Kevin Bretonnel Cohen
Director, Biomedical Text Mining Group
Computational Bioscience Program
University of Colorado School of Medicine

Office: RC-1 S. Room L18-6102
Phone: 303-916-2417
E-mail: Kevin.Cohen@gmail.com

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Publications

2020

2019

  • Margo Mieskes, Karen Fort, Aurelie Neveol, and K. Bretonnel Cohen (2019) NLP Community Perspectives on Replicability. Recent Advances in Natural Language Processing.
  • Peter S. Pressman, Elliott D. Ross, Kevin B. Cohen, Kuan-Hua Chen, Bruce L. Miller, Lawrence E. Hunter, Maria Luisa Gorno-Tempini, and Robert W. Levenson (2019). Interpersonal prosodic correlation in frontotemporal dementia. Annals of Clinical and Translational Neurology.
  • Zhou KY, Wang YX, Zhang S, Gachloo M, Kim JD, Luo Q, Cohen KB, Xia JB (2019) GOF/LOF knowledge inference with tensor decomposition in support of high order link discovery for gene, mutation and disease Mathematical Biosciences and Engineering, 16(3): 1376-1391. doi: 10.3934/mbe.2019067.
  • Jin-Dong Kim, Yue Wang, Toyofumi Fujiwara, Shujiro Okuda, Tiffany J. Callahan, and K. Bretonnel Cohen (2019) Open Agile Text Mining for Bioinformatics: The PubAnnotation Ecosystem Bioinformatics, btz227, https://doi.org/10.1093/bioinformatics/btz227.
  • Zhou, K. Y., Wang, Y. X., Zhang, S., Gachloo, M., Kim, J. D., Luo, Q., Cohen, K.B., & Xia, J. B. (2019). GOF/LOF knowledge inference with tensor decomposition in support of high order link discovery for gene, mutation and disease. Math Biosci Eng, 16(3), 1376-1391.
  • Wang, Y., Zhou, K., Kim, J. D., Cohen, K. B., Gachloo, M., Ren, Y., ... & Xia, J. (2019, November). An Active Gene Annotation Corpus and Its Application on Anti-epilepsy Drug Discovery. In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 512-519). IEEE.

2018

  • Sonia Cardoso, Xavier Aimé, Vincent Meininger, David Grabli, Kevin Bretonnel Cohen, and Jean Charlet (2018) De l'intrêt des ontologies modulaires. Application à la modélisation de la prise en charge de la SLA 29es journées francophones d'Ingénierie des Connaissances (IC), 121-136.
  • Boguslav, M., Cohen, K. B., Baumgartner Jr, W. A., & Hunter, L. E. (2018). Improving precision in concept normalization. In Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (Vol. 23, pp. 566-577). NIH Public Access.
  • Cohen, K. B., Xia, J., Zweigenbaum, P., Callahan, T. J., Hargraves, O., Goss, F., ... & Hunter, L. E. (2018, May). Three Dimensions of Reproducibility in Natural Language Processing. In LREC... International Conference on Language Resources & Evaluation:[proceedings]. International Conference on Language Resources and Evaluation (Vol. 2018, p. 156). NIH Public Access.
  • Cardoso, S., Aimé, X., Meininger, V., Grabli, D., Melo, L. M., Cohen, K. B., & Charlet, J. (2018). A Modular Ontology for Modeling Service Provision in a Communication Network for Coordination of Care. Studies in health technology and informatics, 247, 890-894.
  • Wang, Y., Yao, X., Zhou, K., Qin, X., Kim, J. D., Cohen, K. B., & Xia, J. (2018). Guideline design of an active gene annotation corpus for the purpose of drug repurposing. In 2018 11th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI) (pp. 1-5). IEEE.
  • Zhou, K., Zhang, S., Meng, X., Luo, Q., Wang, Y., Ding, K., Feng, Y., Chen, M., Cohen, K.B., & Xia, J. (2018). CRF-LSTM Text Mining Method Unveiling the Pharmacological Mechanism of Off-target Side Effect of Anti-Multiple Myeloma Drugs. In Proceedings of the BioNLP 2018 workshop (pp. 166-171).
  • Zhou, K., Yao, X., Wang, S., Kim, J. D., Cohen, K. B., Chen, R., ... & Xia, J. (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. In Chinese Computational Linguistics and Natural Language Processing Based on Naturally Annotated Big Data (pp. 398-409). Springer, Cham.

2017

2016

2015

2014

2013

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

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

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2006

2005

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This document last modified 05/05/20 13:05.