Faculty Profile: John Holmes, PhD, applies medical informatics to epidemiologic research and has developed several computer programs to assist in his work
MARCH 23, 2007
John H. Holmes, PhD, was born and raised in Cherry Hill, NJ. After graduating high school from Cherry Hill West, John joined the United States Navy where he served in the Hospital Corps from 1969-71. He describes his training as a hospital corpsman as "the last two years of medical school crammed into 14 weeks." During this period, John learned various skills, such as physical diagnosis, surgical procedures, patient care, and pharmacology. As he characterizes it now, his training as a hospital corpsman provided him with the skills of today's physician assistants.
During and following his stint in the Navy, John spent nearly four years in Emergency Medicine and Critical Care at Methodist Hospital; while there, he was privileged to work in one of the region's first cardiac care units. He then worked as a pulmonary technologist in what was then the Pulmonary Disease Section at the Hospital of the University of Pennsylvania. John looks back with particular fondness on his experiences in field studies in occupational medicine, which included trips to Hazleton, PA, to screen beryllium miners for lung disease. However, it was also during this time that John got a chance to work on computer applications in health care, setting the stage for what would become his primary research interest as a faculty member.
While employed at Methodist and HUP, John was studying for his Bachelor of Arts in Sociology at the University of Pennsylvania. He earned an AB in 1976 and went to work the next year in the Department of Laboratory Medicine at Pennsylvania Hospital, where he worked as a technologist in the hematology, blood bank, and microbiology labs. During his five years there, John continued his studies not in sociology, research, or medicine, but in musicology, intending to pursue graduate study in medieval music performance practice. John had had early training and experience as an organist and was interested in medieval history.
The lure of a research career drew John back into the health sciences, and in 1982 he joined the CCEB's precursor, the Clinical Epidemiology Unit (CEU), at the University of Pennsylvania. He served as Research Coordinator for two of the four faculty members in the Unit at that time. As a coordinator, he was able to apply his health economics, health services research, statistics and medical sociology course knowledge from his undergraduate career. His clinical work as a hospital corpsman also helped him, but so too did the experience in computing that he gained while working in the Pulmonary Disease Section. John set up and ran the first "computer facility" in the CEU, which at that time consisted of two Apple-II+ computers. He developed and taught courses in computing for fellows in the International Clinical Epidemiology Network (INCLEN) training program. John rose to senior research coordinator and then Medical Information Scientist after receiving a Master of Science in Information Systems degree from Drexel University.
In 1996, John earned a PhD from Drexel University in Information Science, where his focus was on the development of new algorithms for knowledge discovery in databases (KDD, or "data mining") in epidemiologic surveillance. In 2000, Dr. Holmes became a Senior Scholar at the CCEB and joined the Penn Medicine faculty as Assistant Professor of Medical Informatics in Epidemiology at HUP.
Dr. Holmes's primary research interest is in the application of medical informatics to epidemiologic research. His work on KDD in epidemiologic surveillance focuses on discovering patterns in data that suggest new hypotheses about associations between exposures and outcomes. Dr. Holmes has developed several computer programs to assist with this work, including EpiCS and EpiXCS. These programs use an approach called "evolutionary computation," in which knowledge is modeled from data using a "survival of the fittest," or Darwinistic, paradigm. His doctoral dissertation, "Evolution-Assisted Discovery of Sentinel Features in Epidemiologic Surveillance," was the first effort to adapt and apply evolutionary computation methods called "learning classifier systems" to biomedical data mining. He has published and presented extensively in national and international venues on using evolutionary computation in biomedical KDD.
Dr. Holmes is particularly interested in injury research. He has worked with Drs. Dennis Durbin, a CCEB Senior Scholar, and Flaura Winston on Partners for Child Passenger Safety, a project sponsored by the State Farm Insurance Company, and a project currently funded by the Center for Child Injury Prevention Science to investigate causes of death in children killed in motor vehicle crashes. Dr. Holmes is also extending his work in KDD to the bioinformatics domain, where he is working with a team led by Dr. Harold Feldman to investigate patterns of amino acids in the HLA molecule that may be associated with renal allograft rejection.
Dr. Holmes's research also involves creating computerized interventions that are designed to encourage health communication and shared decision-making between patients and physicians. This field, while well-known in the health communication and psychology domains, is relatively new to medical informatics. Dr. Holmes has worked on several such projects, including Heart Sense, an interactive, game-based, computerized intervention to reduce delay in seeking care for acute coronary syndrome, developed under the leadership of Dr. Barry Silverman in Penn's School of Engineering and Applied Science and in collaboration with Drs. Stephen Kimmel and William Holmes in the CCEB. Currently, Dr. Holmes is Principal Investigator of a project looking at physician and patient factors involved in discussing prostate cancer screening, with the goal of designing a computerized intervention to provide men with the skills needed to engage in this discussion with their physicians. This study is one of four interrelated projects within the Penn Center for Population Health and Health Disparities, led by Dr. Timothy Rebbeck, that looks to bring knowledge about biological, behavioral, social environmental and physical environmental factors that create health disparities in men at risk of or diagnosed with prostate cancer. Dr. Holmes is also working on a game-based computer intervention to teach children about the proper use of antibiotics in common respiratory infections. An article on which he collaborated titled "Computer games may be good for your health" was published in the Journal of Healthcare Information Management, and he has presented or co-authored numerous abstracts on this topic at national meetings.
In addition to his research, Dr. Holmes has a busy teaching schedule in the CCEB's masters', doctoral, and certificate programs. He is a course director and instructor for Database Management for Clinical Epidemiology, Introduction to Medical Informatics, Introduction to Epidemiologic Research Methods, Practical Applications in Clinical Research Methods, and Database Management here at Penn. Dr. Holmes is also very active in the American Medical Informatics Association, where he serves as the Chair of the Education Committee and member of a number of steering committees, and is co-leading a national effort to establish essential competencies in medical informatics. He was the founding Chair of AMIA's Knowledge Discovery and Data Mining Working Group. His contributions to the field of medical informatics were recognized formally this past November, when he was inducted as a Fellow in the American College of Medical Informatics.
Dr. Holmes is also active outside the informatics world, serving as Chair of the Evaluation Working Group for the Centers for Population Health and Health Disparities, a national group consisting of eight NIH-funded centers including the University of Pennsylvania.
Dr. Holmes resides in University City with his wife Jennifer, and daughters Hazel and Monika. They are (slowly) restoring their 100-year-old house, which gives John plenty of opportunity to engage in a favorite hobby, woodworking. That is, when he's not busy cooking, which he does a lot. John is also an avid bicyclist and enjoys exploring the many miles of trails and paths in Fairmount Park and beyond. He is looking forward to training for the MS150 and several other long-distance rides this year.
