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Linking genes to literature: text mining, information extraction, and retrieval applications for biology
Martin Krallinger, Alfonso Valencia, Lynette Hirschman
Genome Biol. 2008; 9(Suppl 2): S8. Published online 2008 September 1. doi: 10.1186/gb-2008-9-s2-s8
PMCID:
PMC2559992
Abstract Full Text PDF–2.6M

Is Cited by the Following 26 Articles in this Archive:

Rise and Demise of Bioinformatics? Promise and Progress
Christos A. Ouzounis
PLoS Comput Biol. 2012 April; 8(4): e1002487. Published online 2012 April 26. doi: 10.1371/journal.pcbi.1002487
PMCID:
PMC3343106
Abstract Full Text PDF–120K
Text Mining Improves Prediction of Protein Functional Sites
Karin M. Verspoor, Judith D. Cohn, Komandur E. Ravikumar, Michael E. Wall
PLoS One. 2012; 7(2): e32171. Published online 2012 February 29. doi: 10.1371/journal.pone.0032171
PMCID:
PMC3290545
Abstract Full Text PDF–722K Supplementary Material
Biblio-MetReS: A bibliometric network reconstruction application and server
Anabel Usié, Hiren Karathia, Ivan Teixidó, Joan Valls, Xavier Faus, Rui Alves, Francesc Solsona
BMC Bioinformatics. 2011; 12: 387. Published online 2011 October 5. doi: 10.1186/1471-2105-12-387
PMCID:
PMC3228545
Abstract Full Text PDF–1.0M Supplementary Material
Overview of the BioCreative III Workshop
Cecilia N Arighi, Zhiyong Lu, Martin Krallinger, Kevin B Cohen, W John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H Wu
BMC Bioinformatics. 2011; 12(Suppl 8): S1. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S1
PMCID:
PMC3269932
Abstract Full Text PDF–228K
pubmed2ensembl: A Resource for Mining the Biological Literature on Genes
Joachim Baran, Martin Gerner, Maximilian Haeussler, Goran Nenadic, Casey M. Bergman
PLoS One. 2011; 6(9): e24716. Published online 2011 September 29. doi: 10.1371/journal.pone.0024716
PMCID:
PMC3183000
Abstract Full Text PDF–857K Supplementary Material
Integrating GPCR-specific information with full text articles
Bas Vroling, David Thorne, Philip McDermott, Teresa K Attwood, Gert Vriend, Steve Pettifer
BMC Bioinformatics. 2011; 12: 362. Published online 2011 September 12. doi: 10.1186/1471-2105-12-362
PMCID:
PMC3179973
Abstract Full Text PDF–7.5M
A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
Jeroen F J Laros, André Blavier, Johan T den Dunnen, Peter E M Taschner
BMC Bioinformatics. 2011; 12(Suppl 4): S5. Published online 2011 July 5. doi: 10.1186/1471-2105-12-S4-S5
PMCID:
PMC3194197
Abstract Full Text PDF–224K Supplementary Material
BICEPP: an example-based statistical text mining method for predicting the binary characteristics of drugs
Frank PY Lin, Stephen Anthony, Thomas M Polasek, Guy Tsafnat, Matthew P Doogue
BMC Bioinformatics. 2011; 12: 112. Published online 2011 April 21. doi: 10.1186/1471-2105-12-112
PMCID:
PMC3110144
Abstract Full Text PDF–487K Supplementary Material
Gene List significance at-a-glance with GeneValorization
Bryan Brancotte, Anne Biton, Isabelle Bernard-Pierrot, François Radvanyi, Fabien Reyal, Sarah Cohen-Boulakia
Bioinformatics. 2011 April 15; 27(8): 1187–1189. Published online 2011 February 23. doi: 10.1093/bioinformatics/btr073
PMCID:
PMC3072546
Abstract Full Text PDF–231K Supplementary Material
Annotating genes and genomes with DNA sequences extracted from biomedical articles
Maximilian Haeussler, Martin Gerner, Casey M. Bergman
Bioinformatics. 2011 April 1; 27(7): 980–986. Published online 2011 February 16. doi: 10.1093/bioinformatics/btr043
PMCID:
PMC3065681
Abstract Full Text PDF–614K
PubMed and beyond: a survey of web tools for searching biomedical literature
Zhiyong Lu
Database (Oxford) 2011; 2011: baq036. Published online 2011 January 17. doi: 10.1093/database/baq036
PMCID:
PMC3025693
Abstract Full Text PDF–573K
miRBase: integrating microRNA annotation and deep-sequencing data
Ana Kozomara, Sam Griffiths-Jones
Nucleic Acids Res. 2011 January; 39(Database issue): D152–D157. Published online 2010 October 30. doi: 10.1093/nar/gkq1027
PMCID:
PMC3013655
Abstract Full Text PDF–5.1M
Recent progress in automatically extracting information from the pharmacogenomic literature
Yael Garten, Adrien Coulet, Russ B Altman
Pharmacogenomics. Author manuscript; available in PMC 2011 August 1.
Published in final edited form as: Pharmacogenomics. 2010 October; 11(10): 1467–1489. doi: 10.2217/pgs.10.136
PMCID:
PMC3035632
Abstract Full Text PDF–990K
Text mining meets workflow: linking U-Compare with Taverna
Yoshinobu Kano, Paul Dobson, Mio Nakanishi, Jun'ichi Tsujii, Sophia Ananiadou
Bioinformatics. 2010 October 1; 26(19): 2486–2487. Published online 2010 August 12. doi: 10.1093/bioinformatics/btq464
PMCID:
PMC2944208
Abstract Full Text PDF–173K
CCancer: a bird’s eye view on gene lists reported in cancer-related studies
Sabine Dietmann, Wanseon Lee, Philip Wong, Igor Rodchenkov, Alexey V. Antonov
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W118–W123. Published online 2010 June 5. doi: 10.1093/nar/gkq515
PMCID:
PMC2896190
Abstract Full Text PDF–97K
EnvMine: A text-mining system for the automatic extraction of contextual information
Javier Tamames, Victor de Lorenzo
BMC Bioinformatics. 2010; 11: 294. Published online 2010 June 1. doi: 10.1186/1471-2105-11-294
PMCID:
PMC2901371
Abstract Full Text PDF–1.1M Supplementary Material
For I dipped into the future
Andrea Rinaldi
EMBO Rep. 2010 May; 11(5): 345–349. doi: 10.1038/embor.2010.57
PMCID:
PMC2868544
Full Text PDF–713K
TopoGSA: network topological gene set analysis
Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Alfonso Valencia
Bioinformatics. 2010 May 1; 26(9): 1271–1272. Published online 2010 March 24. doi: 10.1093/bioinformatics/btq131
PMCID:
PMC2859135
Abstract Full Text PDF–161K
Word add-in for ontology recognition: semantic enrichment of scientific literature
J Lynn Fink, Pablo Fernicola, Rahul Chandran, Savas Parastatidis, Alex Wade, Oscar Naim, Gregory B Quinn, Philip E Bourne
BMC Bioinformatics. 2010; 11: 103. Published online 2010 February 24. doi: 10.1186/1471-2105-11-103
PMCID:
PMC2837026
Abstract Full Text PDF–658K
LINNAEUS: A species name identification system for biomedical literature
Martin Gerner, Goran Nenadic, Casey M Bergman
BMC Bioinformatics. 2010; 11: 85. Published online 2010 February 11. doi: 10.1186/1471-2105-11-85
PMCID:
PMC2836304
Abstract Full Text PDF–532K Supplementary Material
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
Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)
Thomas C Wiegers, Allan Peter Davis, K Bretonnel Cohen, Lynette Hirschman, Carolyn J Mattingly
BMC Bioinformatics. 2009; 10: 326. Published online 2009 October 8. doi: 10.1186/1471-2105-10-326
PMCID:
PMC2768719
Abstract Full Text PDF–736K Supplementary Material
Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns
Karen R. Christie, Eurie L. Hong, J. Michael Cherry
Trends Microbiol. Author manuscript; available in PMC 2011 March 15.
Published in final edited form as: Trends Microbiol. 2009 July; 17(7): 286–294. Published online 2009 July 2. doi: 10.1016/j.tim.2009.04.005
PMCID:
PMC3057094
Abstract Full Text PDF–273K
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction
Martin Krallinger, Carlos Rodriguez-Penagos, Ashish Tendulkar, Alfonso Valencia
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W160–W165. Published online 2009 July 1. doi: 10.1093/nar/gkp484
PMCID:
PMC2703909
Abstract Full Text PDF–3.9M
Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens
Sam Zaremba, Mila Ramos-Santacruz, Thomas Hampton, Panna Shetty, Joel Fedorko, Jon Whitmore, John M Greene, Nicole T Perna, Jeremy D Glasner, Guy Plunkett, III, Matthew Shaker, David Pot
BMC Bioinformatics. 2009; 10: 177. Published online 2009 June 10. doi: 10.1186/1471-2105-10-177
PMCID:
PMC2704210
Abstract Full Text PDF–1.0M Supplementary Material
Designing and encoding models for synthetic biology
Lukas Endler, Nicolas Rodriguez, Nick Juty, Vijayalakshmi Chelliah, Camille Laibe, Chen Li, Nicolas Le Novère
J R Soc Interface. 2009 August 6; 6(Suppl_4): S405–S417. Published online 2009 April 1. doi: 10.1098/rsif.2009.0035.focus
PMCID:
PMC2843962
Abstract Full Text PDF–491K
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