The University of Minnesota has named a new medical school dean and vice president for health sciences, choosing an internationally known AIDS researcher from Johns Hopkins University and ending a period of leadership uncertainty that dates back to 2009.

The new dean, Dr. J. Brooks Jackson, has led the pathology department at the Johns Hopkins School of Medicine for the past 12 years. During his tenure, the department rose from fifth to first nationally in funding from the National Institutes of Health — a widely watched barometer of medical school research — according to a U statement. Jackson is also principal investigator for a major international NIH project on AIDS, and his research contributed to development of a breakthrough drug for the prevention of HIV transmission in newborns.

The appointment will place Jackson at the helm of one of Minnesota’s flagship institutions, a school that trains nearly 70 percent of the state’s doctors and other health care professionals. It also brings the state more than $300 million in federal research grants each year, and has been mentioned by Gov. Mark Dayton as the cornerstone of an emerging research collaborative with Mayo Clinic that could push Minnesota to the forefront of medical science nationally.

“I’m very interested in leading a world-class academic health system,” Jackson said in a phone interview Thursday. “I am a program builder, and this gives me more of an opportunity to do that.”

The U, he added, is in a position “to lead the world in the treatment and prevention of disease and produce the top leaders, educators, students and health scientists.”

Jackson, who holds MBA and M.D. degrees from Dartmouth, served a residency at the U Hospitals from 1982 to 1985, worked at the Minneapolis VA Medical Center, and was an assistant professor of medicine and pathology at the U from 1985 to 1989.

The pathology department at Johns Hopkins has a $250 million annual budget and employs about 1,500 people. By contrast, the U’s medical school and health sciences division operates on a budget of $1.6 billion.

Jackson will replace Dr. Aaron Friedman, a pediatrician who was named to the post in 2010 as university President Robert Bruininks was approaching retirement and the medical school was preparing a national search for a dean. Friedman, in turn, replaced Dr. Frank Cerra, who had held the post on an interim basis since 2009, when the U announced the departure of the previous dean, Dr. Deborah Powell.

Jackson, who is expected to start in February, says he knows big challenges lie ahead.

“Everybody in medicine [is] seeing that there will be tremendous change in the next decade or so with our health care system as it transitions to more of a large-population health management system” and away from the current fee-for-service, acute-care model, Jackson said. “The future really is about more prevention, more interdisciplinary care.”

According to Jackson, the U is prepared to deal with those challenges because its various health sciences branches — including their partner, Fairview Health Services — already collaborate closely.

Jackson said the U’s history of training doctors, nurses and other professionals gives it a strong base of alumni support — a topic he knows well. Jackson said he and his colleagues raised $60 million in philanthropy for the Johns Hopkins pathology department during his tenure.

“Pathology,’’ he quipped, “does not have a lot of grateful patients, as opposed to oncology.”

Jackson has had a prolific career in research, contributing to more than 200 peer-reviewed articles. He also saw patients and taught courses. He said he hopes to keep up some of those activities at the U, but is unlikely to remain the principal investigator overseeing the NIH-funded AIDS research because of the time involved in managing a multi-center study.

The Board of Regents will consider Jackson’s appointment in December. His annual salary would be $725,000. If approved, Jackson said he will be moving to the Twin Cities with his wife, Kathleen House, who grew up in Worthington and Moorhead, Minn., and is a graduate of the U’s Carlson School of Management. They have three sons in their 20s, none of whom work in health sciences.

“Computer science — seems to be the rage these days,” he said with a chuckle.