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

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

Natural Language Processing and Systems Biology. - K. Bretonnel Cohen; Lawrence Hunter (Artificial Intelligence Methods And Tools For Systems Biology, 2004)

Empirical data on corpus design and usage in biomedical natural language processing. - K. Bretonnel Cohen; Philip V. Ogren; Lynne M. Fox; Lawrence Hunter (AMIA, 2005)

Corpus Design for Biomedical Natural Language Processing. - K. Bretonnel Cohen; Lynne M. Fox; Philip V. Ogren; Lawrence Hunter (LBLODMBS@IDMB, 2005)

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

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)

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

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

Session Introduction. - K. Bretonnel Cohen; Olivier Bodenreider; Lynette Hirschman (Pacific Symposium on Biocomputing, 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)

Finding GeneRIFs via Gene Ontology Annotations. - Zhiyong Lu; K. Bretonnel Cohen; 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 critical review of PASBio's argument structures for biomedical verbs. - K. Bretonnel Cohen; Lawrence Hunter (BMC Bioinform., 2006)

A shared task involving multi-label classification of clinical free text. - John P. Pestian; Chris Brew; Pawel Matykiewicz; D. J. Hovermale; Neil Johnson; K. Bretonnel Cohen; Wlodzislaw Duch (BioNLP@ACL, 2007)

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

BioNLP. - K. Bretonnel Cohen (HLT-NAACL (Tutorial Abstracts), 2007)

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

Generif Quality Assurance as Summary Revision. - Zhiyong Lu; K. Bretonnel Cohen; Lawrence Hunter (Pacific Symposium on Biocomputing, 2007)

Session Introduction. - Pierre Zweigenbaum; Dina Demner-Fushman; Hong Yu 001; K. Bretonnel Cohen (Pacific Symposium on Biocomputing, 2007)

Frontiers of biomedical text mining: current progress. - Pierre Zweigenbaum; Dina Demner-Fushman; Hong Yu 001; Kevin Bretonnel Cohen (Briefings Bioinform., 2007)

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

Rapid Pattern Development for Concept Recognition Systems: Application to Point mutations. - J. Gregory Caporaso; William A. Baumgartner Jr.; David A. Randolph; K. Bretonnel Cohen; Lawrence Hunter (J. Bioinform. Comput. Biol., 2007)

Software Testing and the Naturally Occurring Data Assumption in Natural Language Processing. - K. Bretonnel Cohen; William A. Baumgartner Jr.; Lawrence Hunter (SETQALNLP, 2008)

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

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

Session Introduction. - K. Bretonnel Cohen; Hong Yu 001; Philip E. Bourne; Lynette Hirschman (Pacific Symposium on Biocomputing, 2008)

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

Getting Started in Text Mining. - K. Bretonnel Cohen; Lawrence Hunter (PLoS Comput. Biol., 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)

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

Ontology quality assurance through analysis of term transformations. - Karin Verspoor; Daniel Dvorkin; K. Bretonnel Cohen; Lawrence Hunter (Bioinform., 2009)

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

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

Current issues in biomedical text mining and natural language processing. - Wendy Webber Chapman; K. Bretonnel Cohen (J. Biomed. Informatics, 2009)

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

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

Integrating text mining into high-throughput assay analysis. - Kevin Bretonnel Cohen (BMC Bioinform., 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)

BioNLP. - K. Bretonnel Cohen (Handbook of Natural Language Processing, 2010)

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

Fast and simple semantic class assignment for biomedical text. - K. Bretonnel Cohen; Tom Christiansen; William A. Baumgartner Jr.; Karin Verspoor; Lawrence Hunter (BioNLP@ACL, 2011)

Hypothesis and Evidence Extraction from Full-Text Scientific Journal Articles. - Elizabeth K. White; K. Bretonnel Cohen; Lawrence Hunter (BioNLP@ACL, 2011)

Workshop Introduction. - Kevin Bretonnel Cohen; Yael Garten; Udo Hahn; Nigam H. Shah (Pacific Symposium on Biocomputing, 2011)

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

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

U-Compare bio-event meta-service: compatible BioNLP event extraction services. - 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; et al. (BMC Bioinform., 2011)

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)

Amazon Mechanical Turk: Gold Mine or Coal Mine? - Karën Fort; Gilles Adda; K. Bretonnel Cohen (Comput. Linguistics, 2011)

U-Compare: A modular NLP workflow construction and evaluation system. - Yoshinobu Kano; Makoto Miwa; K. Bretonnel Cohen; Lawrence Hunter; Sophia Ananiadou; Jun'ichi Tsujii (IBM J. Res. Dev., 2011)

Assessment of Software Testing and Quality Assurance in Natural Language Processing Applications and a Linguistically Inspired Approach to Improving It. - K. Bretonnel Cohen; Lawrence E. Hunter; Martha Palmer (EternalS@ECAI, 2012)

Session introduction. - Kevin Bretonnel Cohen; Yael Garten; Nigam Shah; Udo Hahn (Pacific Symposium on Biocomputing, 2012)

Mining the pharmacogenomics literature - a survey of the state of the art. - Udo Hahn; Kevin Bretonnel Cohen; Yael Garten; Nigam H. Shah (Briefings Bioinform., 2012)

Text mining for the biocuration workflow. - Lynette Hirschman; Gully A. P. C. Burns; Martin Krallinger; Cecilia N. Arighi; K. Bretonnel Cohen; Alfonso Valencia; Cathy H. Wu; Andrew Chatr-aryamontri; Karen G. Dowell; Eva Huala; Anália Lourenço; Robert S. Nash; et al. (Database J. Biol. Databases Curation, 2012)

BioCreative-2012 Virtual Issue. - Cathy H. Wu; Cecilia N. Arighi; Kevin Bretonnel Cohen; Lynette Hirschman; Martin Krallinger; Zhiyong Lu; Carolyn J. Mattingly; Alfonso Valencia; Thomas C. Wiegers; W. John Wilbur (Database J. Biol. Databases Curation, 2012)

Concept annotation in the CRAFT corpus. - 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 (BMC Bioinform., 2012)

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)

The state of the art in text mining and natural language processing for pharmacogenomics. - Adrien Coulet; K. Bretonnel Cohen; Russ B. Altman (J. Biomed. Informatics, 2012)

Evaluation of SPARQL query generation from natural language questions. - K. Bretonnel Cohen; Jin-Dong Kim (SWAIE@RANLP, 2013)

Earlier Identification of Epilepsy Surgery Candidates Using Natural Language Processing. - Pawel Matykiewicz; Kevin Bretonnel Cohen; Katherine D. Holland; Tracy A. Glauser; Shannon M. Standridge; Karin M. Verspoor; John Pestian (BioNLP@ACL, 2013)

Recognizing Sublanguages in Scientific Journal Articles through Closure Properties. - Irina P. Temnikova; Kevin Bretonnel Cohen (BioNLP@ACL, 2013)

Session introduction. - Graciela Gonzalez 001; Kevin Bretonnel Cohen; Casey S. Greene; Udo Hahn; Maricel G. Kann; Robert Leaman; Nigam Shah; Jieping Ye (Pacific Symposium on Biocomputing, 2013)

Measuring Closure Properties of Patent Sublanguages. - Irina P. Temnikova; Negacy D. Hailu; Galia Angelova; K. Bretonnel Cohen (RANLP, 2013)

Closure Properties of Bulgarian Clinical Text. - Irina P. Temnikova; Ivelina Nikolova; William A. Baumgartner Jr.; Galia Angelova; K. Bretonnel Cohen (RANLP, 2013)

UColorado_SOM: Extraction of Drug-Drug Interactions from Biomedical Text using Knowledge-rich and Knowledge-poor Features. - Negacy D. Hailu; Lawrence E. Hunter; K. Bretonnel Cohen (SemEval@NAACL-HLT, 2013)

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. - Cecilia N. Arighi; Ben Carterette; K. Bretonnel Cohen; Martin Krallinger; W. John Wilbur; Petra Fey; Robert J. Dodson; Laurel Cooper; Ceri E. Van Slyke; Wasila M. Dahdul; Paula M. Mabee; Donghui Li; et al. (Database J. Biol. Databases Curation, 2013)

BioC: a minimalist approach to interoperability for biomedical text processing. - Donald C. Comeau; Rezarta Islamaj Dogan; Paolo Ciccarese; Kevin Bretonnel Cohen; Martin Krallinger; Florian Leitner; Zhiyong Lu; Yifan Peng 002; Fabio Rinaldi 001; Manabu Torii; Alfonso Valencia; Karin Verspoor; et al. (Database J. Biol. Databases Curation, 2013)

Mining FDA drug labels for medical conditions. - Qi Li 004; Louise Deléger; Todd Lingren; Haijun Zhai; Megan Kaiser; Laura Stoutenborough; Anil G. Jegga; Kevin Bretonnel Cohen; Imre Solti (BMC Medical Informatics Decis. Mak., 2013)

Chapter 16: Text Mining for Translational Bioinformatics. - K. Bretonnel Cohen; Lawrence E. Hunter (PLoS Comput. Biol., 2013)

Temporal Expression Recognition for Cell Cycle Phase Concepts in Biomedical Literature. - Negacy D. Hailu; Natalya Panteleyeva; Kevin Bretonnel Cohen (BioNLP@ACL, 2014)

A repository of semantic types in the MIMIC II database clinical notes. - Richard Osborne; Alan R. Aronson; Kevin Bretonnel Cohen (BioNLP@ACL, 2014)

Sublanguage Corpus Analysis Toolkit: A tool for assessing the representativeness and sublanguage characteristics of corpora. - Irina P. Temnikova; William A. Baumgartner Jr.; Negacy D. Hailu; Ivelina Nikolova; Tony McEnery; Adam Kilgarriff; Galia Angelova; K. Bretonnel Cohen (LREC, 2014)

Ontology Translation: A Case Study on Translating the Gene Ontology from English to German. - Negacy D. Hailu; K. Bretonnel Cohen; Lawrence E. Hunter (NLDB, 2014)

Combining Heterogenous Data for Prediction of Disease Related and Pharmacogenes. - Christopher S. Funk; Lawrence E. Hunter; K. Bretonnel Cohen (Pacific Symposium on Biocomputing, 2014)

Session introduction. - Graciela Gonzalez 001; Kevin Bretonnel Cohen; Robert Leaman; Casey S. Greene; Nigam Shah; Maricel G. Kann; Jieping Ye (Pacific Symposium on Biocomputing, 2014)

BioCreative-IV virtual issue. - Cecilia N. Arighi; Cathy H. Wu; Kevin Bretonnel Cohen; Lynette Hirschman; Martin Krallinger; Alfonso Valencia; Zhiyong Lu; W. John Wilbur; Thomas C. Wiegers (Database J. Biol. Databases Curation, 2014)

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. - Toshiaki Katayama; Mark D. Wilkinson; Kiyoko F. Aoki-Kinoshita; Shuichi Kawashima; Yasunori Yamamoto; Atsuko Yamaguchi; Shinobu Okamoto; Shin Kawano; Jin-Dong Kim; Yue Wang 040; Hongyan Wu; Yoshinobu Kano; et al. (J. Biomed. Semant., 2014)

Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. - Christopher S. Funk; William A. Baumgartner Jr.; Benjamin Garcia; Christophe Roeder; Michael Bada; K. Bretonnel Cohen; Lawrence E. Hunter; Karin Verspoor (BMC Bioinform., 2014)

Research and applications: Assessing the similarity of surface linguistic features related to epilepsy across pediatric hospitals. - Brian Connolly; Pawel Matykiewicz; K. Bretonnel Cohen; Shannon M. Standridge; Tracy A. Glauser; Dennis J. Dlugos; Susan Koh; Eric Tham; John Pestian (J. Am. Medical Informatics Assoc., 2014)

Measuring the readability of medical research journal abstracts. - Samuel J. Severance; K. Bretonnel Cohen (BioNLP@IJCNLP, 2015)

Training the Next Generation of Quantitative Biologists in the Era of Big Data. - Kristine A. Pattin; Anna C. Greene; Russ B. Altman; Kevin Bretonnel Cohen; Elizabeth Wethington; Carsten Görg; Lawrence E. Hunter; Spencer V. Muse; Predrag Radivojac; Jason H. Moore (Pacific Symposium on Biocomputing, 2015)

Replicability of Research in Biomedical Natural Language Processing: a pilot evaluation for a coding task. - Aurélie Névéol; Kevin Bretonnel Cohen; Cyril Grouin; Aude Robert (Louhi@EMNLP, 2016)

Clinical Information Extraction at the CLEF eHealth Evaluation lab 2016. - Aurélie Névéol; Kevin Bretonnel Cohen; Cyril Grouin; Thierry Hamon; Thomas Lavergne; Liadh Kelly; Lorraine Goeuriot; Grégoire Rey; Aude Robert; Xavier Tannier; Pierre Zweigenbaum (CLEF (Working Notes), 2016)

SuperCAT: The (New and Improved) Corpus Analysis Toolkit. - K. Bretonnel Cohen; William A. Baumgartner Jr.; Irina P. Temnikova (LREC, 2016)

Crowdsourcing and curation: perspectives from biology and natural language processing. - Lynette Hirschman; Karën Fort; Stéphanie Boué; Nikos Kyrpides; Rezarta Islamaj Dogan; Kevin Bretonnel Cohen (Database J. Biol. Databases Curation, 2016)

Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition. - Christopher S. Funk; K. Bretonnel Cohen; Lawrence E. Hunter; Karin M. Verspoor (J. Biomed. Semant., 2016)

Introduction. - Karën Fort; Gilles Adda; K. Bretonnel Cohen (Trait. Autom. des Langues, 2016)

Reproducibility in Biomedical Natural Language Processing. - Kevin Bretonnel Cohen; Aurélie Névéol; Jingbo Xia; Negacy D. Hailu; Cyril Grouin; Lawrence E. Hunter; Pierre Zweigenbaum (AMIA, 2017)

A semantic knowledge-base approach to drug-drug interaction discovery. - Ignacio Tripodi; Kevin Bretonnel Cohen; Lawrence E. Hunter (BIBM, 2017)

CLEF eHealth 2017 Multilingual Information Extraction task Overview: ICD10 Coding of Death Certificates in English and French. - Aurélie Névéol; Aude Robert; Robert Anderson; Kevin Bretonnel Cohen; Cyril Grouin; Thomas Lavergne; Grégoire Rey; Claire Rondet; Pierre Zweigenbaum (CLEF (Working Notes), 2017)

Inter-Annotator Agreement and the Upper Limit on Machine Performance: Evidence from Biomedical Natural Language Processing. - Mayla Boguslav; Kevin Bretonnel Cohen (MedInfo, 2017)

Translational Morphosyntax: Distribution of Negation in Clinical Records and Biomedical Journal Articles. - K. Bretonnel Cohen; Foster R. Goss; Pierre Zweigenbaum; Lawrence E. Hunter (MedInfo, 2017)

Semantic Relations in Compound Nouns: Perspectives from Inter-Annotator Agreement. - Prabha Yadav; Elisabetta Jezek; Pierrette Bouillon; Tiffany J. Callahan; Michael Bada; Lawrence E. Hunter; K. Bretonnel Cohen (MedInfo, 2017)

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. - K. Bretonnel Cohen; Arrick Lanfranchi; Miji Joo-young Choi; Michael Bada; William A. Baumgartner Jr.; Natalya Panteleyeva; Karin Verspoor; Martha Palmer; Lawrence E. Hunter (BMC Bioinform., 2017)

A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support. - Brian Connolly; K. Bretonnel Cohen; Daniel Santel; Ulya Bayram; John Pestian (BMC Bioinform., 2017)

Replicability and reproducibility of research results for human language technology: introducing an LRE special section. - António Branco; Kevin Bretonnel Cohen; Piek Vossen; Nancy Ide; Nicoletta Calzolari (Lang. Resour. Evaluation, 2017)

Erratum to: Replicability and reproducibility of research results for human language technology: introducing an LRE special section. - António Branco; Kevin Bretonnel Cohen; Piek Vossen; Nancy Ide; Nicoletta Calzolari (Lang. Resour. Evaluation, 2017)

CRF-LSTM Text Mining Method Unveiling the Pharmacological Mechanism of Off-target Side Effect of Anti-Multiple Myeloma Drugs. - Kaiyin Zhou; Sheng Zhang; Xiangyu Meng; Qi Luo; Yuxing Wang; Ke Ding; Yukun Feng; Mo Chen; Kevin Cohen 001; Jingbo Xia (BioNLP, 2018)

Guideline Design of an Active Gene Annotation Corpus for the Purpose of Drug Repurposing. - Yuxing Wang; Xinzhi Yao; Kaiyin Zhou; Xuan Qin; Jin-Dong Kim; Kevin Bretonnel Cohen; Jingbo Xia (CISP-BMEI, 2018)

Trigger Words Detection by Integrating Attention Mechanism into Bi-LSTM Neural Network - A Case Study in PubMED-Wide Trigger Words Detection for Pancreatic Cancer. - Kaiyin Zhou; Xinzhi Yao; Shuguang Wang; Jin-Dong Kim; Kevin Bretonnel Cohen; Ruiying Chen; Yuxing Wang; Jingbo Xia (CCL, 2018)

De l'intérêt des ontologies modulaires. Application à la modélisation de la prise en charge de la SLA. - Sonia Cardoso; Xavier Aimé; Vincent Meininger; David Grabli; K. Bretonnel Cohen; Jean Charlet (IC, 2018)

The Curative Power of Medical Data. - Daniela Gîfu; Diana Trandabat; Kevin Bretonnel Cohen; Jingbo Xia (JCDL, 2018)

Three Dimensions of Reproducibility in Natural Language Processing. - K. Bretonnel Cohen; Jingbo Xia; Pierre Zweigenbaum; Tiffany Callahan; Orin Hargraves; Foster R. Goss; Nancy Ide; Aurélie Névéol; Cyril Grouin; Lawrence E. Hunter (LREC, 2018)

A Modular Ontology for Modeling Service Provision in a Communication Network for Coordination of Care. - Sonia Cardoso; Xavier Aimé; Vincent Meininger; David Grabli; Luis Felipe Melo Mora; K. Bretonnel Cohen; Jean Charlet (MIE, 2018)

Improving precision in concept normalization. - Mayla Boguslav; K. Bretonnel Cohen; William A. Baumgartner Jr.; Lawrence E. Hunter (PSB, 2018)

An Active Gene Annotation Corpus and Its Application on Anti-epilepsy Drug Discovery. - Yuxing Wang; Jingbo Xia; Kaiyin Zhou; Jin-Dong Kim; Kevin Cohen 001; Mina Gachloo; Yuxin Ren; Shanghui Nie; Xuan Qin; Panzhong Lu (BIBM, 2019)

P-Hacking Lexical Richness Through Definitions of "Type" and "Token". - K. Bretonnel Cohen; Lawrence E. Hunter; Peter S. Pressman (MedInfo, 2019)

Community Perspective on Replicability in Natural Language Processing. - Margot Mieskes; Karën Fort; Aurélie Névéol; Cyril Grouin; K. Bretonnel Cohen (RANLP, 2019)

Findings of the WMT 2019 Biomedical Translation Shared Task: Evaluation for MEDLINE Abstracts and Biomedical Terminologies. - Rachel Bawden; Kevin Bretonnel Cohen; Cristian Grozea; Antonio Jimeno-Yepes; Madeleine Kittner; Martin Krallinger; Nancy Mah; Aurélie Névéol; Mariana L. Neves; Felipe Soares; Amy Siu; Karin Verspoor; et al. (WMT (3), 2019)

Open Agile text mining for bioinformatics: the PubAnnotation ecosystem. - Jin-Dong Kim; Yue Wang 040; Toyofumi Fujiwara; Shujiro Okuda; Tiffany J. Callahan; K. Bretonnel Cohen (Bioinform., 2019)

Special Issue on the Curative Power of Medical Data. - Daniela Gîfu; Diana Trandabat; Kevin Cohen 001; Jingbo Xia (Data, 2019)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. - Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin-Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang 040; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

Reviewing Natural Language Processing Research. - K. Bretonnel Cohen; Karën Fort; Margot Mieskes; Aurélie Névéol (ACL (tutorial), 2020)

Writing about Data Science Research for Digital Libraries. - K. Bretonnel Cohen; Daniela Gîfu (JCDL, 2020)

MEDA 2020: The Curative Power of Medical Data. - K. Bretonnel Cohen; Daniela Gîfu; Youzhu Li; Anna Ripple; Jingbo Xia (JCDL, 2020)

BioHackathon 2015: Semantics of data for life sciences and reproducible research. - Rutger A. Vos; Toshiaki Katayama; Hiroyuki Mishima; Shin Kawano; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Toshiaki Tokimatsu; Atsuko Yamaguchi; Yasunori Yamamoto; Hongyan Wu; Peter Amstutz; et al. (F1000Research, 2020)

Reproducibility in biomedical natural language processing: A FAIR approach to what we need to know. - Kevin Bretonnel Cohen; Anna M. Ripple; Asma Ben Abacha; Olivier Bodenreider; Orin Hargraves; Karin Verspoor; Pierre Zweigenbaum; Dina Demner-Fushman (AMIA, 2021)

Reviewing Natural Language Processing Research. - Kevin Cohen 001; Karën Fort; Margot Mieskes; Aurélie Névéol; Anna Rogers (EACL (Tutorial Abstracts), 2021)

Bridging heterogeneous mutation data to enhance disease gene discovery. - Kaiyin Zhou; Yuxing Wang; Kevin Bretonnel Cohen; Jin-Dong Kim; Xiaohang Ma; Zhixue Shen; Xiangyu Meng; Jingbo Xia (Briefings Bioinform., 2021)

Unsupervised clinical relevancy ranking of structured medical records to retrieve condition-specific information in the emergency department. - Zfania Tom Korach; Stephen C. Gradwohl; Amanda I. Messinger; Kelly Bookman; Kevin Cohen 001; Li Zhou 007; Foster R. Goss (Int. J. Medical Informatics, 2021)

High-quality gene/disease embedding in a multi-relational heterogeneous graph after a joint matrix/tensor decomposition. - Kaiyin Zhou; Sheng Zhang; Yuxing Wang; Kevin Bretonnel Cohen; Jin-Dong Kim; Qi Luo; Xinzhi Yao; Xingyu Zhou 003; Jingbo Xia (J. Biomed. Informatics, 2022)