Ellie Park, Multimedia Managing Editor

For the first time, University President Maurie McInnis released a public statement expressing an opinion about a contentious topic, condemning a National Institutes of Health plan to dramatically strip funding for indirect research costs in a Monday afternoon email to the Yale community.

After attorneys general sued the Trump administration over the policy, a federal judge temporarily blocked the cuts, set to go into effect on Monday, in those 22 states, including Connecticut. Yale was one of dozens of universities that made public declarations supporting the lawsuit.

After the judge’s block, a hearing was scheduled for Feb. 21. If implemented, the NIH policy would cap indirect research costs at 15 percent. Indirect costs are individually negotiated and Yale’s – currently set at 67.5 percent – fund research overhead such as infrastructure and staff salaries. In a post on X, the NIH cited Yale as a university with a multibillion-dollar endowment yet a high indirect cost rate to illustrate the expenses the agency incurs to reimburse these costs.

McInnis called the move a “considerable threat” to research at Yale.

“Since the moment I learned of this news, I have been working with my colleagues at America’s leading research universities to explore all options to oppose this action,” McInnis wrote in her statement. “Curtailing funding threatens not just academic and research communities but also the well-being of our nation.”

McInnis has previously limited her public comments, telling the News that she prefers to work behind closed doors with colleagues and legislators. Early in her tenure, she adopted a faculty report advising that Yale leaders refrain from commenting on topics of public importance. However, the report specifies that leaders should speak when events of significance “directly implicate” Yale’s mission and functions and are sometimes even “obligated” to speak to defend them.

“The NIH indirect cost cap substantially harms Yale’s core research mission and has severe consequences for institutions of higher education in this nation, and that is why I commented,” McInnis wrote to the News.

Still, she established that given the deluge of changes from the federal government, “leaders of each affected area” will henceforth be sending the messages related to federal policy changes instead of her.

In her Monday statement, McInnis wrote that Yale is “unwavering” in its commitment to research, a more direct affirmation than she made in an earlier statement that she released when Trump issued an executive order freezing all federal funding. 

She added that “indirect costs are research costs” and that the areas they fund are necessary for research to happen. She explained that although the University itself contributes toward research “more than double” what NIH indirect cost reimbursements do, the endowment is “not a limitless resource” as much of it is legally allocated or earmarked for other priorities including student financial aid.

At the end of her email, McInnis asked Yale community members to believe that she was working diligently to advocate for Yale’s mission. She wrote that she strives to protect Yale “in ways that are most effective, in public or behind the scenes,” echoing what she previously told the News.

Last week, the Office of the Vice Provost for Research created a webpage titled “2025 Federal Administration Transition” that lists executive orders affecting university research, directives from relevant government agencies and Yale’s recommendations for how researchers should respond.

The webpage, which requires a Yale NetID login, tells researchers that parts of their research proposals may need to be “altered or eliminated” in response to Trump’s executive orders and that submission timelines may shift as agencies figure out how to implement the orders. It advises that they continue to submit proposals unless they were directly sent a stop-work order or notification that an award they received would change.

“This is a dynamic situation that has created uncertainty for researchers at Yale and across the country. I share the same concerns that many of you have expressed to me over the last two weeks,” Vice Provost for Research Michael Crair wrote in a statement launching the webpage. “You have my support.”

Several universities, including Brown and the University of Pennsylvania, filed a joint lawsuit against the NIH to block cuts to federal funding. The suit claims that the action is “ill-conceived” and “self-defeating” for the nation by undermining medical research and innovation. Yale did not join the lawsuit.

Leaders of other universities including Harvard, Brown and the Massachusetts Institute of Technology have also issued similar statements about the indirect cost cap.

“When other nations are expanding their investment in science, America should not drop knowingly and willingly from her lead position on the endless frontier,” Harvard President Alan Garber wrote to Harvard affiliates.

Yale received over $643 million from the NIH in fiscal year 2024.