John H. Holmes, PhD
|Office Location||726, Blockley Hall|
|CCEB Appointment||Senior Scholar, Epidemiology|
|Primary Faculty Appointment||Professor of Medical Informatics in Epidemiology at HUP, University of Pennsylvania Perelman SOM|
Interim Director, Penn Institute for Biomedical Informatics
Chair, Graduate Group in Epidemiology and Biostatistics
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
Dr. Holmes earned his M.S. in Information Systems and his Ph.D. in Information Science from Drexel University. He collaborates extensively with epidemiologists, biostatisticians, and clinical researchers from a wide variety of disciplines within and beyond Penn. He has been recognized nationally and internationally for his work on developing and applying new approaches to mining epidemiologic surveillance data, as well as his efforts at furthering educational initiatives in biomedical informatics. Dr. Holmes has published over 125 peer-reviewed manuscripts, conference papers, abstracts, and book chapters. He has developed graduate-level courses in informatics, clinical research methods, and epidemiology, and has supervised post-doctoral Master’s and PhD students in epidemiology and informatics at Penn, other institutions in the United States, and in Europe and Africa.
Dr. Holmes is the Interim Director of the Penn Institute for Biomedical Informatics and he chairs the Graduate Group in Epidemiology and Biostatistics.
Dr. Holmes’ research interests are focused on several areas in medical informatics, including evolutionary computation and machine learning approaches to knowledge discovery in clinical databases (data mining), interoperable information systems infrastructures for epidemiologic surveillance, clinical decision support systems, semantic analysis, shared decision making and patient-physician communication, and information systems user behavior. Dr. Holmes is a principal or co-investigator on projects funded by the National Cancer Institute, the National Library of Medicine, and the Agency for Healthcare Research and Quality, and he directs the Training Core and the Contextual Analysis Core for the NIH-funded Penn Center of Excellence in Prostate Cancer Disparities. Dr. Holmes is engaged with the Botswana-UPenn Partnership, assisting in building informatics education and clinical research capacity in Botswana.
Dr. Holmes serves on numerous national and international committees, including as a chartered member and now chair of the Biomedical Computing and Health Informatics study section at the NIH, as well as numerous ad hoc review committees for several institutes at the NIH, the Office of the National Coordinator for Health IT, the Agency for Healthcare Research and Quality, and several US foundations and European funding agencies. Dr. Holmes sits on the Board of Directors of the American Medical Informatics Association (AMIA) , and is Chair of the International Affairs Committee of AMIA and the AMIA Representative to the International Medical Informatics Association (IMIA).. Internationally, he serves as Vice President of IMIA for North America, Vice Chair of the IMIA Working Group on Data Mining and Big Data Analytics. and on the Board of Directors of the Artificial Intelligence in Medicine Society (Europe).
Dr. Holmes is an elected Fellow of the American College of Medical Informatics (ACMI) and the American College of Epidemiology.
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
- Holmes JH, Elliot TE, Brown JS, Raebel MA, Davidson A, Nelson AF, Chung A, La Chance P, Steiner JF: Clinical research data warehouse governance for distributed research networks in the United States: a systematic review of the literature. Journal of the American Medical Informatics Association 21(4):730-736, 2014.
- Paccioti B, Roberts KE, Tibbetts KM, Weirich C, Keren R, Barg FK, Holmes JH, Bonafide CP: Physician attitudes toward family-activated medical emergency teams for hospitalized children. The Joint Commission Journal on Quality and Patient Safety 40(4):187-192, 2014.
- Craven CK, Sievert ME, Alexander GL, Hicks LL, Hearne L, Holmes JH. CAH to CAH: EHR implementation advice to Critical Access Hospitals from peer experts and other key informants. Applied Clinical Informatics 5(1):92-117, 2014.
- Holmes JH, Nelson AF, Raebel MA, Brown J, Davidson A, Elliott TE, et al.: Scalable PArtnering Network (SPAN) for Comparative Effectiveness Research (CER): Purpose, Structure, and Operations. (2013). Governance Toolkit. Paper 3. http://repository.academyhealth.org/govtoolkit/3
- Brown JS, Davidson A, Elliott TE, Glanz J, Holmes JH, La Chance P-A, et al.: "Scalable PArtnering Network (SPAN) for Comparative Effectiveness Research (CER): Research User Interface Principles and Requirements" (2013). Governance Toolkit. Paper 2. http://repository.academyhealth.org/govtoolkit/2
- Elliott TE, Holmes JH, Davidson AJ, La Chance P-A, Nelson AF, Steiner JF: Data Warehouse Governance Programs in Healthcare Settings: A Literature Review and a Call to Action, eGEMs (Generating Evidence & Methods to improve patient outcomes).1(1):15, 2013. http://repository.academyhealth.org/egems/vol1/iss1/15
- Roberts KE, Bonafide CP, Weirich CM, Paciotti B, Tibbetts KM, Keren R, Barg FK, Holmes JH: Barriers to calling for urgent assistance that exist despite implementation of a comprehensive pediatric rapid response system. American Journal of Critical Care 23(3): 223-29, 2013.
- Bowles KH, Potashnik S, Ratcliffe SJ, Rosenberg M, Shih N-W, Topaz M, Holmes JH, Naylor MD: Conducting Research Using the Electronic Health Record Across MultiHospital Systems: Semantic Harmonization Implications for Administrators. Journal of Nursing Administration 43(6):355-60 2013.
- Mao JJ, Chung A, Benton A, Hill S, Ungar L, Leonard C, Hennessy S, Holmes JH. Online discussion of drug side effects and discontinuation among breast cancer survivors. Pharmacoepidemiology and Drug Safety 22(3):256-62, 2013.
- Huang EJ, Bonafide CP, Keren R, Nadkarni VM, Holmes JH: Medications associated with clinical deterioration in hospitalized children. Journal of Hospital Medicine 8(5):254-260, 2013.
- Bonafide CP, Roberts KE, Weirich C, Paciotti B, Tibbetts KM, Keren R, Barg FK, Holmes JH: Beyond statistical prediction: Qualitative evaluation of the mechanisms by which pediatric early warning scores impact patient safety. Journal of Hospital Medicine 8(5):248-253, 2013.
- Rivera-Lebron B, Forfia P, Krieder M, Lee J, Holmes JH**, Kawut S**: Echocardiographic and Hemodynamic Predictors of Mortality in Idiopathic Pulmonary Fibrosis. Chest 144(2):564-70, 2013. **Note: co-senior authors.
- Maffei RM, Dunn K, Zhang J, Hsu CE, Holmes JH: Understanding Behavioral Intent to Participate in Shared Decision-making in Medically Uncertain Situations. Methods of Information in Medicine 51:301–308, 2012.
- Massoudi BL, Goodman KW, Gotham IJ, Holmes JH, Lang, L, Miner K, Potenziani DD, Richards J, Turner AM, Fu, PC: An informatics agenda for public health: summarized recommendations from the 2011 AMIA PHI Conference. Journal of the American Medical Informatics Association 19(5):688-695, 2012.
- Benton A, Ungar L, Hill S, Hennessy S, Mao J, Chung A, Leonard C, Holmes JH: Identifying potential adverse effects using the web: a new approach to medical hypothesis generation. Journal of Biomedical Informatics 44(6):989-996, 2011.
- Bonafide CP, Holmes JH, Nadkarni VM, Lin R, Landis JR, Keren R. Development of a predictive score to identify pediatric inpatients at risk of deterioration. Journal of Hospital Medicine. 7(4): 345-349, 2011.
- 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, 2011.
- 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.
- 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.