Vaccines, the most impressive public health intervention in medical history, and where we could be headed if there was not efforts to negate truth, facts, and evidence A great, open-access, review and perspective by @scientificdiscovery.dev

Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.

Now published in gigascience: academic.oup.com/gigascience/.... Key messages: SVs are highly enriched in low-complexity/tandem-repeat regions and are harder to call. They behave differently from transposon insertions. Always stratify if you study SVs.

Excited to see this out www.nature.com/articles/s41...! Nonparametric kernel-based tests for spatially variable isoform usage in spatial transcriptomics. So many interesting examples in the CNS and cancer, we're only scratching the surface!

Nature research paper: Uncovering the role of LINE-1 in the evolution of lung adenocarcinoma go.nature.com/4oUHIPb

That’s a wrap on #SABCS25! Thank you to Dr. Lee Schwartzberg for presenting data demonstrating our platform’s ability to detect early stage breast cancer with high accuracy. #AI #RNA #earlydetection Learn more here: www.exai.bio/publications...

Important new, large (N>28,000 women) randomized clinical trial of breast cancer screening: age-based vs risk-based by polygenic risk score, genomics "opportunity to modernize screening" jamanetwork.com/journals/jam...

Even though the highest-profile names in today’s corporate Cambridge are in biotech and software, the influx of defense startups hearkens back to an earlier era — which, in 1922, saw the birth of Raytheon, now synonymous with the old guard of defense contractors. www.thecrimson.com/article/2025...

SCIENCE SAVES LIVES. Overall pediatric cancer survival rate increased from 63% in mid 1970s to 87%‼️between 2015 & 2021. And this isn’t due to supplements, eating better or avoiding red food dye. It’s due to science & industry working together to develop & approve therapies!

JASPAR 2026 is out 🎉 The new release massively expands the TF motif collections and adds a dedicated DeepLearning collection of motifs learned from deep learning models. Database: jaspar.elixir.no Paper (NAR): doi.org/10.1093/nar/... 🧵1/2

579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm

A nice paper on distilling AI-based splicing models into much simpler additive models: "[...] the distilled models achieve this without modeling RNA structure or feature interactions, indicating that [AI]-based splicing models recognize exons primarily through simple additive sequence features."

Abbott Laboratories is nearing a potential acquisition of Exact Sciences Corp, in what would be its largest deal in nearly a decade, people familiar with the matter said. www.bloomberg.com/news/article...

Are you an early-stage graduate student (2nd or 3rd year) or early-stage postdoc based in the US or Canada, working primarily in Drosophila? Would you like to help improve the experience of all trainees working in Drosophila research? If so, read on. (Please repost to reach a broad audience.)

First time on Bsky and first big announcement! I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature. Our manuscript is here: www.nature.com/articles/s41....

Yesterday our co-founder and CSO @babak-a.bsky.social presented at the Biotech-Pharma Statistics Workshop (BBSW) about the powerful combination of AI and cell-free RNA to detect early-stage lung cancer in the blood.

This version of the Persian dish tahchin incorporates common Thanksgiving ingredients. It is deeply savory and buttery, like stuffing, and some may say even better because it has a whole lot more texture coming from the crispy rice that everyone will be fighting over.

Introducing Molview - the ipython/jupyter widget version of nano-protein-viewer🔍:

Neurodevelopmental Outcomes of 3-Year-Old Children Exposed to Maternal Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Utero I hate to say “I told you so…” but nevertheless: I told you so.

Delighted to see our method, PRSformer, at #NeurIPS2025! PRSformer is AI model for population-scale disease-risk prediction from individual genomes. It lays the groundwork for phenome-wide risk prediction. www.biorxiv.org/content/10.1...

Simultaneously comical and tragic.

Are you a PhD student interested in ML and biology or health? Come do an internship with me, @avapamini.bsky.social, Alex Lu, @lcrawford.bsky.social, or Kristen Severson at MSRNE! Applications are due Dec 1: make sure you include a research statement! jobs.careers.microsoft.com/global/en/jo...

What do you do if you are part of the tech-bro uber-rich cabal? Try and become immortal! There are now about a dozen biotech companies in the loosely defined space of "Longevity"

Consumer Reports expressed concern about high levels of lead in some two dozen protein powders, but only with repeated high exposure. Here's what to know before you make your next grocery run.

The strongest predictor of autism is genetics. Data: • If one identical twin has ASD, the other has a 90–99% chance. • Compare that to 31–67% chance for fraternal twins. • Non-twin siblings have ~20% likelihood of ASD, 7-fold higher than general population. 1/

Wow...what? Apple does protein folding now? As the name implies, it is a "simple" and general-purpose transformer-based method, which relies on a non-domain-specific flow-matching objective rather than domain knowledge.

Such an amazing method and such a good study! Have to read it more carefully, but shows huge potential. Combining evolutionary and population genomics + language model is a great idea.

I'm a science journalist for @statnews.com looking to talk with folks who applied to biomedical Ph.D. programs and had offers rescinded earlier this year. What have you been up to since then? You can reach me at [email protected] or via Signal (username jwosen.27). #journorequest

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵

This is a pretty stark reminder that every methods paper needs proper baselines: "We compared five foundation and two deep learning models against deliberately simple baselines for predicting transcriptome changes after single or double perturbations. None outperformed the baselines."

RNA for the win! The once-overlooked black sheep of the macromolecules is slowly yet surely claiming its rightful place and prominence.

🧬 Happy RNA Day! 🎉 A tiny molecule with a massive impact #RNA! From translating genetic code to fighting diseases through mRNA vaccines, RNA is currently at the heart of innovation in science and medicine.

Didn't know Ben Blencowe has a part-time appointment at Crick! Should be a productive collaboration!

Predicting the translation efficiency of messenger RNA in mammalian cells go.nature.com/4mgXR0C

@atulbutte.bsky.social's last paper. He will be dearly missed.

How did the pandemic start? I have avoided publicly commenting on this for 5 years. Here's my take as someone who has no stake at all in the game. gidmk.substack.com/p/pandemic-r...

Summary Table of the massive defunding of biomedical research in the United States www.nytimes.com/interactive/...

Amgen’s MariTide (GLP‑1 agonist + GIP antagonist), a once‑monthly injection, is demonstrating strong efficacy. The mean percentage change in body weight from baseline to week 52 ranged from −12.3% to −16.2%. Impressive results! www.nejm.org/doi/full/10....

‘Huge advances in cancer and rare diseases’: 25 years of the human genome 🧬 Our Director, Matt Hurles, spoke to the Guardian @scienceweekly.bsky.social podcast about the Human Genome Project, and what could be in store over the next 25 years 🎧 www.theguardian.com/science/audi...

Great article on cancer vaccines by @mackenziejem.bsky.social www.mackenziemorehead.com/the-failures...

The first draft of the human genome turns 25 today! 🎂 On 26 June 2000, the UK & US announced the first full map of the 3 billion DNA base pairs that make us human. 🌍 A milestone for humanity, powered by global collaboration. www.youtube.com/watch?v=pnWA... #HumanGenome #ScienceHistory 🖥️🧬

Allowing Netanyahu to drag us into another endless war in the Middle East would be a catastrophic error by President Trump and Republicans in Congress. Every lawmaker needs to ring the alarm against U.S. military action in Iran. Only Congress has the authority to declare war.

I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...

Less than 200 years ago, one in three Dutch children died before the age of five

In case you needed a smile this Tuesday: 10-month-old baby KJ, who received a bespoke gene-editing therapy after a six month scientific sprint - "graduated" from the hospital @childrensphila.bsky.social today and went HOME! YAY SCIENCE! Here's his story: wapo.st/451ZQjT

Wow! What a way to surrender your scientific advantage just so that #MAHA can keep needles away from children. #NIH #NASA #NSF

We're thrilled to introduce PromoterAI — a tool for accurately identifying promoter variants that impact gene expression. 🧵 (1/)

Industry friends, now is the time for MUCH more speaking out on behalf of academic colleagues under duress. Here are core open source methods that many of your products doubtlessly depend on either directly or indirectly (see en.wikipedia.org/wiki/HMMER) being abruptly defunded. Make noise.

My father worked in a tire factory in Appalachia. Friends and family in the military. Used to vote Republican. Got into college on a diversity program for the underprivileged. Ended up a Harvard professor. And now my funding is terminated because we're trying to stick it to the elites.

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.