John Quackenbush

The system has been corrupted so that research will no longer serve the needs of the people but instead will be used to advance the will of the state. We have surrendered 80 years of world leadership in biomedical research because of the small-mindedness of the Project 2025 authors and its enablers.

The executive order adding a layer of Soviet-style political review before final grant approval means that even good science could be killed by some bureaucrat who has no idea what the science means but sets standards based on political dogma.

What its supporters call "the big, beautiful bill" includes a 40% cut in the NIH budget and a vast restructuring of the institutes. The announced changes in funding structure likely will mean that instead of 1/10 grant applications being funded, 1/25 will be--and maybe worse when combined with cuts.

Don't mention mRNA vaccines as a way of treating infectious disease or for individualized cancer therapy. That is dead too. Training grants for PhD students have not been funded since inauguration day. Grant funding rates have been about 60% of previous years with the fiscal year running out.

Other programs have been axed because they rewarded expertise in the field--such as NCI's R35 Outstanding Investigator program, whose grantees read like a "Who's Who" of luminaries in the field. Vaccine research and clinical trials programs are gone.

The situation with science and the universities is so dire that the best path forward is unclear. Entire programs have been terminated by word search because they addressed questions involving equity or gender--as if some members of the population do not deserve their health issues addressed.

What pains me as a person is that my family has to think about a trip to Canada for a vaccine that used to be available, with a certificate for $20 of free groceries, a six-minute drive from our house.

What pains me as a scientist is the devastation of our nation's intellectual capital and future.

Put it in a Jupyter Notebook/R Markdown Document so that the analysis can be run from start to finish and reproduce all of the figures in the paper. In the process, make sure the code is documented so that each step is explained and each variable is defined.

SEAHORSE: A Serendipity Engine Assaying Heterogeneous Omics-Related Sampling Experiments Large-scale, open-access data sets such as the Genotype Tissue Expression Project (GTEx) and The Cancer Genome Atlas (TCGA) include multi-omic data on large numbers of samples along with extensive cli...

We view science as hypothesis testing, but where do hypotheses originate? From observing associations in systems we study—whether to fill known gaps or reveal the unexpected. SEAHORSE engineers serendipity—finding unexpected associations, beginning with GTEx and TCGA.
www.biorxiv.org/content/10.1...

Wish I could be there to celebrate with you. This is a great piece of work.

After a long journey, a paper by my colleagues @maudfagny.bsky.social, John Platig, and Katherine Stone was published today. It builds on our earlier work in eQTL networks and casts polygenic trait selection in the context of regulatory network models, shedding new light on the process. Take a look!

How does cancer progress? Gene behavior holds clues. | Harvard T.H. Chan School of Public Health John Quackenbush does groundbreaking research that uses massive gene datasets to explore how diseases progress, particularly cancer.

This is a nice overview of both my work and the impact of federal research cuts. I am at the point where I need to think about reinventing myself because we are watching the destruction of the research enterprise in the US.

hsph.harvard.edu/news/how-doe...

They are attacking Harvard and using anti-antisemitism as a pretense. But they are also trying to eliminate expertise and any long-term investment in science. There is no logic other than breaking things because they can. It's like a high school bully who attacks smart kids because we threaten him.

@baym.lol, so sorry to hear this. I had an NCI R35, submitted my competitive renewal (more than 40 papers and a slew of new methods- with one NCI called one of 2024's most significant advances). I got a good score and was hopeful. Pre-council, I got an e-mail saying NCI was terminating the program.

Government word search is killing my cutting-edge research The Trump administration seems to believe that some words and ideas fail an ill-posed and completely nonscientific test of orthodoxy.

The irrationality of the war on science that the Trump Administration has been waging manifests as indiscriminate termination of individual projects and whole lines of inquiry based solely on "bad words" appearing in their descriptions. #WarOnScience @statnews.com
www.statnews.com/2025/04/23/u...

If my institution has DEIA policies, so we recruit highly qualified personnel from a range of backgrounds, treat them equitably, create an environment where certain members aren't excluded, and comply with the Americans with Disabilities Act, we can't work to cure disease. Please, someone, explain.

And now the funds supporting this work are at risk. We've already been told that one funding program has been discontinued and that the grant application won't be reassigned. The project is dead with no attention to the actual work to be done.

My own work sheds light on how diseases such as cancer and emphysema develop, progress, and respond to treatment-and why these differ between the sexes. This isn't "woke science." It addresses real problems and points to better treatments for everyone. We deliver new methods in open-source software.

iPhones and GPS wouldn’t exist without research funded by the US government. What’s at stake in Trump cuts to university funding | CNN Imagine a world without the internet, or GPS, MRNA vaccines or the touchscreen on your iPhone. The science and technology that have become integral to our daily lives may never have existed, experts s...

I'm a proud Harvard Professor, and the University stands behind academic freedom that powers discovery. Grants are not gifts; they are contracts on which we have to deliver. We work long, hard hours, train students, and return innovation and value to the US. #Harvard

www.cnn.com/2025/04/17/u...

A federal research grant is not a gift, but a contract in which the grantee has to complete the work for which they were funded. Receiving a grant comes through a competitive process, and the terms of those contracts are not arbitrary. Harvard doesn't get free money. Grants are hard-won.

NIH funding delivers exponential economic returns — Harvard Gazette Report finds all 50 states reap gains in patient health, job creation, research resources, business development.

Our history of investment in funding biomedical research has positioned the US as the world leader, improved human health, trained generations of highly talented individuals who have founded biotech and lead pharmaceutical companies that employ tens of thousands.
news.harvard.edu/gazette/stor...

‘This is life or death’: Mass. scientists fear consequences of funding cuts by federal government New changes in how the federal government plans to fund research are sending a chill through many local laboratories.

I was interviewed by a local news channel about the disruptions in NIH funding. While the news story concentrates on the proposed reduction in facilities and administration costs, what they left out of the story is the significant risks of wider funding slowdown.
www.boston25news.com/news/local/t...