID:
PMC2447808
Abstract Full Text PDF–493K
Anni 2.0: a multipurpose text-mining tool for the life sciences
Rob Jelier, Martijn J Schuemie, Antoine Veldhoven, Lambert CJ Dorssers, Guido Jenster, Jan A Kors
Genome Biol. 2008; 9(6): R96. Published online 2008 June 12. doi: 10.1186/gb-2008-9-6-r96
PMCID:
PMC2481428
Abstract Full Text PDF–746K Supplementary Material
Text-mining assisted regulatory annotation
Stein Aerts, Maximilian Haeussler, Steven van Vooren, Obi L Griffith, Paco Hulpiau, Steven JM Jones, Stephen B Montgomery, Casey M Bergman, The Open Regulatory Annotation Consortium
Genome Biol. 2008; 9(2): R31. Published online 2008 February 13. doi: 10.1186/gb-2008-9-2-r31
PMCID:
PMC2374703
Abstract Full Text PDF–538K Supplementary Material
ORegAnno: an open-access community-driven resource for regulatory annotation
Obi L. Griffith, Stephen B. Montgomery, Bridget Bernier, Bryan Chu, Katayoon Kasaian, Stein Aerts, Shaun Mahony, Monica C. Sleumer, Mikhail Bilenky, Maximilian Haeussler, Malachi Griffith, Steven M. Gallo, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth Wasserman, Ross Hardison, Casey M. Bergman, Steven J.M. Jones, The Open Regulatory Annotation Consortium
Nucleic Acids Res. 2008 January; 36(Database issue): D107–D113. Published online 2008 January. doi: 10.1093/nar/gkm967
PMCID:
PMC2239002
Abstract Full Text PDF–360K
Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations
Steven Van Vooren, Bernard Thienpont, Björn Menten, Frank Speleman, Bart De Moor, Joris Vermeesch, Yves Moreau
Nucleic Acids Res. 2007 April; 35(8): 2533–2543. Published online 2007 April 1. doi: 10.1093/nar/gkm054
PMCID:
PMC1885641
Abstract Full Text PDF–130K Supplementary Material
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. Published online 2007 January 18. doi: 10.1186/1471-2105-8-14
PMCID:
PMC1784107
Abstract Full Text PDF–500K Supplementary Material
New directions in biomedical text annotation: definitions, guidelines and corpus construction
W John Wilbur, Andrey Rzhetsky, Hagit Shatkay
BMC Bioinformatics. 2006; 7: 356. Published online 2006 July 25. doi: 10.1186/1471-2105-7-356
PMCID:
PMC1559725
Abstract Full Text PDF–289K
GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions
Jason M Doherty, Lynn K Carmichael, Jason C Mills
BMC Bioinformatics. 2006; 7: 151. Published online 2006 March 17. doi: 10.1186/1471-2105-7-151
PMCID:
PMC1459206
Abstract Full Text PDF–323K
Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features
JR Semeiks, A Rizki, MJ Bissell, IS Mian
BMC Bioinformatics. 2006; 7: 147. Published online 2006 March 16. doi: 10.1186/1471-2105-7-147
PMCID:
PMC1435935
Abstract Full Text PDF–316K Supplementary Material
Discovering semantic features in the literature: a foundation for building functional associations
Monica Chagoyen, Pedro Carmona-Saez, Hagit Shatkay, Jose M Carazo, Alberto Pascual-Montano
BMC Bioinformatics. 2006; 7: 41. Published online 2006 January 26. doi: 10.1186/1471-2105-7-41
PMCID:
PMC1386711
Abstract Full Text PDF–1.2M Supplementary Material
L2L: a simple tool for discovering the hidden significance in microarray expression data
John C Newman, Alan M Weiner
Genome Biol. 2005; 6(9): R81. Published online 2005 August 31. doi: 10.1186/gb-2005-6-9-r81
PMCID:
PMC1242216
Abstract Full Text PDF–1.2M
TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis
Stein Aerts, Peter Van Loo, Gert Thijs, Herbert Mayer, Rainer de Martin, Yves Moreau, Bart De Moor
Nucleic Acids Res. 2005 July 1; 33(Web Server issue): W393–W396. Published online 2005 June 27. doi: 10.1093/nar/gki354
PMCID:
PMC1160115
Abstract Full Text PDF–228K
CoPub Mapper: mining MEDLINE based on search term co-publication
Blaise TF Alako, Antoine Veldhoven, Sjozef van Baal, Rob Jelier, Stefan Verhoeven, Ton Rullmann, Jan Polman, Guido Jenster
BMC Bioinformatics. 2005; 6: 51. Published online 2005 March 11. doi: 10.1186/1471-2105-6-51
PMCID:
PMC1274248
Abstract Full Text PDF–1015K
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