🚨first Bartman lab preprint! it's an LC-MS method to measure "total Coenzyme A" (sum of all acyl-CoAs). this will let us study coA synthesis flux using heavy-isotope tracing! huge congrats to first author Amelia Taylor and star coauthor @mzspectrum.bsky.social ! www.biorxiv.org/content/10.6...

If you know a graduating undergraduate looking for the chance to spend 1-2 years in a lab before graduate school, we're hiring! Our lab explores morphogenesis, defining how the cell adhesion & cytoskeletal machinery work together to allow cells to change shape & move tarheels.live/peiferlab/ 1/n RT

Insightful summary of an extraordinary person being extraordinarily fired: "you don't silence a woman of color who raised concerns about racism by silencing her...The fingerprints are distributed perfectly across the system." www.linkedin.com/pulse/uclas-...

When the tech companies built their entire empire on algorithmically pushing what people want to hear to confirm their biases, why would they not do the same with LLMs

Well here's an answer to a question I hadn't thought of asking www.nature.com/articles/s41...

@mukherja.bsky.social work on RNAPII clusters is in print today: www.nature.com/articles/s41... Congrats! TLDR: RNAPII clusters represent transcriptonally engaged molecules at single genes, not super-stochiometric assemblies. Please check it out and see the the thread below for a summary.

There is accumulating evidence that sperm miRNAs function to regulate embryonic gene expression and transmit inherited phenotypes to offspring but how does this work since sperm cargo is massively diluted in the egg upon fertilization. Here we directly address this ? www.biorxiv.org/content/10.6...

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social doi.org/10.1016/j.ce... Read the thread👇 for the highlights of our findings.

Free markets are supposed to select for the good businesses and kill the bad. But, the hyper efficient capital markets allow transient feasting & abandoning the dying carcass. What we have now is a bunch of parasites on the economy evolving unbridled virulence. Now the viruses want to rule.

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n doi.org/10.64898/202...

🚨New preprint! We built a cell-free genomics platform (GATO-seq) to probe transcriptional regulation and discovered a “super pause” sequence that triggers a new Pol II active-site conformation. Huge shout-out to @robertovn.bsky.social for pulling off this monster of a project. tinyurl.com/superpause

Now in print at ACS Synbio! Introducing Aviatar: a concept for inducible translocation to any cell compartment using only a 1-component probe pubs.acs.org/doi/10.1021/...

Warren Center faculty affiliate Greg Ridgeway has developed and tested a statistical model using real-world data that could help police departments take steps to prevent future excessive force. penntoday.upenn.edu/...

Well that's cool Source: Nature search.app/FLn5P

This is how we first teach chirality to our undergrads !

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

Since there are so much happenings that I can't breath, ill just have to take it out on this little irritant. What makes a workshop "prestigous" ? Does attending this give trainees prestige? Do organizers give themselves prestige for running it? Can we stop using language like this?

Every week, Nature publishes yet another breathless puff piece about some AI startup, based only unpublished claims from the company and interviewing only those who work there. How can the leading scientific journal publish piece after piece that would make Kevin Roose blush? I think it's that...

and the winner of the "2025 best thing on Internet" has just arrived neal.fun/size-of-life/ @carlbergstrom.com

I just finished my 28th yr of teaching grad compbio. Following the inevitable trend, a 3rd of the course is now Deep Learning (DL). One activity we did was a deep dive into the AlphaGenome pre-print (www.biorxiv.org/content/10.1...). Question is, how do we evaluate it as a science paper? 1/n

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...

Check out this terrific thread by first author, @sungyalin.bsky.social, whose creativity, bravery, exactitude, and perseverance made this project a reality.

How to keep in step when your (protein) partner speeds up… Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection. Congrats to whole team! www.science.org/doi/10.1126/...

Open faculty position (Assistant or Associate) in UW Medical Genetics. As you might expect, faculty often end up also interacting with Genome Sciences, so we're hoping for some great prospects! Note the clinical requirements for the position. apply.interfolio.com/176466

I feel irrationally annoyed at journals that ask for numerical scores and/or structured review responses. Assessing the reviews themselves is the job of the editors. I will refuse all review requests from journals who use such rubric devices for scientific papers as if they were term papers.

So awesome to have this great paper from Sam Reffsin and Sara Cherry out! In it, we use retrospective clone tracing to show that there are particular single cell states that are more susceptible to viral infection (both SARS-CoV-2 and flu)! www.cell.com/cell/fulltex...

Scientific breakthroughs are rarely unique; someone else would’ve made them soon enough. But when prominent scientists cause harm, that harm isn’t inevitable; the world might simply have been better had the harm not been inflicted. liorpachter.wordpress.com/2018/05/18/j...

After almost 30 years, the Tree of Life Web Project has been retired as an actively growing site. It will be unavailable until we can build a static site that contains its final content. More details at subulatepalpomere.com/2025/11/02/t...

Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here: www.biorxiv.org/content/10.1...

Our paper (Brieuc Lehmann is the first author) is now online in Genetics. academic.oup.com/genetics/adv...

To contribute to common knowledge :-) I too have been integrating AI tools closely into my research. This paper arxiv.org/abs/2507.09683 with @mkearnsphilly.bsky.social and Emily was my first experiment with this, and it was just accepted to SODA. I'll describe the process in thread.

Check out this new Levine-Lampson collaboration, led by the talented Hyuk-Joon Jeon. We explored the consequences of inheriting long telomeres from dad and short telomeres from mom. Or the reciprocal. Turns out, parent-of-origin matters (in mice, at least). authors.elsevier.com/c/1loW-3QW8S...

Excited to share a new method developed from my group thats published at Genome Biology. This was an amazing effort by my grad student Linh @linhngk.bsky.social. We developed Topsicle, a method that analyzes long read data for telomere analysis and length measuring. doi.org/10.1186/s130...

We've been busy in the lab, and I'm super proud of the team right now. These three papers are great examples of "Night Science", creative, curiosity driven work at its best! All are works in progress. www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

The #Drosophila Dscam1 gene generates 10000s of isoforms, but only a small fraction supports neuronal functions. This study shows that #fitness & #immunity are the likely primary evolutionary drivers of Dscam1 isoform diversity in #arthropods @plosbiology.org 🧪 plos.io/4gp8cWd

SINGER, our ARG inference method, is finally published and freely available online: doi.org/10.1038/s415... It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...

Pretty amazing observation in nature rdcu.be/eEebw

Our latest: We developed a chemo-optogenetic system for precise spatiotemporal control of morphogen production. Using dual light + small molecule control of Sonic Hedgehog production, we recapitulated neural tube patterning in vitro & measured spread of Shh 🧵 www.sciencedirect.com/science/arti...

The 2025 Cold Spring Harbor Labs, Single Cell Analysis Meetings are here. This is the longest running single cell meeting, started in 2009. Please register and send an abstract! with streetslab.berkeley.edu ‪@saukaspengler.bsky.social‬ meetings.cshl.edu/meetings.asp...

Here’s some Gemini gaslighting: • giving a wrong answer to a puzzle • giving Python code that could test its claim • asserting it obtained results from the code supporting its claim • but when I ran the code myself, it showed the claim was false. g.co/gemini/share...

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! 🧵

I have some BIG NEWS to share today! Today I begin my next adventure as Chief Editor of Nature Biomedical Engineering!! (a thread) @natmethods.nature.com @natbiomedeng.nature.com @natureportfolio.nature.com

Happy to see our latest work out in @molbioevol.bsky.social. We revisit the evolution of 5-methylcytosine across neglected eukaryotic supergroups, establishing an ancestral repressive role silencing genome invaders, both transposons and viral elements👾: academic.oup.com/mbe/advance-... 🧵 1/7

My talk from this year's probgen is finally out. Where do linear mixed models and random effects come from? They emerge from *mutations* on Ancestral Recombination Graphs.

Discovery of a pH sensor that regulates inflammation. Zhou and Medzhitov provide a mechanistic tour-de-force in defining how BRD4 links changes in pH to inflammatory gene expression. Kudos to the authors on this exciting finding. www.sciencedirect.com/science/arti...

Wowee! Super-resolution stimulated X-ray Raman spectroscopy | Nature share.google/Mdn4Z0ddIy2t...

My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful. It’s available on Amazon: tinyurl.com/mx2hewen

At #ICML 2025 to present our paper on single cell lineage tracing. Being one of "big 3, AI/ML", confs, I guess this is the ground zero of current AI. I'll have more to say about my obs, but one thing---it certainly is a lot more posh than your usual bio meetings. acrobat.adobe.com/id/urn:aaid:...

Happy to share my postdoc work—our new preprint is out! 🧬 It’s been a privilege to lead this project. I'm immensely grateful to Anton @golobor.bsky.social for being such an inspiring and supportive supervisor. Also truly thankful to @danielgerlich.bsky.social for his guidance and collaboration.