Thomas Peterson Jr, PhD

Title(s)Assistant Professor, Orthopaedic Surgery
SchoolSchool of Medicine
Address550 16th Street, #001
San Francisco CA 94158
Phone415-514-0528
ORCID ORCID Icon0000-0002-2562-6574 Additional info
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    Collapse Biography 
    Collapse education and training
    University of California, San FranciscoPostdoctoral Research2020Biomedical Informatics
    University of Maryland, Baltimore CountyPh.D.2016Biological Sciences, with Focus in Biomedical Informatics & Computational Biology
    University of Maryland, Baltimore CountyB.S.2011Information Systems, with Web Development Certificate
    Collapse awards and honors
    PLOS Computational Biology 20182018 Research Prize for Public Impact
    Phi Kappa Phi Honors Society2015Selected to be a member of Phi Kappa Phi Honors Society for achieving a perfect GPA
    GABS Graduate Student Research Symposium2013Best graduate poster award
    UMB’s Second Annual Cancer Biology Research Retreat2012Best pre-doctoral poster award

    Collapse Overview 
    Collapse overview
    Core member, Bakar Computational Health Sciences Institute
    Director, UCSF REACH Analytics Core
    Leadership Team, UCSF Musculoskeletal Center
    Investigator, San Francisco Veteran's Administration Health Care System

    Collapse Research 
    Collapse research activities and funding
    UCSF Core Center for Patient-centric Mechanistic Phenotyping in Chronic Low Back Pain
    NIH U19AR076737Sep 25, 2019 - May 31, 2024
    Role: Director, REACH Informatics Core

    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. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Unlocking Gait Analysis Beyond the Gait Lab: High-Fidelity Replication of Knee Kinematics Using Inertial Motion Units and a Convolutional Neural Network. Arthroplast Today. 2025 Jun; 33:101656. Bini SA, Gillian N, Peterson TA, Souza RB, Schultz B, Mormul W, Cichon MK, Szczotka AB, Poupyrev I. PMID: 40276526; PMCID: PMC12020888.
      View in: PubMed   Mentions:
    2. Evaluating associations between social risks and health care utilization in patients with chronic low back pain. Pain Rep. 2024 Dec; 9(6):e1191. Pak SS, Jiang Y, Lituiev DS, De Marchis EH, Peterson TA. PMID: 39391767; PMCID: PMC11463208.
      View in: PubMed   Mentions:
    3. Machine Learning Models for Low Back Pain Detection and Factor Identification: Insights From a 6-Year Nationwide Survey. J Pain. 2024 Aug; 25(8):104497. Bhak Y, Ahn TK, Peterson TA, Han HW, Nam SM. PMID: 38342191.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    4. Automatic extraction of social determinants of health from medical notes of chronic lower back pain patients. J Am Med Inform Assoc. 2023 07 19; 30(8):1438-1447. Lituiev DS, Lacar B, Pak S, Abramowitsch PL, De Marchis EH, Peterson TA. PMID: 37080559; PMCID: PMC10354762.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    5. Risk factors for extended length of stay and non-home discharge in adults treated with multi-level fusion for lumbar degenerative pathology and deformity. Spine Deform. 2023 05; 11(3):685-697. Arora A, Wague A, Srinivas R, Callahan M, Peterson TA, Theologis AA, Berven S. PMID: 36520257; PMCID: PMC10147745.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    6. Predictive Models for Length of Stay and Discharge Disposition in Elective Spine Surgery: Development, Validation, and Comparison to the ACS NSQIP Risk Calculator. Spine (Phila Pa 1976). 2023 Jan 01; 48(1):E1-E13. Arora A, Lituiev D, Jain D, Hadley D, Butte AJ, Berven S, Peterson TA. PMID: 36398784; PMCID: PMC9772082.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    7. Unsupervised Machine Learning on Motion Capture Data Uncovers Movement Strategies in Low Back Pain. Front Bioeng Biotechnol. 2022; 10:868684. Keller AV, Torres-Espin A, Peterson TA, Booker J, O'Neill C, Lotz JC, Bailey JF, Ferguson AR, Matthew RP. PMID: 35497350; PMCID: PMC9047543.
      View in: PubMed   Mentions:
    8. Discovery of Depression-Associated Factors From a Nationwide Population-Based Survey: Epidemiological Study Using Machine Learning and Network Analysis. J Med Internet Res. 2021 06 24; 23(6):e27344. Nam SM, Peterson TA, Seo KY, Han HW, Kang JI. PMID: 34184998; PMCID: PMC8277318.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    9. Quantifying Variation in Treatment Utilization for Type 2 Diabetes Across Five Major University of California Health Systems. Diabetes Care. 2021 04; 44(4):908-914. Peterson TA, Fontil V, Koliwad SK, Patel A, Butte AJ. PMID: 33531419; PMCID: PMC7985428.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    10. Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes. NPJ Digit Med. 2020; 3:57. Norgeot B, Muenzen K, Peterson TA, Fan X, Glicksberg BS, Schenk G, Rutenberg E, Oskotsky B, Sirota M, Yazdany J, Schmajuk G, Ludwig D, Goldstein T, Butte AJ. PMID: 32337372; PMCID: PMC7156708.
      View in: PubMed   Mentions: 37  
    11. Explanatory Model of Dry Eye Disease Using Health and Nutrition Examinations: Machine Learning and Network-Based Factor Analysis From a National Survey. JMIR Med Inform. 2020 Feb 20; 8(2):e16153. Nam SM, Peterson TA, Butte AJ, Seo KY, Han HW. PMID: 32130150; PMCID: PMC7059080.
      View in: PubMed   Mentions: 7  
    12. Empirical null estimation using zero-inflated discrete mixture distributions and its application to protein domain data. Biometrics. 2018 06; 74(2):458-471. Gauran IIM, Park J, Lim J, Park D, Zylstra J, Peterson T, Kann M, Spouge JL. PMID: 28940296; PMCID: PMC5862774.
      View in: PubMed   Mentions: 5     Fields:    
    13. Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples. PLoS Comput Biol. 2017 04; 13(4):e1005428. Peterson TA, Gauran IIM, Park J, Park D, Kann MG. PMID: 28426665; PMCID: PMC5398485.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    14. Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants. Hum Mutat. 2016 11; 37(11):1137-1143. Peterson TA, Mort M, Cooper DN, Radivojac P, Kann MG, Mooney SD. PMID: 27406314; PMCID: PMC6192032.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    15. Towards precision medicine: advances in computational approaches for the analysis of human variants. J Mol Biol. 2013 Nov 01; 425(21):4047-63. Peterson TA, Doughty E, Kann MG. PMID: 23962656; PMCID: PMC3807015.
      View in: PubMed   Mentions: 63     Fields:    Translation:Humans
    16. Crosstalk between the circadian clock and innate immunity in Arabidopsis. PLoS Pathog. 2013; 9(6):e1003370. Zhang C, Xie Q, Anderson RG, Ng G, Seitz NC, Peterson T, McClung CR, McDowell JM, Kong D, Kwak JM, Lu H. PMID: 23754942; PMCID: PMC3675028.
      View in: PubMed   Mentions: 76     Fields:    Translation:AnimalsCells
    17. A protein domain-centric approach for the comparative analysis of human and yeast phenotypically relevant mutations. BMC Genomics. 2013; 14 Suppl 3:S5. Peterson TA, Park D, Kann MG. PMID: 23819456; PMCID: PMC3665522.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    18. Domain landscapes of somatic mutations in cancer. AMIA Jt Summits Transl Sci Proc. 2013; 2013:136. Peterson TA, Park D, Kann MG. PMID: 24303323.
      View in: PubMed   Mentions: 1  
    19. Domain landscapes of somatic mutations in cancer. BMC Genomics. 2012 Jun 18; 13 Suppl 4:S9. Nehrt NL, Peterson TA, Park D, Kann MG. PMID: 22759657; PMCID: PMC3394412.
      View in: PubMed   Mentions: 33     Fields:    Translation:Humans
    20. Incorporating molecular and functional context into the analysis and prioritization of human variants associated with cancer. J Am Med Inform Assoc. 2012 Mar-Apr; 19(2):275-83. Peterson TA, Nehrt NL, Park D, Kann MG. PMID: 22319177; PMCID: PMC3277632.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    21. Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature. Bioinformatics. 2011 Feb 01; 27(3):408-15. Doughty E, Kertesz-Farkas A, Bodenreider O, Thompson G, Adadey A, Peterson T, Kann MG. PMID: 21138947; PMCID: PMC3031038.
      View in: PubMed   Mentions: 44     Fields:    
    22. DMDM: domain mapping of disease mutations. Bioinformatics. 2010 Oct 01; 26(19):2458-9. Peterson TA, Adadey A, Santana-Cruz I, Sun Y, Winder A, Kann MG. PMID: 20685956; PMCID: PMC2944201.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
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