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Janet E. Penksa, a top official in the Brown administration, is leaving City Hall to join a small but innovative nonprofit institute on the Buffalo Niagara Medical Campus.

Penksa’s departure will leave a void in the mayor’s Cabinet, where for the last six years she oversaw Buffalo’s finances and many facets of city government, including handling state and federal grants and analyzing operations.

Penksa, 53, said that the decision to leave was difficult but that the move allows her to return to the academic world.

As an associate vice president at the University at Buffalo, she worked closely with the Center of Excellence in Bioinformatics.

“There’s a whole host of these types of projects that I worked on, in my other life,” Penksa said.

The Jacobs Institute, where she will become executive director in early December, fosters partnerships involving UB, Kaleida Health, doctors and medical companies.

Penksa, who holds a Ph.D. in economic geography from UB, wrote her dissertation on innovative relationships, which will be a core responsibility in her new job.

“It’s been my plan now to go back into this type of work,” she said.

In separate interviews, Mayor Byron W. Brown and Penksa praised each other and said the departure was more than amicable.

“I love this mayor,” Penksa said. “It’s been an honor to serve him, to work with him.”

Penksa learned about the Jacobs Institute, an independent nonprofit organization, on a tour there and connected with its world-renowned CEO, Dr. Leo Nelson “Nick” Hopkins.

“We want to develop a high-tech corridor in Western New York that would lead to jobs – biotechnology jobs,” Hopkins said.

For that to happen, the institute needs people with skills in governmental relations. “She’s a terrific fit for us and a phenomenal person,” Hopkins said.

Penksa will oversee administrative responsibilities and new business development.

Although the institute has just four full-time employees, Penksa said, she is looking forward to working on a growing enterprise.

The institute essentially got off the ground in September when it moved into the building that houses the Gates Vascular Institute. It started with a $10 million gift from Jeremy M. Jacobs and his wife, Margaret, to honor Dr. Lawrence D. Jacobs, Jeremy’s brother and a prominent neurologist, who died in 2001. The institute also received a $4 million state grant last year through the Western New York Regional Economic Development Council.

It is on the fifth floor of the Ellicott Street building and serves as a bridge between the doctors in the vascular institute on the lower floors and the researchers above, who work at the UB Clinical and Translational Research Center.

Penksa has been an important member of Brown’s team, one of just four people who question city department heads every week as a member of the CitiStat panel. The city’s bond rating increased dramatically during her tenure, though the city was also under a state-appointed financial control board during the same period.

“She has served the city incredibly well,” Brown said, adding that she is leaving “on incredibly good terms.”

Brown has asked her to stay on the Buffalo Urban Renewal Agency board as a citizen member.

Penksa is the highest-ranking woman in the Brown administration and the highest-paid member of the Cabinet, including the mayor. She was well-regarded when Brown appointed her, and he persuaded the control board to raise the salary for the position from $83,000 to $104,000. Penksa’s salary in 2012-13 is $119,239, according to the city budget.

Brown’s Cabinet includes one other woman, Human Resources Commissioner Patricia P. Folts, though the last five hires on his management team have been women, said spokesman Michael J. DeGeorge.

Brown hired Penksa in late 2006 to be commissioner of administration, finance, policy and urban affairs, after she worked as a lobbyist with Hinman Straub. She also was a member of the Erie County control board and has been the Assembly’s top budget negotiator.

“It kind of spices it up and keeps you alive,” Penksa said of her diverse resume.

In a Buffalo News profile of Deputy Mayor Steven M. Casey published in September, Assemblywoman Crystal D. Peoples-Stokes credited Penksa with being a key to Brown’s success. The mayor said he will appoint Budget Director Donna J. Estrich as interim commissioner until a successor to Penksa is found.

email: jterreri@buffnews.com