Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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Lawrence E Hunter

TitleProfessor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM - Pharmacology
Address2RC1N
Research North Tower
12800 E 19th Ave, Bldg. RC1 North Room P18-9103
Aurora CO 80010
Phone303/724-3574

     Bibliographic 
     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. Vehlow C, Kao DP, Bristow MR, Hunter LE, Weiskopf D, Görg C. Visual analysis of biological data-knowledge networks. BMC Bioinformatics. 2015; 16(1):135.
      View in: PubMed
    2. Livingston KM, Bada M, Baumgartner WA, Hunter LE. KaBOB: ontology-based semantic integration of biomedical databases. BMC Bioinformatics. 2015; 16(1):126.
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    3. Hewett D, Whirl-Carrillo M, Hunter LE, Altman RB, Klein TE. A twentieth anniversary tribute to psb. Pac Symp Biocomput. 2015; 20:1-7.
      View in: PubMed
    4. Hinterberg MA, Kao DP, Bristow MR, Hunter LE, Port JD, Görg C. Peax: interactive visual analysis and exploration of complex clinical phenotype and gene expression association. Pac Symp Biocomput. 2015; 20:419-30.
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    5. 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; 20:488-92.
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    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; 15:59.
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    7. Pattin KA, Greene AC, Altman RB, Hunter LE, Ross DA, Foster JA, Moore JH. Building the next generation of quantitative biologists. Pac Symp Biocomput. 2014; 417-21.
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    8. Funk CS, Hunter LE, Cohen KB. Combining heterogenous data for prediction of disease related and pharmacogenes. Pac Symp Biocomput. 2014; 328-39.
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    9. Livingston KM, Bada M, Hunter LE, Verspoor K. Representing annotation compositionality and provenance for the Semantic Web. J Biomed Semantics. 2013; 4:38.
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    10. Hunter LE. Rocky mountain conference on bioinformatics celebrates 10 years. PLoS Comput Biol. 2013; 9(5):e1003076.
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    11. Cohen KB, Hunter LE. Chapter 16: text mining for translational bioinformatics. PLoS Comput Biol. 2013 Apr; 9(4):e1003044.
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    12. Liu H, Hunter L, Kešelj V, Verspoor K. Approximate subgraph matching-based literature mining for biomedical events and relations. PLoS One. 2013; 8(4):e60954.
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    13. Hunter L. Computational challenges of mass phenotyping. Pac Symp Biocomput. 2013; 454-5.
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    14. 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; 13:207.
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    15. Sarkar SA, Lee CE, Tipney H, Karimpour-Fard A, Dinella JD, Juhl K, Walters JA, Hutton JC, Hunter LE. Synergizing genomic analysis with biological knowledge to identify and validate novel genes in pancreatic development. Pancreas. 2012 Aug; 41(6):962-9.
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    16. Hunter LE, Hopfer C, Terry SF, Coors ME. Reporting actionable research results: shared secrets can save lives. Sci Transl Med. 2012 Jul 18; 4(143):143cm8.
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    17. 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; 13:161.
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    18. Kulikowski CA, Shortliffe EH, Currie LM, Elkin PL, Hunter LE, Johnson TR, Kalet IJ, Lenert LA, Musen MA, Ozbolt JG, Smith JW, Tarczy-Hornoch PZ, Williamson JJ. AMIA Board white paper: definition of biomedical informatics and specification of core competencies for graduate education in the discipline. J Am Med Inform Assoc. 2012 Nov-Dec; 19(6):931-8.
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    19. Jani A, Orlicky DJ, Karimpour-Fard A, Epperson LE, Russell RL, Hunter LE, Martin SL. Kidney proteome changes provide evidence for a dynamic metabolism and regional redistribution of plasma proteins during torpor-arousal cycles of hibernation. Physiol Genomics. 2012 Jul 15; 44(14):717-27.
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    20. Rehrer CW, Karimpour-Fard A, Hernandez TL, Law CK, Stob NR, Hunter LE, Eckel RH. Regional differences in subcutaneous adipose tissue gene expression. Obesity (Silver Spring). 2012 Nov; 20(11):2168-73.
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    21. Galligan JJ, Smathers RL, Fritz KS, Epperson LE, Hunter LE, Petersen DR. Protein carbonylation in a murine model for early alcoholic liver disease. Chem Res Toxicol. 2012 May 21; 25(5):1012-21.
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    22. 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; 12:481.
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    23. Cohen KB, Christiansen T, Hunter LE. Parenthetically speaking: classifying the contents of parentheses for text mining. AMIA Annu Symp Proc. 2011; 2011:267-72.
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    24. Grabek KR, Karimpour-Fard A, Epperson LE, Hindle A, Hunter LE, Martin SL. Multistate proteomics analysis reveals novel strategies used by a hibernator to precondition the heart and conserve ATP for winter heterothermy. Physiol Genomics. 2011 Nov 21; 43(22):1263-75.
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    25. Hindle AG, Karimpour-Fard A, Epperson LE, Hunter LE, Martin SL. Skeletal muscle proteomics: carbohydrate metabolism oscillates with seasonal and torpor-arousal physiology of hibernation. Am J Physiol Regul Integr Comp Physiol. 2011 Nov; 301(5):R1440-52.
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    26. Ryan VH, Trayhurn P, Hunter L, Morris PJ, German AJ. 11-Hydroxy-ß-steroid dehydrogenase gene expression in canine adipose tissue and adipocytes: stimulation by lipopolysaccharide and tumor necrosis factor a. Domest Anim Endocrinol. 2011 Oct; 41(3):150-61.
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    27. Scott MC, Sarver AL, Gavin KJ, Thayanithy V, Getzy DM, Newman RA, Cutter GR, Lindblad-Toh K, Kisseberth WC, Hunter LE, Subramanian S, Breen M, Modiano JF. Molecular subtypes of osteosarcoma identified by reducing tumor heterogeneity through an interspecies comparative approach. Bone. 2011 Sep; 49(3):356-67.
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    28. Epperson LE, Karimpour-Fard A, Hunter LE, Martin SL. Metabolic cycles in a circannual hibernator. Physiol Genomics. 2011 Jul 14; 43(13):799-807.
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    29. Galligan JJ, Fritz KS, Tipney H, Smathers RL, Roede JR, Shearn CT, Hunter LE, Petersen DR. Profiling impaired hepatic endoplasmic reticulum glycosylation as a consequence of ethanol ingestion. J Proteome Res. 2011 Apr 1; 10(4):1837-47.
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    30. Tamburini BA, Phang TL, Fosmire SP, Scott MC, Trapp SC, Duckett MM, Robinson SR, Slansky JE, Sharkey LC, Cutter GR, Wojcieszyn JW, Bellgrau D, Gemmill RM, Hunter LE, Modiano JF. Gene expression profiling identifies inflammation and angiogenesis as distinguishing features of canine hemangiosarcoma. BMC Cancer. 2010; 10:619.
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    31. Bada M, Hunter L. Desiderata for ontologies to be used in semantic annotation of biomedical documents. J Biomed Inform. 2011 Feb; 44(1):94-101.
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    32. 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; 11:492.
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    33. Karimpour-Fard A, Dumas L, Phang T, Sikela JM, Hunter LE. A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation. Hum Genomics. 2010 Aug; 4(6):421-7.
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    34. 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.
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    35. Roeder C, Jonquet C, Shah NH, Baumgartner WA, Verspoor K, Hunter L. A UIMA wrapper for the NCBO annotator. Bioinformatics. 2010 Jul 15; 26(14):1800-1.
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    36. Lussier YA, Butte AJ, Hunter L. Current methodologies for translational bioinformatics. J Biomed Inform. 2010 Jun; 43(3):355-7.
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    37. Tipney H, Hunter L. An introduction to effective use of enrichment analysis software. Hum Genomics. 2010 Feb; 4(3):202-6.
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    38. Coulet A, Shah N, Hunter L, Barral C, Altman RB. Extraction of genotype-phenotype-drug relationships from text: from entity recognition to bioinformatics application. Pac Symp Biocomput. 2010; 485-7.
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    39. Feng W, Leach SM, Tipney H, Phang T, Geraci M, Spritz RA, Hunter LE, Williams T. Spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences. PLoS One. 2009; 4(12):e8066.
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    40. Verspoor K, Dvorkin D, Cohen KB, Hunter L. Ontology quality assurance through analysis of term transformations. Bioinformatics. 2009 Jun 15; 25(12):i77-84.
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    41. Verspoor K, Cohen KB, Hunter L. The textual characteristics of traditional and Open Access scientific journals are similar. BMC Bioinformatics. 2009; 10:183.
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    42. Tamburini BA, Trapp S, Phang TL, Schappa JT, Hunter LE, Modiano JF. Gene expression profiles of sporadic canine hemangiosarcoma are uniquely associated with breed. PLoS One. 2009; 4(5):e5549.
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    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 1; 25(15):1997-8.
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    44. Shortliffe EH, Califano A, Hunter L. New JBI emphasis on translational bioinformatics. J Biomed Inform. 2009 Apr; 42(2):199-200.
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    45. Leach SM, Tipney H, Feng W, Baumgartner WA, Kasliwal P, Schuyler RP, Williams T, Spritz RA, Hunter L. Biomedical discovery acceleration, with applications to craniofacial development. PLoS Comput Biol. 2009 Mar; 5(3):e1000215.
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    46. Tipney HJ, Schuyler RP, Hunter L. Consistent visualizations of changing knowledge. Summit on Translat Bioinforma. 2009; 2009:129-32.
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    47. Tipney HJ, Leach SM, Feng W, Spritz R, Williams T, Hunter L. Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology. BMC Bioinformatics. 2009; 10 Suppl 2:S12.
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    48. Yen CY, Meyer-Arendt K, Eichelberger B, Sun S, Houel S, Old WM, Knight R, Ahn NG, Hunter LE, Resing KA. A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins. Mol Cell Proteomics. 2009 Apr; 8(4):857-69.
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    49. Caporaso JG, Smit S, Easton BC, Hunter L, Huttley GA, Knight R. Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics. BMC Evol Biol. 2008; 8:327.
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    50. Karimpour-Fard A, Leach SM, Gill RT, Hunter LE. Predicting protein linkages in bacteria: which method is best depends on task. BMC Bioinformatics. 2008; 9:397.
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    51. Cohen KB, Palmer M, Hunter L. Nominalization and alternations in biomedical language. PLoS One. 2008; 3(9):e3158.
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    52. Smith L, Tanabe LK, Ando RJ, Kuo CJ, Chung IF, Hsu CN, Lin YS, Klinger R, Friedrich CM, Ganchev K, Torii M, Liu H, Haddow B, Struble CA, Povinelli RJ, Vlachos A, Baumgartner WA, Hunter L, Carpenter B, Tsai RT, Dai HJ, Liu F, Chen Y, Sun C, Katrenko S, Adriaans P, Blaschke C, Torres R, Neves M, Nakov P, Divoli A, Maña-López M, Mata J, Wilbur WJ. Overview of BioCreative II gene mention recognition. Genome Biol. 2008; 9 Suppl 2:S2.
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    53. Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, Shin SY, Zhang BT, Baumgartner WA, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozgür A, Erkan G, Radev DR, Krauthammer M, Luong T, Hoffmann R, Sander C, Valencia A. Introducing meta-services for biomedical information extraction. Genome Biol. 2008; 9 Suppl 2:S6.
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    54. 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.
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    55. Karimpour-Fard A, Leach SM, Hunter LE, Gill RT. The topology of the bacterial co-conserved protein network and its implications for predicting protein function. BMC Genomics. 2008; 9:313.
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    56. Bethard S, Lu Z, Martin JH, Hunter L. Semantic role labeling for protein transport predicates. BMC Bioinformatics. 2008; 9:277.
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    57. Bada M, Hunter L. Identification of OBO nonalignments and its implications for OBO enrichment. Bioinformatics. 2008 Jun 15; 24(12):1448-55.
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    58. Gabow AP, Leach SM, Baumgartner WA, Hunter LE, Goldberg DS. Improving protein function prediction methods with integrated literature data. BMC Bioinformatics. 2008; 9:198.
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    59. Harvell DM, Spoelstra NS, Singh M, McManaman JL, Finlayson C, Phang T, Trapp S, Hunter L, Dye WW, Borges VF, Elias A, Horwitz KB, Richer JK. Molecular signatures of neoadjuvant endocrine therapy for breast cancer: characteristics of response or intrinsic resistance. Breast Cancer Res Treat. 2008 Dec; 112(3):475-88.
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    60. 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; 9:78.
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    61. 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; 3:1.
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    62. Cohen KB, Hunter L. Getting started in text mining. PLoS Comput Biol. 2008 Jan; 4(1):e20.
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    63. Glueck DH, Mandel J, Karimpour-Fard A, Hunter L, Muller KE. Exact calculations of average power for the Benjamini-Hochberg procedure. Int J Biostat. 2008; 4(1):Article 11.
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    64. 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.
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    65. 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.
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    66. Karimpour-Fard A, Hunter L, Gill RT. Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling. BMC Genomics. 2007; 8:393.
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    67. Johnson HL, Baumgartner WA, Krallinger M, Cohen KB, Hunter L. Corpus refactoring: a feasibility study. J Biomed Discov Collab. 2007; 2:4.
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    68. Bhave SV, Hornbaker C, Phang TL, Saba L, Lapadat R, Kechris K, Gaydos J, McGoldrick D, Dolbey A, Leach S, Soriano B, Ellington A, Ellington E, Jones K, Mangion J, Belknap JK, Williams RW, Hunter LE, Hoffman PL, Tabakoff B. The PhenoGen informatics website: tools for analyses of complex traits. BMC Genet. 2007; 8:59.
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    69. Baumgartner WA, Cohen KB, Fox LM, Acquaah-Mensah G, Hunter L. Manual curation is not sufficient for annotation of genomic databases. Bioinformatics. 2007 Jul 1; 23(13):i41-8.
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    70. 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.
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    71. Serkova NJ, Zhang Y, Coatney JL, Hunter L, Wachs ME, Niemann CU, Mandell MS. Early detection of graft failure using the blood metabolic profile of a liver recipient. Transplantation. 2007 Feb 27; 83(4):517-21.
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    72. Karimpour-Fard A, Detweiler CS, Erickson KD, Hunter L, Gill RT. Cross-species cluster co-conservation: a new method for generating protein interaction networks. Genome Biol. 2007; 8(9):R185.
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    73. Leach S, Gabow A, Hunter L, Goldberg DS. Assessing and combining reliability of protein interaction sources. Pac Symp Biocomput. 2007; 433-44.
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    74. Lu Z, Cohen KB, Hunter L. GeneRIF quality assurance as summary revision. Pac Symp Biocomput. 2007; 269-80.
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    75. Johnson HL, Cohen KB, Hunter L. A fault model for ontology mapping, alignment, and linking systems. Pac Symp Biocomput. 2007; 233-44.
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    76. Cohen KB, Hunter L. A critical review of PASBio's argument structures for biomedical verbs. BMC Bioinformatics. 2006; 7 Suppl 3:S5.
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    77. Guzelian J, Barwick JL, Hunter L, Phang TL, Quattrochi LC, Guzelian PS. Identification of genes controlled by the pregnane X receptor by microarray analysis of mRNAs from pregnenolone 16alpha-carbonitrile-treated rats. Toxicol Sci. 2006 Dec; 94(2):379-87.
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    78. Bada M, Hunter L. Enrichment of OBO ontologies. J Biomed Inform. 2007 Jun; 40(3):300-15.
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    79. Lowes BD, Zolty R, Minobe WA, Robertson AD, Leach S, Hunter L, Bristow MR. Serial gene expression profiling in the intact human heart. J Heart Lung Transplant. 2006 May; 25(5):579-88.
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    80. Hunter L, Cohen KB. Biomedical language processing: what's beyond PubMed? Mol Cell. 2006 Mar 3; 21(5):589-94.
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    81. 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.
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    82. Lu Z, Cohen KB, Hunter L. Finding GeneRIFs via gene ontology annotations. Pac Symp Biocomput. 2006; 52-63.
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    83. Hu X, Friedman D, Hill S, Caprioli R, Nicholson W, Powers AC, Hunter L, Limbird LE. Proteomic exploration of pancreatic islets in mice null for the alpha2A adrenergic receptor. J Mol Endocrinol. 2005 Aug; 35(1):73-88.
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    84. Kinoshita S, Cohen KB, Ogren PV, Hunter L. BioCreAtIvE task1A: entity identification with a stochastic tagger. BMC Bioinformatics. 2005; 6 Suppl 1:S4.
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    85. Ogren PV, Cohen KB, Hunter L. Implications of compositionality in the gene ontology for its curation and usage. Pac Symp Biocomput. 2005; 174-85.
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    86. Coors ME, Hunter L. Evaluation of genetic enhancement: will human wisdom properly acknowledge the value of evolution? Am J Bioeth. 2005; 5(3):21-2; discussion W4-9.
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    87. Lu Z, Hunter L. Go molecular function terms are predictive of subcellular localization. Pac Symp Biocomput. 2005; 151-61.
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    88. 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.
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    89. Ogren PV, Cohen KB, Acquaah-Mensah GK, Eberlein J, Hunter L. The compositional structure of Gene Ontology terms. Pac Symp Biocomput. 2004; 214-25.
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    90. Russell SA, Old W, Resing KA, Hunter L. Proteomic informatics. Int Rev Neurobiol. 2004; 61:127-57.
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    91. Shenkar R, Elliott JP, Diener K, Gault J, Hu LJ, Cohrs RJ, Phang T, Hunter L, Breeze RE, Awad IA. Differential gene expression in human cerebrovascular malformations. Neurosurgery. 2003 Feb; 52(2):465-77; discussion 477-8.
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    92. Phang TL, Neville MC, Rudolph M, Hunter L. Trajectory clustering: a non-parametric method for grouping gene expression time courses, with applications to mammary development. Pac Symp Biocomput. 2003; 351-62.
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    93. Hunter L. Ontologies for programs, not people. Genome Biol. 2002; 3(6):INTERACTIONS1002.
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    94. Edgerton ME, Taylor R, Powell JI, Hunter L, Simon R, Liu ET. A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis. Bioinformatics. 2002 May; 18(5):774-5.
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    95. Hunter L, Taylor RC, Leach SM, Simon R. GEST: a gene expression search tool based on a novel Bayesian similarity metric. Bioinformatics. 2001; 17 Suppl 1:S115-22.
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    96. Rindflesch TC, Tanabe L, Weinstein JN, Hunter L. EDGAR: extraction of drugs, genes and relations from the biomedical literature. Pac Symp Biocomput. 2000; 517-28.
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    97. Shah I, Hunter L. Visual management of large scale data mining projects. Pac Symp Biocomput. 2000; 278-90.
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    98. Tanabe L, Scherf U, Smith LH, Lee JK, Hunter L, Weinstein JN. MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling. Biotechniques. 1999 Dec; 27(6):1210-4, 1216-7.
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    99. Rindflesch TC, Hunter L, Aronson AR. Mining molecular binding terminology from biomedical text. Proc AMIA Symp. 1999; 127-31.
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    100. Shah I, Hunter L. Visualization based on the Enzyme Commission nomenclature. Pac Symp Biocomput. 1998; 142-52.
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    101. Dowe DL, Allison L, Dix TI, Hunter L, Wallace CS, Edgoose T. Circular clustering of protein dihedral angles by Minimum Message Length. Pac Symp Biocomput. 1996; 242-55.
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    102. Hunter L, Klein T. Finding relevant biomolecular features. Proc Int Conf Intell Syst Mol Biol. 1993; 1:190-7.
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    103. Hunter L, Pring T, Martin S. The use of strategies to increase speech intelligibility in cerebral palsy: an experimental evaluation. Br J Disord Commun. 1991 Aug; 26(2):163-74.
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