Dr. Cooney served as program director for the Internal Medicine Residency Program from 1984 to 2010 and Vice Chair for Education 1995-2019. He has focused his scholarly interests on several areas, including HIV medicine, headache, health policy and medical education. Dr. Cooney has held training grants from the Department of Veterans Affairs and the Department of Health and Human Services and workforce-related research grants from the Robert Wood Johnson Foundation (“Influences on career choices of Internal Medicine Residents”) and the HRSA Bureau of Health Professions (“National Data Base on General Internal Medicine”).

Dr. Cooney is a former Chair of the Board of Governors, and current Chair of the Board of Regents of the American College of Physicians. He has served as an Associate Editor at the Journal of Graduate Medical Education since 2012.