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John H. Holmes, PhD, FACE, FACMI

Professor of Medical Informatics in Epidemiology in Biostatistics and Epidemiology at the Hospital of the University of Pennsylvania
Department: Biostatistics and Epidemiology

Contact information
726 Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104
Office: 215-898-4833
Fax: 215-573-5325
A.B. (Sociology)
University of Pennsylvania, 1976.
M.S. (Information Systems)
Drexel University, 1987.
Ph.D. (Information Science)
Drexel University, 1996.
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Description of CCEB Expertise

Dr. Holmes conducts research in medical informatics and epidemiology. His interests are in evolutionary computation and machine learning approaches to knowledge discovery in databases (data mining), information systems infrastructures for epidemiologic surveillance, clinical decision support systems, semantic analysis, text mining, and information systems user (physician and patient) behavior. He is principal investigator on a project funded by the National Library of Medicine to investigate the use of online discussions as potential sources of adverse drug event data.

As a member of the University of Pennsylvania Comprehensive Cancer Center, Dr. Holmes also works on several cancer-related projects, including as a project principal investigator in the Penn Center for Population Health and Health Disparities. He is a co-investigator on numerous other NIH-funded projects.

Dr. Holmes collaborates with investigators nationwide on data governance issues associated with distributed research networks and comparative effectiveness research. He serves as co-chair of the Data Governance Core of SPAN, a Kaiser-Colorado based project supported by the Agency for Healthcare Research and Quality.

Dr. Holmes' methodologic focus is in evolutionary computation, especially learning classifier systems. His work in evolutionary computation focuses on translational research that bridges the gap between theoretical, genetics-based computing and epidemiologic practice. This work includes adapting evolutionary computational techniques to risk assessment and discovery of clinical decision rules in large clinical databases. Dr. Holmes is continuing this work with extensions to distributed databases and the deployment of genetics-based intelligent agents in wide-scale knowledge discovery tasks in biomedicine and epidemiology. He is active in the international Learning Classifier System community.

Dr. Holmes is an active member of the American Medical Informatics Association (AMIA) having served as Chair of the Education Committee, and member of the Membership, Working Group Steering and 10x10 Steering Committees. He currently serves on the AMIA Board of Directors and is Chair of the Board of Directors of the Global Health Informatics Partnership. He is an elected Fellow of the American College of Medical Informatics (ACMI) and the American College of Epidemiology.

Description of Content-based Expertise

Adherence, Cancer Epidemiology, Cardiovascular Epidemiology, Infectious Diseases, Injury, Medical Informatics, Molecular Epidemiology, Patient-Oriented Research, Pharmacoepidemiology, Prevention, Public Health, Pulmonary Epidemiology

Description of Methodology Expertise

Bayesian Modeling, Causal Inference, Diagnostic Testing, Functional Genomics, Gene Expression Profiling, Health Services Research, Microarray Methods, Missing Data, Data Mining, Machine Learning, Decision Support

Selected Publications

Maro JC, Platt R, Holmes JH, Strom BL, Hennessy S, Lazarus R, Brown JS: Design of a national distributed health data network. Annals of Internal Medicine 151(5): 1-4, July 2009.

Bowles KH, Holmes JH, Ratcliffe SJ, Liberatore M, Nydick R, Naylor MD: Factors Identified by Experts to Support Decision Making for Post-Acute Referral. Nursing Research 58(2): 115-122, In Press 2009.

Safran C, Shabot MM, Munger BS, Holmes JH, Steen EB, Lumpkin JR, Detmer DE: ACGME Program Requirements for Fellowship Education in the Subspecialty of Clinical Informatics. Journal of the American Medical Informatics Association December (epub ahead of print) 2008.

Kamoun M**, Holmes JH**, Israni AK, Kearns JD, Teal V, Yang WP, Rosas SE, Joffe MM, Li H, Feldman HI: HLA-A amino acid polymorphism and delayed kidney allograft function. Proceedings of the National Academy of Sciences 105(48): 18883-18888, December 2008 Notes: Co-first author.

Gardner RM, Overhage JM, Steen EB, Munger BS, Holmes JH, Williamson JJ, Detmer DE: Core Content for the Subspecialty of Clinical Informatics. Journal of the American Medical Informatics Association December (epub ahead of print) 2008.

Holmes JH, Lehman A, Hade E, Ferketich A, Gehlert S, Rauscher GH, Abrams J, Bird C: Challenges to Multi-Level Analysis in Health Disparities Research in a transdisciplinary environment. American Journal of Preventive Medicine 35(2): 182-192, August 2008.

Baumgarten M, Margolis DJ, Localio AR, Kagan SH, Lowe RA, Kinosian B, Holmes JH, Abbuhl SB, Kavesh W, Ruffin A, Mehari T: Extrinsic risk factors for pressure ulcers early in the hospital stay: A nested case-control study. Journal of Gerontology: Medical Sciences 63(4): 408-413, April 2008.

Bowles KH, Holmes JH, Ratcliffe SJ, Liberatore M, Nydick R, Naylor MD: Post-acute referral decisions made by multidisciplinary experts compared to hospital clinicians and the patients' 12-week outcomes. Medical Care 46(2): 158-166, February 2008.

Bair-Merritt MH, Holmes WC, Holmes JH, Feinstein J, Feudtner C : Does Intimate Partner Violence Epidemiology Differ Between Homes With and Without Children? A Population-Based Study of Annual Prevalence and Associated Risk Factors. Journal of Family Violence February 2008 Notes: accepted August 2007; published online February 18, 2008.

Nguyen GT, Barg FK, Armstrong K, Holmes JH, Hornik RC: Cancer and communication in the healthcare setting: Experiences of older Vietnamese immigrants, a qualitative study. Journal of General Internal Medicine 23(1): 45-50, January 2008.

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Last updated: 10/30/2014
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