Sign in

John Quackenbush

@johnquackenbush.bsky.social
1.3K followers 2.1K following 83 posts

Father, husband, scientist, professor, martial artist, scuba diver (in about that order).

PostsRepliesMedia
John Quackenbush @johnquackenbush.bsky.social · 27/07/2026
What makes each cell in an individual different despite having the same DNA? Inferring Gene Regulatory Networks (GRNs) for single cells provides an answer, but are the GRN models right? Simple answer: similar cells should have similar networks. #networkmedicine www.biorxiv.org/content/10.6...
biorxiv.org
FERRET: Framework to Evaluate Robustness in Regulatory Networks Using Heterogeneous Cell Types
Techniques for evaluating gene regulatory network (GRN) inference methods typically focus on recovering small ground-truth networks or on benchmarking against simulated data. However, both approaches ...
021
John Quackenbush @johnquackenbush.bsky.social · 29/06/2026
Can common analytical methods generate spurious molecular #waves_of_aging? We show LOESS and DE-SWAN produce wave-like patterns from random noise, casting doubt on reported “waves." With MaddyCarbonneau, Kate Shutta, Jeff Miller, Michael Snyder, and Xiaotao Shen. www.biorxiv.org/content/10.6...
biorxiv.org
LOESS and DE-SWAN can induce artifactual "waves" of molecular aging
A growing literature has investigated the relationship between age and biomolecular changes, leading to conclusions that aging occurs in discrete molecular "waves." Data summary tools such as LOESS an...
151
John Quackenbush @johnquackenbush.bsky.social · 20/03/2026
@joshuaholland.bsky.social, even cooler is the "Wall of Hammerheads" (with a Galapagos shark along the bottom and a few Silky sharks barely visible in the distance). Shot from ~30m/100ft below the surface at Wolf Island in the Galapagos.
010
John Quackenbush @johnquackenbush.bsky.social · 11/03/2026
As the US spends >$1B per day on Trump's war in Iran, and following on the devastation of US science wreaked by the DOGE bros, other countries are making substantial investments in science in ways that will help them lead in inventing the future. www.nature.com/articles/d41...
nature.com
China pledges billion-dollar spending boost for science
Funding for national laboratories and important research projects would increase under the government’s plans.
086
John Quackenbush @johnquackenbush.bsky.social · 09/03/2026
One of the people in the DOGE braintrust who made the executive decisions to terminate federally funded research programs. A person who can't articulate what "DEI" is killed research programs, including our work to develop methods to better understand why diseases differ between men and women.
010
Reposted by John Quackenbush
Jeremy Berg @jeremymberg.bsky.social · 21/02/2026
A second email, this with a more substantial insight about "The Replication Crisis"... 1/5
Dear Director Bhattacharya and Deputy Director Lorsch: I saw a post Director Bhattacharya retweeted about replication in economics. This begins with:

Between 1974 and 2014, only 0.1% of publications in the top 50 economics journals were replication studies.
That's 40 years. Thousands of papers. Almost none replicated.
We've built careers on findings no one has verified.
When economists finally replicate studies, 40-67% fail depending on the study.
67427
John Quackenbush @johnquackenbush.bsky.social · 20/02/2026
I caught Covid and am working from home, perplexing our two cats. One comes to the door of the "office," sits outside, cries, is let in, and settles next to the desk. Then the other one repeats the process, causing the other cat to leave. I believe I have evidence of the Paw-li exclusion principle.
040
John Quackenbush @johnquackenbush.bsky.social · 25/08/2025
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...
biorxiv.org
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...
2100
John Quackenbush @johnquackenbush.bsky.social · 19/08/2025
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!
052
John Quackenbush @johnquackenbush.bsky.social · 18/06/2025
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
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.
0174
John Quackenbush @johnquackenbush.bsky.social · 23/04/2025
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...
statnews.com
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.
424173
John Quackenbush @johnquackenbush.bsky.social · 17/04/2025
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...
cnn.com
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...
24311
John Quackenbush @johnquackenbush.bsky.social · 12/03/2025
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
NIH funding delivers exponential economic returns — Harvard Gazette
Report finds all 50 states reap gains in patient health, job creation, research resources, business development.
2122
John Quackenbush @johnquackenbush.bsky.social · 07/03/2025
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...
boston25news.com
‘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.
0113