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{shortcode-24643cedbe14221289878261864001a8ceef067a}ver the past two decades, Professor John Quackenbush has made Harvard his home.
He’s filled his office at the School of Public Health with artifacts from his life. His L-shaped desk is crowded with popular science magazines, academic books, and piles of papers. Lining the wall are art prints from friends and framed photographs taken by his wife. Plaques and trophies litter the office — prestigious awards from universities, research institutes, and even the White House.
According to Quackenbush, a prominent computational biologist, Harvard is built on the talent it attracts. He can take a short walk to Brigham and Women’s Hospital and strike up a casual chat with the world’s expert in chronic obstructive pulmonary disease, and his questions can fundamentally change the way he’s thinking about his research.
“The thing that makes this University such an exquisite place to work are the people who are here, who are the world’s experts in everything,” he says.
Quackenbush always thought that Harvard would be his last workplace. But now, he is on the verge of leaving. The Trump administration’s attacks on the University have made him question whether Harvard is the best place to continue his life’s work.
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In April, the Trump administration froze $2.2 billion in grants and $60 million in contracts to Harvard. One month later, the administration cut an additional $450 million. The University laid off employees in waves. Projects came to a halt, or were terminated altogether. Researchers scrambled to mitigate the damage, unsure of how long the freeze would last. Labs closed down, biospecimens died, and researchers cleared out their offices.
Funding began to flow back to the University in September. While the announcement granted some reprieve, the damage of the five-month freeze could not be undone.
Some, like Quackenbush, considered leaving Harvard. Researchers that choose to stay struggle to fund the research they have spent years, or even decades, pursuing. And while there are some options — University bridge funding, corporate sponsorships, foundation grants — none can replace government funding. Early-career researchers now hesitate to join one of the world’s best research institutions, backing away as the federal government continues to target the University. With funding at a constant risk of revocation, Harvard is not out of the clear — and researchers are still fighting for their futures.
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{shortcode-a0fafb3727a5405eac46bd1741f1eafab86bbf7e}SPH Professor Shahin Lockman has been fighting the AIDS epidemic in Botswana for 26 years. After medical school, she began working at an epidemiology training program at the Centers for Disease Control and Prevention, studying tuberculosis. When she requested to continue her work internationally, she ended up in Botswana for two years, and “fell in love with the place.”
At the time, tuberculosis was raging through southern Africa because of the ongoing AIDS epidemic. AIDS weakens the immune system and increases the risk of catching diseases like tuberculosis. But the crisis was “getting no attention,” Lockman says. “There was no testing, no treatment, nothing.”
After her stint abroad, Lockman returned to America before joining the Botswana Harvard Health Partnership in 1999. Though she now works out of Boston, she frequently travels to Botswana.
Lockman’s lab, like so many others, is primarily funded through federal grants. Eight were terminated — the equivalent of $7.1 million per year. The lab employed 300 people full-time, and 240 had their contracts ended. Though some have been rehired on short-term contracts, dozens have been laid off permanently.
Lockman recalls feeling a profound sadness on her employees’ behalf. “Feeling bad that we had to let them go, and also just frustration at how unnecessarily damaging this is to their lives and to science,” she says.
The Trump administration first put Harvard’s funding under review at the end of March, as part of an investigation by the Federal Task Force to Combat Antisemitism. The White House issued a list of demands to the University, an ultimatum that asked Harvard to axe diversity initiatives, ensure “ideological diversity” in faculty hires, and subject itself to unprecedented levels of federal scrutiny. Harvard President Alan M. Garber ’76 rebuked the offer, dismissing the administration’s demands as coercive and beyond federal authority. The White House rescinded $2.2 billion in federal grants weeks later.
The cuts did not stop there. The Trump administration terminated 350 research grants to Harvard Medical School in May and cut nearly all direct federal grants to HSPH.
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Harvard sued the Trump administration almost immediately, and a judge restored its funds in September, but the damage extends beyond the institutional freeze. The National Institutes of Health began terminating hundreds of grants across the country in February, targeting project abstracts that mentioned “race,” “transgender,” “inequity,” and “minority.” By April, the NIH had axed $110 million from Harvard and its hospitals. A lawsuit filed against the NIH revocations made its way to the Supreme Court, which ruled in August that the White House could continue to withhold the funds.
In her 26 years at Harvard’s Botswana lab, Lockman has never seen this level of instability. While it’s true that government funding for research has historically waxed and waned for a variety of reasons, these cuts were massive and sudden. “This was basically the rug being pulled out from under everybody in one fell swoop, without warning,” she says.
The devastating impact that Lockman and other scientists are facing represents the breaking of a decades-long compact between university research and government funding. Prior to the 20th century, universities operated without federal research funding.
On the precipice of World War II, the government contracted universities to develop tools for the war. Seeing the breakthroughs made by university researchers — such as large-scale penicillin manufacturing, malaria therapies, and communication and aviation technology — the government formalized the relationship between science and the state. The first official NIH grant was awarded in 1945.
“The idea that you just invest in that for the good of the country was unquestioned,” Jesse B. Bump, a lecturer at HSPH, says. “It had an easy demonstration in the World War II technologies, but there was great faith in that, and it’s continued until the Trump administration.”
Now, Harvard’s research relies in no small part on government funding — federal research funding made up 11 percent of the University’s total operating revenue in the 2024 fiscal year. The reliance is particularly visible in the University’s biomedical and health research. Government and private funding supplies more than half of the HSPH operating budget, and more than a third of the HMS operating budget. (A Harvard spokesperson declined to comment, but redirected The Crimson to a publicly available website page of University communications relating to updates on federal research policy.)
A key part of this funding dynamic is the salaries of researchers, which are mainly funded by federal grants. Many of the faculty at HMS and HSPH are not on full salaries from Harvard. Instead, they are partially paid by the University, while a substantial part of their salary is paid through grants, mainly from the federal government.
The impact of grant losses is especially difficult for junior faculty and trainees.
Sungwhan F. Oh came to Harvard from South Korea in 2003 to get a Ph.D. in Biological Chemistry and Molecular Pharmacology. Now, he works as an assistant professor in Immunology and a principal investigator at the Center for Experimental Therapeutics and Reperfusion Injury.
According to Oh, while tenured faculty may have six to eight sources of funding, those running smaller labs usually will have fewer avenues to support their research.
Prior to funding cuts, Oh had two sources of funding: a subcontract through HMS and an NIH grant. When the federal government cut Havard’s funding, Oh was one of many scientists who received a termination notice. Meanwhile, Oh’s NIH grant, which involved international collaboration with researchers in Australia, was put on hold when the NIH changed grant rules for foreign collaborations. Oh’s team was out of funding for several months as they re-budgeted their NIH grant for reapproval.
Funding cuts have also had significant effects on early-career scientists like graduate students and postdoctoral researchers, who are on a race against the clock to complete research before they leave Harvard. “They have only short amounts of time to do the research and prove themselves,” says Oh. “If they get disturbed during that critical period, that’s a big blow for them.”
Oh says he needed to let go of two of his postdocs a year earlier than expected as a result of funding restrictions. While one found a research position at a top Korean university, the other was unable to get a job in U.S. industry due to visa issues. Unable to help her renew her visa, Oh scrambled with friends in different universities to help her find a new research position.
“That was the best I could do,” he says.
Oh analogizes the experience of running his lab like managing “a hole in the wall restaurant” and making sure everything runs smoothly. “We basically do everything. We cook, we take orders, we negotiate with the vendor, and then we pay people,” he says.
For a bigger lab — or restaurant — losing two people might not be such a significant loss. But for Oh, whose lab only consisted of five researchers prior to funding cuts, losing two people has major impacts.
“We lose a lot of time, and we lose a few people who contributed to the science. So it’s very depressing,” Oh says.
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Oh shares a space with two other labs. Scientists dart up and down the narrow hallway — any free walking space not taken up by benches is lined tightly with biohazard fridges and equipment.
Most of Oh’s work happens on one of these benches. There’s an HPLC machine, which his team uses to separate symbiotic microbe molecules. In the back, there’s anaerobic and aerobic chambers where they cultivate microbacteria. If the microbacteria is removed from the machines and “if you put it in the bench, not too many of them will survive,” Oh notes.
Due to funding cuts after grant terminations at HMS, his lab hasn’t made significant progress on research. While he can run analysis or use machines that have already been paid for, he can’t buy new materials or equipment to use for his research.
According to Oh, “Science feeds on hope and expectation and enthusiasm.” But due to the precariousness of the funding environment, Oh feels that there are low expectations around how sustainable the work can be. “The big, big challenge is we don’t really know how this uncertainty will last.”
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{shortcode-69a9ed06c887cb075e6988b5c6d61980cc21c96c}ary B. Rice ’99, associate professor at HSPH, was in the fourth year of a five-year randomized control trial studying the effects of air purifiers for people with chronic lung disease when the NIH terminated her $3.8 million grant in May.
This left Rice with a fully enrolled trial, but none of the resources to continue the work. As a temporary remedy, Rice secured internal bridge funding from the University, allowing for researchers to finish the trials.
She was one beneficiary of a I $250 million initiative announced by Garber in May, which allocated funding over the next year to support research projects that were hit by the funding freeze.
HSPH professor Walter C. Willet has a hundred freezers filled with biological samples — blood, urine, and feces — from more decades of longitudinal nutrition studies. When funding was cut, he was at risk of losing all of his material. University bridge funding, alongside other sources, enabled him to continue his project.
“If we lost our samples and follow-up of the cohort, if somebody wanted to reproduce this, it would take 50 years to get to where we are now,” Willet says.
But bridge funding is temporary, used to fund the remainder of a project or a small portion of the work being done. It’s not intended as a substitute or replacement for federal funding.
For Rice’s project, bridge funding covers the money she needs to oversee the trials, but doesn’t account for resources her team will need to analyze their data and draw conclusions. “We’re collecting information, but we don’t actually have the money to complete the trial or answer the questions that we set out to answer.”
Researchers are also looking for support from philanthropic foundations. Erica Kenney, an associate professor at HSPH, plans to apply for a grant from the Robert Wood Johnson Foundation in order to continue her lab’s work.
But philanthropic funding also has its limitations.
David Blumenthal ’70, a professor at HSPH, has spent the last few months helping colleagues navigate the complexities of foundation funding. He worked at HSPH before serving as health advisor in a number of government roles — including as a National Coordinator for Health Information Technology under the Obama administration. In 2013, he was asked to run the Commonwealth Fund, a non-profit supporting health research. He remained there for 10 years before leaving and later deciding to return to HSPH as a professor.
“I went back and decided that among the schools I had worked at, the School of Public Health would be the most appropriate and enjoyable,” Blumenthal says.
And his mentorship is especially necessary now — using his knowledge of philanthropic funding, he can advise his fellow researchers on how to apply to private funding, an unfamiliar application process for researchers to navigate.
“There are lots of very, very experienced and accomplished investigators at the School of Public Health, and I expect the medical school as well, who have never written a foundation grant,” says Blumenthal. “They’ve been so successful attracting federal support, which has its own methodology and its own approach, so they can be really quite uninformed about how to begin that process.”
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The funding cuts have been so wide-ranging that scientists applying for private funding must compete with an influx of other researchers in the same situation. “It’s like musical chairs, you know, there’s just a limited number of resources, and you have to try and get them, and they’re not even going to quite be enough,” Kenney says.
And even if they navigate the countless grant applications, private funding is inconsistent — “smaller in amount and shorter in duration,” Blumenthal says. Federal grants tend to be allocated for three to five years, but private foundations tend to fund projects for a year or two, he adds.
Because foundations have much less funding than the federal government, they tend to be very purposeful in their spending, Blumenthal says. While working at the Commonwealth Fund, instead of funding risky projects, Blumenthal was focused on finding grantees that could do consistent work that supported the goals of the foundation.
Even when foundations fund university research projects, they can’t compensate for the overhead costs of big research institutions like Harvard. In February, before any of the sweeping grant cuts, the Trump administration proposed slashing indirect cost rates — a percentage of funding set aside for administrative costs of research — to 15 percent across the board, a devastating cut to Harvard, which has an indirect cost rate of almost 70 percent. Though a federal judge blocked the 15 percent cap in a June ruling, it is still uncertain whether the ruling will hold.
The other primary form of private funding comes from for-profit companies. Industry funding supports research that benefits a specific company. It rose in popularity around the biotechnology revolution of the 1980s and 1990s, when many companies partnered with universities to develop new technologies.
But corporate and academic interests don’t always align. “Universities want the right to publish, they don’t want to be censored, they don’t want to be controlled, and they don’t want to have to keep things secret,” Blumenthal explains. “Not all companies have the same philosophy in that regard.”
Many researchers agree that private funding, whether from foundations or corporations, can’t make up for the loss of federal funding.
Andrea L. Roberts ’88, principal research scientist at HSPH, notes that the small size of foundation funding may inhibit researchers’ work. “There’s just a limited amount of things you can do with that amount of money,” she says. “That’s a big difference.”
For industry funding, the situation isn’t much better. Bump, the HSPH lecturer, says, “If you’re working on a social scientific problem that doesn’t lead to a drug at all, then pharma is not going to be interested.”
For Bump, what makes government funding so special is that it allows for “basic research” — research that is interested in exploring fundamental phenomena to expand scientific knowledge. “Basic researchers, they’re busy competing with each other to create the best science that’s most interesting in their peer group,” he says. “That’s really different than what you’d get out of a competitive, private market process.”
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{shortcode-be29865d8a9c7908fa05930b7f2d42574eaa573c}n September, United States District Judge Allison D. Burroughs struck down the Trump administration’s funding freeze. By October, a majority of Harvard’s funding had been restored.
Initially, researchers were relieved. “I’m very very happy that I get to finish the work that I had, that I had planned to do and that I was doing before the federal grant cancelations. And I know for a fact that my colleagues are equally ecstatic to be able to get their work restarted,,” says Jorge E. Chavarro, HSPH dean for academic affairs. “This is fantastic, fantastic news for everybody who is currently funded.”
Still, this doesn’t mean that Harvard’s research programs have returned to normal. Many of the long-term structural and psychological impacts of the months-long funding freeze are still affecting Harvard’s researchers. And with the Trump administration’s ongoing attack on scientific research, Harvard affiliates are worried about what policy or funding changes are to come.
“We know that regardless of the additional actions the federal government may or may not take in the coming months, there are drastic changes that are probably going to become law that make it very very hard to continue to operate as we were operating in 2024,” Chavarro says.
Quackenbush compares the recovery of NIH funds to a power outage. Turn off the lights, and six months later, you can turn them back on without issue. But research is more like buying ingredients and preparing an elaborate dinner for his wife, he says. If the power goes out for fifteen minutes or so, it won’t be a problem.
“The power is out for three months, whatever I made is rotted, right?” Quackenbush says. “Even though I still have all this stuff sitting on the counter, I can’t just start cooking again.”
People have left, expertise is gone, networks and collaborations have been dissolved entirely — research is rotting.
Some projects, like Lockman’s research on HIV in Botswana, were stopped shortly after the beginning of the funding freeze — preventing scientists from finishing their studies or making breakthroughs in their research.
“It’s also just a waste potentially of all that investment,” Lockman says. “You don’t necessarily get the scientific answers after having invested so much.”
Lockman searched for private funders to continue the remainder of the study, and she managed to fund “most, but not all” of the final interviews for the study. But the infrastructure she built in Botswana — a team of nurses, doctors, and researchers — is permanently damaged.
“If you lose so much funding overnight, and you start to lose staff,” Lockman says. “ It’s going to take years and years to build that back up, if we are even able to.”
Some researchers are not sure what the restoration will look like — or how long it will last. “This is a temporary situation, and that could end any day, given the roller coaster that we’ve been on, especially at Harvard,” says Lockman.
Some projects may not receive funding at all. “Projects that address issues that are at odds with the overall political vision of the current administration would not be funded,” says Chavarro, the HSPH dean.
Quackenbush had previously received a grant to conduct sex-based disease research. While the language of the grant had previously discussed gender, after the elections in November, they decided to strictly concentrate on biological sex and chromosomal content.
Despite submitting a renewal application for the project, their grant was never reviewed — Quackenbush says the review date changed until it disappeared entirely. He called the program officer in April, only to learn that the entire program had been terminated because of its discussion of sex and gender.
Beyond that, even though NIH grants are restored, less funding will be available as a result of changes to the ways that grants are funded.
Even though the budget of the NIH has remained relatively similar, from $47.3 billion in 2024 to $46.9 billion in 2026, there are many changes that impact the amount of grants that can be funded. The NIH is also shifting towards a one-time payment model where the funding is distributed upfront, as opposed to multi-year grants where researchers receive more money for their research each year.
Instead of funding five separate projects, the NIH is funding five years of a single project, Quackenbush says. As a result, the NIH will be funding less grants overall. Some projections indicate that grants issued by the NIH will drop almost a third, from almost 40,000 in 2025 to 27,000 in 2026.
Many young researchers now feel uncertain about joining the field.
“You’re going to stop the flow of young people from this country, and also, obviously the flow of people from other countries,” says Lockman. “People will look to other countries for training and for jobs.”
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{shortcode-dd08abb0bb2b02bf4881baaa9fb305566107f8d4}o Quackenbush, the future of research is the future of Harvard.
“The University is built not on buildings, not on endowments. It’s built on people,” he says. “The greatest asset this University has, what gives it its character, and what makes it the world’s leader in research and education are the people who are here.”
Many believe Harvard’s researchers are some of the best and brightest in the world. But several say that they’re now unable to focus on making progress. Instead, they’re trying to save specimens, frantically applying for grants, and rebuilding their scattered teams. Meanwhile, the Trump administration continues to attack Harvard, discouraging people from joining the University in the first place.
Quackenbush puts the long-term consequences in clear terms. “Losing those people is going to fundamentally change the quality of the institution,” he says.
—Staff writer Megan L. Blonigen can be reached at megan.blonigen@thecrimson.com. Follow her on X at @MeganBlonigen.
—Magazine writer Jona P. Liu can be reached at jona.liu@thecrimson.com.
