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Kevin Cohen 0001

K. Bretonnel Cohen – Kevin Bretonnel Cohen

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affiliation: University of Colorado Denver, School of Medicine, Aurora, CO, USA
affiliation (PhD 2010): University of Colorado Boulder, CO, USA

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2020 – today

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2023
[e24]
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Dina Demner-Fushman, Sophia Ananiadou, Kevin Cohen:
The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, BioNLP@ACL 2023, Toronto, Canada, 13 July 2023. Association for Computational Linguistics 2023 [contents]
2022
[j47]
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Kaiyin Zhou, Sheng Zhang, Yuxing Wang, Kevin Bretonnel Cohen, Jin-Dong Kim, Qi Luo, Xinzhi Yao, Xingyu Zhou, Jingbo Xia:
High-quality gene/disease embedding in a multi-relational heterogeneous graph after a joint matrix/tensor decomposition. J. Biomed. Informatics 126: 103973 (2022)
[e23]
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Dina Demner-Fushman, Kevin Bretonnel Cohen, Sophia Ananiadou, Junichi Tsujii:
Proceedings of the 21st Workshop on Biomedical Language Processing, BioNLP@ACL 2022, Dublin, Ireland, May 26, 2022. Association for Computational Linguistics 2022, ISBN 978-1-955917-27-8 [contents]
2021
[j46]
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Kaiyin Zhou, Yuxing Wang, Kevin Bretonnel Cohen, Jin-Dong Kim, Xiaohang Ma, Zhixue Shen, Xiangyu Meng, Jingbo Xia:
Bridging heterogeneous mutation data to enhance disease gene discovery. Briefings Bioinform. 22(5) (2021)
[j45]
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Zfania Tom Korach, Stephen C. Gradwohl, Amanda I. Messinger, Kelly Bookman, Kevin Cohen, Li Zhou, Foster R. Goss:
Unsupervised clinical relevancy ranking of structured medical records to retrieve condition-specific information in the emergency department. Int. J. Medical Informatics 149: 104410 (2021)
[c73]
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Kevin Bretonnel Cohen, Anna M. Ripple, Asma Ben Abacha, Olivier Bodenreider, Orin Hargraves, Karin Verspoor, Pierre Zweigenbaum, Dina Demner-Fushman:
Reproducibility in biomedical natural language processing: A FAIR approach to what we need to know. AMIA 2021
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Kevin Cohen, Karën Fort, Margot Mieskes, Aurélie Névéol, Anna Rogers:
Reviewing Natural Language Processing Research. EACL (Tutorial Abstracts) 2021: 14-16
[e22]
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Dina Demner-Fushman, Kevin Bretonnel Cohen, Sophia Ananiadou, Junichi Tsujii:
Proceedings of the 20th Workshop on Biomedical Language Processing, BioNLP@NAACL-HLT 2021, Online, June 11, 2021. Association for Computational Linguistics 2021, ISBN 978-1-954085-40-4 [contents]
2020
[c71]
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K. Bretonnel Cohen, Karën Fort, Margot Mieskes, Aurélie Névéol:
Reviewing Natural Language Processing Research. ACL (tutorial) 2020: 16-18
[c70]
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K. Bretonnel Cohen, Daniela Gîfu:
Writing about Data Science Research for Digital Libraries. JCDL 2020: 569-570
[c69]
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K. Bretonnel Cohen, Daniela Gîfu, Youzhu Li, Anna Ripple, Jingbo Xia:
MEDA 2020: The Curative Power of Medical Data. JCDL 2020: 575-576
[e21]
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Dina Demner-Fushman, Kevin Bretonnel Cohen, Sophia Ananiadou, Junichi Tsujii:
Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing, BioNLP 2020, Online, July 9, 2020. Association for Computational Linguistics 2020, ISBN 978-1-952148-09-5 [contents]
[e20]
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Karin Verspoor, Kevin Bretonnel Cohen, Michael Conway, Berry de Bruijn, Mark Dredze, Rada Mihalcea, Byron C. Wallace:
Proceedings of the 1st Workshop on NLP for COVID-19@ EMNLP 2020, Online, December 2020. Association for Computational Linguistics 2020 [contents]
[i2]
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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, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan E. Bolton, Raoul Jean Pierre Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García Castro, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick S. Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy NguyenXuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron R. Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi:
BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research 9: 136 (2020)

2010 – 2019

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2019
[j44]
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Jin-Dong Kim, Yue Wang, Toyofumi Fujiwara, Shujiro Okuda, Tiffany J. Callahan, K. Bretonnel Cohen:
Open Agile text mining for bioinformatics: the PubAnnotation ecosystem. Bioinform. 35(21): 4372-4380 (2019)
[j43]
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Daniela Gîfu, Diana Trandabat, Kevin Cohen, Jingbo Xia:
Special Issue on the Curative Power of Medical Data. Data 4(2): 85 (2019)
[c68]
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Yuxing Wang, Jingbo Xia, Kaiyin Zhou, Jin-Dong Kim, Kevin Cohen, Mina Gachloo, Yuxin Ren, Shanghui Nie, Xuan Qin, Panzhong Lu:
An Active Gene Annotation Corpus and Its Application on Anti-epilepsy Drug Discovery. BIBM 2019: 512-519
[c67]
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K. Bretonnel Cohen, Lawrence E. Hunter, Peter S. Pressman:
P-Hacking Lexical Richness Through Definitions of "Type" and "Token". MedInfo 2019: 1433-1434
[c66]
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Margot Mieskes, Karën Fort, Aurélie Névéol, Cyril Grouin, K. Bretonnel Cohen:
Community Perspective on Replicability in Natural Language Processing. RANLP 2019: 768-775
[c65]
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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, Maika Vicente Navarro:
Findings of the WMT 2019 Biomedical Translation Shared Task: Evaluation for MEDLINE Abstracts and Biomedical Terminologies. WMT (3) 2019: 29-53
[e19]
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Dina Demner-Fushman, Kevin Bretonnel Cohen, Sophia Ananiadou, Junichi Tsujii:
Proceedings of the 18th BioNLP Workshop and Shared Task, BioNLP@ACL 2019, Florence, Italy, August 1, 2019. Association for Computational Linguistics 2019, ISBN 978-1-950737-28-4 [contents]
[i1]
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Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Hidemasa Bono, Jesualdo Tomás Fernández-Breis, Robert M. Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla J. García, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick S. Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Pérez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala M. Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi:
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. F1000Research 8: 1677 (2019)
2018
[c64]
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Kaiyin Zhou, Sheng Zhang, Xiangyu Meng, Qi Luo, Yuxing Wang, Ke Ding, Yukun Feng, Mo Chen, Kevin Cohen, Jingbo Xia:
CRF-LSTM Text Mining Method Unveiling the Pharmacological Mechanism of Off-target Side Effect of Anti-Multiple Myeloma Drugs. BioNLP 2018: 166-171
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Yuxing Wang, Xinzhi Yao, Kaiyin Zhou, Xuan Qin, Jin-Dong Kim, Kevin Bretonnel Cohen, Jingbo Xia:
Guideline Design of an Active Gene Annotation Corpus for the Purpose of Drug Repurposing. CISP-BMEI 2018: 1-5
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Kaiyin Zhou, Xinzhi Yao, Shuguang Wang, Jin-Dong Kim, Kevin Bretonnel Cohen, Ruiying Chen, Yuxing Wang, Jingbo Xia:
Trigger Words Detection by Integrating Attention Mechanism into Bi-LSTM Neural Network - A Case Study in PubMED-Wide Trigger Words Detection for Pancreatic Cancer. CCL 2018: 398-409
[c61]
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Sonia Cardoso, Xavier Aimé, Vincent Meininger, David Grabli, K. Bretonnel Cohen, Jean Charlet:
De l'intérêt des ontologies modulaires. Application à la modélisation de la prise en charge de la SLA. IC 2018: 121-128
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Daniela Gîfu, Diana Trandabat, Kevin Bretonnel Cohen, Jingbo Xia:
The Curative Power of Medical Data. JCDL 2018: 431-432
[c59]
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K. Bretonnel Cohen, Jingbo Xia, Pierre Zweigenbaum, Tiffany Callahan, Orin Hargraves, Foster R. Goss, Nancy Ide, Aurélie Névéol, Cyril Grouin, Lawrence E. Hunter:
Three Dimensions of Reproducibility in Natural Language Processing. LREC 2018
[c58]
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Sonia Cardoso, Xavier Aimé, Vincent Meininger, David Grabli, Luis Felipe Melo Mora, K. Bretonnel Cohen, Jean Charlet:
A Modular Ontology for Modeling Service Provision in a Communication Network for Coordination of Care. MIE 2018: 890-894
[c57]
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Mayla Boguslav, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence E. Hunter:
Improving precision in concept normalization. PSB 2018: 566-577
[e18]
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Dina Demner-Fushman, Kevin Bretonnel Cohen, Sophia Ananiadou, Junichi Tsujii:
Proceedings of the BioNLP 2018 workshop, Melbourne, Australia, July 19, 2018. Association for Computational Linguistics 2018, ISBN 978-1-948087-33-9 [contents]
2017
[j42]
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Brian Connolly, K. Bretonnel Cohen, Daniel Santel, Ulya Bayram, John Pestian:
A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support. BMC Bioinform. 18(1): 361 (2017)
[j41]
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K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer, Lawrence E. Hunter:
Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. BMC Bioinform. 18(1): 372:1-372:14 (2017)
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  - journals/lre/BrancoCVIC17
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António Branco, Kevin Bretonnel Cohen, Piek Vossen, Nancy Ide, Nicoletta Calzolari:
Replicability and reproducibility of research results for human language technology: introducing an LRE special section. Lang. Resour. Evaluation 51(1): 1-5 (2017)
[j39]
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António Branco, Kevin Bretonnel Cohen, Piek Vossen, Nancy Ide, Nicoletta Calzolari:
Erratum to: Replicability and reproducibility of research results for human language technology: introducing an LRE special section. Lang. Resour. Evaluation 51(1): 7 (2017)
[c56]
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Kevin Bretonnel Cohen, Aurélie Névéol, Jingbo Xia, Negacy D. Hailu, Cyril Grouin, Lawrence E. Hunter, Pierre Zweigenbaum:
Reproducibility in Biomedical Natural Language Processing. AMIA 2017
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Ignacio Tripodi, Kevin Bretonnel Cohen, Lawrence E. Hunter:
A semantic knowledge-base approach to drug-drug interaction discovery. BIBM 2017: 1123-1126
[c54]
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Aurélie Névéol, Aude Robert, Robert Anderson, Kevin Bretonnel Cohen, Cyril Grouin, Thomas Lavergne, Grégoire Rey, Claire Rondet, Pierre Zweigenbaum:
CLEF eHealth 2017 Multilingual Information Extraction task Overview: ICD10 Coding of Death Certificates in English and French. CLEF (Working Notes) 2017
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Mayla Boguslav, Kevin Bretonnel Cohen:
Inter-Annotator Agreement and the Upper Limit on Machine Performance: Evidence from Biomedical Natural Language Processing. MedInfo 2017: 298-302
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K. Bretonnel Cohen, Foster R. Goss, Pierre Zweigenbaum, Lawrence E. Hunter:
Translational Morphosyntax: Distribution of Negation in Clinical Records and Biomedical Journal Articles. MedInfo 2017: 346-350
[c51]
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Prabha Yadav, Elisabetta Jezek, Pierrette Bouillon, Tiffany J. Callahan, Michael Bada, Lawrence E. Hunter, K. Bretonnel Cohen:
Semantic Relations in Compound Nouns: Perspectives from Inter-Annotator Agreement. MedInfo 2017: 644-648
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Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, Junichi Tsujii:
BioNLP 2017, Vancouver, Canada, August 4, 2017. Association for Computational Linguistics 2017, ISBN 978-1-945626-59-3 [contents]
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Svetla Boytcheva, Kevin Bretonnel Cohen, Guergana Savova, Galia Angelova:
Proceedings of the Biomedical NLP Workshop associated with RANLP 2017, Varna, Bulgaria, September 2017. INCOMA Ltd. 2017 [contents]
2016
[j38]
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Lynette Hirschman, Karën Fort, Stéphanie Boué, Nikos Kyrpides, Rezarta Islamaj Dogan, Kevin Bretonnel Cohen:
Crowdsourcing and curation: perspectives from biology and natural language processing. Database J. Biol. Databases Curation 2016 (2016)
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Christopher S. Funk, K. Bretonnel Cohen, Lawrence E. Hunter, Karin M. Verspoor:
Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition. J. Biomed. Semant. 7: 52 (2016)
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Karën Fort, Gilles Adda, K. Bretonnel Cohen:
Introduction. Trait. Autom. des Langues 57(2) (2016)
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Aurélie Névéol, Kevin Bretonnel Cohen, Cyril Grouin, Aude Robert:
Replicability of Research in Biomedical Natural Language Processing: a pilot evaluation for a coding task. Louhi@EMNLP 2016: 78-84
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Aurélie Névéol, Kevin Bretonnel Cohen, Cyril Grouin, Thierry Hamon, Thomas Lavergne, Liadh Kelly, Lorraine Goeuriot, Grégoire Rey, Aude Robert, Xavier Tannier, Pierre Zweigenbaum:
Clinical Information Extraction at the CLEF eHealth Evaluation lab 2016. CLEF (Working Notes) 2016: 28-42
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K. Bretonnel Cohen, William A. Baumgartner Jr., Irina P. Temnikova:
SuperCAT: The (New and Improved) Corpus Analysis Toolkit. LREC 2016
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Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, Jun'ichi Tsujii:
Proceedings of the 15th Workshop on Biomedical Natural Language Processing, BioNLP@ACL 2016, Berlin, Germany, August 12, 2016. Association for Computational Linguistics 2016, ISBN 978-1-945626-12-8 [contents]
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Sophia Ananiadou, Riza Batista-Navarro, Kevin Bretonnel Cohen, Dina Demner-Fushman, Paul Thompson:
Proceedings of the Fifth Workshop on Building and Evaluating Resources for Biomedical Text Mining, BioTxtM@COLING 2016, Osaka, Japan, December 12, 2016. The COLING 2016 Organizing Committee 2016, ISBN 978-4-87974-719-8 [contents]
2015
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Samuel J. Severance, K. Bretonnel Cohen:
Measuring the readability of medical research journal abstracts. BioNLP@IJCNLP 2015: 127-133
[c46]
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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:
Training the Next Generation of Quantitative Biologists in the Era of Big Data. Pacific Symposium on Biocomputing 2015: 488-492
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Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, Jun'ichi Tsujii:
Proceedings of the Workshop on Biomedical Natural Language Processing, BioNLP@IJCNLP 2015, Beijing, China, July 30, 2015. Association for Computational Linguistics 2015 [contents]
2014
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Cecilia N. Arighi, Cathy H. Wu, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, W. John Wilbur, Thomas C. Wiegers:
BioCreative-IV virtual issue. Database J. Biol. Databases Curation 2014 (2014)
[j34]
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Toshiaki Katayama, Mark D. Wilkinson, Kiyoko F. Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, Jan Aerts, Yukie Akune, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Pier Luigi Buttigieg, Matthew P. Campbell, Yi-an Chen, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Alexandru Constantin:
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J. Biomed. Semant. 5: 5 (2014)
[j33]
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Christopher S. Funk, William A. Baumgartner Jr., Benjamin Garcia, Christophe Roeder, Michael Bada, K. Bretonnel Cohen, Lawrence E. Hunter, Karin Verspoor:
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinform. 15: 59 (2014)
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Brian Connolly, Pawel Matykiewicz, K. Bretonnel Cohen, Shannon M. Standridge, Tracy A. Glauser, Dennis J. Dlugos, Susan Koh, Eric Tham, John Pestian:
Research and applications: Assessing the similarity of surface linguistic features related to epilepsy across pediatric hospitals. J. Am. Medical Informatics Assoc. 21(5): 866-870 (2014)
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Negacy D. Hailu, Natalya Panteleyeva, Kevin Bretonnel Cohen:
Temporal Expression Recognition for Cell Cycle Phase Concepts in Biomedical Literature. BioNLP@ACL 2014: 10-18
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Richard Osborne, Alan R. Aronson, Kevin Bretonnel Cohen:
A repository of semantic types in the MIMIC II database clinical notes. BioNLP@ACL 2014: 93-97
[c43]
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Irina P. Temnikova, William A. Baumgartner Jr., Negacy D. Hailu, Ivelina Nikolova, Tony McEnery, Adam Kilgarriff, Galia Angelova, K. Bretonnel Cohen:
Sublanguage Corpus Analysis Toolkit: A tool for assessing the representativeness and sublanguage characteristics of corpora. LREC 2014: 1714-1718
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Negacy D. Hailu, K. Bretonnel Cohen, Lawrence E. Hunter:
Ontology Translation: A Case Study on Translating the Gene Ontology from English to German. NLDB 2014: 33-38
[c41]
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Graciela Gonzalez, Kevin Bretonnel Cohen, Robert Leaman, Casey S. Greene, Nigam Shah, Maricel G. Kann, Jieping Ye:
Session introduction. Pacific Symposium on Biocomputing 2014: 312-315
[c40]
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Christopher S. Funk, Lawrence E. Hunter, K. Bretonnel Cohen:
Combining Heterogenous Data for Prediction of Disease Related and Pharmacogenes. Pacific Symposium on Biocomputing 2014: 328-339
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Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, Jun'ichi Tsujii:
Proceedings of BioNLP, Baltimore, Maryland, USA, BioNLP@ACL 2014, June 27-28, 2014. Association for Computational Linguistics 2014, ISBN 978-1-941643-18-1 [contents]
2013
[j31]
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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, Bethany R. Harris, Marc Gillespie, Silvia Jimenez, Phoebe M. Roberts, Lisa Matthews, Kevin G. Becker, Harold J. Drabkin, Susan M. Bello, Luana Licata, Andrew Chatr-aryamontri, Mary L. Schaeffer, Julie Park, Melissa A. Haendel, Kimberly Van Auken, Yuling Li, Juancarlos Chan, Hans-Michael Müller, Hong Cui, James P. Balhoff, Chi-Yang Wu, Zhiyong Lu, Chih-Hsuan Wei, Catalina O. Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan Miguel Cejuela, Pratibha Dubey, Cathy H. Wu:
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database J. Biol. Databases Curation 2013 (2013)
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Donald C. Comeau, Rezarta Islamaj Dogan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur:
BioC: a minimalist approach to interoperability for biomedical text processing. Database J. Biol. Databases Curation 2013 (2013)
[j29]
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Qi Li, Louise Deléger, Todd Lingren, Haijun Zhai, Megan Kaiser, Laura Stoutenborough, Anil G. Jegga, Kevin Bretonnel Cohen, Imre Solti:
Mining FDA drug labels for medical conditions. BMC Medical Informatics Decis. Mak. 13: 53 (2013)
[j28]
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K. Bretonnel Cohen, Lawrence E. Hunter:
Chapter 16: Text Mining for Translational Bioinformatics. PLoS Comput. Biol. 9(4) (2013)
[c39]
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K. Bretonnel Cohen, Jin-Dong Kim:
Evaluation of SPARQL query generation from natural language questions. SWAIE@RANLP 2013: 3-7
[c38]
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Pawel Matykiewicz, Kevin Bretonnel Cohen, Katherine D. Holland, Tracy A. Glauser, Shannon M. Standridge, Karin M. Verspoor, John Pestian:
Earlier Identification of Epilepsy Surgery Candidates Using Natural Language Processing. BioNLP@ACL 2013: 1-9
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Irina P. Temnikova, Kevin Bretonnel Cohen:
Recognizing Sublanguages in Scientific Journal Articles through Closure Properties. BioNLP@ACL 2013: 72-79
[c36]
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Graciela Gonzalez, Kevin Bretonnel Cohen, Casey S. Greene, Udo Hahn, Maricel G. Kann, Robert Leaman, Nigam Shah, Jieping Ye:
Session introduction. Pacific Symposium on Biocomputing 2013: 368-372
[c35]
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Irina P. Temnikova, Negacy D. Hailu, Galia Angelova, K. Bretonnel Cohen:
Measuring Closure Properties of Patent Sublanguages. RANLP 2013: 659-666
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Irina P. Temnikova, Ivelina Nikolova, William A. Baumgartner Jr., Galia Angelova, K. Bretonnel Cohen:
Closure Properties of Bulgarian Clinical Text. RANLP 2013: 667-675
[c33]
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Negacy D. Hailu, Lawrence E. Hunter, K. Bretonnel Cohen:
UColorado_SOM: Extraction of Drug-Drug Interactions from Biomedical Text using Knowledge-rich and Knowledge-poor Features. SemEval@NAACL-HLT 2013: 684-688
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Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, John Pestian, Junichi Tsujii:
Proceedings of the 2013 Workshop on Biomedical Natural Language Processing, BioNLP@ACL 2013, Sofia, Bulgaria, August 8, 2013. Association for Computational Linguistics 2013, ISBN 978-1-937284-54-1 [contents]
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Guergana Savova, Kevin Bretonnel Cohen, Galia Angelova:
Proceedings of the Workshop on NLP for Medicine and Biology associated with RANLP 2013, Hissar, Bulgaria, September 13, 2013. INCOMA Ltd. Shoumen, BULGARIA 2013, ISBN 978-954-452-024-3 [contents]
2012
[j27]
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Udo Hahn, Kevin Bretonnel Cohen, Yael Garten, Nigam H. Shah:
Mining the pharmacogenomics literature - a survey of the state of the art. Briefings Bioinform. 13(4): 460-494 (2012)
[j26]
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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, Anne-Lise Veuthey, Thomas C. Wiegers, Andrew G. Winter:
Text mining for the biocuration workflow. Database J. Biol. Databases Curation 2012 (2012)
[j25]
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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:
BioCreative-2012 Virtual Issue. Database J. Biol. Databases Curation 2012 (2012)
[j24]
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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 Bioinform. 13: 161 (2012)
[j23]
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Karin Verspoor, Kevin Bretonnel Cohen, Arrick Lanfranchi, Colin Warner, Helen L. Johnson, Christophe Roeder, Jinho D. Choi, Christopher S. 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 Bioinform. 13: 207 (2012)
[j22]
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Adrien Coulet, K. Bretonnel Cohen, Russ B. Altman:
The state of the art in text mining and natural language processing for pharmacogenomics. J. Biomed. Informatics 45(5): 825-826 (2012)
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K. Bretonnel Cohen, Lawrence E. Hunter, Martha Palmer:
Assessment of Software Testing and Quality Assurance in Natural Language Processing Applications and a Linguistically Inspired Approach to Improving It. EternalS@ECAI 2012: 77-90
[c31]
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Kevin Bretonnel Cohen, Yael Garten, Nigam Shah, Udo Hahn:
Session introduction. Pacific Symposium on Biocomputing 2012: 375
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Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, Bonnie L. Webber, Jun'ichi Tsujii, John Pestian:
Proceedings of the 2012 Workshop on Biomedical Natural Language Processing, BioNLP@HLT-NAACL Montrèal, Canada, June 8, 2012. Association for Computational Linguistics 2012, ISBN 978-1-937284-20-6 [contents]
2011
[j21]
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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 Bioinform. 12: 481 (2011)
[j20]
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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 Bioinform. 12(S-8): S1 (2011)
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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. Comput. Intell. 27(4): 681-701 (2011)
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Karën Fort, Gilles Adda, K. Bretonnel Cohen:
Amazon Mechanical Turk: Gold Mine or Coal Mine? Comput. Linguistics 37(2): 413-420 (2011)
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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 J. Res. Dev. 55(3): 11 (2011)
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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
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K. Bretonnel Cohen, Tom Christiansen, William A. Baumgartner Jr., Karin Verspoor, Lawrence Hunter:
Fast and simple semantic class assignment for biomedical text. BioNLP@ACL 2011: 38-45
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Elizabeth K. White, K. Bretonnel Cohen, Lawrence Hunter:
Hypothesis and Evidence Extraction from Full-Text Scientific Journal Articles. BioNLP@ACL 2011: 134-135
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Kevin Bretonnel Cohen, Yael Garten, Udo Hahn, Nigam H. Shah:
Workshop Introduction. Pacific Symposium on Biocomputing 2011: 362-363
[c26]
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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
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Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, John Pestian, Jun'ichi Tsujii, Bonnie L. Webber:
Proceedings of the 2011 Workshop on Biomedical Natural Language Processing, BioNLP@ACL, Portland, Oregon, USA, June 23-24, 2011. Association for Computational Linguistics 2011, ISBN 978-1-932432-91-6 [contents]
2010
[j16]
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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 Bioinform. 11: 492 (2010)
[j15]
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Kevin Bretonnel Cohen:
Integrating text mining into high-throughput assay analysis. BMC Bioinform. 11(S-5): O3 (2010)
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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. Biol. Bioinform. 7(3): 462-471 (2010)
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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
[c24]
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K. Bretonnel Cohen, Christophe Roeder, William A. Baumgartner Jr., Lawrence Hunter, Karin Verspoor:
Test Suite Design for Biomedical Ontology Concept Recognition Systems. LREC 2010
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K. Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, John Pestian, Jun'ichi Tsujii, Bonnie L. Webber:
Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, BioNLP@ACL 2010, Uppsala, Sweden, July 15, 2010. Association for Computational Linguistics 2010, ISBN 978-1-932432-73-2 [contents]
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K. Bretonnel Cohen:
BioNLP. Handbook of Natural Language Processing 2010: 605-625

2000 – 2009

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2009
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Karin Verspoor, Daniel Dvorkin, K. Bretonnel Cohen, Lawrence Hunter:
Ontology quality assurance through analysis of term transformations. Bioinform. 25(12) (2009)
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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. Bioinform. 25(15): 1997-1998 (2009)
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Karin Verspoor, K. Bretonnel Cohen, Lawrence Hunter:
The textual characteristics of traditional and Open Access scientific journals are similar. BMC Bioinform. 10 (2009)
[j10]
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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 Bioinform. 10: 326 (2009)
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Wendy Webber Chapman, K. Bretonnel Cohen:
Current issues in biomedical text mining and natural language processing. J. Biomed. Informatics 42(5): 757-759 (2009)
[c23]
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K. Bretonnel Cohen, Karin Verspoor, Helen L. Johnson, Christophe Roeder, Philip V. Ogren, William A. Baumgartner Jr., Elizabeth K. White, Lawrence Hunter:
High-precision biological event extraction with a concept recognizer. BioNLP@HLT-NAACL (Shared Task) 2009: 50-58
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Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, John Pestian, Jun'ichi Tsujii, Bonnie L. Webber:
Proceedings of the BioNLP Workshop, BioNLP@HLT-NAACL 2009, Boulder, Colorado, USA, June 4-5, 2009. Association for Computational Linguistics 2009, ISBN 978-1-932432-30-5 [contents]
2008
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Dina Demner-Fushman, Sophia Ananiadou, K. Bretonnel Cohen, John Pestian, Jun'ichi Tsujii, Bonnie L. Webber:
Themes in biomedical natural language processing: BioNLP08. BMC Bioinform. 9(S-11) (2008)
[j7]
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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 Bioinform. 9 (2008)
[j6]
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K. Bretonnel Cohen, Lawrence Hunter:
Getting Started in Text Mining. PLoS Comput. Biol. 4(1) (2008)
[c22]
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K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter:
Software Testing and the Naturally Occurring Data Assumption in Natural Language Processing. SETQALNLP 2008: 23-30
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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
[c20]
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K. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman:
Session Introduction. Pacific Symposium on Biocomputing 2008: 551-555
[c19]
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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
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K. Bretonnel Cohen, Bob Carpenter:
Software Engineering, Testing, and Quality Assurance for Natural Language Processing@ACL 2008, Columbus, Ohio, USA, June 20, 2008. Association for Computational Linguistics 2008, ISBN 978-1-932432-10-7 [contents]
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Dina Demner-Fushman, Sophia Ananiadou, Kevin Bretonnel Cohen, John Pestian, Jun'ichi Tsujii, Bonnie L. Webber:
Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing, BioNLP 2008, Columbus, Ohio, USA, June 19, 2008. Association for Computational Linguistics 2008, ISBN 978-1-932432-11-4 [contents]
2007
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Pierre Zweigenbaum, Dina Demner-Fushman, Hong Yu, Kevin Bretonnel Cohen:
Frontiers of biomedical text mining: current progress. Briefings Bioinform. 8(5): 358-375 (2007)
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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. Bioinform. 23(14): 1862-1865 (2007)
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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. Bioinform. Comput. Biol. 5(6): 1233-1259 (2007)
[c18]
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John P. Pestian, Chris Brew, Pawel Matykiewicz, D. J. Hovermale, Neil Johnson, K. Bretonnel Cohen, Wlodzislaw Duch:
A shared task involving multi-label classification of clinical free text. BioNLP@ACL 2007: 97-104
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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
[c16]
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K. Bretonnel Cohen:
BioNLP. HLT-NAACL (Tutorial Abstracts) 2007: 1-2
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Pierre Zweigenbaum, Dina Demner-Fushman, Hong Yu, K. Bretonnel Cohen:
Session Introduction. Pacific Symposium on Biocomputing 2007: 205-208
[c14]
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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
[c13]
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Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter:
Generif Quality Assurance as Summary Revision. Pacific Symposium on Biocomputing 2007: 269-280
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K. Bretonnel Cohen, Dina Demner-Fushman, Carol Friedman, Lynette Hirschman, John Pestian:
Biological, translational, and clinical language processing, BioNLP@ACL 2007, Prague, Czech Republic, June 29, 2007. Association for Computational Linguistics 2007 [contents]
2006
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K. Bretonnel Cohen, Lawrence Hunter:
A critical review of PASBio's argument structures for biomedical verbs. BMC Bioinform. 7(S-3) (2006)
[c12]
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Helen L. Johnson, William A. Baumgartner Jr., Martin Krallinger, K. Bretonnel Cohen, Lawrence Hunter:
Refactoring Corpora. BioNLP@NAACL-HLT 2006: 116-117
[c11]
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K. Bretonnel Cohen, Olivier Bodenreider, Lynette Hirschman:
Session Introduction. Pacific Symposium on Biocomputing 2006: 1-3
[c10]
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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
[c9]
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Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter:
Finding GeneRIFs via Gene Ontology Annotations. Pacific Symposium on Biocomputing 2006: 52-63
[c8]
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K. Bretonnel Cohen, Lawrence Hunter:
A critical review of PASBio's argument structures for biomedical verbs. SMBM 2006
[c7]
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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
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Karin Verspoor, Kevin Bretonnel Cohen, Ben Goertzel, Inderjeet Mani:
Proceedings of the Workshop on Linking Natural Language and Biology, BioNLP@NAACL-HLT 2006, New York, NY, USA, June 8, 2006. Association for Computational Linguistics 2006 [contents]
2005
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Shuhei Kinoshita, K. Bretonnel Cohen, Philip V. Ogren, Lawrence Hunter:
BioCreAtIvE Task1A: entity identification with a stochastic tagger. BMC Bioinform. 6(S-1) (2005)
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K. Bretonnel Cohen, Philip V. Ogren, Lynne M. Fox, Lawrence Hunter:
Empirical data on corpus design and usage in biomedical natural language processing. AMIA 2005
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K. Bretonnel Cohen, Lynne M. Fox, Philip V. Ogren, Lawrence Hunter:
Corpus Design for Biomedical Natural Language Processing. LBLODMBS@IDMB 2005: 38-45
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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
[c3]
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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
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K. Bretonnel Cohen, Lynette Hirschman, Hagit Shatkay, Christian Blaschke:
Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics@ISMB 2005, Detroit, MI, USA June 24, 2005. Association for Computational Linguistics 2005 [contents]
2004
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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
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K. Bretonnel Cohen, Lawrence Hunter:
Natural Language Processing and Systems Biology. Artificial Intelligence Methods And Tools For Systems Biology 2004: 147-173
2002
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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

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