Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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Last Name
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William Anthony Baumgartner

TitleAssistant Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-MED
ORCID ORCID Icon0000-0001-6717-5313 Additional info

    Collapse Research 
    Collapse research activities and funding
    R01LM013400     (BAUMGARTNER, WILLIAM ANTHONY)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, 2024
    NIH
    High Performance Text Mining for Translator
    Role: Co-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. Shoaibi A, Ostropolets A, Weaver J, Rao GA, Golozar A, Swerdel J, Huser V, Adam A, Alshammari T, Anikpezie N, Baumgartner WA, Brand M, Fan R, Kanter AS, Kern D, Melisa S, Minty E, Mo J, Oluwalade B, Schilling LM, Spence H, Stocking JC, Zhang L, Ryan P. Variation in Phenotype Definitions in Observational Clinical Research: A Review of Three Conditions. AMIA Annu Symp Proc. 2024; 2024:1021-1029. PMID: 40417462.
      View in: PubMed
    2. Rizaldi AA, Larson EL, Zhou AL, Alejo DE, Wang H, Baumgartner WA, Sussman MS. Engaging the Next Generation: Evaluating the Long-term Success of a Premedical Program in Cardiothoracic Surgery. Ann Thorac Surg. 2025 Apr 25. PMID: 40288730.
      View in: PubMed
    3. Calhoon J, Cleveland J, Baumgartner W. In Memoriam: David Fullerton, STS Past President and Superb Cardiac Surgeon, Educator, Investigator and Leader (1952 - 2024). Ann Thorac Surg. 2025 Feb 13. PMID: 39955020.
      View in: PubMed
    4. Callahan TJ, Tripodi IJ, Stefanski AL, Cappelletti L, Taneja SB, Wyrwa JM, Casiraghi E, Matentzoglu NA, Reese J, Silverstein JC, Hoyt CT, Boyce RD, Malec SA, Unni DR, Joachimiak MP, Robinson PN, Mungall CJ, Cavalleri E, Fontana T, Valentini G, Mesiti M, Gillenwater LA, Santangelo B, Vasilevsky NA, Hoehndorf R, Bennett TD, Ryan PB, Hripcsak G, Kahn MG, Bada M, Baumgartner WA, Hunter LE. An open source knowledge graph ecosystem for the life sciences. Sci Data. 2024 Apr 11; 11(1):363. PMID: 38605048.
      View in: PubMed
    5. Baumgartner WA. The Exit Strategy: Preparing for Retirement. Thorac Surg Clin. 2024 Feb; 34(1):105-110. PMID: 37953047.
      View in: PubMed
    6. 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
    7. Ostropolets A, Albogami Y, Conover M, Banda JM, Baumgartner WA, Blacketer C, Desai P, DuVall SL, Fortin S, Gilbert JP, Golozar A, Ide J, Kanter AS, Kern DM, Kim C, Lai LYH, Li C, Liu F, Lynch KE, Minty E, Neves MI, Ng DQ, Obene T, Pera V, Pratt N, Rao G, Rappoport N, Reinecke I, Saroufim P, Shoaibi A, Simon K, Suchard MA, Swerdel JN, Voss EA, Weaver J, Zhang L, Hripcsak G, Ryan PB. Reproducible variability: assessing investigator discordance across 9 research teams attempting to reproduce the same observational study. J Am Med Inform Assoc. 2023 04 19; 30(5):859-868. PMID: 36826399.
      View in: PubMed
    8. 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
    9. 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
    10. 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
    11. 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
    12. 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
    13. Cohen KB, Baumgartner WA, Temnikova I. SuperCAT: The (New and Improved) Corpus Analysis Toolkit. LREC Int Conf Lang Resour Eval. 2016 May; 2016:2784-2788. PMID: 29568820.
      View in: PubMed
    14. 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
    15. Temnikova IP, Baumgartner WA, Hailu ND, Nikolova I, McEnery T, Kilgarriff A, Angelova G, Cohen KB. Sublanguage Corpus Analysis Toolkit: A tool for assessing the representativeness and sublanguage characteristics of corpora. LREC Int Conf Lang Resour Eval. 2014 May; 2014:1714-1718. PMID: 29568819.
      View in: PubMed
    16. 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
    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 Jul 09; 13:161. PMID: 22776079.
      View in: PubMed
    18. Liu H, Christiansen T, Baumgartner WA, Verspoor K. BioLemmatizer: a lemmatization tool for morphological processing of biomedical text. J Biomed Semantics. 2012 Apr 01; 3:3. PMID: 22464129.
      View in: PubMed
    19. Cohen KB, Verspoor K, Johnson HL, Roeder C, Ogren PV, Baumgartner WA, White E, Tipney H, Hunter L. HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA. Comput Intell. 2011 Nov; 27(4):681-701. PMID: 25937701.
      View in: PubMed
    20. 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
    21. 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.
      View in: PubMed
    22. Kano Y, Baumgartner WA, McCrohon L, Ananiadou S, Cohen KB, Hunter L, Tsujii J. U-Compare: share and compare text mining tools with UIMA. Bioinformatics. 2009 Aug 01; 25(15):1997-8. PMID: 19414535.
      View in: PubMed
    23. 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.
      View in: PubMed
    24. Baumgartner WA, Lu Z, Johnson HL, Caporaso JG, Paquette J, Lindemann A, White EK, Medvedeva O, Cohen KB, Hunter L. Concept recognition for extracting protein interaction relations from biomedical text. Genome Biol. 2008; 9 Suppl 2:S9. PMID: 18834500.
      View in: PubMed
    25. 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.
      View in: PubMed
    26. Hunter L, Lu Z, Firby J, Baumgartner WA, Johnson HL, Ogren PV, Cohen KB. OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinformatics. 2008 Jan 31; 9:78. PMID: 18237434.
      View in: PubMed
    27. Baumgartner WA, Cohen KB, Hunter L. An open-source framework for large-scale, flexible evaluation of biomedical text mining systems. J Biomed Discov Collab. 2008 Jan 29; 3:1. PMID: 18230184.
      View in: PubMed
    28. Johnson HL, Baumgartner WA, Krallinger M, Cohen KB, Hunter L. Corpus refactoring: a feasibility study. J Biomed Discov Collab. 2007 Sep 13; 2:4. PMID: 17854502.
      View in: PubMed
    29. Baumgartner WA, Cohen KB, Fox LM, Acquaah-Mensah G, Hunter L. Manual curation is not sufficient for annotation of genomic databases. Bioinformatics. 2007 Jul 01; 23(13):i41-8. PMID: 17646325.
      View in: PubMed
    30. Caporaso JG, Baumgartner WA, Randolph DA, Cohen KB, Hunter L. MutationFinder: a high-performance system for extracting point mutation mentions from text. Bioinformatics. 2007 Jul 15; 23(14):1862-5. PMID: 17495998.
      View in: PubMed
    31. Johnson HL, Cohen KB, Baumgartner WA, Lu Z, Bada M, Kester T, Kim H, Hunter L. Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies. Pac Symp Biocomput. 2006; 28-39. PMID: 17094225.
      View in: PubMed
    32. Baumgartner WA, Peterson AJ, Presson RG, Tanabe N, Jaryszak EM, Wagner WW. Blood flow switching among pulmonary capillaries is decreased during high hematocrit. J Appl Physiol (1985). 2004 Aug; 97(2):522-6. PMID: 15247197.
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    33. Baumgartner WA, Jaryszak EM, Peterson AJ, Presson RG, Wagner WW. Heterogeneous capillary recruitment among adjoining alveoli. J Appl Physiol (1985). 2003 Aug; 95(2):469-76. PMID: 12851416.
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    34. Nabors LK, Baumgartner WA, Janke SJ, Rose JR, Wagner WW, Capen RL. Red blood cell orientation in pulmonary capillaries and its effect on gas diffusion. J Appl Physiol (1985). 2003 Apr; 94(4):1634-40. PMID: 12626477.
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    35. Doty JR, Walinsky PL, Salazar JD, Brawn J, Haggerty M, Redmond JM, Baumgartner WA, Gott VL. Left atrial-inferior vena cava bypass achieves retroperfusion of the porcine spinal cord: morphologic and preliminary physiologic studies. J Surg Res. 2002 Nov; 108(1):157-64. PMID: 12443728.
      View in: PubMed
    36. Conte JV, Baumgartner WA. Commentary on Cadaveric-donor organ recovery at a hospital-independent facility. Transplantation. 2002 Oct 15; 74(7):931-2. PMID: 12408165.
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    37. Presson RG, Baumgartner WA, Peterson AJ, Glenny RW, Wagner WW. Pulmonary capillaries are recruited during pulsatile flow. J Appl Physiol (1985). 2002 Mar; 92(3):1183-90. PMID: 11842057.
      View in: PubMed
    38. Jaryszak EM, Baumgartner WA, Peterson AJ, Presson RG, Glenny RW, Wagner WW. Selected contribution: measuring the response time of pulmonary capillary recruitment to sudden flow changes. J Appl Physiol (1985). 2000 Sep; 89(3):1233-8. PMID: 10956374.
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    39. Conte JV, Baumgartner WA. Overview and future practice patterns in cardiac and pulmonary preservation. J Card Surg. 2000 Mar-Apr; 15(2):91-107. PMID: 11221975.
      View in: PubMed
    Baumgartner's Networks
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