Publications

2013

• K. Bretonnel Cohen and Lawrence E. Hunter (2013) Text mining for translational bioinformatics. PLOS Computational Biology: Translational Bioinformatics.
• John P. Pestian, Pawel Matykiewicz, K. Bretonnel Cohen, Jacqueline Grupp-Phelan, Linda A. Richey, Gabriel Meyers, Christina M. Canter, and Michael T. Sorter (2013) Suicidal thought markers: A controlled trial examining the language of suicidal adolescents. 46th Annual Conference of the American Association of Suicidology.
• K. Bretonnel Cohen, Lawrence E. Hunter, and Martha Palmer (2013) Assessment of software testing and quality assurance in natural language processing applications and a linguistically inspired approach to improving it. JIMSE.
• Qi Li, Louise Deleger, Todd Lingren, Haijun Zhai, Megan Kaiser, Laura Stoutenborough, Anil G. Jegga, K. Bretonnel Cohen, and Imre Solti (2013) Mining FDA drug labels for medical conditions. BMC Medical Informatics and Decision Making 13:53.

2012

• Karin Verspoor, Kevin Cohen, Arrick Lanfranchi, Colin Warner, Helen L Johnson, Christophe Roeder, Jinho D. Choi, Christopher Funk, Yuriy Malenkiy, Miriam Eckert, Nianwen Xue, William A. Baumgartner, Michael Bada, Martha Palmer, and Lawrence E. Hunter (2012) 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.
• Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A Baumgartner, Kevin Cohen, Karin Verspoor, Judith A Blake, and Lawrence E. Hunter (2012) Concept annotation in the CRAFT corpus. BMC Bioinformatics 13:161.
• Lynette Hirschman, Gully A. P. C Burns, Martin Krallinger, Cecilia Arighi, K. Bretonnel Cohen, Alfonso Valencia, Cathy H. Wu, Andrew Chatr-Aryamontri, Karen G. Dowell, Eva Huala, Analia Lourenco, Robert Nash, Anne-Lise Veuthey, Thomas Wiegers, and Andrew G. Winter (2012) Text mining for the biocuration workflow. DATABASE: The journal of biological databases and curation.
• K. Bretonnel Cohen, Tom Christiansen, and Lawrence E. Hunter (2011) MetaMap is a superior baseline to a standard document retrieval engine for the task of finding patient cohorts in clinical free text. 20th Text Retrieval Conference.
• Irina Temnikova and K. Bretonnel Cohen (2012) The Crisis Management Corpus and its application to the study of the crisis management sub-language. Language Resources for Public Security Applications.
• Adrien Coulet, K. Bretonnel Cohen, and Russ B. Altman (2012) The state of the art in text mining and natural language processing for pharmacogenomics. Journal of Biomedical Informatics 45(5):825-826.
• John P. Pestian, Pawel Matykiewicz, Michelle Linn-Gust, Brett South, Ozlem Uzuner, Jan Wiebe, K. Bretonnel Cohen, John Hurdle, and Christopher Brew (2012) Sentiment analysis of suicide notes: A shared task. Biomedical Informatics Insights 2012:5 (Suppl. 1) 1-14.
• Yoshinobu Kano, Jari Bjorne, 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 Neves, Alberto Pascual-Montano, Arzucan Ozgur, Dragomir R. Radev, Sebastian Riedel, Rune Saetre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, and Jun'ichi Tsujii (2011) U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics 12:481.

2011

• K. Bretonnel Cohen, Thomas Christiansen, William A. Baumgartner Jr., Karin Verspoor, and Lawrence E. Hunter (2011) Fast and simple semantic class assignment for biomedical text. BioNLP 2011, pp. 38-45.
• K. Bretonnel Cohen, Lawrence E. Hunter, and Martha Palmer (2011) A scaleable automated quality assurance technique for semantic representations and proposition banks. Linguistic Annotation Workshop V, pp. 82-91.
• K. Bretonnel Cohen, Thomas Christiansen, and Lawrence E. Hunter (2011) Parenthetically speaking: Classifying the contents of parentheses for text mining. AMIA 2011, pp. 267-272.
• K. Bretonnel Cohen, Karin Verspoor, Helen L. Johnson, Christophe Roeder, Philip V. Ogren, William A. Baumgartner Jr., Elizabeth White, Hannah Tipney, and Lawrence Hunter (accepted) High-precision biological event extraction: Effects of system and data. (preprint) Computational Intelligence.
• Cecilia N. Arighi, Zhiyong Lu, Martin Krallinger, Kevin B. Cohen, W. John Wilbur, Alfonso Valencia, Lynette Hirschman, and Cathy H. Wu (2011) Overview of the BioCreative III workshop. BMC Bioinformatics 12(Suppl. 8).

2010

• K. Bretonnel Cohen, Helen L. Johnson, Karin Verspoor, Christophe Roeder, and Lawrence E. Hunter (2010) The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC Bioinformatics 11:492.
• K. Bretonnel Cohen, Christophe Roeder, William A. Baumgartner Jr., Lawrence Hunter, and Karin Verspoor (2010) Test suite design for biomedical ontology concept recognition systems. Language Resources and Evaluation Conference, pp. 441-446.
• K. Bretonnel Cohen (2010) Biomedical text mining. Chapter 27 of Handbook of natural language processing, 2nd edition, Nitin Indurkhya and Fred J. Damerau, editors. Write me for uncorrected proofs.
• Karin Verspoor, Christophe Roeder, Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., and Lawrence Hunter (2010) Exploring species-based strategies for gene normalization. IEEE/ACM Transactions in Computational Biology and Bioinformatics 7(3):462-471.
• K. Bretonnel Cohen, Arrick Lanfranchi, William Corvey, William A. Baumgartner Jr., Christophe Roeder, Philip V. Ogren, Martha Palmer, and Lawrence Hunter (2010) Annotation of all coreference in biomedical text: Guideline selection and adaptation. BioTxtM 2010: 2nd workshop on building and evaluating resources for biomedical text mining, pp. 37-41.
• Cartic Ramakrishnan, William A. Baumgartner Jr., Judith A. Blake, Gully A.P.C. Burns, K. Bretonnel Cohen, Harold Drabkin, Janan Eppig, Eduard Hovy, Chun-Nan Hsu, Lawrence E. Hunter, Tommy Ingulfsen, Hiroaki 'Rocky' Onda, Sandeep Pokkunuri, Ellen Riloff, Christophe Roeder, and Karin Verspoor (2010) Building the Scientific Knowledge Mine (SciKnowMine): A community-driven framework for text mining tools in direct service to biocuration. New challenges for NLP frameworks, pp. 9-14.
• Carsten Goerg, Hannah Tipney, Karin Verspoor, William A. Baumgartner Jr., K. Bretonnel Cohen, John Stasko, and Lawrence E. Hunter (2010) Visualization and language processing for supporting analysis across the biomedical literature. Workshop on 3D visualization of natural language, 14th international conference on knowledge-based and intelligent information and engineering systems.

2009

• Karin Verspoor, Daniel Dvorkin, K. Bretonnel Cohen, and Lawrence Hunter (2009) Ontology quality assurance through analysis of term transformations. Bioinformatics 25(12):i77-i84.
• K. Bretonnel Cohen, Karin Verspoor, Helen L. Johnson, Chris Roeder, Philip V. Ogren, William A. Baumgartner Jr., Elizabeth White, Hannah Tipney, and Lawrence Hunter (2009) High-precision biological event extraction with a concept recognizer. BioNLP 2009 Companion Volume: Shared Task on Event Extraction, pp. 50-58.
• Thomas C. Wiegers, Allan P. Davis, K. Bretonnel Cohen, Lynette Hirschman, and Carolyn J. Mattingly (2009) Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD). BMC Bioinformatics 10:326.
• Wendy Chapman and K. Bretonnel Cohen (2009) Current issues in biomedical text mining and natural language processing. Journal of Biomedical Informatics 42(5):757-759.
• Karin Verspoor, K. Bretonnel Cohen, and Lawrence Hunter (2009) The textual characteristics of traditional and Open Access scientific journals are similar. BMC Bioinformatics 10:183.
• Yoshinobu Kano, William A. Baumgartner Jr., Luke McCrohon, Sophia Ananiadou, K. Bretonnel Cohen, Lawrence Hunter, and Jun'ichi Tsujii (2009) U-Compare: share and compare text mining tools with UIMA. Bioinformatics 25(15):1997-1998.

2008

• K. Bretonnel Cohen, Martha Palmer, and Lawrence Hunter (2008) Nominalization and alternations in biomedical language. PLoS ONE 3(9).
• K. Bretonnel Cohen, William A. Baumgartner Jr., and Lawrence Hunter (2008) Software testing and the naturally occurring data assumption in natural language processing. Software engineering, testing, and quality assurance for natural language processing 2008, pp. 23-30. Association for Computational Linguistics.
• William A. Baumgartner Jr., Zhiyong Lu, Helen L. Johnson, J. Gregory Caporaso, Jesse Paquette, Anna Lindemann, Elizabeth K. White, Olga Medvedeva, K. Bretonnel Cohen, and Lawrence Hunter (2008) Concept recognition for extracting protein interaction relations from biomedical text. Genome Biology 9(Suppl. 2).
• Alexander A. Morgan, 17 other people, K. Bretonnel Cohen, and Lynette Hirschman (2008) Overview of BioCreative II gene normalization. Genome Biology 9(Suppl. 2).
• Lynette Hirschman, Cheryl Clark, K. Bretonnel Cohen, et al. (2008) Habitat-Lite: A GSC case study based on free text terms for environmental metadata. OMICS: A Journal of Integrative Biology 12(2).
• K. Bretonnel Cohen and Lawrence Hunter (2008) Getting started in text mining. PLoS Computational Biology 4(1).
• Guergana Savova, Cheryl Clark, Jiaping Zheng, K. Bretonnel Cohen, Sean Murphy, Ben Wellner, David Harris, Marcia Lazo, John Aberdeen, Qian Hu, Christopher Chute, and Lynette Hirschman (2008) The Mayo/MITRE system for discovery of obesity and its comorbidities. Proceedings of the i2b2 Workshop on Challenges in Natural Language Processing for Clinical Data 2008.
• William A. Baumgartner Jr., K. Bretonnel Cohen, and Lawrence Hunter An open-source framework for large-scale, flexible evaluation of biomedical text mining systems Journal of Biomedical Discovery and Collaboration 3:1.
• Lawrence Hunter, Zhiyong Lu, James Firby, William A. Baumgartner Jr., Helen L. Johnson, Philip V. Ogren, and K. Bretonnel Cohen (2008) OpenDMAP: An open-source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-specific gene expression. BMC Bioinformatics 9(78).
• J. Gregory Caporaso, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, and Lawrence Hunter (2008) Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pacific Symposium on Biocomputing 13:640-651.

2007

• Pierre Zweigenbaum, Dina Demner-Fushman, Hong Yu, and Kevin B. Cohen (2007) Frontiers of biomedical text mining: current progress. Briefings in Bioinformatics 8:358-375.
• John P. Pestian, Chris Brew, Pawel Matykiewicz, DJ Hovermale, Neil Johnson, K. Bretonnel Cohen, and Wlodzislaw Duch (2007) A shared task involving multi-label classification of clinical free text. BioNLP 2007: Biological, translational, and clinical language processing, pp. 97-104.
• William A. Baumgartner Jr., K. Bretonnel Cohen, Lynne Fox, George Acquaah-Mensah, and Lawrence Hunter (in press, July 2007) Manual annotation is not sufficient for curating genomic databases. Bioinformatics 23:i41-i48.
• J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, and Lawrence Hunter (in press, Dec. 2007) Developing high-performance information extraction systems by bootstrapping automatic regular expression generation. Journal of Bioinformatics and Computational Biology 5(6):1233-1259.
• Helen L. Johnson, William A. Baumgartner Jr., Martin Krallinger, K. Bretonnel Cohen, and Lawrence Hunter (2007) Corpus refactoring: a feasibility study. Journal of Biomedical Discovery and Collaboration 2:4.
• J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, and Lawrence Hunter (2007) MutationFinder: A high-performance system for extracting point mutations from text. Bioinformatics 23(14):1862-1865.
• Helen L. Johnson, K. Bretonnel Cohen, and Lawrence Hunter (2007) A fault model for ontology mapping, alignment, and linking systems. Pacific Symposium on Biocomputing 12:233-244.
• Zhiyong Lu, K. Bretonnel Cohen, and Lawrence Hunter (2007) GeneRIF quality assurance as summary revision. Pacific Symposium on Biocomputing 12:269-280.

2006

• K. Bretonnel Cohen and Lawrence Hunter (2006) A critical review of PASBio's argument structures for biomedical verbs. BMC Bioinformatics 7(Suppl. 3):S5.
• Lawrence Hunter and K. Bretonnel Cohen (2006) Biomedical language processing: what's beyond PubMed? Molecular Cell 21:589-594.
• J. Gregory Caporaso, William A. Baumgartner Jr., Hyunmin Kim, Zhiyong Lu, Helen L. Johnson, Olga Medvedeva, Anna Lindemann, Lynne Fox, Elizabeth White, K. Bretonnel Cohen, and Lawrence Hunter (2006) Concept recognition, information retrieval, and machine learning in genomics question-answering (2006) Proceedings of the Fifteenth Text Retrieval Conference.
• Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, and Lawrence Hunter (2006) Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies. Pacific Symposium on Biocomputing 11:28-39.
• Zhiyong Lu, K. Bretonnel Cohen, and Lawrence Hunter (2006) Finding GeneRIFs via Gene Ontology annotations. Pacific Symposium on Biocomputing 11:52-63.

2005

• J. Gregory Caporaso, William A. Baumgartner Jr., K. Bretonnel Cohen, Helen L. Johnson, Jesse Paquette, and Lawrence Hunter (2005) Concept recognition and the TREC Genomics tasks. Proceedings of the Fourteenth Text Retrieval Conference, National Institute of Standards and Technology.
• K. Bretonnel Cohen, Lynne Fox, Philip V. Ogren, and Lawrence Hunter (2005). Corpus design for biomedical natural language processing. Proceedings of the ACL-ISMB workshop on linking biological literature, ontologies and databases, pp. 38-45. Association for Computational Linguistics.
• Cohen, K. Bretonnel; Lynne Fox; Philip Ogren; and Lawrence Hunter (2005). Empirical data on corpus design and usage in biomedical natural language processing. AMIA 2005 symposium proceedings, pp. 156-160.
• Shuhei Kinoshita, K. Bretonnel Cohen, Philip V. Ogren, and Lawrence Hunter (2005). BioCreative Task 1A: entity identification with a stochastic tagger. BMC Bioinformatics 6(Suppl. 1):S4.
• Philip V. Ogren, K. Bretonnel Cohen, and Lawrence Hunter (2005). Implications of compositionality in the Gene Ontology for its curation and usage. Pacific Symposium on Biocomputing 2005, pp. 174-185.

2004

• K. Bretonnel Cohen and Lawrence Hunter (2004) Natural language processing and systems biology. In Dubitzky and Pereira, Artificial intelligence methods and tools for systems biology. Springer Verlag.
• K. Bretonnel Cohen, Lorraine Tanabe, Shuhei Kinoshita, and Lawrence Hunter (2004). A resource for constructing customized test suites for molecular biology entity identification systems. BioLINK 2004: Linking biological literature, ontologies, and databases: tools for users, pp. 1-8. Association for Computational Linguistics.
• Philip V. Ogren, K. Bretonnel Cohen, George K. Acquaah-Mensah, Jens Eberlein, and Lawrence Hunter (2004). The compositional structure of Gene Ontology terms. Proceedings of the Pacific Symposium on Biocomputing 2004, pp. 214-225.

2002

• K. Bretonnel Cohen, Andrew E. Dolbey, George K. Acquaah-Mensah, and Lawrence Hunter (2002). Contrast and variability in gene names. Proceedings of the workshop on natural language processing in the biomedical domain, pp. 14-20. Association for Computational Linguistics.

2000

• Kevin Bretonnel Cohen (2000). Aspects of the grammar of Kukú. LINCOM-EUROPA.
• Beckman, M. E., & Cohen, K. B. (2000). Modeling the articulatory dynamics of two levels of stress contrast. In M. Horne, ed., Prosody: Theory and Experiment. Studies Presented to Gosta Bruce, pp. 169-200. Kluwer.

1995

• Beckman, M. E., Jung, T.-P., Lee, S., de Jong, K., Krishnamurthy, A. K., Ahalt, S. C., Cohen, K. B. & Collins, M. (1995). Variability in the production of quantal vowels revisited. Journal of the Acoustical Society of America, 97(1), 471-490.