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Kevin Bretonnel Cohen

InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM - Pharmacology

    Collapse Research 
    Collapse research activities and funding
    R13GM109648     (COHEN, KEVIN B.)Sep 1, 2014 - Aug 31, 2017
    Biocreative Conference Grant
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Cohen KB, Xia J, Zweigenbaum P, Callahan TJ, Hargraves O, Goss F, Ide N, Névéol A, Grouin C, Hunter LE. Three Dimensions of Reproducibility in Natural Language Processing. LREC Int Conf Lang Resour Eval. 2018 May; 2018:156-165. PMID: 29911205.
      View in: PubMed
    2. Boguslav M, Cohen KB, Baumgartner WA, Hunter LE. Improving precision in concept normalization. Pac Symp Biocomput. 2018; 23:566-577. PMID: 29218915.
      View in: PubMed
    3. Cohen KB, Lanfranchi A, Choi MJ, Bada M, Baumgartner WA, Panteleyeva N, Verspoor K, Palmer M, Hunter LE. Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. BMC Bioinformatics. 2017 Aug 17; 18(1):372. PMID: 28818042.
      View in: PubMed
    4. Connolly B, Cohen KB, Santel D, Bayram U, Pestian J. A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support. BMC Bioinformatics. 2017 Aug 07; 18(1):361. PMID: 28784111.
      View in: PubMed
    5. Boguslav M, Cohen KB. Inter-Annotator Agreement and the Upper Limit on Machine Performance: Evidence from Biomedical Natural Language Processing. Stud Health Technol Inform. 2017; 245:298-302. PMID: 29295103.
      View in: PubMed
    6. Cohen KB, Goss FR, Zweigenbaum P, Hunter LE. Translational Morphosyntax: Distribution of Negation in Clinical Records and Biomedical Journal Articles. Stud Health Technol Inform. 2017; 245:346-350. PMID: 29295113.
      View in: PubMed
    7. Yadav P, Jezek E, Bouillon P, Callahan TJ, Bada M, Hunter LE, Cohen KB. Semantic Relations in Compound Nouns: Perspectives from Inter-Annotator Agreement. Stud Health Technol Inform. 2017; 245:644-648. PMID: 29295175.
      View in: PubMed
    8. Funk CS, Cohen KB, Hunter LE, Verspoor KM. Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition. J Biomed Semantics. 2016 Sep 09; 7:52. PMID: 27613112.
      View in: PubMed
    9. Névéol A, Cohen KB, Grouin C, Hamon T, Lavergne T, Kelly L, Goeuriot L, Rey G, Robert A, Tannier X, Zweigenbaum P. Clinical Information Extraction at the CLEF eHealth Evaluation lab 2016. CEUR Workshop Proc. 2016 Sep; 1609:28-42. PMID: 29308065.
      View in: PubMed
    10. Hirschman L, Fort K, Boué S, Kyrpides N, Islamaj Dogan R, Cohen KB. Crowdsourcing and curation: perspectives from biology and natural language processing. Database (Oxford). 2016; 2016. PMID: 27504010; PMCID: PMC4976298.
    11. Cohen KB, Glass B, Greiner HM, Holland-Bouley K, Standridge S, Arya R, Faist R, Morita D, Mangano F, Connolly B, Glauser T, Pestian J. Methodological Issues in Predicting Pediatric Epilepsy Surgery Candidates Through Natural Language Processing and Machine Learning. Biomed Inform Insights. 2016; 8:11-8. PMID: 27257386; PMCID: PMC4876984.
    12. Cohen KB, Xia J, Roeder C, Hunter LE. Reproducibility in Natural Language Processing: A Case Study of Two R Libraries for Mining PubMed/MEDLINE. LREC Int Conf Lang Resour Eval. 2016 May; 2016(W23):6-12. PMID: 29568821.
      View in: PubMed
    13. Cohen KB, Baumgartner WA, Temnikova I. SuperCAT: The (New and Improved) Corpus Analysis Toolkit. LREC Int Conf Lang Resour Eval. 2016 May; 2016:2784-2788. PMID: 29568820.
      View in: PubMed
    14. Cohen KB, Fort K, Adda G, Zhou S, Farri D. Ethical Issues in Corpus Linguistics And Annotation: Pay Per Hit Does Not Affect Effective Hourly Rate For Linguistic Resource Development On Amazon Mechanical Turk. LREC Int Conf Lang Resour Eval. 2016 May; 2016(W40):8-12. PMID: 29568822.
      View in: PubMed
    15. Pattin KA, Greene AC, Altman RB, Cohen KB, Wethington E, Görg C, Hunter LE, Muse SV, Radivojac P, Moore JH. Training the next generation of quantitative biologists in the era of big data. Pac Symp Biocomput. 2015; 488-92. PMID: 25592609.
      View in: PubMed
    16. Hailu ND, Cohen KB, Hunter LE. Ontology translation: A case study on translating the Gene Ontology from English to German. Nat Lang Process Inf Syst. 2014 Jun; 8455:33-38. PMID: 29780975.
      View in: PubMed
    17. Arighi CN, Wu CH, Cohen KB, Hirschman L, Krallinger M, Valencia A, Lu Z, Wilbur JW, Wiegers TC. BioCreative-IV virtual issue. Database (Oxford). 2014; 2014. PMID: 24852177.
      View in: PubMed
    18. Temnikova IP, Baumgartner WA, Hailu ND, Nikolova I, McEnery T, Kilgarriff A, Angelova G, Cohen KB. Sublanguage Corpus Analysis Toolkit: A tool for assessing the representativeness and sublanguage characteristics of corpora. LREC Int Conf Lang Resour Eval. 2014 May; 2014:1714-1718. PMID: 29568819.
      View in: PubMed
    19. Funk C, Baumgartner W, Garcia B, Roeder C, Bada M, Cohen KB, Hunter LE, Verspoor K. Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinformatics. 2014 Feb 26; 15:59. PMID: 24571547; PMCID: PMC4015610.
    20. Funk CS, Hunter LE, Cohen KB. Combining heterogenous data for prediction of disease related and pharmacogenes. Pac Symp Biocomput. 2014; 328-39. PMID: 24297559; PMCID: PMC3910248.
    21. Comeau DC, Islamaj Dogan R, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013; 2013:bat064. PMID: 24048470; PMCID: PMC3889917.
    22. Cohen KB, Hunter LE. Chapter 16: text mining for translational bioinformatics. PLoS Comput Biol. 2013 Apr; 9(4):e1003044. PMID: 23633944; PMCID: PMC3635962.
    23. Li Q, Deleger L, Lingren T, Zhai H, Kaiser M, Stoutenborough L, Jegga AG, Cohen KB, Solti I. Mining FDA drug labels for medical conditions. BMC Med Inform Decis Mak. 2013 Apr 24; 13:53. PMID: 23617267; PMCID: PMC3646673.
    24. Arighi CN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE, Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, Roberts P, Matthews L, Becker K, Drabkin H, Bello S, Licata L, Chatr-aryamontri A, Schaeffer ML, Park J, Haendel M, Van Auken K, Li Y, Chan J, Muller HM, Cui H, Balhoff JP, Chi-Yang Wu J, Lu Z, Wei CH, Tudor CO, Raja K, Subramani S, Natarajan J, Cejuela JM, Dubey P, Wu C. An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database (Oxford). 2013; 2013:bas056. PMID: 23327936.
      View in: PubMed
    25. Gonzalez G, Cohen KB, Greene CS, Hahn U, Kann MG, Leaman R, Shah N, Ye J. Text and data mining for biomedical discovery. Pac Symp Biocomput. 2013; 368-72. PMID: 23424141.
      View in: PubMed
    26. Wu CH, Arighi CN, Cohen KB, Hirschman L, Krallinger M, Lu Z, Mattingly C, Valencia A, Wiegers TC, John Wilbur W. BioCreative-2012 virtual issue. Database (Oxford). 2012; 2012:bas049. PMID: 23221175; PMCID: PMC3514749.
    27. Verspoor K, Cohen KB, Lanfranchi A, Warner C, Johnson HL, Roeder C, Choi JD, Funk C, Malenkiy Y, Eckert M, Xue N, Baumgartner WA, Bada M, Palmer M, Hunter LE. 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. 2012 Aug 17; 13:207. PMID: 22901054; PMCID: PMC3483229.
    28. Bada M, Eckert M, Evans D, Garcia K, Shipley K, Sitnikov D, Baumgartner WA, Cohen KB, Verspoor K, Blake JA, Hunter LE. Concept annotation in the CRAFT corpus. BMC Bioinformatics. 2012 Jul 09; 13:161. PMID: 22776079; PMCID: PMC3476437.
    29. Hahn U, Cohen KB, Garten Y, Shah NH. Mining the pharmacogenomics literature--a survey of the state of the art. Brief Bioinform. 2012 Jul; 13(4):460-94. PMID: 22833496.
      View in: PubMed
    30. Hirschman L, Burns GA, Krallinger M, Arighi C, Cohen KB, Valencia A, Wu CH, Chatr-Aryamontri A, Dowell KG, Huala E, Lourenço A, Nash R, Veuthey AL, Wiegers T, Winter AG. Text mining for the biocuration workflow. Database (Oxford). 2012; 2012:bas020. PMID: 22513129; PMCID: PMC3328793.
    31. Pestian JP, Matykiewicz P, Linn-Gust M, South B, Uzuner O, Wiebe J, Cohen KB, Hurdle J, Brew C. Sentiment Analysis of Suicide Notes: A Shared Task. Biomed Inform Insights. 2012 Jan 30; 5(Suppl 1):3-16. PMID: 22419877.
      View in: PubMed
    32. Kano Y, Björne J, Ginter F, Salakoski T, Buyko E, Hahn U, Cohen KB, Verspoor K, Roeder C, Hunter LE, Kilicoglu H, Bergler S, Van Landeghem S, Van Parys T, Van de Peer Y, Miwa M, Ananiadou S, Neves M, Pascual-Montano A, Özgür A, Radev DR, Riedel S, Sætre R, Chun HW, Kim JD, Pyysalo S, Ohta T, Tsujii J. U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics. 2011 Dec 18; 12:481. PMID: 22177292; PMCID: PMC3299809.
    33. Cohen KB, Verspoor K, Johnson HL, Roeder C, Ogren PV, Baumgartner WA, White E, Tipney H, Hunter L. HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA. Comput Intell. 2011 Nov; 27(4):681-701. PMID: 25937701.
      View in: PubMed
    34. Cohen KB, Christiansen T, Hunter LE. Parenthetically speaking: classifying the contents of parentheses for text mining. AMIA Annu Symp Proc. 2011; 2011:267-72. PMID: 22195078; PMCID: PMC3243264.
    35. Arighi CN, Lu Z, Krallinger M, Cohen KB, Wilbur WJ, Valencia A, Hirschman L, Wu CH. Overview of the BioCreative III Workshop. BMC Bioinformatics. 2011 Oct 03; 12 Suppl 8:S1. PMID: 22151647; PMCID: PMC3269932.
    36. Cohen KB, Christiansen T, Hunter LE. MetaMap is a superior baseline to a standard document retrieval engine for the task of finding patient cohorts in clinical free text. Text Retr Conf. 2011; 2011. PMID: 30417177.
      View in: PubMed
    37. Cohen KB, Johnson HL, Verspoor K, Roeder C, Hunter LE. The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC Bioinformatics. 2010 Sep 29; 11:492. PMID: 20920264; PMCID: PMC3098079.
    38. Verspoor K, Roeder C, Johnson HL, Cohen KB, Baumgartner WA, Hunter LE. Exploring species-based strategies for gene normalization. IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul-Sep; 7(3):462-71. PMID: 20671318; PMCID: PMC2929766.
    39. Wiegers TC, Davis AP, Cohen KB, Hirschman L, Mattingly CJ. Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD). BMC Bioinformatics. 2009 Oct 08; 10:326. PMID: 19814812; PMCID: PMC2768719.
    40. Chapman WW, Cohen KB. Current issues in biomedical text mining and natural language processing. J Biomed Inform. 2009 Oct; 42(5):757-9. PMID: 19735740.
      View in: PubMed
    41. Verspoor K, Dvorkin D, Cohen KB, Hunter L. Ontology quality assurance through analysis of term transformations. Bioinformatics. 2009 Jun 15; 25(12):i77-84. PMID: 19478020; PMCID: PMC2687949.
    42. Verspoor K, Cohen KB, Hunter L. The textual characteristics of traditional and Open Access scientific journals are similar. BMC Bioinformatics. 2009 Jun 15; 10:183. PMID: 19527520; PMCID: PMC2714574.
    43. Kano Y, Baumgartner WA, McCrohon L, Ananiadou S, Cohen KB, Hunter L, Tsujii J. U-Compare: share and compare text mining tools with UIMA. Bioinformatics. 2009 Aug 01; 25(15):1997-8. PMID: 19414535; PMCID: PMC2712335.
    44. Demner-Fushman D, Ananiadou S, Cohen KB, Pestian J, Tsujii J, Webber B. Themes in biomedical natural language processing: BioNLP08. BMC Bioinformatics. 2008 Nov 19; 9 Suppl 11:S1. PMID: 19025685; PMCID: PMC2586759.
    45. Cohen KB, Palmer M, Hunter L. Nominalization and alternations in biomedical language. PLoS One. 2008 Sep 09; 3(9):e3158. PMID: 18779866; PMCID: PMC2527518.
    46. Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Fundel K, Leaman R, Hakenberg J, Sun C, Liu HH, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, Hirschman L. Overview of BioCreative II gene normalization. Genome Biol. 2008; 9 Suppl 2:S3. PMID: 18834494; PMCID: PMC2559987.
    47. Baumgartner WA, Lu Z, Johnson HL, Caporaso JG, Paquette J, Lindemann A, White EK, Medvedeva O, Cohen KB, Hunter L. Concept recognition for extracting protein interaction relations from biomedical text. Genome Biol. 2008; 9 Suppl 2:S9. PMID: 18834500; PMCID: PMC2559993.
    48. Hirschman L, Clark C, Cohen KB, Mardis S, Luciano J, Kottmann R, Cole J, Markowitz V, Kyrpides N, Morrison N, Schriml LM, Field D. Habitat-Lite: a GSC case study based on free text terms for environmental metadata. OMICS. 2008 Jun; 12(2):129-36. PMID: 18416669.
      View in: PubMed
    49. Hunter L, Lu Z, Firby J, Baumgartner WA, Johnson HL, Ogren PV, Cohen KB. 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 Bioinformatics. 2008 Jan 31; 9:78. PMID: 18237434; PMCID: PMC2275248.
    50. Baumgartner WA, Cohen KB, Hunter L. An open-source framework for large-scale, flexible evaluation of biomedical text mining systems. J Biomed Discov Collab. 2008 Jan 29; 3:1. PMID: 18230184; PMCID: PMC2276192.
    51. Caporaso JG, Deshpande N, Fink JL, Bourne PE, Cohen KB, Hunter L. Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pac Symp Biocomput. 2008; 640-51. PMID: 18229722; PMCID: PMC2517250.
    52. Cohen KB, Hunter L. Getting started in text mining. PLoS Comput Biol. 2008 Jan; 4(1):e20. PMID: 18225946; PMCID: PMC2217579.
    53. Cohen KB, Yu H, Bourne PE, Hirschman L. TRANSLATING BIOLOGY: TEXT MINING TOOLS THAT WORK. Pac Symp Biocomput. 2008 Jan 01; 13:551-555. PMID: 20827444.
      View in: PubMed
    54. Caporaso JG, Baumgartner WA, Randolph DA, Cohen KB, Hunter L. Rapid pattern development for concept recognition systems: application to point mutations. J Bioinform Comput Biol. 2007 Dec; 5(6):1233-59. PMID: 18172927.
      View in: PubMed
    55. Zweigenbaum P, Demner-Fushman D, Yu H, Cohen KB. Frontiers of biomedical text mining: current progress. Brief Bioinform. 2007 Sep; 8(5):358-75. PMID: 17977867; PMCID: PMC2516302.
    56. Johnson HL, Baumgartner WA, Krallinger M, Cohen KB, Hunter L. Corpus refactoring: a feasibility study. J Biomed Discov Collab. 2007 Sep 13; 2:4. PMID: 17854502; PMCID: PMC2072937.
    57. Baumgartner WA, Cohen KB, Fox LM, Acquaah-Mensah G, Hunter L. Manual curation is not sufficient for annotation of genomic databases. Bioinformatics. 2007 Jul 01; 23(13):i41-8. PMID: 17646325; PMCID: PMC2516305.
    58. Caporaso JG, Baumgartner WA, Randolph DA, Cohen KB, Hunter L. MutationFinder: a high-performance system for extracting point mutation mentions from text. Bioinformatics. 2007 Jul 15; 23(14):1862-5. PMID: 17495998; PMCID: PMC2516306.
    59. Johnson HL, Cohen KB, Hunter L. A fault model for ontology mapping, alignment, and linking systems. Pac Symp Biocomput. 2007; 233-44. PMID: 17990495; PMCID: PMC2516303.
    60. Lu Z, Cohen KB, Hunter L. GeneRIF quality assurance as summary revision. Pac Symp Biocomput. 2007; 269-80. PMID: 17990498; PMCID: PMC2652871.
    61. Cohen KB, Hunter L. A critical review of PASBio's argument structures for biomedical verbs. BMC Bioinformatics. 2006 Nov 24; 7 Suppl 3:S5. PMID: 17134478; PMCID: PMC1764449.
    62. Hunter L, Cohen KB. Biomedical language processing: what's beyond PubMed? Mol Cell. 2006 Mar 03; 21(5):589-94. PMID: 16507357; PMCID: PMC1702322.
    63. Johnson HL, Cohen KB, Baumgartner WA, Lu Z, Bada M, Kester T, Kim H, Hunter L. Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies. Pac Symp Biocomput. 2006; 28-39. PMID: 17094225; PMCID: PMC1810343.
    64. Lu Z, Cohen KB, Hunter L. Finding GeneRIFs via gene ontology annotations. Pac Symp Biocomput. 2006; 52-63. PMID: 17094227; PMCID: PMC2652876.
    65. Kinoshita S, Cohen KB, Ogren PV, Hunter L. BioCreAtIvE task1A: entity identification with a stochastic tagger. BMC Bioinformatics. 2005; 6 Suppl 1:S4. PMID: 15960838; PMCID: PMC1869018.
    66. Ogren PV, Cohen KB, Hunter L. Implications of compositionality in the gene ontology for its curation and usage. Pac Symp Biocomput. 2005; 174-85. PMID: 15759624.
      View in: PubMed
    67. Cohen KB, Fox L, Ogren P, Hunter L. Empirical data on corpus design and usage in biomedical natural language processing. AMIA Annu Symp Proc. 2005; 156-60. PMID: 16779021; PMCID: PMC1560643.
    68. Ogren PV, Cohen KB, Acquaah-Mensah GK, Eberlein J, Hunter L. The compositional structure of Gene Ontology terms. Pac Symp Biocomput. 2004; 214-25. PMID: 14992505; PMCID: PMC2490823.
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