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Text-mining and information-retrieval services for molecular biology
Martin Krallinger, Alfonso Valencia
Genome Biol. 2005; 6(7): 224. Published online 2005 June 28. doi: 10.1186/gb-2005-6-7-224
PMCID:
PMC1175978
Abstract Full Text PDF–708K
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 Is Cited by the Following 31 Articles in this Archive:
Discovering Disease Associations by Integrating Electronic Clinical Data and Medical Literature
Antony B. Holmes, Alexander Hawson, Feng Liu, Carol Friedman, Hossein Khiabanian, Raul Rabadan
PLoS One. 2011; 6(6): e21132. Published online 2011 June 23. doi: 10.1371/journal.pone.0021132
PMCID:
PMC3121722
Abstract Full Text PDF–371K Supplementary Material
The biomedical discourse relation bank
Rashmi Prasad, Susan McRoy, Nadya Frid, Aravind Joshi, Hong Yu
BMC Bioinformatics. 2011; 12: 188. Published online 2011 May 23. doi: 10.1186/1471-2105-12-188
PMCID:
PMC3130691
Abstract Full Text PDF–304K
Toward an interactive article: integrating journals and biological databases
Arun Rangarajan, Tim Schedl, Karen Yook, Juancarlos Chan, Stephen Haenel, Lolly Otis, Sharon Faelten, Tracey DePellegrin-Connelly, Ruth Isaacson, Marek S Skrzypek, Steven J Marygold, Raymund Stefancsik , J Michael Cherry, Paul W Sternberg, Hans-Michael Müller
BMC Bioinformatics. 2011; 12: 175. Published online 2011 May 19. doi: 10.1186/1471-2105-12-175
PMCID:
PMC3213741
Abstract Full Text PDF–1.9M
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. Published online 2010 October 7. doi: 10.1186/1471-2105-11-S6-S14
PMCID:
PMC3026361
Abstract Full Text PDF–2.2M
Concept-based query expansion for retrieving gene related publications from MEDLINE
Sérgio Matos, Joel P Arrais, João Maia-Rodrigues, José Luis Oliveira
BMC Bioinformatics. 2010; 11: 212. Published online 2010 April 28. doi: 10.1186/1471-2105-11-212
PMCID:
PMC2873540
Abstract Full Text PDF–604K
LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships
Adriano Barbosa-Silva, Theodoros G Soldatos, Ivan LF Magalhães, Georgios A Pavlopoulos, Jean-Fred Fontaine, Miguel A Andrade-Navarro, Reinhard Schneider, J Miguel Ortega
BMC Bioinformatics. 2010; 11: 70. Published online 2010 February 1. doi: 10.1186/1471-2105-11-70
PMCID:
PMC3098111
Abstract Full Text PDF–381K Supplementary Material
Computational Epigenetics: the new scientific paradigm
Shen Jean Lim, Tin Wee Tan, Joo Chuan Tong
Bioinformation. 2010; 4(7): 331–337. Published online 2010 January 23.
PMCID:
PMC2957762
Abstract Full Text PDF–241K 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
BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature
Guillermo de la Calle, Miguel García-Remesal, Stefano Chiesa, Diana de la Iglesia, Victor Maojo
BMC Bioinformatics. 2009; 10: 320. Published online 2009 October 7. doi: 10.1186/1471-2105-10-320
PMCID:
PMC2765974
Abstract Full Text PDF–1.9M Supplementary Material
Enhancing navigation in biomedical databases by community voting and database-driven text classification
Timo Duchrow, Timur Shtatland, Daniel Guettler, Misha Pivovarov, Stefan Kramer, Ralph Weissleder
BMC Bioinformatics. 2009; 10: 317. Published online 2009 October 3. doi: 10.1186/1471-2105-10-317
PMCID:
PMC2768718
Abstract Full Text PDF–1.0M
Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions
Soumya Raychaudhuri, Robert M. Plenge, Elizabeth J. Rossin, Aylwin C. Y. Ng, International Schizophrenia Consortium, Shaun M. Purcell, Pamela Sklar, Edward M. Scolnick, Ramnik J. Xavier, David Altshuler, Mark J. Daly
PLoS Genet. 2009 June; 5(6): e1000534. Published online 2009 June 26. doi: 10.1371/journal.pgen.1000534
PMCID:
PMC2694358
Abstract Full Text PDF–554K Supplementary Material
PPI Finder: A Mining Tool for Human Protein-Protein Interactions
Min He, Yi Wang, Wei Li
PLoS ONE. 2009; 4(2): e4554. Published online 2009 February 23. doi: 10.1371/journal.pone.0004554
PMCID:
PMC2641004
Abstract Full Text PDF–439K
OntoGene in BioCreative II
Fabio Rinaldi, Thomas Kappeler, Kaarel Kaljurand, Gerold Schneider, Manfred Klenner, Simon Clematide, Michael Hess, Jean-Marc von Allmen, Pierre Parisot, Martin Romacker, Therese Vachon
Genome Biol. 2008; 9(Suppl 2): S13. Published online 2008 September 1. doi: 10.1186/gb-2008-9-s2-s13
PMCID:
PMC2559984
Abstract Full Text PDF–702K
Introducing meta-services for biomedical information extraction
Florian Leitner, Martin Krallinger, Carlos Rodriguez-Penagos, Jörg Hakenberg, Conrad Plake, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hsi-Chuan Hung, William W Lau, Calvin A Johnson, Rune Sætre, Kazuhiro Yoshida, Yan Hua Chen, Sun Kim, Soo-Yong Shin, Byoung-Tak Zhang, William A Baumgartner, Jr, Lawrence Hunter, Barry Haddow, Michael Matthews, Xinglong Wang, Patrick Ruch, Frédéric Ehrler, Arzucan Özgür, Güneş Erkan, Dragomir R Radev, Michael Krauthammer, ThaiBinh Luong, Robert Hoffmann, Chris Sander, Alfonso Valencia
Genome Biol. 2008; 9(Suppl 2): S6. Published online 2008 September 1. doi: 10.1186/gb-2008-9-s2-s6
PMCID:
PMC2559990
Abstract Full Text PDF–1.7M
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
Network integration and graph analysis in mammalian molecular systems biology
A. Ma'ayan
IET Syst Biol. Author manuscript; available in PMC 2009 September 16.
Published in final edited form as: IET Syst Biol. 2008 September; 2(5): 206–221. doi: 10.1049/iet-syb:20070075
PMCID:
PMC2745214
Abstract Full Text PDF–461K
Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users
Hagit Shatkay, Fengxia Pan, Andrey Rzhetsky, W. John Wilbur
Bioinformatics. 2008 September 15; 24(18): 2086–2093. Published online 2008 August 20. doi: 10.1093/bioinformatics/btn381
PMCID:
PMC2530883
Abstract Full Text PDF–132K
Seeking a New Biology through Text Mining
Andrey Rzhetsky, Michael Seringhaus, Mark Gerstein
Cell. Author manuscript; available in PMC 2009 September 1.
Published in final edited form as: Cell. 2008 July 11; 134(1): 9–13. doi: 10.1016/j.cell.2008.06.029
PMCID:
PMC2735884
Abstract Full Text PDF–36K Supplementary Material
PIE: an online prediction system for protein–protein interactions from text
Sun Kim, Soo-Yong Shin, In-Hee Lee, Soo-Jin Kim, Ram Sriram, Byoung-Tak Zhang
Nucleic Acids Res. 2008 July 1; 36(Web Server issue): W411–W415. Published online 2008 July 1. doi: 10.1093/nar/gkn281
PMCID:
PMC2447724
Abstract Full Text PDF–3.5M
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments
Fátima Al-Shahrour, José Carbonell, Pablo Minguez, Stefan Goetz, Ana Conesa, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, Joaquín Dopazo
Nucleic Acids Res. 2008 July 1; 36(Web Server issue): W341–W346. Published online 2008 July 1. doi: 10.1093/nar/gkn318
PMCID:
PMC2447758
Abstract Full Text PDF–96K
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. Published online 2008 April 15. doi: 10.1186/1471-2105-9-198
PMCID:
PMC2375131
Abstract Full Text PDF–746K Supplementary Material
MeInfoText: associated gene methylation and cancer information from text mining
Yu-Ching Fang, Hsuan-Cheng Huang, Hsueh-Fen Juan
BMC Bioinformatics. 2008; 9: 22. Published online 2008 January 14. doi: 10.1186/1471-2105-9-22
PMCID:
PMC2258285
Abstract Full Text PDF–978K
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
iHOP web services
José M. Fernández, Robert Hoffmann, Alfonso Valencia
Nucleic Acids Res. 2007 July; 35(Web Server issue): W21–W26. Published online 2007 July. doi: 10.1093/nar/gkm298
PMCID:
PMC1933131
Abstract Full Text PDF–626K
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments
Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, Joaquín Dopazo
Nucleic Acids Res. 2007 July; 35(Web Server issue): W91–W96. Published online 2007 July. doi: 10.1093/nar/gkm260
PMCID:
PMC1933151
Abstract Full Text PDF–744K Supplementary Material
CellCircuits: a database of protein network models
H. Craig Mak, Mike Daly, Bianca Gruebel, Trey Ideker
Nucleic Acids Res. 2007 January; 35(Database issue): D538–D545. Published online 2006 November 29. doi: 10.1093/nar/gkl937
PMCID:
PMC1751555
Abstract Full Text PDF–606K
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
Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues
Hua Xu, Marianthi Markatou, Rositsa Dimova, Hongfang Liu, Carol Friedman
BMC Bioinformatics. 2006; 7: 334. Published online 2006 July 5. doi: 10.1186/1471-2105-7-334
PMCID:
PMC1550263
Abstract Full Text PDF–332K Supplementary Material
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, Bobby-Joe Breitkreutz, Gary C Hon, Chad L Myers, Ainslie Parsons, Helena Friesen, Rose Oughtred, Amy Tong, Chris Stark, Yuen Ho, David Botstein, Brenda Andrews, Charles Boone, Olga G Troyanskya, Trey Ideker, Kara Dolinski, Nizar N Batada, Mike Tyers
J Biol. 2006; 5(4): 11. Published online 2006 June 8. doi: 10.1186/jbiol36
PMCID:
PMC1561585
Abstract Full Text PDF–1.7M 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
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