John Quackenbush
@johnquackenbush.bsky.social
Father, husband, scientist, professor, department chair, martial artist, scuba diver (in about that order).
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
August 25, 2025 at 2:55 PM
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...
www.biorxiv.org/content/10.1...
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!
I’m happy to share our new paper, just published in @molbioevol.bsky.social , that shows how complex traits heritability and adaptation is supported by mutations holding key local hubs positions in eQTL networks !
doi.org/10.1093/molb...
@ideevl.bsky.social
@johnquackenbush.bsky.social
doi.org/10.1093/molb...
@ideevl.bsky.social
@johnquackenbush.bsky.social
The Importance of Regulatory Network Structure for Complex Trait Heritability and Evolution
Abstract. Complex traits are determined by many loci—mostly regulatory elements—that, through combinatorial interactions, can affect multiple traits. Such
doi.org
August 19, 2025 at 4:14 PM
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!
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...
hsph.harvard.edu/news/how-doe...
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.
hsph.harvard.edu
June 18, 2025 at 1:57 PM
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...
hsph.harvard.edu/news/how-doe...
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...
www.statnews.com/2025/04/23/u...
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.
www.statnews.com
April 23, 2025 at 1:56 PM
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...
www.statnews.com/2025/04/23/u...
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...
www.cnn.com/2025/04/17/u...
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...
www.cnn.com
April 17, 2025 at 4:25 PM
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...
www.cnn.com/2025/04/17/u...
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...
news.harvard.edu/gazette/stor...
NIH funding delivers exponential economic returns — Harvard Gazette
Report finds all 50 states reap gains in patient health, job creation, research resources, business development.
news.harvard.edu
March 12, 2025 at 1:13 PM
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...
news.harvard.edu/gazette/stor...
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...
www.boston25news.com/news/local/t...
‘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.
www.boston25news.com
March 7, 2025 at 2:39 AM
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...
www.boston25news.com/news/local/t...