John H. Holmes, PhD
| Office Location | 726, Blockley Hall |
| Office Phone | 215-898-4833 |
| jhholmes@mail.med.upenn.edu | |
Faculty Information | |
| CCEB Appointment | Senior Scholar, Epidemiology |
| Primary Faculty Appointment | Associate Professor of Medical Informatics in Epidemiology at HUP, University of Pennsylvania Perelman SOM |
Additional Positions
Director, Doctoral Program in Epidemiology
Senior Fellow, The Leonard Davis Institute of Health Economics
Senior Fellow, Center for Public Health Initiatives
Senior Fellow, Center for Health Behavior Research
Research Statement
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.
Courses Taught
EPID532 Database Management for Clinical Epidemiology
EPID632 Introduction to Medical Informatics
EPID633 Advanced Data Management for Clinical Research
EPID700 Doctoral Seminar in Epidemiology
EPID805 Applications of Epidemiologic Research
EPID811 Introduction to Epidemiologic Research
EPID814 Database Management
Selected Publications
- Hill S, Mao, J, Ungar L, Hennessy S, Leonard CE, Holmes JH. The rise of H1N1 influenza and internet search for natural supplements. Journal of Medical Internet Research. Journal of Medical Internet Research. 2011 (May 10); 13(2):e36
- Benton A, Hill S, Ungar L, Chung A, Leonard C, Freeman C, Holmes JH. A system for deidentifying medical message board text. BMC Bioinformatics. 12(Suppl 3):S2 (18 May 2011).
- Westra BL, Savik K, Oancea C, Choromanski L, Holmes JH, Bliss D: Predicting improvement in urinary and bowel incontinence for home health patients using electronic health record data. Journal of Wound, Ostomy, and Continence Nursing. 38(1):77-87, 2011.
- Israni AJ, Leduc R, Holmes JH, Jacobson PA, Lamba V, Guan W, Schladt D, Chen J, Matas AJ, Oetting WS: Single nucleotide polymorphisms, acute rejection and severity of tubulitis in kidney transplantation, accounting for center-to-center variation. Transplantation. 90(12):1401-8, 2010.
- Nguyen GT, Shungu NP, Niederdeppe J, Barg FK, Holmes JH, Armstrong K, Hornik RC: Cancer-related information seeking and scanning behavior of older Vietnamese immigrants. Journal of Health Communication. 15(7):754-68, 2010.
- Brown JS, Holmes JH, Shah K, Hall K, Lazarus R, Platt R. Distributed health data networks: A practical and preferred approach to multi-institutional evaluations of comparative effectiveness, safety, and quality of care. Medical Care 48:S45-S51, 2010.
- Stawicki SP, Holmes JH, Kallan MJ, Nance ML: Fatal child cervical spine injuries in motor vehicle collisions: Analysis using unique linked national datasets. Injury 40(8):864-7, 2009.
- 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 16(2):153-157, 2009.
- Safran C, Shabot MM, Munger BS, Holmes JH, Steen EB, Lumpkin JR, Detmer DE, and AMIA Board of Directors: Program Requirements for Fellowship Education in the Subspecialty of Clinical Informatics. Journal of the American Medical Informatics Association 16(2):158-166, 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, 2009.
- 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 (** co-first author).
- 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, 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, published online February 18, 2008.
- Bowles KH, Holmes JH, Ratcliffe SJ, Liberatore M, Nydick R, Naylor MD: Expert Discharge Referral Decisions and 12 Week Post Discharge Outcomes. Medical Care, 46(2):158-166, 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, 63A (4): 408-413, 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, 2008.
- Holmes JH, Sager JA: The EpiXCS workbench: A tool for experimentation and visualization. Advances at the frontier of Learning Classifier Systems, LNCS 4399. New York: Springer Verlag: 343-356, 2007.
- Holmes JH: Detection of sentinel predictor-class associations with XCS: A sensitivity analysis. Advances at the frontier of Learning Classifier Systems, LNCS 4399. New York: Springer Verlag: 276-289, 2007.
- Holmes JH, Sager JA, Bilker WB: Three methods for covering missing input data in XCS. Advances at the frontier of Learning Classifier Systems, LNCS 4399. New York: Springer Verlag: 184-196, 2007.
- Baumann B,Holmes JH, Chansky M, Levey H, Bourdreaux E: Pain assessments and the provision of analgesia: The effects of a templated chart. Academic Emergency Medicine, 14: 47-52, 2007.
- Hughes-Halbert C, Armstrong K, Holmes JH, Fenstermacher D, Weiner J, Guerra C, Schwartz S, Johnson JC, Weisberg E, Montagnet C, Weathers B, Zeigler-Johnson C, Rebbeck TR: Transdisciplinary approaches to ameliorating disparities in prostate cancer outcomes. Journal of Health Disparities 1(1):19-46, 2006.
- M'ikinatha NM, Holmes JH, Polachek C, Lautenbach E: Use of the Internet to Enhance Infectious Disease Surveillance and Outbreak Investigation. Biosecurity and Bioterrorism, 4(3):293-300, 2006.
- Localio AR, Margolis DJ, Kagan SH, Lowe RA, Kinosian B, Abbuhl S, Kavesh W, Holmes JH, Ruffin A, Baumgarten M: Use of Photographs for the Identification of Pressure Ulcers in Elderly Hospitalized Patients: Validity and Reliability. Wound Repair and Regeneration 14:506-13, 2006.
- Baumgarten M, Margolis DJ, Localio AR, Kagan SH, Lowe RA, Kinosian B, Holmes JH, Abbuhl SB, Kavesh W, Ruffin A: Pressure Ulcers Among Elderly Patients Early in the Hospital Stay. Journal of Gerontology: Medical Sciences 61A: 749-654, 2006.
- Synnesvedt MB, Chen C,Holmes JH: CiteSpace II: Visualization and knowledge discovery in bibliographic databases. Journal of the American Medical Informatics Association Suppl724-728, 2005.
- Holmes JH and Sager JA: Rule discovery in epidemiologic surveillance data using EpiXCS: An evolutionary computation approach. Miksch S, Hunter J, and Keravnou E (eds): Artificial Intelligence in Medicine. 10th Conference on Artificial Intelligence in Medicine, AIME 2005. Lecture Notes in Artificial Intelligence, LNAI 3581. Berlin: Springer, pp. 444-452, 2005.
- Armstrong K, Weber B, Ubel P, Peters BA, Holmes JH, Schwartz JS: Decision Support with Individualized Estimated Survival Curves Improves Satisfaction with Decisions about Cancer Risk Reduction among Women with BRCA1/2 Mutations. Journal of Clinical Oncology 23(36):9319-9328, 2005.
