The federal government annually spends billions funding research at Harvard, part of a decades-old system that is little understood by the public but essential to American science.

This spring, nearly every dollar of that payment was cut off by the Trump administration, endangering much of the university’s research.

The New York Times was able to identify more than 900 terminated grants, using court records, government databases and other internal university sources — a near-complete accounting of the cuts in the Trump administration’s escalating campaign to cripple the university.

The White House and Harvard have resumed negotiations to resolve the government’s claims that the nation’s oldest university has “failed to live up to both the intellectual and civil rights conditions that justify federal investment.” But while researchers await the outcome — or that of a parallel lawsuit brought by Harvard — the federal support for every one of these projects remains halted.

The Trump administration has canceled research grants at other universities, too, ending studies related to racial diversity and equity, scaling back the reach of federal science agencies, and sometimes attacking universities it views as ideological foes.

But Harvard is unique both in the volume of its research output and the extent of these cuts — the government has threatened to end every research dollar to the university. The canceled grants accounted for here add up to about $2.6 billion in awarded federal funds, nearly half of which has already been spent according to government data.

“Even ‘grant’ is a problematic word, because people think they’re just sort of handing this money out for us to do what we want with,” said Marc Weisskopf, who directs a center for environmental health at Harvard that lost its funding from the National Institute of Environmental Health Sciences.

On the contrary, the government is much more explicit in competitive research applications and grant reviews: It wants more neuroscientists. It wants better opioid treatment. It wants to know how lightweight origami-inspired shelters and antennas can be unfurled in war zones.

The money the government sends to Harvard is, in effect, not a subsidy to advance the university’s mission. It’s a payment for the role Harvard plays in advancing the research mission of the United States.

This is the science model the U.S. has developed over 80 years: The government sets the agenda and funds the work; university scientists design the studies and find the answers. The president’s willingness to upend that model has revealed its fragility. There is no alternative in the U.S. to produce the kind of scientific advancements represented by these grants.

Foundational discoveries and future cures

Much of what the government funds at universities is “basic” research — the foundational knowledge that lays the groundwork for technological advances, disease cures and improvements in quality of life.

Daniel Nocera, a Harvard chemist, had four total grants terminated from the Department of Defense, the Department of Energy and the National Science Foundation. His lab develops new chemical methods to address practical problems, such as developing an artificial leaf that can convert air and sunlight into biofuels, or extracting oxygen from seawater so that divers could one day swim without a heavy oxygen tank.

“I have to answer these questions that a company doesn’t have time to answer,” he said.

That’s because basic research takes years. And it produces insights that aren’t profitable on the time scale of corporate quarterly earnings.

Stephen Buratowski’s project to understand how genes are expressed and regulated is in its 25th year of federal funding. An early discovery in his lab used yeast cells to reveal how different steps are coordinated in the formation of messenger RNA, a mechanism later confirmed in human cells by researchers at other universities. Today, 20 years later, several companies are testing potential cancer treatments built on that knowledge.

Such long-term federal investments are inherently risky and expensive (a single tube containing a teardrop size of purified enzyme used in Professor Buratowski’s lab costs $400 to $500). And some ideas don’t prove as fruitful. But the government can bear this risk better than industry or individual universities can.

“It’s almost as if the government is acting as a venture capitalist,” Professor Buratowski said. “They’re putting out an ad saying, ‘We’ve got a pool of money, send us your best ideas.’”

Dragana Rogulja’s Harvard lab studies how chronic sleep deprivation harms the body. Her lab discovered that when fruit flies or mice are deprived of sleep, it damages their gut, which can be fatal. But when sleep-deprived flies were then treated with antioxidant drugs, they had normal life spans.

She received a grant from the Department of Defense’s health agency to detect biological signals in samples of blood, urine or saliva that warn of organ damage from sleep loss in mice. “If we are right,” her research proposal stated, “this would be a major breakthrough that would offer practical ways to mitigate health damage caused by poor sleep.”

Without researchers at Harvard or other universities doing this foundational work, it’s not clear who would. The government doesn’t have the expertise. Companies don’t have the luxury of time. And this same research would cost far more outside academia, where it runs on graduate students working long hours at relatively low cost.

Evidence for public policy

Other grants at Harvard produce something different from a lab discovery or a medical cure. This research provides evidence that shapes public policy, like nutritional guidelines, federal laws or local education initiatives.

A federal rule in 2018 banned artificial trans fats, following the findings of a decades-long longitudinal study of women’s health based at Harvard.

“A lot of things we take for granted — ‘Oh, everybody always knew that’ — no actually, we published those findings,” said Walter Willett, a professor of epidemiology and nutrition who leads that study.

Of similar direct interest to the government, other Harvard researchers are trying to determine how well telemedicine appointments — sometimes paid for by Medicaid and Medicare — connect opioid use disorder patients with lifesaving treatments. (Some of the National Institutes of Health funding for that research goes right back to the government, in the form of fees to access Centers for Medicare and Medicaid Services health data).

Other researchers are studying how well community college students have fared amid remote learning, after a pandemic boost in federal support for community colleges. Others are working on how to implement smoke-free policies in low-income housing after a move by the Department of Housing and Urban Development to curb secondhand smoke.

“We are directly informing the government’s capacity to work to serve its constituents,” said Vaughan Rees, the lead investigator on that HUD-funded research.

Just as much of basic research couldn’t be done in corporate labs, this kind of work — often relying on large-scale surveys, or partnerships that cross universities, hospitals and countries — couldn’t be funded by Harvard alone.

“No university could do that,” said Lisa Berkman, a professor of public policy and epidemiology who works on international studies. “This is science that rests on a public investment.”

Training the next generation of scientists

Federal funding also fosters not just science, but scientists. Grants pay the salaries of graduate students and postdoctoral researchers. Grant terms regularly require that lead researchers incorporate student training into their work.

Jessica Whited, a professor of stem cell and regenerative biology, was the first in her family to become a scientist. As an undergraduate, she earned a scholarship at the University of Missouri and worked part-time under the federal work-study program. As an early-career researcher, her research was funded by competitive N.I.H. grants.

“I wouldn’t be sitting here today without the government,” she said.

Her lab studies how the axolotl, a salamander species, can regenerate its limbs, producing insights that could lead to treatments for human amputees. In 2019, President Trump awarded her the Presidential Early Career Award, the nation’s highest honor for early-career scientists and engineers. Last month, the government canceled the grants that provided nearly all of her funding.

The canceled grants highlighted below are specifically designed for training and professional development. They include National Science Foundation fellowships for undergraduates, graduate students, postdoctoral researchers and early-career researchers, and similar training opportunities from the N.I.H. Together, these awards cover about a tenth of the total funding cut by the government at Harvard.

Paul Bump, a postdoctoral fellow, was just awarded one of these grants — the first of his career — in January. He wants to uncover the fundamental mechanisms of where stem cells come from in certain animals that, unlike humans, continue to produce them throughout their lives. (He works, in particular, on the three-banded panther worm, which can regenerate into two worms when cut in half.)

“What are the grand biological processes that explain that?” he said, describing what amounts to nature’s solution for making stem cells. The public’s down payment on the answer was about $75,000 a year to fund Mr. Bump’s work for two years.

Harvard is trying for now to provide stopgap funding for many of these researchers and students, but it can’t permanently replace the government. That’s also because federal funds support much of the infrastructure that researchers rely on. Grants also cover the indirect costs Harvard pays to maintain facilities and research support staff. And some larger grants directly fund research hubs that assemble shared resources and facilities for many scientists from different specialties working on related topics.

For 18 years, Harvard has hosted a center studying worker safety, health and well-being funded by the National Institute for Occupational Safety and Health, an arm of the C.D.C., where researchers from multiple institutions have studied the health of construction workers, Sept. 11 first responders, health care workers and warehouse workers.

The center’s canceled grant jeopardizes its active research projects, but also the partnerships with hospitals, insurance companies and employers that have taken years to develop, said Glorian Sorensen, a Harvard professor who co-directs the center.

“This is larger than any individual grant,” she said. “What we are losing is a future.”

Explore the data

Click on the chart below to explore the canceled grants for yourself: