My NCBISign In
Overview of BioCreative II gene normalization
Alexander A Morgan, Zhiyong Lu, Xinglong Wang, Aaron M Cohen, Juliane Fluck, Patrick Ruch, Anna Divoli, Katrin Fundel, Robert Leaman, Jörg Hakenberg, Chengjie Sun, Heng-hui Liu, Rafael Torres, Michael Krauthammer, William W Lau, Hongfang Liu, Chun-Nan Hsu, Martijn Schuemie, K Bretonnel Cohen, Lynette Hirschman
Genome Biol. 2008; 9(Suppl 2): S3. Published online 2008 September 1. doi: 10.1186/gb-2008-9-s2-s3
PMCID:
PMC2559987
Abstract Full Text PDF–368K Supplementary Material

Is Cited by the Following 29 Articles in this Archive:

Context-Specific Protein Network Miner – An Online System for Exploring Context-Specific Protein Interaction Networks from the Literature
Rajesh Chowdhary, Sin Lam Tan, Jinfeng Zhang, Shreyas Karnik, Vladimir B. Bajic, Jun S. Liu
PLoS One. 2012; 7(4): e34480. Published online 2012 April 6. doi: 10.1371/journal.pone.0034480
PMCID:
PMC3321019
Abstract Full Text PDF–724K Supplementary Material
Industrial methodology for process verification in research (IMPROVER): toward systems biology verification
Pablo Meyer, Julia Hoeng, J. Jeremy Rice, Raquel Norel, Jörg Sprengel, Katrin Stolle, Thomas Bonk, Stephanie Corthesy, Ajay Royyuru, Manuel C. Peitsch, Gustavo Stolovitzky
Bioinformatics. 2012 May 1; 28(9): 1193–1201. Published online 2012 March 14. doi: 10.1093/bioinformatics/bts116
PMCID:
PMC3338013
Abstract Full Text PDF–398K
Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature
Xinglong Wang, Rafal Rak, Angelo Restificar, Chikashi Nobata, CJ Rupp, Riza Theresa B Batista-Navarro, Raheel Nawaz, Sophia Ananiadou
BMC Bioinformatics. 2011; 12(Suppl 8): S11. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S11
PMCID:
PMC3269934
Abstract Full Text PDF–524K
The gene normalization task in BioCreative III
Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illes Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sergio Matos, David Campos, Karin Verspoor, Kevin M Livingston, W John Wilbur
BMC Bioinformatics. 2011; 12(Suppl 8): S2. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S2
PMCID:
PMC3269937
Abstract Full Text PDF–441K Supplementary Material
Cross-species gene normalization by species inference
Chih-Hsuan Wei, Hung-Yu Kao
BMC Bioinformatics. 2011; 12(Suppl 8): S5. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S5
PMCID:
PMC3269940
Abstract Full Text PDF–654K
Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization
Cheng-Ju Kuo, Maurice HT Ling, Chun-Nan Hsu
BMC Bioinformatics. 2011; 12(Suppl 8): S6. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S6
PMCID:
PMC3269941
Abstract Full Text PDF–668K
Multi-stage gene normalization for full-text articles with context-based species filtering for dynamic dictionary entry selection
Richard Tzong-Han Tsai, Po-Ting Lai
BMC Bioinformatics. 2011; 12(Suppl 8): S7. Published online 2011 October 3. doi: 10.1186/1471-2105-12-S8-S7
PMCID:
PMC3269942
Abstract Full Text PDF–493K
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
Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network
Junguk Hur, Zuoshuang Xiang, Eva L Feldman, Yongqun He
BMC Immunol. 2011; 12: 49. Published online 2011 August 26. doi: 10.1186/1471-2172-12-49
PMCID:
PMC3180695
Abstract Full Text PDF–13M
The GNAT library for local and remote gene mention normalization
Jörg Hakenberg, Martin Gerner, Maximilian Haeussler, Illés Solt, Conrad Plake, Michael Schroeder, Graciela Gonzalez, Goran Nenadic, Casey M. Bergman
Bioinformatics. 2011 October 1; 27(19): 2769–2771. Published online 2011 August 3. doi: 10.1093/bioinformatics/btr455
PMCID:
PMC3179658
Abstract Full Text PDF–151K
Exploring subdomain variation in biomedical language
Thomas Lippincott, Diarmuid Ó Séaghdha, Anna Korhonen
BMC Bioinformatics. 2011; 12: 212. Published online 2011 May 27. doi: 10.1186/1471-2105-12-212
PMCID:
PMC3118171
Abstract Full Text PDF–11M
Génie: literature-based gene prioritization at multi genomic scale
Jean-Fred Fontaine, Florian Priller, Adriano Barbosa-Silva, Miguel A. Andrade-Navarro
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W455–W461. Published online 2011 May 23. doi: 10.1093/nar/gkr246
PMCID:
PMC3125729
Abstract Full Text PDF–2.7M
Advancing Science through Mining Libraries, Ontologies, and Communities
James A. Evans, Andrey Rzhetsky
J Biol Chem. 2011 July 8; 286(27): 23659–23666. Published online 2011 May 12. doi: 10.1074/jbc.R110.176370
PMCID:
PMC3129146
Abstract Full Text
PLIO: an ontology for formal description of protein–ligand interactions
Olga Ivchenko, Erfan Younesi, Mohammad Shahid, Antje Wolf, Bernd Müller, Martin Hofmann-Apitius
Bioinformatics. 2011 June 15; 27(12): 1684–1690. Published online 2011 May 5. doi: 10.1093/bioinformatics/btr256
PMCID:
PMC3106195
Free in PMC on 2012/06/15
Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles
Richard Tzong-Han Tsai, Po-Ting Lai
BMC Bioinformatics. 2011; 12: 60. Published online 2011 February 23. doi: 10.1186/1471-2105-12-60
PMCID:
PMC3053256
Abstract Full Text PDF–551K
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
Semi-automatic semantic annotation of PubMed Queries: a study on quality, efficiency, satisfaction
Aurélie Névéol, Rezarta Islamaj-Doğan, Zhiyong Lu
J Biomed Inform. Author manuscript; available in PMC 2012 April 1.
Published in final edited form as: J Biomed Inform. 2011 April; 44(2): 310–318. Published online 2010 November 20. doi: 10.1016/j.jbi.2010.11.001
PMCID:
PMC3063330
Abstract Full Text PDF–706K Supplementary Material
NEMO: Extraction and normalization of organization names from PubMed affiliation strings
Siddhartha Jonnalagadda, Philip Topham
J Biomed Discov Collab. 2010; 5: 50–75. Published online 2010 October 4.
PMCID:
PMC2990275
Abstract Full Text PDF–866K Supplementary Material
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
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
Exploring species-based strategies for gene normalization
Karin Verspoor, Christophe Roeder, Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner, Jr., Lawrence E. Hunter
IEEE/ACM Trans Comput Biol Bioinform. Author manuscript; available in PMC 2010 August 30.
Published in final edited form as: IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul–Sep; 7(3): 462–471. doi: 10.1109/TCBB.2010.48
PMCID:
PMC2929766
Abstract Full Text PDF–270K
Moara: a Java library for extracting and normalizing gene and protein mentions
Mariana L Neves, José-María Carazo, Alberto Pascual-Montano
BMC Bioinformatics. 2010; 11: 157. Published online 2010 March 26. doi: 10.1186/1471-2105-11-157
PMCID:
PMC2851609
Abstract Full Text PDF–3.1M
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
BIOADI: a machine learning approach to identifying abbreviations and definitions in biological literature
Cheng-Ju Kuo, Maurice HT Ling, Kuan-Ting Lin, Chun-Nan Hsu
BMC Bioinformatics. 2009; 10(Suppl 15): S7. Published online 2009 December 3. doi: 10.1186/1471-2105-10-S15-S7
PMCID:
PMC2788358
Abstract Full Text PDF–321K
Novel Protein-Protein Interactions Inferred from Literature Context
Herman H. H. B. M. van Haagen, Peter A. C. 't Hoen, Alessandro Botelho Bovo, Antoine de Morrée, Erik M. van Mulligen, Christine Chichester, Jan A. Kors, Johan T. den Dunnen, Gert-Jan B. van Ommen, Silvère M. van der Maarel, Vinícius Medina Kern, Barend Mons, Martijn J. Schuemie
PLoS One. 2009; 4(11): e7894. Published online 2009 November 18. doi: 10.1371/journal.pone.0007894
PMCID:
PMC2774517
Abstract Full Text PDF–128K Supplementary Material
Extraction of human kinase mutations from literature, databases and genotyping studies
Martin Krallinger, Jose MG Izarzugaza, Carlos Rodriguez-Penagos, Alfonso Valencia
BMC Bioinformatics. 2009; 10(Suppl 8): S1. Published online 2009 August 27. doi: 10.1186/1471-2105-10-S8-S1
PMCID:
PMC2745582
Abstract Full Text PDF–1.6M Supplementary Material
SciMiner: web-based literature mining tool for target identification and functional enrichment analysis
Junguk Hur, Adam D. Schuyler, David J. States, Eva L. Feldman
Bioinformatics. 2009 March 15; 25(6): 838–840. Published online 2009 February 2. doi: 10.1093/bioinformatics/btp049
PMCID:
PMC2654801
Abstract Full Text PDF–69K Supplementary Material
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