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Lawrence E Hunter

InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM - Pharmacology

    Collapse Research 
    Collapse research activities and funding
    U01AA013524     (HUNTER, LAWRENCE E)Sep 27, 2001 - Aug 31, 2006
    Integrated Neuroinformatics Resource for Alcoholism (IN*
    Role: Principal Investigator

    R01LM008111     (HUNTER, LAWRENCE E.)Dec 1, 2003 - Jun 30, 2022
    Developing and applying information extraction resources and technology to create
    Role: Principal Investigator

    R01LM009254     (HUNTER, LAWRENCE E.)Sep 15, 2006 - Apr 30, 2019
    Bio Text NLP
    Role: Principal Investigator

    T15LM009451     (HUNTER, LAWRENCE E.)Jul 1, 2007 - Jun 30, 2022
    Colorado Biomedical Informatics Training Program
    Role: Principal Investigator

    G08LM009639     (HUNTER, LAWRENCE E)Sep 15, 2007 - Sep 14, 2010
    Construction of a Full Text Corpus for Biomedical Text Mining
    Role: Principal Investigator

    R01GM083649     (HUNTER, LAWRENCE E)Sep 30, 2007 - Aug 31, 2012
    Ontologies and Biomedical Language Processing
    Role: Principal Investigator

    R01LM010120     (HUNTER, LAWRENCE E)Jul 1, 2009 - Jun 30, 2012
    Automated Literature Mining for Validation of High-Throughput Function Prediction
    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. Callahan TJ, Baumgartner WA, Bada M, Stefanski AL, Tripodi I, White EK, Hunter LE. OWL-NETS: Transforming OWL Representations for Improved Network Inference. Pac Symp Biocomput. 2018; 23:133-144. PMID: 29218876.
      View in: PubMed
    3. 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
    4. Hunter LE. Knowledge-based biomedical Data Science. EPJ Data Sci. 2017; 1(1-2):19-25. PMID: 30294517.
      View in: PubMed
    5. 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
    6. Pouille F, McTavish TS, Hunter LE, Restrepo D, Schoppa NE. Intraglomerular gap junctions enhance interglomerular synchrony in a sparsely connected olfactory bulb network. J Physiol. 2017 09 01; 595(17):5965-5986. PMID: 28640508.
      View in: PubMed
    7. Greene CS, Garmire LX, Gilbert JA, Ritchie MD, Hunter LE. Celebrating parasites. Nat Genet. 2017 Mar 30; 49(4):483-484. PMID: 28358134.
      View in: PubMed
    8. Hooper JE, Feng W, Li H, Leach SM, Phang T, Siska C, Jones KL, Spritz RA, Hunter LE, Williams T. Systems biology of facial development: contributions of ectoderm and mesenchyme. Dev Biol. 2017 06 01; 426(1):97-114. PMID: 28363736.
      View in: PubMed
    9. Moore JH, Jennings SF, Greene CS, Hunter LE, Perkins AD, Williams-Devane C, Wunsch DC, Zhao Z, Huang X. NO-BOUNDARY THINKING IN BIOINFORMATICS. Pac Symp Biocomput. 2017; 22:646-648. PMID: 27897015.
      View in: PubMed
    10. 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
    11. 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
    12. Eberlein J, Davenport B, Nguyen T, Victorino F, Haist K, Jhun K, Karimpour-Fard A, Hunter L, Kedl R, Clambey ET, Homann D. Aging promotes acquisition of naive-like CD8+ memory T cell traits and enhanced functionalities. J Clin Invest. 2016 10 03; 126(10):3942-3960. PMID: 27617858.
      View in: PubMed
    13. 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
    14. 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
    15. Karimpour-Fard A, Epperson LE, Hunter LE. A survey of computational tools for downstream analysis of proteomic and other omic datasets. Hum Genomics. 2015 Oct 28; 9:28. PMID: 26510531; PMCID: PMC4624643.
    16. Vehlow C, Kao DP, Bristow MR, Hunter LE, Weiskopf D, Görg C. Visual analysis of biological data-knowledge networks. BMC Bioinformatics. 2015 Apr 29; 16:135. PMID: 25925016.
      View in: PubMed
    17. Livingston KM, Bada M, Baumgartner WA, Hunter LE. KaBOB: ontology-based semantic integration of biomedical databases. BMC Bioinformatics. 2015 Apr 23; 16:126. PMID: 25903923; PMCID: PMC4448321.
    18. Hewett D, Whirl-Carrillo M, Hunter LE, Altman RB, Klein TE. A twentieth anniversary tribute to PSB. Pac Symp Biocomput. 2015; 1-7. PMID: 25592562.
      View in: PubMed
    19. 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; 419-30. PMID: 25592601.
      View in: PubMed
    20. 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
    21. 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.
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    22. 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.
    23. 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. PMID: 24297567; PMCID: PMC3935419.
    24. 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.
    25. Livingston KM, Bada M, Hunter LE, Verspoor K. Representing annotation compositionality and provenance for the Semantic Web. J Biomed Semantics. 2013; 4:38. PMID: 24268021; PMCID: PMC4129183.
    26. Hunter LE. Rocky mountain conference on bioinformatics celebrates 10 years. PLoS Comput Biol. 2013; 9(5):e1003076. PMID: 23737739; PMCID: PMC3667766.
    27. Cohen KB, Hunter LE. Chapter 16: text mining for translational bioinformatics. PLoS Comput Biol. 2013 Apr; 9(4):e1003044. PMID: 23633944; PMCID: PMC3635962.
    28. 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. PMID: 23613763.
      View in: PubMed
    29. Hunter L. Computational challenges of mass phenotyping. Pac Symp Biocomput. 2013; 454-5. PMID: 23424150.
      View in: PubMed
    30. Frantz AM, Sarver AL, Ito D, Phang TL, Karimpour-Fard A, Scott MC, Valli VE, Lindblad-Toh K, Burgess KE, Husbands BD, Henson MS, Borgatti A, Kisseberth WC, Hunter LE, Breen M, O'Brien TD, Modiano JF. Molecular profiling reveals prognostically significant subtypes of canine lymphoma. Vet Pathol. 2013 Jul; 50(4):693-703. PMID: 23125145.
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    31. 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.
    32. 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. PMID: 22450367; PMCID: PMC3387325.
    33. 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. PMID: 22814848; PMCID: PMC3501742.
    34. 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.
    35. 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. PMID: 22683918; PMCID: PMC3534470.
    36. 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. PMID: 22643061; PMCID: PMC3426438.
    37. 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. PMID: 22627919; PMCID: PMC3434286.
    38. 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. PMID: 22502949; PMCID: PMC3423195.
    39. 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.
    40. 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
    41. 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.
    42. 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. PMID: 21914784; PMCID: PMC3217319.
    43. 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. PMID: 21865542; PMCID: PMC3213940.
    44. 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. PMID: 21798686.
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    45. 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. PMID: 21621658; PMCID: PMC3143255.
    46. Epperson LE, Karimpour-Fard A, Hunter LE, Martin SL. Metabolic cycles in a circannual hibernator. Physiol Genomics. 2011 Jul 14; 43(13):799-807. PMID: 21540299; PMCID: PMC3132838.
    47. 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 01; 10(4):1837-47. PMID: 21319786; PMCID: PMC3501204.
    48. 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
    49. 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 Nov 09; 10:619. PMID: 21062482; PMCID: PMC2994824.
    50. 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. PMID: 20971216.
      View in: PubMed
    51. 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.
    52. 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. PMID: 20846932; PMCID: PMC3525224.
    53. 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.
    54. 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. PMID: 20505005; PMCID: PMC2894505.
    55. Tipney H, Hunter L. An introduction to effective use of enrichment analysis software. Hum Genomics. 2010 Feb; 4(3):202-6. PMID: 20368141; PMCID: PMC3525973.
    56. 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. PMID: 19904832; PMCID: PMC3501138.
    57. 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 Dec 16; 4(12):e8066. PMID: 20016822; PMCID: PMC2789411.
    58. 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.
    59. 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.
    60. 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 May 20; 4(5):e5549. PMID: 19461996.
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    61. 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.
    62. Shortliffe EH, Califano A, Hunter L. New JBI emphasis on translational bioinformatics. J Biomed Inform. 2009 Apr; 42(2):199-200. PMID: 19298948.
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    63. 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. PMID: 19325874; PMCID: PMC2653649.
    64. Tipney HJ, Schuyler RP, Hunter L. Consistent visualizations of changing knowledge. Summit Transl Bioinform. 2009 Mar 01; 2009:129-32. PMID: 21347184; PMCID: PMC3041575.
    65. 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 Feb 05; 10 Suppl 2:S12. PMID: 19208187; PMCID: PMC2646237.
    66. 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. PMID: 19106086; PMCID: PMC2667364.
    67. 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 Dec 03; 8:327. PMID: 19055758; PMCID: PMC2637866.
    68. Karimpour-Fard A, Leach SM, Gill RT, Hunter LE. Predicting protein linkages in bacteria: which method is best depends on task. BMC Bioinformatics. 2008 Sep 24; 9:397. PMID: 18816389; PMCID: PMC2570368.
    69. Cohen KB, Palmer M, Hunter L. Nominalization and alternations in biomedical language. PLoS One. 2008 Sep 09; 3(9):e3158. PMID: 18779866; PMCID: PMC2527518.
    70. 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.
    71. 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. PMID: 18834493; PMCID: PMC2559986.
    72. 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. PMID: 18834497; PMCID: PMC2559990.
    73. 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 Jun 30; 9:313. PMID: 18590549; PMCID: PMC2488357.
    74. Bethard S, Lu Z, Martin JH, Hunter L. Semantic role labeling for protein transport predicates. BMC Bioinformatics. 2008 Jun 11; 9:277. PMID: 18547432; PMCID: PMC2474622.
    75. Bada M, Hunter L. Identification of OBO nonalignments and its implications for OBO enrichment. Bioinformatics. 2008 Jun 15; 24(12):1448-55. PMID: 18463117; PMCID: PMC2427163.
    76. Gabow AP, Leach SM, Baumgartner WA, Hunter LE, Goldberg DS. Improving protein function prediction methods with integrated literature data. BMC Bioinformatics. 2008 Apr 15; 9:198. PMID: 18412966; PMCID: PMC2375131.
    77. 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. PMID: 18327671.
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    78. 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.
    79. 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.
    80. Cohen KB, Hunter L. Getting started in text mining. PLoS Comput Biol. 2008 Jan; 4(1):e20. PMID: 18225946; PMCID: PMC2217579.
    81. 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. PMID: 21243075; PMCID: PMC3020656.
    82. 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.
    83. Glueck DH, Muller KE, Karimpour-Fard A, Hunter L. Expected Power for the False Discovery Rate with Independence. Commun Stat Theory Methods. 2008 Jan; 37(12):1855-1866. PMID: 20975846.
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    84. Glueck DH, Karimpour-Fard A, Mandel J, Hunter L, Muller KE. Fast Computation by Block Permanents of Cumulative Distribution Functions of Order Statistics from Several Populations. Commun Stat Theory Methods. 2008 Jan 01; 37(18):2815-2824. PMID: 19865590.
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    85. 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.
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    86. Karimpour-Fard A, Hunter L, Gill RT. Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling. BMC Genomics. 2007 Oct 29; 8:393. PMID: 17967189; PMCID: PMC2204017.
    87. 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.
    88. 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 Aug 30; 8:59. PMID: 17760997; PMCID: PMC2034588.
    89. 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.
    90. 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.
    91. 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. PMID: 17318087; PMCID: PMC2709529.
    92. 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. PMID: 17803817; PMCID: PMC2375023.
    93. Leach S, Gabow A, Hunter L, Goldberg DS. Assessing and combining reliability of protein interaction sources. Pac Symp Biocomput. 2007; 433-44. PMID: 17990508.
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    94. 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.
    95. Lu Z, Cohen KB, Hunter L. GeneRIF quality assurance as summary revision. Pac Symp Biocomput. 2007; 269-80. PMID: 17990498; PMCID: PMC2652871.
    96. 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.
    97. 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. PMID: 16997903; PMCID: PMC1636678.
    98. Bada M, Hunter L. Enrichment of OBO ontologies. J Biomed Inform. 2007 Jun; 40(3):300-15. PMID: 17011833; PMCID: PMC2084396.
    99. 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. PMID: 16678038; PMCID: PMC2709530.
    100. Hunter L, Cohen KB. Biomedical language processing: what's beyond PubMed? Mol Cell. 2006 Mar 03; 21(5):589-94. PMID: 16507357; PMCID: PMC1702322.
    101. Lu Z, Cohen KB, Hunter L. Finding GeneRIFs via gene ontology annotations. Pac Symp Biocomput. 2006; 52-63. PMID: 17094227; PMCID: PMC2652876.
    102. 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.
    103. 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. PMID: 16087723.
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    104. 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.
    105. 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.
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    106. Lu Z, Hunter L. Go molecular function terms are predictive of subcellular localization. Pac Symp Biocomput. 2005; 151-61. PMID: 15759622; PMCID: PMC2652875.
    107. 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. PMID: 16006358; PMCID: PMC2517247.
    108. 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.
    109. Russell SA, Old W, Resing KA, Hunter L. Proteomic informatics. Int Rev Neurobiol. 2004; 61:127-57. PMID: 15482814.
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    110. 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.
    111. 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. PMID: 12535382; PMCID: PMC2709524.
    112. 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. PMID: 12603041; PMCID: PMC2527819.
    113. Hunter L. Ontologies for programs, not people. Genome Biol. 2002; 3(6):INTERACTIONS1002. PMID: 12093368; PMCID: PMC139366.
    114. 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. PMID: 12050079.
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    115. 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. PMID: 11473000.
      View in: PubMed
    116. 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. PMID: 10902199.
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    117. Shah I, Hunter L. Visual management of large scale data mining projects. Pac Symp Biocomput. 2000; 278-90. PMID: 10902176; PMCID: PMC2709531.
    118. 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. PMID: 10631500.
      View in: PubMed
    119. Rindflesch TC, Hunter L, Aronson AR. Mining molecular binding terminology from biomedical text. Proc AMIA Symp. 1999; 127-31. PMID: 10566334; PMCID: PMC2232739.
    120. Shah I, Hunter L. Visualization based on the Enzyme Commission nomenclature. Pac Symp Biocomput. 1998; 142-52. PMID: 9697178.
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    121. 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. PMID: 9390236.
      View in: PubMed
    122. Hunter L, Klein T. Finding relevant biomolecular features. Proc Int Conf Intell Syst Mol Biol. 1993; 1:190-7. PMID: 7584335.
      View in: PubMed
    123. 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. PMID: 1777397.
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