Standing in his laboratory, Harvard professor Sean Eddy gazes at a row of vacant work stations. More than a year ago, this lab was filled with over a dozen researchers. On a given day they might be working independently on analyzing genomic sequencing or gathered around the group table, drinking coffee and helping each other troubleshoot questions about genomic data from different species.

Now, after his funding was terminated under the Trump administration, the computer screens are gone and the room is silent. He's one of the last people left.

" Seeing these labs empty — this is not the way it's supposed to be," he says. "This was a very vibrant lab."

Eddy is a computational biologist. He has devoted his career to one fundamental question. " I'm really interested in the origin of life," he says. "I want to know where it all came from."

He and his colleagues spent years developing software that could be used to seek out an answer. Scientists around the world now use the tools his team created to compare DNA and protein sequences, identify genes, and predict what they do. Their work underpins countless studies, including research related to cancer and neurodevelopmental disorders.

It's hard to quantify how much modern science relies on what his team built. Eddy describes its use as being as ubiquitous as microscopes or pipettes.

"It's very affirming for me to pick up sort of semi-random papers in the literature in fields that I care about and see them using our software over and over again," he says.

When the lab was designed more than a decade ago, he worked closely with an architect. On the wall are pictures of animals. His daughter, who was 12 at the time, stenciled them for him. Mixed in with pictures of mice and fish are laboratory creatures. "There's a bacterial virus called T4 that I did my thesis on," he says, pointing to the wall.

In 2025, Eddy received a letter from the National Institutes of Health, informing him that his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," he recalls.

Eddy is one of thousands of researchers across the U.S. still grappling with the damage inflicted on science in 2025 under the Trump administration — despite a restoration of funding earlier this year.

Left guessing 

At the time he received the letter, Eddy had more than a dozen people working for him. Over the last year he's had to let almost all of them go. He's worked closely with them to help find jobs elsewhere.

Eddy says he has given up on any dream that his funding would be restored. "I haven't talked to my program officer in years now," he says. "My guess is that he's under instructions not to talk to me. So we're just sort of left guessing what the status of the grant is."

He estimates the funding loss set him and his lab back by a decade. At 60, Eddy had planned to continue working through the next decade with his team. "For someone of my career stage, this is probably not recoverable," he says.

Walking through the empty lab, he looks at the bare desks where his team used to sit. He'd like to see this lab taken over by a younger computational biologist, someone who could pick up where he left off. But with Harvard now on a hiring freeze, he says, he doesn't see that happening anytime soon.

Money on paper — but not in practice

Champions of science celebrated a rare bipartisan victory in the early months of 2026. After the Trump administration tried to cut, freeze or suspend billions of dollars the previous year, a handful of Republicans — at the urging of their constituents — joined Democratic colleagues in an effort to quietly restore significant portions of that funding through the appropriations process.

Now, many of those same advocates are warning that money is not reaching scientists at the rate it should be, and that a lack of transparency at the agency is compromising the integrity and reliability of its research.

"In the past you had a pretty good sense of how NIH was gonna behave," says Jeremy Berg, a former high-ranking official at NIH who has become a kind of watchdog for the organization. When the Trump administration started slashing funding for NIH, Berg took it personally. " Now that level of trust is pretty much gone," he says.

In the past, says Berg, there was an ethos in the agency that dictated clear deadlines, funding forecasts, and expectations from researchers. This reliability fostered good science, Berg says. He credits the institution with funding and fostering much of the progress in biomedical research in the past few decades — such as mapping the human genome, major advances in cancer care, or new therapies for HIV and AIDS.

Berg recalls something a Republican senator once told him about the agency. "He used to refer to it not just as the crown jewel in biomedical research, but as the crown jewel in the federal government," he says. "I think that one can make a pretty strong case for that."

When the cuts hit, he started tracking their progress, charting the changes over the last year. In 2026, Berg says the budget may look intact on paper. However, he says NIH has switched the strategy to making fewer grants with more money over more years, an accounting shift that means fewer scientists are getting funding.

Berg's analysis showed that at one point earlier this year, NIH had issued roughly 2,300 new grants — about half as many as at the same point the previous year.

"There's a lot of pain and a lot of science that isn't gonna get done," he says.

Advocacy groups have also been sounding alarm bells about a lack of transparency at NIH. Money approved by Congress this year has been slow to reach researchers, they say. Analysis from the Association of American Universities showed that NIH issued 66 percent fewer grant awards in the first few months of 2026 than they did the previous year.

" I'm sadly watching the agency where I worked for so many years be dismantled," says Elizabeth Ginexi, who was a program officer at the agency for 22 years, working on substance use prevention. She left when the Trump administration started making cuts, fearing she would be cut anyway.

She's been looking for a job for over a year.

In the meantime, Ginexi's been analyzing something on the NIH website called forecasts, areas of research the agency would like to fund. Typically these forecasts give direction to scientists who are applying for research money.

Ginexi started tracking them when she observed that they were not being filled as quickly as they had in the past. "There are tons and tons of them — starting from last year — that are still sitting as forecasts and were never published," she explains.

Her research shows that of 336 NIH funding forecasts still listed as open, 205 were already past their promised posting date with no full announcement ever published. It's a way, she says, of giving the illusion of funding opportunities, even as they fail to materialize.

Chances of funding? "Basically zero"

Sitting at her lab, cancer researcher Rachael Sirianni scrolls down the website for the NIH, monitoring the grants she's submitted that are waiting for the agency to review. She looks at one application. " The chances of that grant being funded in 2026 are basically zero," she says.

Sirianni had been counting on that grant to continue evaluating a combination of medications for treating children with cancer that had metastasized to the brain. The drugs together offered a "one-two punch," she says, and was showing a lot of promise. She figured with this progress, she'd be able to secure more funding for her work. But she hasn't been able to see it through the normal review process at NIH.

Many of the families grappling with this condition have no other options for dealing with this kind of pediatric cancer, which is basically impossible to remove or mitigate.

"It's thin and it's across the soft tissues of the brain and spinal cord," she explains. "There isn't really a consistent neurosurgical solution to that cancer complication."

Sirianni is a biomedical engineer. Earlier in her career, while working at a research institute, she met a family who lost a child to a type of cancer considered unsurvivable. "Being exposed to that family's pain, especially when I had become a parent myself," she says, "was pretty personally transformative."

In 2022, she moved her young family from Texas to Worcester, Mass., a city of a little over 200,000 an hour outside Boston, to build a lab at the University of Massachusetts Chan Medical School and run pediatric cancer studies.

For this particular grant, Sirianni worked with a colleague for several years before they submitted their proposal for funding, carefully tracking compliance requirements and watching deadlines. In the last year, these deadlines have been repeatedly moved, making it now impossible for the grant to even be reviewed in time for funding.

Sirianni looks at one laboratory bench that is full of equipment — reagent bottles and pipettes. She's had to lay off the researcher who was working here. "I can't bring myself to clear his bench," she says. "It makes me sad."

In response to her concerns and those laid out by other researchers in this story, a spokesperson from Health and Human Services, Andrew Nixon, acknowledged the slowdown in funding and attributed the delays to the government shutdown and congressional Democrats.

"Timelines have returned to typical funding patterns," he wrote in an email to NPR.

Both Sirianni and Eddy say for them, it's too late to restart their research. "That means that the therapeutic development work that taxpayers previously invested in is now hitting a brick wall," says Sirianni.

"Even as just a citizen of the country, this frustrates me," she says. "It's a loss of investment. It's a loss of momentum for the families that have children that are affected by these tumors. Every month, every week — that matters to them."