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Lawrence E Hunter

TitleProfessor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-BIOMED Informatics Gen Ops
Phone303/724-3574

    Collapse Research 
    Collapse research activities and funding
    R01LM013400     (HUNTER, LAWRENCE E)Aug 1, 2020 - Jul 31, 2024
    NIH
    Scientific Questions: A New Target for Biomedical NLP
    Role: Principal Investigator
    OT2TR003422     (HUNTER, LAWRENCE E.)Jan 23, 2020 - Nov 30, 2022
    NIH
    High Performance Text Mining for Translator
    Role: Principal Investigator
    R01LM010120     (HUNTER, LAWRENCE E)Jul 1, 2009 - Jun 30, 2012
    NIH
    Automated Literature Mining for Validation of High-Throughput Function Prediction
    Role: Principal Investigator
    R01GM083649     (HUNTER, LAWRENCE E)Sep 30, 2007 - Aug 31, 2012
    NIH
    Ontologies and Biomedical Language Processing
    Role: Principal Investigator
    G08LM009639     (HUNTER, LAWRENCE E)Sep 15, 2007 - Sep 14, 2010
    NIH
    Construction of a Full Text Corpus for Biomedical Text Mining
    Role: Principal Investigator
    T15LM009451     (KECHRIS-MAYS, KATHERINA)Jul 1, 2007 - Jun 30, 2027
    NIH
    Colorado Biomedical Informatics Training Program
    Role: Principal Investigator
    R01LM009254     (HUNTER, LAWRENCE E.)Sep 15, 2006 - Apr 30, 2019
    NIH
    Bio Text NLP
    Role: Principal Investigator
    R01LM008111     (HUNTER, LAWRENCE E)Dec 1, 2003 - Jun 30, 2022
    NIH
    Knowledge-Based Biomedical Data Science
    Role: Principal Investigator
    U01AA013524     (HUNTER, LAWRENCE E)Sep 27, 2001 - Aug 31, 2006
    NIH
    Integrated Neuroinformatics Resource for Alcoholism (IN*
    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. Gupta S, Westacott MJ, Ayers DG, Weiss SJ, Whitley P, Mueller C, Weaver DC, Schneider DJ, Karimpour-Fard A, Hunter LE, Drolet DW, Janjic N. Plasma proteome of growing tumors. Sci Rep. 2023 07 27; 13(1):12195. PMID: 37500700.
      View in: PubMed
    2. Boguslav MR, Salem NM, White EK, Sullivan KJ, Bada M, Hernandez TL, Leach SM, Hunter LE. Creating an ignorance-base: Exploring known unknowns in the scientific literature. J Biomed Inform. 2023 07; 143:104405. PMID: 37270143.
      View in: PubMed
    3. Callahan TJ, Stefanski AL, Wyrwa JM, Zeng C, Ostropolets A, Banda JM, Baumgartner WA, Boyce RD, Casiraghi E, Coleman BD, Collins JH, Deakyne Davies SJ, Feinstein JA, Lin AY, Martin B, Matentzoglu NA, Meeker D, Reese J, Sinclair J, Taneja SB, Trinkley KE, Vasilevsky NA, Williams AE, Zhang XA, Denny JC, Ryan PB, Hripcsak G, Bennett TD, Haendel MA, Robinson PN, Hunter LE, Kahn MG. Ontologizing health systems data at scale: making translational discovery a reality. NPJ Digit Med. 2023 May 19; 6(1):89. PMID: 37208468.
      View in: PubMed
    4. Callahan TJ, Stefanksi AL, Ostendorf DM, Wyrwa JM, Davies SJD, Hripcsak G, Hunter LE, Kahn MG. Characterizing Patient Representations for Computational Phenotyping. AMIA Annu Symp Proc. 2022; 2022:319-328. PMID: 37128436.
      View in: PubMed
    5. Callahan TJ, Stefanski AL, Kim JD, Baumgartner WA, Wyrwa JM, Hunter LE. Knowledge-Driven Mechanistic Enrichment of the Preeclampsia Ignorome. Pac Symp Biocomput. 2023; 28:371-382. PMID: 36540992.
      View in: PubMed
    6. Santangelo BE, Gillenwater LA, Salem NM, Hunter LE. Molecular cartooning with knowledge graphs. Front Bioinform. 2022; 2:1054578. PMID: 36568701.
      View in: PubMed
    7. Nicholson DN, Rubinetti V, Hu D, Thielk M, Hunter LE, Greene CS. Examining linguistic shifts between preprints and publications. PLoS Biol. 2022 02; 20(2):e3001470. PMID: 35104289.
      View in: PubMed
    8. Boguslav MR, Hailu ND, Bada M, Baumgartner WA, Hunter LE. Concept recognition as a machine translation problem. BMC Bioinformatics. 2021 Dec 17; 22(Suppl 1):598. PMID: 34920707.
      View in: PubMed
    9. Boguslav MR, Salem NM, White EK, Leach SM, Hunter LE. Identifying and classifying goals for scientific knowledge. Bioinform Adv. 2021; 1(1):vbab012. PMID: 34661112.
      View in: PubMed
    10. Sullivan KJ, Burden M, Keniston A, Banda JM, Hunter LE. Characterization of Anonymous Physician Perspectives on COVID-19 Using Social Media Data. Pac Symp Biocomput. 2021; 26:95-106. PMID: 33691008.
      View in: PubMed
    11. Tripodi IJ, Callahan TJ, Westfall JT, Meitzer NS, Dowell RD, Hunter LE. Applying knowledge-driven mechanistic inference to toxicogenomics. Toxicol In Vitro. 2020 Aug; 66:104877. PMID: 32387679.
      View in: PubMed
    12. Callahan TJ, Tripodi IJ, Pielke-Lombardo H, Hunter LE. Knowledge-Based Biomedical Data Science. Annu Rev Biomed Data Sci. 2020 Jul; 3:23-41. PMID: 33954284.
      View in: PubMed
    13. Cohen KB, Hunter LE, Pressman PS. P-Hacking Lexical Richness Through Definitions of "Type" and "Token". Stud Health Technol Inform. 2019 Aug 21; 264:1433-1434. PMID: 31438167.
      View in: PubMed
    14. Pressman PS, Ross ED, Cohen KB, Chen KH, Miller BL, Hunter LE, Gorno-Tempini ML, Levenson RW. Interpersonal prosodic correlation in frontotemporal dementia. Ann Clin Transl Neurol. 2019 07; 6(7):1352-1357. PMID: 31353851.
      View in: PubMed
    15. Zhang XA, Yates A, Vasilevsky N, Gourdine JP, Callahan TJ, Carmody LC, Danis D, Joachimiak MP, Ravanmehr V, Pfaff ER, Champion J, Robasky K, Xu H, Fecho K, Walton NA, Zhu RL, Ramsdill J, Mungall CJ, K?hler S, Haendel MA, McDonald CJ, Vreeman DJ, Peden DB, Bennett TD, Feinstein JA, Martin B, Stefanski AL, Hunter LE, Chute CG, Robinson PN. Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery. NPJ Digit Med. 2019; 2. PMID: 31119199.
      View in: PubMed
    16. Cohen KB, Xia J, Zweigenbaum P, Callahan TJ, Hargraves O, Goss F, Ide N, N?v?ol 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
    17. 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
    18. 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
    19. Hunter LE. Knowledge-based biomedical Data Science. EPJ Data Sci. 2017; 1(1-2):19-25. PMID: 30294517.
      View in: PubMed
    20. 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
    21. 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
    22. Greene CS, Garmire LX, Gilbert JA, Ritchie MD, Hunter LE. Celebrating parasites. Nat Genet. 2017 03 30; 49(4):483-484. PMID: 28358134.
      View in: PubMed
    23. 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
    24. 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
    25. 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
    26. 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
    27. Bada M, Vasilevsky N, Baumgartner WA, Haendel M, Hunter LE. Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. Database (Oxford). 2017 Jan 01; 2017. PMID: 31725864.
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    28. 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
    29. 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
    30. 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
    31. 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.
      View in: PubMed
    32. Vehlow C, Kao DP, Bristow MR, Hunter LE, Weiskopf D, G?rg C. Visual analysis of biological data-knowledge networks. BMC Bioinformatics. 2015 Apr 29; 16:135. PMID: 25925016.
      View in: PubMed
    33. 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.
      View in: PubMed
    34. 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.
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    35. Hinterberg MA, Kao DP, Bristow MR, Hunter LE, Port JD, G?rg 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
    36. Pattin KA, Greene AC, Altman RB, Cohen KB, Wethington E, G?rg 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
    37. 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
    38. 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
    39. 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.
      View in: PubMed
    40. 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
    41. 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.
      View in: PubMed
    42. Hunter LE. Rocky mountain conference on bioinformatics celebrates 10 years. PLoS Comput Biol. 2013; 9(5):e1003076. PMID: 23737739.
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    43. Cohen KB, Hunter LE. Chapter 16: text mining for translational bioinformatics. PLoS Comput Biol. 2013 Apr; 9(4):e1003044. PMID: 23633944.
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    44. Liu H, Hunter L, Ke?elj V, Verspoor K. Approximate subgraph matching-based literature mining for biomedical events and relations. PLoS One. 2013; 8(4):e60954. PMID: 23613763.
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    45. Hunter L. Computational challenges of mass phenotyping. Pac Symp Biocomput. 2013; 454-5. PMID: 23424150.
      View in: PubMed
    46. Cohen KB, Hunter LE, Palmer M. Assessment of software testing and quality assurance in natural language processing applications and a linguistically inspired approach to improving it. Trust Eternal Syst Via Evol Softw Data Knowl (2012). 2013; 379:77-90. PMID: 34308448.
      View in: PubMed
    47. 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
    48. 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.
      View in: PubMed
    49. 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.
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    50. 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
    51. 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.
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    52. 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.
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    53. 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.
      View in: PubMed
    54. 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.
      View in: PubMed
    55. Kano Y, Bj?rne 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, ?zg?r A, Radev DR, Riedel S, S?tre 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.
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    56. 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
    57. 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.
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    58. 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.
      View in: PubMed
    59. 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.
      View in: PubMed
    60. 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.
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    61. 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.
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    62. 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.
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    63. 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.
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    64. 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.
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    65. 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.
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    66. 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.
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    67. 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.
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    68. 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
    69. 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.
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    70. Lussier YA, Butte AJ, Hunter L. Current methodologies for translational bioinformatics. J Biomed Inform. 2010 Jun; 43(3):355-7. PMID: 20470899.
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    71. Tipney H, Hunter L. An introduction to effective use of enrichment analysis software. Hum Genomics. 2010 Feb; 4(3):202-6. PMID: 20368141.
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    72. 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.
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    73. 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.
      View in: PubMed
    74. 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
    75. 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.
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    76. 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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    77. 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.
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    78. 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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    79. 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.
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    80. Tipney HJ, Schuyler RP, Hunter L. Consistent visualizations of changing knowledge. Summit Transl Bioinform. 2009 Mar 01; 2009:129-32. PMID: 21347184.
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    81. 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.
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    82. 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.
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    83. 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.
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    84. 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.
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    85. Cohen KB, Palmer M, Hunter L. Nominalization and alternations in biomedical language. PLoS One. 2008 Sep 09; 3(9):e3158. PMID: 18779866.
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    86. 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.
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    87. 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, Ma?a-L?pez M, Mata J, Wilbur WJ. Overview of BioCreative II gene mention recognition. Genome Biol. 2008; 9 Suppl 2:S2. PMID: 18834493.
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    88. 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, Ozg?r 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.
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    89. 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.
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    90. Bethard S, Lu Z, Martin JH, Hunter L. Semantic role labeling for protein transport predicates. BMC Bioinformatics. 2008 Jun 11; 9:277. PMID: 18547432.
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    91. Bada M, Hunter L. Identification of OBO nonalignments and its implications for OBO enrichment. Bioinformatics. 2008 Jun 15; 24(12):1448-55. PMID: 18463117.
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    92. 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.
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    93. 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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    94. 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.
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    95. 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.
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    96. Cohen KB, Hunter L. Getting started in text mining. PLoS Comput Biol. 2008 Jan; 4(1):e20. PMID: 18225946.
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    97. 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.
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    98. 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.
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    99. 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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    100. 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.
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    101. 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.
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    102. 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.
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    103. 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.
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    104. 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.
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    105. 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.
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    106. 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.
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    107. Johnson HL, Cohen KB, Hunter L. A fault model for ontology mapping, alignment, and linking systems. Pac Symp Biocomput. 2007; 233-44. PMID: 17990495.
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    108. Lu Z, Cohen KB, Hunter L. GeneRIF quality assurance as summary revision. Pac Symp Biocomput. 2007; 269-80. PMID: 17990498.
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    109. 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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    110. 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.
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    111. 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.
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    112. Bada M, Hunter L. Enrichment of OBO ontologies. J Biomed Inform. 2007 Jun; 40(3):300-15. PMID: 17011833.
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    113. 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.
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    114. Hunter L, Cohen KB. Biomedical language processing: what's beyond PubMed? Mol Cell. 2006 Mar 03; 21(5):589-94. PMID: 16507357.
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    115. Lu Z, Cohen KB, Hunter L. Finding GeneRIFs via gene ontology annotations. Pac Symp Biocomput. 2006; 52-63. PMID: 17094227.
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    116. 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.
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    117. 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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    118. 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.
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    119. 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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    120. 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.
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    121. 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.
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    122. Russell SA, Old W, Resing KA, Hunter L. Proteomic informatics. Int Rev Neurobiol. 2004; 61:127-57. PMID: 15482814.
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    123. Witzmann FA, Li J, Strother WN, McBride WJ, Hunter L, Crabb DW, Lumeng L, Li TK. Innate differences in protein expression in the nucleus accumbens and hippocampus of inbred alcohol-preferring and -nonpreferring rats. Proteomics. 2003 Jul; 3(7):1335-44. PMID: 12872235.
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    124. 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.
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    125. Hunter L. Ontologies for programs, not people. Genome Biol. 2002; 3(6):INTERACTIONS1002. PMID: 12093368.
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