Johns Hopkins University biomedical engineer Jean Fan and her team develop—and freely share—computational tools that give researchers everywhere the ability to discover breakthrough cancer drugs, gene therapies, and diagnostic tests for neurodegenerative diseases. But sweeping federal cuts to research grants are now threatening the training of the next generation of scientists who make this kind of work possible.
Fan's JEFworks lab, which is entirely supported by the National Science Foundation and National Institutes of Health, creates computational tools as open-source software that uses artificial intelligence to analyze which genes are active in specific cells and pinpoint their exact location within tissue samples—essentially creating a detailed molecular AI portrait for every cell. This capability allows scientists to better understand diseases from acute kidney injury to brain cancers at an unprecedented molecular level.
The impact of this work extends beyond academia. Software pioneered at institutions like Johns Hopkins is frequently adopted by leading companies for their own research and development pipelines.
"Companies often take the free, open-source software developed in university labs and use it to build their own commercial products, creating tremendous economic value downstream," said Fan, an associate professor of biomedical engineering at the university's Whiting School of Engineering and School of Medicine. "Our objective is for the broader scientific community to freely apply our tools to their own biological research questions, helping form the infrastructure of modern biotechnology and pharmaceutical development."
But federal funding cuts are undermining the ability of researchers like Fan to train the teams that make this kind of research possible.
"A significant portion of these federal grants directly supports the training of students," Fan said. "With funding becoming scarcer, we are no longer able to actively recruit or train new scientists."
The decline in student training is creating a "pipeline breakage" that will lead to fewer qualified engineers entering the biotech sector in the coming years.
"This shortage could slow down the development of new treatments for patients," she said.
The stakes of that shortage become clear when considering the role that academic labs like Fan's play in the broader health technology ecosystem. A prime example is STalign, one of several free software programs developed in Fan's lab. The tool simplifies the complicated process of aligning spatial gene profiles, removing the need for tedious, manual labor. STalign has already been built into the LatchBio platform, a company focused on creating next-gen computing tools for genomics research.
Beyond creating new software, university labs also play a critical role in ensuring that new medical technologies are truly effective, reliable, and safe before reaching patients. Fan's lab, for instance, rigorously checks gene mapping technologies developed by private companies. In one case, her team tested a technology that is intended to create a detailed map of gene activity within breast tissue, developed by the company 10X Genomics. By evaluating such technologies, Fan's lab helps ensure that the information they provide is accurate, ultimately supporting new discoveries and gene therapies for diseases like breast cancer.
This independent validation is critical because while private companies can create and test their technologies using their own software tools, they aren't required to disclose how they do it, unlike academic research.
"Because university studies are funded by independent federal grants, rather than by the companies themselves, we can offer unbiased oversight, free from any financial or commercial pressures," Fan said. "This partnership between industry and academia fosters a more transparent and reliable scientific process, ultimately to the benefit of consumers and the public."
The relationship between academic research and private industry also creates a mighty engine for medical advancement, Fan says.
"Those of us in university labs provide foundational tools and independent validation, while the companies scale these innovations into treatments used by real people," Fan said. "Together, we are accelerating the pace of discovery."
