Thomas Peterson Jr, PhD
Assistant Professor
Orthopaedic Surgery
School of Medicine

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

Awards

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• 2018 Research Prize for Public Impact, PLOS Computational Biology, 2018
• Selected to be a member of Phi Kappa Phi Honors Society for achieving a perfect GPA, Phi Kappa Phi Honors Society, 2015
• Best graduate poster award, GABS Graduate Student Research Symposium, 2013
• Best pre-doctoral poster award, UMB’s Second Annual Cancer Biology Research Retreat, 2012

Education & Training

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• Postdoctoral Research Biomedical Informatics University of California, San Francisco 2020
• Ph.D. Biological Sciences, with Focus in Biomedical Informatics & Computational Biology University of Maryland, Baltimore County 2016
• B.S. Information Systems, with Web Development Certificate University of Maryland, Baltimore County 2011

Websites

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• Posts on X TomPetersonPhD (X.com)

Grants and Projects

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• UCSF Core Center for Patient-centric Mechanistic Phenotyping in Chronic Low Back Pain, NIH, 2019-2024

Publications (21)

Top publication keywords:
Databases, ProteinProtein Structure, TertiaryGenome, HumanGenetic Diseases, InbornMachine LearningSequence AnalysisOncogene ProteinsComputational BiologyProtein DomainsSpineMutationQuality ImprovementDiseaseLow Back PainMetformin

• Evaluating associations between social risks and health care utilization in patients with chronic low back pain.
  Pain reports 2024 Pak SS, Jiang Y, Lituiev DS, De Marchis EH, Peterson TA
• Machine Learning Models for Low Back Pain Detection and Factor Identification: Insights From a 6-Year Nationwide Survey.
  The journal of pain 2024 Bhak Y, Ahn TK, Peterson TA, Han HW, Nam SM
• Automatic extraction of social determinants of health from medical notes of chronic lower back pain patients.
  Journal of the American Medical Informatics Association : JAMIA 2023 Lituiev DS, Lacar B, Pak S, Abramowitsch PL, De Marchis EH, Peterson TA
• 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 deformity 2022 Arora A, Wague A, Srinivas R, Callahan M, Peterson TA, Theologis AA, Berven S
• Predictive Models for Length of Stay and Discharge Disposition in Elective Spine Surgery: Development, Validation, and Comparison to the ACS NSQIP Risk Calculator.
  Spine 2022 Arora A, Lituiev D, Jain D, Hadley D, Butte AJ, Berven S, Peterson TA

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• Unsupervised Machine Learning on Motion Capture Data Uncovers Movement Strategies in Low Back Pain.
  Frontiers in bioengineering and biotechnology 2022 Keller AV, Torres-Espin A, Peterson TA, Booker J, O'Neill C, Lotz JC, Bailey JF, Ferguson AR, Matthew RP
• Discovery of Depression-Associated Factors From a Nationwide Population-Based Survey: Epidemiological Study Using Machine Learning and Network Analysis.
  Journal of medical Internet research 2021 Nam SM, Peterson TA, Seo KY, Han HW, Kang JI
• Quantifying Variation in Treatment Utilization for Type 2 Diabetes Across Five Major University of California Health Systems.
  Diabetes care 2021 Peterson TA, Fontil V, Koliwad SK, Patel A, Butte AJ
• Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes.
  NPJ digital medicine 2020 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
• Explanatory Model of Dry Eye Disease Using Health and Nutrition Examinations: Machine Learning and Network-Based Factor Analysis From a National Survey.
  JMIR medical informatics 2020 Nam SM, Peterson TA, Butte AJ, Seo KY, Han HW
• Empirical null estimation using zero-inflated discrete mixture distributions and its application to protein domain data.
  Biometrics 2017 Gauran IIM, Park J, Lim J, Park D, Zylstra J, Peterson T, Kann M, Spouge JL
• Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples.
  PLoS computational biology 2017 Peterson TA, Gauran IIM, Park J, Park D, Kann MG
• Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants.
  Human mutation 2016 Peterson TA, Mort M, Cooper DN, Radivojac P, Kann MG, Mooney SD
• Towards precision medicine: advances in computational approaches for the analysis of human variants.
  Journal of molecular biology 2013 Peterson TA, Doughty E, Kann MG
• Crosstalk between the circadian clock and innate immunity in Arabidopsis.
  PLoS pathogens 2013 Zhang C, Xie Q, Anderson RG, Ng G, Seitz NC, Peterson T, McClung CR, McDowell JM, Kong D, Kwak JM, Lu H
• A protein domain-centric approach for the comparative analysis of human and yeast phenotypically relevant mutations.
  BMC genomics 2013 Peterson TA, Park D, Kann MG
• Domain landscapes of somatic mutations in cancer.
  AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science 2013 Peterson TA, Park D, Kann MG
• Domain landscapes of somatic mutations in cancer.
  BMC genomics 2012 Nehrt NL, Peterson TA, Park D, Kann MG
• Incorporating molecular and functional context into the analysis and prioritization of human variants associated with cancer.
  Journal of the American Medical Informatics Association : JAMIA 2012 Peterson TA, Nehrt NL, Park D, Kann MG
• Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature.
  Bioinformatics (Oxford, England) 2010 Doughty E, Kertesz-Farkas A, Bodenreider O, Thompson G, Adadey A, Peterson T, Kann MG
• DMDM: domain mapping of disease mutations.
  Bioinformatics (Oxford, England) 2010 Peterson TA, Adadey A, Santana-Cruz I, Sun Y, Winder A, Kann MG