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1

A Machine Learning Approach to Identifying the Thought Markers of Suicidal Subjects: A Prospective Multicenter Trial

Pestian, John P., Sorter, Michael, Connolly, Brian, Bretonnel Cohen, Kevin, McCullumsmith, Cheryl, Gee, Jeffry T., Morency, Louis-Philippe, Scherer, Stefan, Rohlfs, Lesley

Journal:

Suicide and Life-Threatening Behavior

Year:

2016

Language:

english

File:

PDF, 117 KB

english, 2016

2

Natural Language Processing for Online Applications: Text Retrieval, Extraction and Categorization (review)

Cohen, Kevin Bretonnel

Journal:

Year:

2004

Language:

english

File:

PDF, 254 KB

english, 2004

3

Replicability and reproducibility of research results for human language technology: introducing anLREspecial section

António Branco,Kevin Bretonnel Cohen,Piek Vossen…

Journal:

Language Resources and Evaluation

Year:

2017

Language:

english

File:

PDF, 363 KB

english, 2017

4

Spanish/English Contrasts: A Course in Spanish Linguistics (review)

Cohen, K. Bretonnel

Journal:

Year:

2004

Language:

english

File:

PDF, 191 KB

english, 2004

5

[untitled]

Review by: K. Bretonnel Cohen

Journal:

Year:

2004

Language:

english

File:

PDF, 217 KB

english, 2004

6

[untitled]

Review by: K. Bretonnel Cohen

Journal:

Year:

2004

Language:

english

File:

PDF, 232 KB

english, 2004

7

[ACM Press the 18th ACM/IEEE - Fort Worth, Texas, USA (2018.06.03-2018.06.07)] Proceedings of the 18th ACM/IEEE on Joint Conference on Digital Libraries - JCDL '18 - The Curative Power of Medical Data

Gifu, Daniela, Trandabat, Diana, Cohen, Kevin Bretonnel, Xia, Jigbo

Year:

2018

Language:

english

File:

PDF, 564 KB

english, 2018

8

[IEEE 2018 11th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI) - Beijing, China (2018.10.13-2018.10.15)] 2018 11th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI) - Guideline Design of an Active Gene Annotation Corpus for the Purpose of Drug Repurposing

Wang, Yuxing, Yao, Xinzhi, Zhou, Kaiyin, Qin, Xuan, Kim, Jin-Dong, Cohen, Kevin Bretonnel, Xia, Jingbo

Year:

2018

Language:

english

File:

PDF, 8 KB

english, 2018

9

Exploring Species-Based Strategies for Gene Normalization

Verspoor, Karin, Roeder, Christophe, Johnson, Helen L, Cohen, Kevin Bretonnel, Baumgartner, William A, Hunter, Lawrence E

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.93 MB

english, 2010

10

A Controlled Trial Using Natural Language Processing to Examine the Language of Suicidal Adolescents in the Emergency Department

Pestian, John P., Grupp-Phelan, Jacqueline, Bretonnel Cohen, Kevin, Meyers, Gabriel, Richey, Linda A., Matykiewicz, Pawel, Sorter, Michael T.

Journal:

Suicide and Life-Threatening Behavior

Year:

2016

Language:

english

File:

PDF, 96 KB

english, 2016

11

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, Helen L Johnson, Philip V Ogren, K Bretonnel Cohen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 543 KB

english, 2008

12

War of Ontology Worlds: Mathematics, Computer Code, or Esperanto?

Rzhetsky, Andrey, Evans, James A., Cohen, Kevin Bretonnel

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 89 KB

english, 2011

13

Introduction to the Biomedical Linked Annotation Hackathon (BLAH) 2015 Symposium

Jin-Dong Kim,Kevin Bretonnel Cohen,Nigel Collier,Zhiyong Lu…

Journal:

BMC Proceedings

Year:

2015

Language:

english

File:

PDF, 200 KB

english, 2015

14

The structural and content aspects of abstracts versus bodies of full text journal articles are different

K Bretonnel Cohen, Helen L Johnson, Karin Verspoor, Christophe Roeder, Lawrence E Hunter

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 306 KB

english, 2010

15

Corpus Refactoring: a Feasibility Study

Johnson, Helen L, Baumgartner, William A, Krallinger, Martin, Cohen, K Bretonnel, Hunter, Lawrence

Journal:

Journal of Biomedical Discovery and Collaboration

Year:

2007

Language:

english

File:

PDF, 303 KB

english, 2007

16

Chapter 16: Text Mining for Translational Bioinformatics

Cohen, K. Bretonnel, Hunter, Lawrence E., Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 193 KB

english, 2013

17

A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support

Connolly, Brian, Cohen, K. Bretonnel, Santel, Daniel, Bayram, Ulya, Pestian, John

Journal:

BMC Bioinformatics

Year:

2017

Language:

english

File:

PDF, 1.40 MB

english, 2017

18

The textual characteristics of traditional and Open Access scientific journals are similar

Karin Verspoor, K Bretonnel Cohen, Lawrence Hunter

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 472 KB

english, 2009

19

PubAnnotation-query: a search tool for corpora with multi-layers of annotation

Jin-Dong Kim,Kevin Bretonnel Cohen,Jung-jae Kim

Journal:

BMC Proceedings

Year:

2015

Language:

english

File:

PDF, 350 KB

english, 2015

20

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles

Cohen, K. Bretonnel, Lanfranchi, Arrick, Choi, Miji Joo-young, Bada, Michael, Baumgartner, William A., Panteleyeva, Natalya, Verspoor, Karin, Palmer, Martha, Hunter, Lawrence E.

Journal:

BMC Bioinformatics

Year:

2017

Language:

english

File:

PDF, 510 KB

english, 2017

21

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

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 736 KB

english, 2009

22

An open-source framework for large-scale, flexible evaluation of biomedical text mining systems

Baumgartner, William A, Cohen, K Bretonnel, Hunter, Lawrence

Journal:

Journal of Biomedical Discovery and Collaboration

Year:

2008

Language:

english

File:

PDF, 670 KB

english, 2008

23

A critical review of PASBio's argument structures for biomedical verbs

K Bretonnel Cohen, Lawrence Hunter

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 269 KB

english, 2006

24

Getting Started in Text Mining

Cohen, K. Bretonnel, Hunter, Lawrence

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 193 KB

english, 2008

25

Habitat-Lite: A GSC Case Study Based on Free Text Terms for Environmental Metadata

Hirschman, Lynette, Clark, Cheryl, Cohen, K. Bretonnel, Mardis, Scott, Luciano, Joanne, Kottmann, Renzo, Cole, James, Markowitz, Victor, Kyrpides, Nikos, Morrison, Norman, Schriml, Lynn M., Field, Daw

Journal:

Omics A Journal of Integrative Biology

Year:

2008

Language:

english

File:

PDF, 189 KB

english, 2008

26

Methodological Issues in Predicting Pediatric Epilepsy Surgery Candidates through Natural Language Processing and Machine Learning

Cohen, Kevin Bretonnel, Glass, Benjamin, Greiner, Hansel M., Holland-Bouley, Katherine, Standridge, Shannon, Arya, Ravindra, Faist, Robert, Morita, Diego, Mangano, Francesco, Connolly, Brian, Glauser,

Journal:

Biomedical Informatics Insights

Year:

2016

Language:

english

File:

PDF, 552 KB

english, 2016

27

Finding the balance between model complexity and performance: Using ventral striatal oscillations to classify feeding behavior in rats

Dwiel, Lucas L., Khokhar, Jibran Y., Connerney, Michael A., Green, Alan I., Doucette, Wilder T., Cohen, K. Bretonnel

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 2.09 MB

english, 2019

28

Current issues in biomedical text mining and natural language processing

Wendy W. Chapman, K. Bretonnel Cohen

Journal:

Journal of Biomedical Informatics

Year:

2009

Language:

english

File:

PDF, 128 KB

english, 2009

29

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, Sofie V

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 257 KB

english, 2011

30

RAPID PATTERN DEVELOPMENT FOR CONCEPT RECOGNITION SYSTEMS: APPLICATION TO POINT MUTATIONS

CAPORASO, J. GREGORY, BAUMGARTNER, WILLIAM A., RANDOLPH, DAVID A., COHEN, K. BRETONNEL, HUNTER, LAWRENCE

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2007

Language:

english

File:

PDF, 405 KB

english, 2007

31

Nominalization and Alternations in Biomedical Language

Cohen, K. Bretonnel, Palmer, Martha, Hunter, Lawrence, Futrelle, Robert P.

Journal:

Year:

2008

Language:

english

File:

PDF, 331 KB

english, 2008

32

Assessing the similarity of surface linguistic features related to epilepsy across pediatric hospitals

Connolly, B., Matykiewicz, P., Bretonnel Cohen, K., Standridge, S. M., Glauser, T. A., Dlugos, D. J., Koh, S., Tham, E., Pestian, J.

Journal:

Journal of the American Medical Informatics Association

Year:

2014

Language:

english

File:

PDF, 240 KB

english, 2014

33

Biomedical Language Processing: What's Beyond PubMed?

Lawrence Hunter, K. Bretonnel Cohen

Journal:

Year:

2006

Language:

english

File:

PDF, 210 KB

english, 2006

34

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, Christophe Roeder, Jinho D Choi, Christopher Funk, Yuriy Malenkiy, Miriam Eckert, Nianwen Xue, William A Baumga

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 383 KB

english, 2012

35

Conflicting Biomedical Assumptions for Mathematical Modeling: The Case of Cancer Metastasis

Divoli, Anna, Mendonça, Eneida A., Evans, James A., Rzhetsky, Andrey, Cohen, Kevin Bretonnel

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.14 MB

english, 2011

36

[IEEE 2008 IEEE International Conference on Bioinformatics and Biomedicine - Philadelphia, PA, USA (2008.11.3-2008.11.5)] 2008 IEEE International Conference on Bioinformatics and Biomedicine - iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology

Hu, Zhang-Zhi, Cohen, K. Bretonnel, Hirschman, Lynette, Valencia, Alfonso, Liu, Hongfang, Giglio, Michelle G., Wu, Cathy H.

Year:

2008

Language:

english

File:

PDF, 1.35 MB

english, 2008

37

Crowdsourcing and curation: perspectives from biology and natural language processing

Hirschman, Lynette, Fort, Karën, Boué, Stéphanie, Kyrpides, Nikos, Islamaj Doğan, Rezarta, Cohen, Kevin Bretonnel

Journal:

Year:

2016

Language:

english

File:

PDF, 1.01 MB

english, 2016

38

Erratum to: Replicability and reproducibility of research results for human language technology: introducing anLREspecial section

António Branco,Kevin Bretonnel Cohen,Piek Vossen…

Journal:

Language Resources and Evaluation

Year:

2017

Language:

english

File:

PDF, 312 KB

english, 2017

39

Predicting the Extension of Biomedical Ontologies

Pesquita, Catia, Couto, Francisco M., Cohen, K. Bretonnel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 999 KB

english, 2012

40

Quantifying the Impact and Extent of Undocumented Biomedical Synonymy

Blair, David R., Wang, Kanix, Nestorov, Svetlozar, Evans, James A., Rzhetsky, Andrey, Cohen, K. Bretonnel

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 3.24 MB

english, 2014

41

Themes in biomedical natural language processing: BioNLP08

Dina Demner-Fushman, Sophia Ananiadou, K Bretonnel Cohen, John Pestian, Jun'ichi Tsujii, Bonnie Webber

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 182 KB

english, 2008

42

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

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 442 KB

english, 2012

43

Methods in Biomedical Informatics || Biomedical Natural Language Processing and Text Mining

Cohen, Kevin Bretonnel

Year:

2014

Language:

english

File:

PDF, 619 KB

english, 2014

44

Amazon Mechanical Turk: Gold Mine or Coal Mine?

Fort, Karën, Adda, Gilles, Cohen, K. Bretonnel

Journal:

Computational Linguistics

Year:

2011

Language:

english

File:

PDF, 96 KB

english, 2011

45

Benchmarking Ontologies: Bigger or Better?

Yao, Lixia, Divoli, Anna, Mayzus, Ilya, Evans, James A., Rzhetsky, Andrey, Cohen, K. Bretonnel

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.32 MB

english, 2011

46

Survey of the State of the Art in Human Language Technologyby Giovanni Varile; Antonio Zampolli; Ronald Cole; Joseph Mariani; Hans Uszkoreit; Annie Zaenen; Victor Zue

Review by: K. Bretonnel Cohen

Journal:

Year:

2000

Language:

english

File:

PDF, 683 KB

english, 2000

47

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Maui, Hawaii (3 – 7 January 2006)] Biocomputing 2006 - LINKING BIOMEDICAL INFORMATION THROUGH TEXT MINING: SESSION INTRODUCTION

COHEN, K. BRETONNEL, BODENREIDER, OLIVIER, HIRSCHMAN, LYNETTE

Language:

english

File:

PDF, 186 KB

english

48

The state of the art in text mining and natural language processing for pharmacogenomics

Adrien Coulet, K. Bretonnel Cohen, Russ B. Altman

Journal:

Journal of Biomedical Informatics

Year:

2012

Language:

english

File:

PDF, 133 KB

english, 2012

49

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Kohala Coast, Hawaii, USA (3 – 7 January 2018)] Biocomputing 2018 - Improving precision in concept normalization

Boguslav, Mayla, Cohen, K. Bretonnel, Baumgartner, William A., Hunter, Lawrence E.

Language:

english

File:

PDF, 663 KB

english

50

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Maui, Hawaii (3 – 7 January 2006)] Biocomputing 2006 - EVALUATION OF LEXICAL METHODS FOR DETECTING RELATIONSHIPS BETWEEN CONCEPTS FROM MULTIPLE ONTOLOGIES

JOHNSON, HELEN L., COHEN, K. BRETONNEL, BAUMGARTNER, WILLIAM A., LU, ZHIYONG, BADA, MICHAEL, KESTER, TODD, KIM, HYUNMIN, HUNTER, LAWRENCE

Language:

english

File:

PDF, 670 KB

english

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