America’s Best Colleges for Research

In February 2025, a baby boy named KJ Muldoon—born with a genetic defect that lets ammonia build to lethal levels in the blood, killing many infants in their first week of life—received an injection that had not existed anywhere on earth until his doctors designed it specifically for him. It made him the first person treated with personalized CRISPR therapy, which lets scientists cut and correct DNA at one exact spot, written for a single patient. But that cure did not come from a private biotech firm’s skunkworks. Instead, it grew out of the public research funding that has underwritten American science for almost 80 years. 

The National Institutes of Health’s Somatic Cell Genome Editing program supported the project, while the cure itself was designed and manufactured in under seven months at Children’s Hospital of Philadelphia and the University of Pennsylvania. And it is only one of many such breakthroughs to recently emerge from that system. Two decades of work in Doug Melton’s Harvard lab—taken up after both of his children were diagnosed with type 1 diabetes—culminated in June 2025 in a stem cell therapy that, in an early trial, freed 83 percent of recipients from insulin injections by growing them fresh insulin-producing cells. Washington University in St. Louis recently followed more than 600,000 veterans with type 2 diabetes and linked GLP-1 drugs not only to weight loss and to heart, kidney, and liver benefits but also to recovery from and protection against substance use disorders involving alcohol, nicotine, opioids, cocaine, and cannabis. And at the University of California, Davis, a federally funded team gave back the voice of a man silenced by ALS, reading his intended words off his brain signals and speaking them aloud, in his own cadence, in real time.

Acknowledging and mapping that system is the purpose of the Washington Monthly’s guide to the Best Colleges for Research, the only ranking of its kind assembled by a journalistic outlet. The universities behind those breakthroughs sit near the top of it: Harvard ranks number three, the University of Pennsylvania number eight, Washington University number 25, and UC Davis number 23—and UC Berkeley, whose scientists helped give the world CRISPR itself, ranks number seven. But the research economy underlying the system runs just as deeply through lesser-known land-grant universities whose discoveries remake the industries around them. That’s why our ranking evaluates the roughly 140 universities that each spend at least $100 million a year on research, scoring them along four equally weighted measures: total research expenditure; the number of science and engineering doctorates awarded; the faculty elected to the National Academies of Sciences, Engineering, and Medicine; and the major national honors a school’s scholars collect. 

We have never had more reason to produce this ranking. Since the beginning of his second term, Donald Trump has mounted the most sweeping assault on university research in the system’s history. Princeton University President Christopher Eisgruber, whose university ranks number 12, has called the campaign “the greatest threat to American universities since the Red Scare of the 1950s.” Trump has made Princeton, Harvard, and their elite peers the face of his assault on higher education. But those schools, with their deep-pocketed donors and high-powered legal teams, have largely recovered their footing—whether by prevailing in court or writing nine-figure checks to the government. The less-famous public universities on the Washington Monthly list, especially those of deep-red America, have no such options. They often cannot wage costly legal battles, and they cannot replace federal grants with other sources of income.

Take Mississippi State University, number 110 on the Monthly’s list. MSU runs the National Warmwater Aquaculture Center, where USDA-funded scientists recently engineered a single-dose vaccine, ESC-NDKL1, that protects farmed catfish against two of the diseases that most threaten the state’s signature but struggling crop. Last year the university lost a USAID aquaculture grant, leading the mayor of Starkville to warn that “every time you touch the university, you, in effect, touch Starkville.” Mississippi State’s president, Mark Keenum, warned that he was “extremely concerned about announcements from Washington that pause or interrupt the research of our faculty, staff and students,” calling the prospect “catastrophic to our university.”

Kansas State University, number 104, used CRISPR to switch off the gluten-coding genes in wheat, a step toward a lower-gluten version of the crop that anchors the state’s economy, and serves as the university partner to the federal government’s new National Bio and Agro-Defense Facility, built to shield the nation’s livestock from foreign disease. West Virginia University, number 121, sent a Department of Energy–funded team to gather the first geological data on whether the geothermal reservoirs beneath Appalachia could become a source of clean power for a region built on coal—exactly the kind of work now imperiled by proposed cuts to the Energy Department’s budget. The administration’s newest proposal includes a 64 percent cut to the Department’s Advanced Research Projects Agency, which supports clean energy research.

By the count of Grant Witness, a crowdsourced tracker two scientists built after the cancellations began, the NIH has terminated roughly 2,100 grants worth about $9.5 billion, and the NSF more than 1,600 worth over $1.5 billion. Such terminations carry immediate human cost: One analysis found that cutting funding for 383 clinical trials pushed more than 74,000 enrolled patients out of studies many were counting on for treatment. The Adolescent Medicine Trials Network, a two-decade-old effort to prevent HIV in teenagers, lost $18 million, halting its trials; the dismantling of USAID ended the global-health grants behind Johns Hopkins’s Jhpiego, a nonprofit that works to keep mothers from dying in childbirth.

The institutions named in last year’s edition of this ranking have moved from bracing for impact to absorbing it. Johns Hopkins—number five in our rankings, and the single largest university recipient of federal research dollars in the country—laid off more than 2,000 people, the largest workforce reduction in its history, after the shuttering of USAID erased $800 million in global-health work. Penn State, number 22, planned nearly $100 million in cuts and imposed a hiring freeze. “Today is a profoundly difficult day for our colleagues and for our university,” Johns Hopkins President Ronald J. Daniels told the campus, mourning “a significant loss of exceptional people … whose work has advanced the mission of our university.”

Much of the assault, though, has run into resistance. After a coalition of 16 states and the American Public Health Association sued over some 900 grants, the courts produced a patchwork of rulings, many of which are in higher education’s favor. A federal judge in San Francisco ordered about 300 NSF awards and 500 NIH grants restored to UCLA, reinstating 114 more across 45 institutions. Then, when the NIH tried to cap the overhead it pays on grants at a flat 15 percent, down from the negotiated rates of 50 percent or more that major universities had long charged, a district court blocked the move within weeks. And Congress refused to ratify the deepest cuts to America’s research complex. The president’s fiscal request for 2026 sought to slash the NIH’s budget by roughly $18 billion, close to 40 percent. But the Senate chose to instead advance a measure increasing its budget by $400 million, or about 1 percent.

Where the government wielded the most direct leverage was over individual campuses. Columbia, after losing $400 million in grants, agreed to pay the government $221 million to make the pressure stop. But Harvard, facing even graver pressure, chose to litigate and, in September, won: Judge Allison Burroughs ruled that freezing roughly $2.6 billion in grants amounted to unconstitutional retaliation for the university’s speech. 

Even so, the Supreme Court’s August order let the NIH continue to withhold terminated funds as targeted scientists wait on the Court of Federal Claims’s proceedings. And a national survey of researchers published in March 2026 found laboratories shedding staff and supplies, with early-career scientists taking the heaviest blows. Nationally, just 35 percent of grantees whose funds were cut or interrupted in 2025 said they had fully regained them by year’s end.

The administration is also no longer only cutting grants but is moving to control which ones get made. In May 2026, the Office of Management and Budget proposed the most sweeping rewrite of federal grant rules in decades, requiring, among other conditions, that senior political appointees review every discretionary award before it is issued to confirm that the research “demonstrably advances the President’s policy priorities.” The proposal would bar grants concerning diversity, “gender ideology,” or transgender medicine, while restricting universities from recovering overhead on the cost of publishing their findings. 

The bitter irony is that the people Washington claims to be protecting from coastal elites are among those the cuts hurt most. Of the 23 states economists identified as most exposed to the overhead cap, most voted for Donald Trump. Consider the University of Alabama at Birmingham—number 87 on our ranking (and not to be confused with the University of Alabama’s flagship campus in Tuscaloosa). UAB brought in $413.7 million in NIH awards in 2023, enough to place it in the top 1 percent of the agency’s recipients, and its 48.5 percent overhead rate left it acutely exposed when the NIH moved to cap reimbursements at 15 percent; the agency canceled millions of dollars in its grants, and administrators warned that “virtually all areas of research would slow.” UAB, too, has produced important medical breakthroughs in the recent past. In 2025, the university served as a lead site for the first therapy ever shown to slow Huntington’s disease. Medicine had long failed to do more than manage the symptoms of the fatal brain disorder. But the gene treatment cut the disease’s progression by 75 percent over three years, in patients for whom medicine had long offered nothing but temporarily alleviating their discomfort. Even Alabama’s junior senator, Katie Britt, a Republican, has warned against gutting the very labs in her state that her party’s president is threatening.

Today KJ Muldoon is a thriving toddler, alive because a federally funded lab could invent a medicine for him and him alone. (“He’s had quite a nice little growth spurt” that “has really helped him grow some nice chubby cheeks,” says a physician-scientist at the Children’s Hospital of Philadelphia.) The next child born with a disorder like his will be surrounded by a research system with fewer labs and thinner budgets. The courts have blunted the worst of the Trumpian assault on American higher education. But whether that child finds a cure still depends on a bet this country’s political leaders once knew to make, and have lately seemed determined to forget.