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Mining microarray expression data by literature profiling
Damien Chaussabel, Alan Sher
Genome Biol. 2002; 3(10): research0055.1–research0055.16. Published online 2002 September 13.
PMCID:
PMC134484
Abstract Full Text PDF–2.5M Supplementary Material
 Is Cited by the Following 20 Articles in this Archive:
Disclosing ambiguous gene aliases by automatic literature profiling
Roney S Coimbra, Dana E Vanderwall, Guilherme C Oliveira
BMC Genomics. 2010; 11(Suppl 5): S3. Published online 2010 December 22. doi: 10.1186/1471-2164-11-S5-S3
PMCID:
PMC3045796
Abstract Full Text PDF–271K Supplementary Material
Simple tricks for improving pattern-based information extraction from the biomedical literature
Quang Long Nguyen, Domonkos Tikk, Ulf Leser
J Biomed Semantics. 2010; 1: 9. Published online 2010 September 24. doi: 10.1186/2041-1480-1-9
PMCID:
PMC2955645
Abstract Full Text PDF–735K Supplementary Material
Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases
Raoul Frijters, Marianne van Vugt, Ruben Smeets, René van Schaik, Jacob de Vlieg, Wynand Alkema
PLoS Comput Biol. 2010 September; 6(9): e1000943. Published online 2010 September 23. doi: 10.1371/journal.pcbi.1000943
PMCID:
PMC2944780
Abstract Full Text PDF–817K Supplementary Material
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
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
Identification and Analysis of Co-Occurrence Networks with NetCutter
Heiko Müller, Francesco Mancuso
PLoS ONE. 2008; 3(9): e3178. Published online 2008 September 10. doi: 10.1371/journal.pone.0003178
PMCID:
PMC2526157
Abstract Full Text PDF–795K Supplementary Material
Methodology capture: discriminating between the "best" and the rest of community practice
James M Eales, John W Pinney, Robert D Stevens, David L Robertson
BMC Bioinformatics. 2008; 9: 359. Published online 2008 September 1. doi: 10.1186/1471-2105-9-359
PMCID:
PMC2553348
Abstract Full Text PDF–1.4M
A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus
Damien Chaussabel, Charles Quinn, Jing Shen, Pinakeen Patel, Casey Glaser, Nicole Baldwin, Dorothee Stichweh, Derek Blankenship, Lei Li, Indira Munagala, Lynda Bennett, Florence Allantaz, Asuncion Mejias, Monica Ardura, Ellen Kaizer, Laurence Monnet, Windy Allman, Henry Randall, Diane Johnson, Aimee Lanier, Marilynn Punaro, Knut M. Wittkowski, Perrin White, Joseph Fay, Goran Klintmalm, Octavio Ramilo, A. Karolina Palucka, Jacques Banchereau, Virginia Pascual
Immunity. Author manuscript; available in PMC 2009 August 17.
Published in final edited form as: Immunity. 2008 July 18; 29(1): 150–164. doi: 10.1016/j.immuni.2008.05.012
PMCID:
PMC2727981
Abstract Full Text PDF–2.1M Supplementary Material
GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords
Zhong-Xi Huang, Hui-Yong Tian, Zhen-Fu Hu, Yi-Bo Zhou, Jin Zhao, Kai-Tai Yao
BMC Bioinformatics. 2008; 9: 308. Published online 2008 July 13. doi: 10.1186/1471-2105-9-308
PMCID:
PMC2483997
Abstract Full Text PDF–692K Supplementary Material
CoPub: a literature-based keyword enrichment tool for microarray data analysis
Raoul Frijters, Bart Heupers, Pieter van Beek, Maurice Bouwhuis, René van Schaik, Jacob de Vlieg, Jan Polman, Wynand Alkema
Nucleic Acids Res. 2008 July 1; 36(Web Server issue): W406–W410. Published online 2008 July 1. doi: 10.1093/nar/gkn215
PMCID:
PMC2447728
Abstract Full Text PDF–644K
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
Functional gene clustering via gene annotation sentences, MeSH and GO keywords from biomedical literature
Jeyakumar Natarajan, Jawahar Ganapathy
Bioinformation. 2007; 2(5): 185–193. Published online 2007 December 30.
PMCID:
PMC2241933
Abstract Full Text PDF–296K 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
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. Published online 2006 July 26. doi: 10.1186/1471-2105-7-363
PMCID:
PMC1579237
Abstract Full Text PDF–366K Supplementary Material
Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets
Marc Aubry, Annabelle Monnier, Celine Chicault, Marie de Tayrac, Marie-Dominique Galibert, Anita Burgun, Jean Mosser
BMC Bioinformatics. 2006; 7: 241. Published online 2006 May 4. doi: 10.1186/1471-2105-7-241
PMCID:
PMC1482722
Abstract Full Text PDF–483K 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
A sentence sliding window approach to extract protein annotations from biomedical articles
Martin Krallinger, Maria Padron, Alfonso Valencia
BMC Bioinformatics. 2005; 6(Suppl 1): S19. Published online 2005 May 24. doi: 10.1186/1471-2105-6-S1-S19
PMCID:
PMC1869011
Abstract Full Text PDF–373K
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
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
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