K. Bretonnel Cohen

Udo Hahn, Kevin Bretonnel Cohen, Yael Garten, Nigam H. Shah: Mining the pharmacogenomics literature - a survey of the state of the art. Briefings in Bioinformatics 13(4): 460-494 (2012)

Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A. Baumgartner Jr., K. Bretonnel Cohen, Karin Verspoor, Judith A. Blake, Lawrence E. Hunter: Concept annotation in the CRAFT corpus. BMC Bioinformatics 13: 161 (2012)

Karin Verspoor, Kevin Bretonnel Cohen, Arrick Lanfranchi, Colin Warner, Helen L. Johnson, Christophe Roeder, Jinho D. Choi, Christopher Funk, Yuriy Malenkiy, Miriam Eckert, Nianwen Xue, William A. Baumgartner Jr., Michael Bada, Martha Palmer, Lawrence E. Hunter: A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. BMC Bioinformatics 13: 207 (2012)

Adrien Coulet, K. Bretonnel Cohen, Russ B. Altman: The state of the art in text mining and natural language processing for pharmacogenomics. Journal of Biomedical Informatics 45(5): 825-826 (2012)

Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, Alberto D. Pascual-Montano, Arzucan Özgür, Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii: U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics 12: 481 (2011)

Cecilia N. Arighi, Zhiyong Lu, Martin Krallinger, Kevin Bretonnel Cohen, W. John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H. Wu: Overview of the BioCreative III Workshop. BMC Bioinformatics 12(S-8): S1 (2011)

K. Bretonnel Cohen, Karin Verspoor, Helen L. Johnson, Christophe Roeder, Philip V. Ogren, William A. Baumgartner Jr., Elizabeth K. White, Hannah J. Tipney, Lawrence Hunter: High-Precision Biological Event Extraction: Effects of System and of Data. Computational Intelligence 27(4): 681-701 (2011)

Karën Fort, Gilles Adda, K. Bretonnel Cohen: Amazon Mechanical Turk: Gold Mine or Coal Mine? Computational Linguistics 37(2): 413-420 (2011)

Yoshinobu Kano, Makoto Miwa, K. Bretonnel Cohen, Lawrence Hunter, Sophia Ananiadou, Jun'ichi Tsujii: U-Compare: A modular NLP workflow construction and evaluation system. IBM Journal of Research and Development 55(3): 11 (2011)

K. Bretonnel Cohen, Lawrence Hunter, Martha Palmer: A scaleable automated quality assurance technique for semantic representations and proposition banks. Linguistic Annotation Workshop 2011: 82-91

Kevin Bretonnel Cohen, Yael Garten, Udo Hahn, Nigam H. Shah: Workshop Introduction. Pacific Symposium on Biocomputing 2011: 362-363

K. Bretonnel Cohen, Tom Christiansen, Lawrence E. Hunter: MetaMap is a Superior Baseline to a Standard Document Retrieval Engine for the Task of Finding Patient Cohorts in Clinical Free Text. TREC 2011

K. Bretonnel Cohen, Helen L. Johnson, Karin Verspoor, Christophe Roeder, Lawrence Hunter: The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC Bioinformatics 11: 492 (2010)

Karin Verspoor, Christophe Roeder, Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter: Exploring Species-Based Strategies for Gene Normalization. IEEE/ACM Trans. Comput. Biology Bioinform. 7(3): 462-471 (2010)

Carsten Görg, Hannah J. Tipney, Karin Verspoor, William A. Baumgartner Jr., K. Bretonnel Cohen, John T. Stasko, Lawrence Hunter: Visualization and Language Processing for Supporting Analysis across the Biomedical Literature. KES (4) 2010: 420-429

K. Bretonnel Cohen, Christophe Roeder, William A. Baumgartner Jr., Lawrence Hunter, Karin Verspoor: Test Suite Design for Biomedical Ontology Concept Recognition Systems. LREC 2010

Karin Verspoor, Daniel Dvorkin, K. Bretonnel Cohen, Lawrence Hunter: Ontology quality assurance through analysis of term transformations. Bioinformatics 25(12) (2009)

Yoshinobu Kano, William A. Baumgartner Jr., Luke McCrohon, Sophia Ananiadou, K. Bretonnel Cohen, Lawrence Hunter, Jun'ichi Tsujii: U-Compare: share and compare text mining tools with UIMA. Bioinformatics 25(15): 1997-1998 (2009)

Karin Verspoor, K. Bretonnel Cohen, Lawrence Hunter: The textual characteristics of traditional and Open Access scientific journals are similar. BMC Bioinformatics 10 (2009)

Thomas C. Wiegers, Allan Peter Davis, K. Bretonnel Cohen, Lynette Hirschman, Carolyn J. Mattingly: Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD). BMC Bioinformatics 10: 326 (2009)

Wendy Webber Chapman, K. Bretonnel Cohen: Current issues in biomedical text mining and natural language processing. Journal of Biomedical Informatics 42(5): 757-759 (2009)

Dina Demner-Fushman, Sophia Ananiadou, K. Bretonnel Cohen, John Pestian, Jun'ichi Tsujii, Bonnie L. Webber: Themes in biomedical natural language processing: BioNLP08. BMC Bioinformatics 9(S-11) (2008)

Lawrence Hunter, Zhiyong Lu, James Firby, William A. Baumgartner Jr., Helen L. Johnson, Philip V. Ogren, K. Bretonnel Cohen: OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinformatics 9 (2008)

K. Bretonnel Cohen, Lawrence Hunter: Getting Started in Text Mining. PLoS Computational Biology 4(1) (2008)

Zhang-Zhi Hu, K. Bretonnel Cohen, Lynette Hirschman, Alfonso Valencia, Hongfang Liu, Michelle G. Giglio, Cathy H. Wu: iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology. BIBM 2008: 467-472

K. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman: Session Introduction. Pacific Symposium on Biocomputing 2008: 551-555

J. Gregory Caporaso, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, Lawrence Hunter: Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks. Pacific Symposium on Biocomputing 2008: 640-651

J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter: MutationFinder: a high-performance system for extracting point mutation mentions from text. Bioinformatics 23(14): 1862-1865 (2007)

J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter: Rapid Pattern Development for Concept Recognition Systems: Application to Point mutations. J. Bioinformatics and Computational Biology 5(6): 1233-1259 (2007)

William A. Baumgartner Jr., K. Bretonnel Cohen, Lynne M. Fox, George K. Acquaah-Mensah, Lawrence Hunter: Manual curation is not sufficient for annotation of genomic databases. ISMB/ECCB (Supplement of Bioinformatics) 2007: 41-48

K. Bretonnel Cohen: BioNLP. HLT-NAACL (Tutorial Abstracts) 2007: 1-2

Pierre Zweigenbaum, Dina Demner-Fushman, Hong Yu, K. Bretonnel Cohen: Session Introduction. Pacific Symposium on Biocomputing 2007: 205-208

Helen L. Johnson, K. Bretonnel Cohen, Lawrence Hunter: A Fault Model for Ontology Mapping, Alignment, and Linking Systems. Pacific Symposium on Biocomputing 2007: 233-268

Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter: Generif Quality Assurance as Summary Revision. Pacific Symposium on Biocomputing 2007: 269-280

K. Bretonnel Cohen, Lawrence Hunter: A critical review of PASBio's argument structures for biomedical verbs. BMC Bioinformatics 7(S-3) (2006)

K. Bretonnel Cohen, Olivier Bodenreider, Lynette Hirschman: Session Introduction. Pacific Symposium on Biocomputing 2006: 1-3

Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, Lawrence Hunter: Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies. Pacific Symposium on Biocomputing 2006: 28-39

Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter: Finding GeneRIFs via Gene Ontology Annotations. Pacific Symposium on Biocomputing 2006: 52-63

J. Gregory Caporaso, William A. Baumgartner Jr., Hyunmin Kim, Zhiyong Lu, Helen L. Johnson, Olga Medvedeva, Anna Lindemann, Lynne M. Fox, Elizabeth K. White, K. Bretonnel Cohen, Lawrence Hunter: Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question-Answering. TREC 2006

Shuhei Kinoshita, K. Bretonnel Cohen, Philip V. Ogren, Lawrence Hunter: BioCreAtIvE Task1A: entity identification with a stochastic tagger. BMC Bioinformatics 6(S-1) (2005)

Philip V. Ogren, K. Bretonnel Cohen, Lawrence Hunter: Implications of Compositionality in the Gene Ontology for Its Curation and Usage . Pacific Symposium on Biocomputing 2005

J. Gregory Caporaso, William A. Baumgartner Jr., K. Bretonnel Cohen, Helen L. Johnson, Jesse Paquette, Lawrence Hunter: Concept Recognition and the TREC Genomics Tasks. TREC 2005

Philip V. Ogren, K. Bretonnel Cohen, George K. Acquaah-Mensah, Jens Eberlein, Lawrence Hunter: The Compositional Structure of Gene Ontology Terms. Pacific Symposium on Biocomputing 2004: 214-225

K. Bretonnel Cohen, Andrew Dolbey, George K. Acquaah-Mensah, Lawrence Hunter: Contrast and variability in gene names. ACL Workshop on Natural Language Processing in the Biomedical Domain 2002: 14-20