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Kevin Bretonnel Cohen

TitleInstructor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM - Pharmacology
Phone303/724-3369

    Collapse Research 
    Collapse research activities and funding
    R13GM109648     (COHEN, KEVIN B.)Sep 1, 2014 - Aug 31, 2017
    NIH/NIGMS
    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. 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
    2. 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.
      View in: PubMed
    3. 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.
      View in: PubMed
    4. 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
    5. 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
    6. 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.
      View in: PubMed
    7. Funk CS, Hunter LE, Cohen KB. Combining heterogenous data for prediction of disease related and pharmacogenes. Pac Symp Biocomput. 2014; 328-39. PMID: 24297559.
      View in: PubMed
    8. 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.
      View in: PubMed
    9. Cohen KB, Hunter LE. Chapter 16: text mining for translational bioinformatics. PLoS Comput Biol. 2013 Apr; 9(4):e1003044. PMID: 23633944.
      View in: PubMed
    10. 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.
      View in: PubMed
    11. 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
    12. 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.
      View in: PubMed
    13. 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.
      View in: PubMed
    14. 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.
      View in: PubMed
    15. 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
    16. 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.
      View in: PubMed
    17. 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
    18. 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.
      View in: PubMed
    19. 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
    20. 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.
      View in: PubMed
    21. 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.
      View in: PubMed
    22. 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.
      View in: PubMed
    23. 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.
      View in: PubMed
    24. 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.
      View in: PubMed
    25. 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
    26. 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.
      View in: PubMed
    27. 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.
      View in: PubMed
    28. 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.
      View in: PubMed
    29. 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.
      View in: PubMed
    30. Cohen KB, Palmer M, Hunter L. Nominalization and alternations in biomedical language. PLoS One. 2008 Sep 09; 3(9):e3158. PMID: 18779866.
      View in: PubMed
    31. 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.
      View in: PubMed
    32. 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.
      View in: PubMed
    33. 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
    34. 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.
      View in: PubMed
    35. 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.
      View in: PubMed
    36. 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.
      View in: PubMed
    37. Cohen KB, Hunter L. Getting started in text mining. PLoS Comput Biol. 2008 Jan; 4(1):e20. PMID: 18225946.
      View in: PubMed
    38. 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
    39. 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
    40. 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.
      View in: PubMed
    41. 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.
      View in: PubMed
    42. 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.
      View in: PubMed
    43. 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.
      View in: PubMed
    44. Johnson HL, Cohen KB, Hunter L. A fault model for ontology mapping, alignment, and linking systems. Pac Symp Biocomput. 2007; 233-44. PMID: 17990495.
      View in: PubMed
    45. Lu Z, Cohen KB, Hunter L. GeneRIF quality assurance as summary revision. Pac Symp Biocomput. 2007; 269-80. PMID: 17990498.
      View in: PubMed
    46. 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.
      View in: PubMed
    47. Hunter L, Cohen KB. Biomedical language processing: what's beyond PubMed? Mol Cell. 2006 Mar 03; 21(5):589-94. PMID: 16507357.
      View in: PubMed
    48. 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.
      View in: PubMed
    49. Lu Z, Cohen KB, Hunter L. Finding GeneRIFs via gene ontology annotations. Pac Symp Biocomput. 2006; 52-63. PMID: 17094227.
      View in: PubMed
    50. 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.
      View in: PubMed
    51. 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
    52. 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.
      View in: PubMed
    53. 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.
      View in: PubMed
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