Concept Recognition and the TREC Genomics Tasks. - J. Gregory Caporaso; William A. Baumgartner Jr.; K. Bretonnel Cohen; Helen L. Johnson 001; Jesse Paquette; Lawrence Hunter (TREC, 2005)

Refactoring Corpora. - Helen L. Johnson 001; William A. Baumgartner Jr.; Martin Krallinger; K. Bretonnel Cohen; Lawrence Hunter (BioNLP@NAACL-HLT, 2006)

Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies. - Helen L. Johnson 001; K. Bretonnel Cohen; William A. Baumgartner Jr.; Zhiyong Lu; Michael Bada; Todd Kester; Hyunmin Kim; Lawrence Hunter (Pacific Symposium on Biocomputing, 2006)

Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question-Answering. - J. Gregory Caporaso; William A. Baumgartner Jr.; Hyunmin Kim; Zhiyong Lu; Helen L. Johnson 001; Olga Medvedeva; Anna Lindemann; Lynne M. Fox; Elizabeth K. White; K. Bretonnel Cohen; Lawrence Hunter (TREC, 2006)

A Fault Model for Ontology Mapping, Alignment, and Linking Systems. - Helen L. Johnson 001; K. Bretonnel Cohen; Lawrence Hunter (Pacific Symposium on Biocomputing, 2007)

Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP. - Andrew D. Fox; William A. Baumgartner Jr.; Helen L. Johnson 001; Lawrence E. Hunter; Donna K. Slonim (BioLINK@ISMB/ECCB, 2008)

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. - Lawrence Hunter; Zhiyong Lu; James Firby; William A. Baumgartner Jr.; Helen L. Johnson 001; Philip V. Ogren; K. Bretonnel Cohen (BMC Bioinform., 2008)

High-precision biological event extraction with a concept recognizer. - K. Bretonnel Cohen; Karin Verspoor; Helen L. Johnson 001; Christophe Roeder; Philip V. Ogren; William A. Baumgartner Jr.; Elizabeth K. White; Lawrence Hunter (BioNLP@HLT-NAACL (Shared Task), 2009)

Leveraging Gene Ontology Annotations to Improve a Memory-Based Language Understanding System. - Kevin M. Livingston; Helen L. Johnson 001; Karin Verspoor; Lawrence Hunter (ICSC, 2010)

The structural and content aspects of abstracts versus bodies of full text journal articles are different. - K. Bretonnel Cohen; Helen L. Johnson 001; Karin Verspoor; Christophe Roeder; Lawrence Hunter (BMC Bioinform., 2010)

Exploring Species-Based Strategies for Gene Normalization. - Karin Verspoor; Christophe Roeder; Helen L. Johnson 001; K. Bretonnel Cohen; William A. Baumgartner Jr.; Lawrence Hunter (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

High-Precision Biological Event Extraction: Effects of System and of Data. - K. Bretonnel Cohen; Karin Verspoor; Helen L. Johnson 001; Christophe Roeder; Philip V. Ogren; William A. Baumgartner Jr.; Elizabeth K. White; Hannah J. Tipney; Lawrence Hunter (Comput. Intell., 2011)

A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. - Karin Verspoor; Kevin Bretonnel Cohen; Arrick Lanfranchi; Colin Warner; Helen L. Johnson 001; Christophe Roeder; Jinho D. Choi; Christopher S. Funk; Yuriy Malenkiy; Miriam Eckert; Nianwen Xue; William A. Baumgartner Jr.; et al. (BMC Bioinform., 2012)

Acquisition and evaluation of verb subcategorization resources for biomedicine. - Laura Rimell; Thomas Lippincott; Karin Verspoor; Helen L. Johnson 001; Anna Korhonen (J. Biomed. Informatics, 2013)