SARS-CoV-2 did not come from a lab. There is no evidence pointing to laboratory origins. There’s been a massive disinformation campaign to convince the public otherwise. It’s scary how effective that campaign has been.
Jeffrey Townsend
@jeffreytownsend.bsky.social
Elihu Professor of Biostatistics @yalesph.bsky.social--Evolutionary biology of cancer, infectious disease, and fungi; sometimes running.
Just published in Journal of Translational Medicine: we investigate mutations driving colon and rectal adenocarcinomas. Deconvolution into mutational supply and selection motivates anatomical specification with BRAF and PIK3CA hotspot status. 🧪 link.springer.com/article/10.1...
A comparative mutation–selection reanalysis of colon and rectal adenocarcinoma highlights PIK3CA variants and BRAF V600E - Journal of Translational Medicine
Journal of Translational Medicine -
link.springer.com
The Trump Administration is sending billions to Amazon, Apple, Walmart, and other big corporations to refund them for Trump’s tariffs. American households were estimated to lose over $1,000 to tariff price hikes. Here's an idea: refund working families before big business.
just out in Frontiers in Genetics: "Evaluating the prognostic value of mutational signatures in small-cell lung cancer" www.frontiersin.org/journals/gen... —a scientific publishing story 🧪: from a curious student, to an investigation, to a journal inquiry, to a new study.
Frontiers | Evaluating the prognostic value of mutational signatures in small-cell lung cancer through reference-based signature assignment and continuous activity analysis
BackgroundSmall-cell lung cancer (SCLC) is an aggressive malignancy with poor survival outcomes. Biomarkers that reliably capture tumor mutational burden (TM...
frontiersin.org
Cannot be more excited about the lineup for the inaugural Function of Evolving Systems GRC conference I am co-organizing with the amazing Joy Bergelson. Less than a month away: August 9 - 14, 2026. Still a few spots left! And do check out the amazing list of speakers: www.grc.org/function-of-...
2026 Function of Evolving Systems Conference GRC
The 2026 Gordon Research Conference on Function of Evolving Systems will be held in Waterville Valley, New Hampshire. Apply today to reserve your spot.
grc.org
Thank you to #SMBE2026 organizers for this great meeting in København! See you next year for #SMBE2027 in Québec City, Canada! smbe2027.org
So excited for #smbe2027 to occur in my hometown, and grateful to @christianlandry.bsky.social, @naubinhorth.bsky.social, the LOC and the student committee for jumping in again! It will be an amazing opportunity for members of the lab to network, learn and share our work!
has accessed the office transcription of Scott Jennings' call to Mitch McConnell: open.substack.com/pub/jeffreyp...
Transcription of Scott Jenning's call to Mitch McConnell
Jennings:
open.substack.com
@multitarga.com was featured in this Yale School of Public Health piece on community and health innovation. Our Multi-Targeted Primer reagents aim to make high-quality RNA-seq more focused, efficient, and accessible across health, agriculture, and surveillance. ysph.yale.edu/news-article...
Tumor driver co-mutation patterns are not conclusions—they are hypotheses. Mutual exclusivity/co-occurrence in cancer genomes become biologically meaningful (i.e. informative of epistasis) only when evaluated in the context of mutation-rate heterogeneity. 🧪: onlinelibrary.wiley.com/doi/10.1002/...
Empowering Inference of Epistasis on the Basis of Mutual Exclusivity, Co‐Occurrence, Functional Antagonism and Synergy in ERK‐Pathway Oncogenes
Click on the article title to read more.
onlinelibrary.wiley.com
Working at the intersection of AI, LLMs, genomics, and evolution, I agree: AI accelerates, but expertise drives. The real question is no longer “Can you use AI” but “Do you know when it’s right—and when it only looks right?” Excellent read: www.nature.com/articles/s41...
prepR4pcm: An R Package for Preparing Data and Trees for Phylo- genetic Comparative Methods https://ecoevorxiv.org/repository/view/13554/
8/n As proof of principle, we used scarless CRISPR-cas9 genome-editing to reconstruct evolutionary intermediates for one candidate, Trio (flybase.org/reports/FBgn...), that harbors a cluster of three putatively adaptive amino acid substitutions unique to the D. melanogaster lineage.
FlyBase Gene Report: Dmel\trio
FlyBase: a database for drosophila genetics and molecular biology
flybase.org
7/n Using genome-wide population genetic approach based on the McDonald-Kreitman test framework (called MASS-PRF, Zhao et al. 2017 10.1093/molbev/msx213, @jeffreytownsend.bsky.social), we identified dozens of potentially experimentally tractable candidate proteins.
2/n Intramolecular epistasis is increasingly recognized as an important feature of adaptive protein evolution. But how do adaptive amino acid substitutions actually accumulate? Do epistatically interacting substitutions fix sequentially, or do favorable combinations assemble before fixation?
1/n Check out our new paper, spearheaded by @fborne.bsky.social, just out in PLoS Genetics doi.org/10.1371/jour....
Epistasis among clustered lineage-specific amino acid substitutions in the Drosophila Trio protein
Author summary Proteins fold into three-dimensional structures that are essential for their function. Because these structures depend on interactions among amino acids, the fitness effect of a mutatio...
doi.org
visited our new "blue" Lincoln Monument reflecting pool.
Politics is entitled to determine the topics and targets for public investment of funds. But the science to be done to accomplish those goals is best decided on by scientists. White House seeks to tighten political oversight of grantmaking | Science | AAAS www.science.org/content/arti...
White House seeks to tighten political oversight of grantmaking
Sweeping proposed rule, now open for comments, would also restrict foreign collaborations and remove federal funding for open-access fees
science.org
I am recruiting PhD students for my new lab housed in the Sam Noble Museum at University of Oklahoma! If you are interested in fish macroevolution, geometric morphometrics, specimen-based research & phylogenomics please reach out. More info here: fishdiversitylab.weebly.com Please share widely!!!
New @plos.org-GENETICS: Borne, Taverner & @pandolfatto.bsky.social use MASS-PRF to detect clustered, lineage-specific amino-acid substitutions in Drosophila proteins—then beautifully validate one case in Trio. journals.plos.org/plosgenetics... 🧪 #EvoDevo
Every cancer case can be associated with a genetic “fingerprint” shaped by both inherited vulnerabilities and acquired mutations. @yalemedicine.bsky.social: an open-access tool to quantify pathway-level disruption and advance personalized cancer risk assessment. medicine.yale.edu/news-article...
Calculating Cancer Risk Through the Genetic Fingerprints of Tumors
A new tool offers insights into understanding why every patient has a unique cancer journey.
medicine.yale.edu
They are indeed. Source: literally me (and a whole bunch of other authors from multiple datasets)
You Might Think of Shrimp as Bugs of the Sea. But a Remarkable Discovery Shows the Opposite: Bugs Are Actually Shrimp of the Land
A recent study suggests that insects branched out from crustaceans on the tree of life
smithsonianmag.com
Older adults benefit from COVID-19 vaccine protection that keeps pace with waning immunity. Nursing home resident data show that antibodies decline substantially over the 12 months after vaccination, supporting biannual vaccine updates for adults 65+. www.sciencedirect.com/science/arti...
Antibody responses to SARS-CoV-2 vaccine in nursing home residents support a Bi-annual update schedule
The COVID-19 pandemic has greatly affected nursing home residents (NHRs), a vulnerable group with high rates of illness and death. While vaccination i…
sciencedirect.com
· #mRNAvaccine · The advent of mRNA vaccines against SARS-CoV-2 in 2020 changed the course of the COVID-19 pandemic. Now, the Nobel Prize–winning technology is being adapted to fight cancer, with mRNA vaccines in clinical trials for melanoma, small-cell lung cancer and bladder cancer, among others…
How mRNA cancer vaccines still destroy tumors when a key immune cell is missing
The advent of mRNA vaccines against SARS-CoV-2 in 2020 changed the course of the COVID-19 pandemic. Now, the Nobel Prize–winning technology is being adapted to fight cancer, with mRNA vaccines in clin...
medicalxpress.com
The U.S. could cut outpatient prescription drug spending by $184 billion per year—a 51% reduction—by aligning prices with those in peer high-income nations. Drug affordability is a policy choice, not an inevitability. ysph.yale.edu/news-article...
Yale study: U.S. could save $184 billion by aligning drug prices with peer nations
Researchers at the Yale School of Public Health estimate that the United States could reduce its annual spending on outpatient prescription drugs by $184
ysph.yale.edu
This is how we do it. 1. Win majorities in the House and Senate. 2. Impeach and remove DJT 3. Impeach and remove JDV 4. Democratic Speaker of the House becomes President. 5. Prosecute, convict, and imprison every one of DJTs cabal 6. Send a message to the world that we can throw out the trash
BREAKING: Victor Orban has CONCEDED to Magyar www.theguardian.com/world/live/2...
Hungary election live: Polls in Hungary close in tightly fought election after 16 years under Viktor Orbán
Prime minister has been trailing in the polls to Péter Magyar in race that could have repercussions for Europe, the US and Russia
theguardian.com