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...

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 ...

biorxiv.org

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...

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...

biorxiv.org

@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.

Joshua Holland@joshuaholland.bsky.social · 5mo ago

I’m sure there are things that are cooler than a school of hammerheads but can’t think of any off the top of my head. 🤿 🦑

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...

China pledges billion-dollar spending boost for science

Funding for national laboratories and important research projects would increase under the government’s plans.

nature.com

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.

Lisa Marie Rhody@lmrhody.bsky.social · 5mo ago

It's stunning how ignorant the DOGE bros were who were sent into agencies. Justin Fox cannot even articulate in his own words what his "present understanding of DEI" is: he can't even formulate a coherent sentence about it. I wouldn't hire him for basic tech support. #NEH youtu.be/jomaMvItnew?...

A second email, this with a more substantial insight about "The Replication Crisis"... 1/5

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.

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...

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...

biorxiv.org

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!

Maud Fagny@maudfagny.bsky.social · 12mo ago

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

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...

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

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...

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.

statnews.com

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...

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...

cnn.com

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...

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

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...

‘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.

boston25news.com