Larry Hunter, PhD
Professor, Biomedical Informatics

Professional Titles

• Professor

Recognition & Awards

• Excellence in Teaching, Pharmacology Department (2017)
• Daniel T. Richards Prize, American Medical Library Association (2016)
  For advancing openness in science and scientific publication
• Outstanding Service Award, International Society for Computational Biology (2016)
  For lifetime contributions to the ISCB

Research Interests

Teaching

Publications

• 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. PubMed PMID: 36540992
• Fecho K, Thessen AE, Baranzini SE, Bizon C, Hadlock JJ, Huang S, Roper RT, Southall N, Ta C, Watkins PB, Williams MD, Xu H, Byrd W, Dancík V, Duby MP, Dumontier M, Glusman G, Harris NL, Hinderer EW, Hyde G, Johs A, Su AI, Qin G, Zhu Q. Progress toward a universal biomedical data translator. Clin Transl Sci. 2022 May 25;15(8):1838-47. [Epub ahead of print] PubMed PMID: 35611543
• Santangelo BE, Gillenwater LA, Salem NM, Hunter LE. Molecular cartooning with knowledge graphs. Front Bioinform. 2022;2:1054578. PubMed PMID: 36568701
• Nicholson DN, Rubinetti V, Hu D, Thielk M, Hunter LE, Greene CS. Examining linguistic shifts between preprints and publications. PLoS Biol. 2022 Feb;20(2):e3001470. PubMed PMID: 35104289
• Zong N, Li N, Wen A, Ngo V, Yu Y, Huang M, Chowdhury S, Jiang C, Fu S, Weinshilboum R, Jiang G, Hunter L, Liu H. BETA: a comprehensive benchmark for computational drug-target prediction. Brief Bioinform. 2022 Jul 18;23(4). PubMed PMID: 35649342
• Unni DR, Moxon SAT, Bada M, Brush M, Bruskiewich R, Caufield JH, Clemons PA, Dancik V, Dumontier M, Fecho K, Glusman G, Hadlock JJ, Harris NL, Joshi A, Putman T, Qin G, Ramsey SA, Shefchek KA, Solbrig H, Soman K, Thessen AE, Haendel MA, Bizon C, Mungall CJ. Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci. 2022 Aug;15(8):1848-1855. PubMed PMID: 36125173
• Boguslav MR, Salem NM, White EK, Leach SM, Hunter LE. Identifying and classifying goals for scientific knowledge. Bioinform Adv. 2021;1(1):vbab012. PubMed PMID: 34661112
• 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. PubMed PMID: 33691008
• Is There Gender Bias In Internal Medicine Grand Rounds Introduction? Rm Hanna, L Hunter, A Keniston, L Mcbeth, A Kara… - Journal Of General Internal Medicine, 2021
• 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. PubMed PMID: 32387679
• Southall NT, Natarajan M, Lau LPL, Jonker AH, Deprez B, Guilliams T, Hunter L, Rademaker CM, Hivert V, Ardigò D. The use or generation of biomedical data and existing medicines to discover and establish new treatments for patients with rare diseases - recommendations of the IRDiRC Data Mining and Repurposing Task Force. Orphanet J Rare Dis. 2019 Oct 15;14(1):225. PubMed PMID: 31615551
• 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. PubMed PMID: 31438167
• 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 Jul;6(7):1352-1357. PubMed PMID: 31353851
• 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, Köhler 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. PubMed PMID: 31119199
• Boguslav M, Cohen KB, Baumgartner WA, Hunter LE. Improving precision in concept normalization. Pac Symp Biocomput. 2018;23:566-577. PubMed PMID: 29218915
• 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. PubMed PMID: 29218876
• 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. PubMed PMID: 29295175
• 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. PubMed PMID: 29295113
• Cohen KB, Lanfranchi A, Choi MJ, Bada M, Baumgartner WA Jr, 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. PubMed PMID: 28818042
• 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 Sep 1;595(17):5965-5986. PubMed PMID: 28640508
• 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 Jun 1;426(1):97-114. PubMed PMID: 28363736
• Greene CS, Garmire LX, Gilbert JA, Ritchie MD, Hunter LE. Celebrating parasites. Nat Genet. 2017 Mar 30;49(4):483-484. PubMed PMID: 28358134
• 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. PubMed PMID: 27897015
• 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. 2016;22:646-648. PubMed PMID: 27897015
• 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 Oct 3;126(10):3942-3960. PubMed PMID: 27617858
• 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 9;7:52. PubMed PMID: 27613112
• 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. PubMed PMID: 25592609
• 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. PubMed PMID: 25592601
• Hewett D, Whirl-Carrillo M, Hunter LE, Altman RB, Klein TE. A twentieth anniversary tribute to PSB. Pac Symp Biocomput. 2015;:1-7. PubMed PMID: 25592562
• 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. PubMed PMID: 25925016
• Livingston KM, Bada M, Baumgartner WA Jr, Hunter LE. KaBOB: ontology-based semantic integration of biomedical databases. BMC Bioinformatics. 2015 Apr 23;16:126. PubMed PMID: 25903923
• 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. PubMed PMID: 26510531
• 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. PubMed PMID: 25592601
• 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. PubMed PMID: 25592609
• Hewett D, Whirl-Carrillo M, Hunter LE, Altman RB, Klein TE. A twentieth anniversary tribute to PSB. Pac Symp Biocomput. 2015;:1-7. PubMed PMID: 25592562
• Funk C, Baumgartner W Jr, 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. PubMed PMID: 24571547
• 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. PubMed PMID: 24297567
• Funk CS, Hunter LE, Cohen KB. Combining heterogenous data for prediction of disease related and pharmacogenes. Pac Symp Biocomput. 2014;:328-39. PubMed PMID: 24297559
• Carpendale S, Chen M, Evanko D, Gehlenborg N, Gorg C, Hunter L, Rowland F, Storey MA, Strobelt H. Ontologies in biological data visualization. IEEE Comput Graph Appl. 2014 Mar-Apr;34(2):8-15. PubMed PMID: 24808195
• Livingston KM, Bada M, Hunter LE, Verspoor K. Representing annotation compositionality and provenance for the Semantic Web. J Biomed Semantics. 2013 Nov 22;4(1):38. [Epub ahead of print] PubMed PMID: 24268021
• Yarborough M, Hunter L. Teaching research ethics better: focus on excellent science, not bad scientists. Clin Transl Sci. 2013 Jun;6(3):201-3. PubMed PMID: 23751025
• Hunter LE. Rocky mountain conference on bioinformatics celebrates 10 years. PLoS Comput Biol. 2013;9(5):e1003076. PubMed PMID: 23737739
• Cohen KB, Hunter LE. Chapter 16: text mining for translational bioinformatics. PLoS Comput Biol. 2013 Apr;9(4):e1003044. PubMed PMID: 23633944
• 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. PubMed PMID: 23613763
• Hunter L. Computational challenges of mass phenotyping. Pac Symp Biocomput. 2013;:454-5. PubMed PMID: 23424150
• 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. PubMed PMID: 23125145

Professional Memberships

• International Society for Computational Biology, Founding President