BOSTON — The Harvard T.H. Chan School of Public Health lab led by John Quackenbush used to buzz with the energy of postdoctoral fellows, graduate students, and interns, all diving into cutting-edge computational biology research. Their work spurred significant discoveries and resulted in the development of essential big data tools, one of which received accolades from the National Cancer Institute as a notable advancement for 2024.
Now, however, those offices sit eerily empty, with only vacant computer stations remaining. The once-busy spots are as desolate as bleached coral reefs.
The downturn began earlier this year when the Trump administration swiftly cut funding that had supported research programs nationwide.
Quackenbush’s lab is just one of many facing challenges. Universities, bracing for potential further reductions in National Institutes of Health funding, have laid off staff, slowed hiring, and enrolled fewer students and fellows.
For years, Quackenbush’s lab was celebrated for its leadership in human genetics and bioinformatics. The tools developed there aid scientists in deciphering gene regulation and understanding diseases ranging from cancer to autism. Collaborating with Quackenbush’s lab has been a goal for many top research teams, according to Kenneth Ramos, a cancer researcher from Texas A&M Health. Quackenbush’s work boasts around 100,000 citations to date.
“John’s contributions have made him one of the most significant bioinformaticians in the last quarter-century,” said Ramos. “He offers many resources freely, is inquisitive, and dives deeply into scientific inquiries. Plus, he’s incredibly collegial.”
Quackenbush had anticipated some difficulties after the 2024 election. He paused new hiring to safeguard his budget, saying, “I was cautious, uncertain about what might happen. Now, it feels like the funding has vanished.”
A significant blow came in April when Quackenbush discovered that a vital research program was terminated. He had applied for a grant renewal to study gender differences in medicine, but delays in communication led to its abrupt end, with officials citing misalignment with current administration priorities — a phrase that became increasingly common among affected researchers.
Additionally, the National Cancer Institute shut down its Outstanding Investigator Award program, a crucial source of Quackenbush’s funding. This program was designed to support high-risk scientific inquiries with fewer administrative burdens and was intended to provide funding for seven years. Although ongoing awards will still be honored, Quackenbush’s expired in 2025, and he was looking forward to a renewal based on promising review scores until the initiative’s termination. The administration also turned down his request for a no-cost extension, which would have allowed him to utilize remaining grant dollars.
“That was a crushing blow. Just as I was flying over Lake Michigan, I learned about the mass terminations of Harvard grants. I felt an intense fear,” he recalled.
With funding disappearing, Quackenbush can no longer afford to hire. As staff members and students move on, there are no resources to replace them, placing his decades’ worth of work and contributions at significant risk.
Many recognize Quackenbush as a thought leader, particularly for his innovative network of applications known as the “Network Zoo,” which helps analyze the complex gene interactions that dictate cellular functions.
Quackenbush emphasizes not just identifying which genes are active in certain cells but also understanding the intricate networks of over 1,600 transcription factors responsible for regulating the human genome’s 20,000 genes. “It’s a complicated web,” he explained.
Such modeling is essential for unpacking human biology and potential disease treatments. The tools from the Network Zoo, including one called PHOENIX, facilitate groundbreaking research across various biological questions. Notably, PHOENIX helped identify gene network dynamics, receiving recognition from the NCI.
Yet, Quackenbush doesn’t define himself merely as a tool builder; the applications are his pathway to investigate scientific questions he finds compelling. Recently, he and his postdoc, Tara Eicher, set out to explore connections among genes linked to glioblastoma, a challenging brain cancer. Eicher conceptualized a method named BLOBFISH, a playful nod to the quirky fish representing her creative take on network analysis.
The Network Zoo applications remain open source and user-friendly, ensuring widespread access for researchers. Ramos, for instance, utilized a Network Zoo tool, ALPACA, to tackle issues related to drug resistance in cancer treatment. Other scientists have also benefited in their investigations of various diseases thanks to Quackenbush’s work.
But with diminishing personnel, Quackenbush’s lab struggles to maintain its resources and further develop new methods. “The software tools require constant updates to remain functional, which has become increasingly challenging,” Quackenbush said.
As of now, only three individuals remain in the lab, down from nine. Meetings have shifted from spacious rooms to smaller offices. Though Quackenbush hasn’t had to lay anyone off, he’s proud that former lab members have moved on to promising positions, despite the mixed feelings surrounding their departures.
“There is a somber tone now. The funding cuts have accelerated decisions to leave,” one postdoc shared. Eicher also worried that her funding might soon dry up, complicating family finances.
“Moving abroad could be an option for some, but not for me. Relocating with my children isn’t pragmatic,” she reflected, hinting at the shifting landscape for scientists amid tightening funding environments.
At Harvard, increasing austerity measures reveal the financial strain — fewer Ph.D. candidates and even the absence of coffee in break rooms. “It’s indicative of how things have changed,” Eicher observed, eyeing the empty coffee station.
The Future is Uncertain
Although Quackenbush has some funding remaining, it won’t sustain his lab for much longer. He estimates losing around $1.2 million this year and potentially facing a broader loss of close to $10 million over the coming years. He’s assessing new job offers and exploring opportunities to transition his work into tech startups.
Quackenbush describes himself as the “luckiest person in the world,” grateful for his journey as a scientist, rooted in public investment. “I owe it to society to yield a return on that investment,” he stated, but now grappling with unprecedented obstacles has made fulfilling that responsibility more daunting.
The search for new funding will undoubtedly be a long and competitive process, while the remaining resources will quickly expire. “What lies beyond spring is a mystery,” he admitted.
Yet, he remains determined: “We will continue pushing forward with our research and strive to achieve what we can,” he said, even if it means a slower pace.
