New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/ www.biorxiv.org/content/10.6...

Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now? www.nature.com/articles/s41... More functional data, many thousands of words removed, and a few other updates from last year's preprint.

Papers are like buses... You wait for ages, then two come along at once. Huge congrats to @bornanovak.bsky.social and @jefflotthammer.bsky.social for pushing and driving every aspect of this work, preprinted ~1 year ago to the day (Friday before BPS), now published! www.nature.com/articles/s41...

Pablo’s work on “condensate Deborah numbers” is now out in #JCP!! Selected as Editor’s Pick and featured as a #Scilight pubs.aip.org/aip/jcp/arti...

I am excited to share the main piece of work from my PhD! In this paper, we investigated the propensities of distinct transcripts in associating with biomolecular condensates, mainly focusing on how heat-induced mRNAs escape condensation and are properly translated. www.biorxiv.org/content/10.6...

Long in the making, but happy to present the Chlamydomonas chlororibosome! Cryo-ET🔬reveals a large new domain on the small subunit, built from multiple extensions in conserved ribosomal proteins. bioRxiv 📖: shorturl.at/q44tG This suggests greater chlororibosome diversity than expected! 1/n 🧵

Happy to share this new, very intentional chapter. I have left UCLA after 14 years to join the University of Colorado Anschutz as Professor of Biomedical Informatics and Neurosurgery and the inaugural Marsico Chair in Excellence in Functional Precision Medicine/n news.cuanschutz.edu/dbmi/cu-ansc...

Out on the #bioRxiv in collaboration with @luciastrader.bsky.social, we probe the molecular basis for thermoresponsive condensation in plants! Work led by Sunita Pathak and @ananyac2000.bsky.social 🥳🥳 www.biorxiv.org/content/10.6...

How does protein folding change inside biomolecular condensates? Our new preprint put forwards a framework for predicting this!! 🥳🥳🥳🥳 work by the talented @nathanieldhess.bsky.social

How titus organizes computational projects: a (very) short presentation. Comments welcome ;)

Physicist and mathematician Isaac Newton was born #OTD in 1643. Newton revolutionized our understanding of mathematics, mechanics, gravity, and optics. Later in life he served as warden of the Royal Mint, reforming currency and foiling counterfeiters. 🧪 🔭 ⚛️ 🪙 Portrait: B. Bramley, after G. Kneller

Physicist Leo Szilard, in a short science fiction story from 1948, describing how to retard science by making the funding application longer and harder than the proposed research - now called the ‘Szilard point’

very unusual - a tRNA regulated anion channel

(1/n) What if you never had to make your bed? What if your laundry could fold itself? Folding is everywhere around us - but did you know that folding flat sheets are at the ❤️ of diversity of shapes in the animal world - since 500 million years ago. Our latest work: www.youtube.com/watch?v=nudC...

Faculty position at the department of medicine, University of Chicago. Please share.

🚨Preprint 2/2: Several studies implicate condensates in RTK fusion onco-signaling. So we were surprised to find that condensates are entirely dispensable😮(!). A study from proteins to mice, by dynamic duo @davidgonzmar.bsky.social and @trmumford.bsky.social. www.biorxiv.org/content/10.6... 👇

🚨New preprint(1/2)! We show that RTK fusion oncoproteins broadly suppress EGFR signaling. How? Sequestration of adapters as the shared principle. Led by superb PhD student Carol Gao. www.biorxiv.org/content/10.1... Implications for drug tolerance/resistance, and includes one big surprise🫧.👇

Organelles do NOT have a single uniform pH. And if you think they must, because “protons diffuse fast,” this paper is for you. A thread on why that assumption is wrong; and what we found instead. 🧵 1/n

Have you ever wondered: just how strong *is* the evidence for Muller's ratchet on mtDNA? Well, wonder no more! (Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social) "No molecular evidence for Muller's ratchet in mitochondrial genomes" www.biorxiv.org/content/10.6...

Become a colleague in my department! Applications close in four days, December 15.

Incredible thread

"I, at any rate, am convinced that He is not playing at dice." Einstein sent a letter to Max Born #OTD in 1926, in which he gave his oft-quoted objection to the probabilistic interpretation of the wavefunction in quantum mechanics. 🧪 ⚛️ You may be surprised by where this is headed. (1/n)

New preprint with @pyjiang.bsky.social and @kelleyharris.bsky.social! The discovery and patterns of the underlying long-standing mild-effect mutator alleles in S. cerevisiae populations www.biorxiv.org/content/10.1...

Our review on the physics of phase separation in cells has been published by Rep. Prog. Phys. 🎉 doi.org/10.1088/1361... We hope that the text and citations are helpful for anyone interested in physical descriptions of condensates in cells!

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

(2/10) We found that disparate drivers of acute myeloid leukemia (AML) – including NPM1c, KMT2A-r, and nucleoporin oncofusions – form nuclear condensates with a shared set of proteins including XPO1 and MENIN to drive leukemic gene expression (e.g. HOXA). www.cell.com/cell/fulltex...

(1/10) How do diverse leukemia mutations converge on the same molecular program? In #RibackLab first manuscript @cp-cell.bsky.social, collaboration with @goodell-lab.bsky.social shows that disparate mutations rewire shared protein networks to form nuclear condensates called C-bodies.

My department at UT Austin is looking to hire an Assistant Professor in Evolutionary Biology, broadly defined. Feel free to reach out to me with any questions you may have. apply.interfolio.com/177547

Happy that our paper just got accepted. Also happy that it's been available as a preprint for more than 1.5 years on @biorxivpreprint.bsky.social, updated 3x with new experiments, with >7,500 full-text downloads and 20 citations. Before publication. www.biorxiv.org/content/10.1...

A wonderful collaboration between my lab and Andy Ellington and Edward Marcotte here at UT. We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)

Please read the thoughtful Blog that @richardsever.bsky.social and the @openrxiv.bsky.social team wrote on integrating pre-prints with AI review openrxiv.org/enabling-rev...

Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n openrxiv.org/enabling-rev...

Slightly less snarkily, manuscript review culture varies a lot. If a person trained in GlamHoundery reviews for a real journal they often are slightly out of step in their demands. So an important editorial function is to enforce the culture of their journal. By saying “nah don’t do all that”.

As an author, I frequently encounter reviewers who should be overruled -- gatekeepers. My main complaint is has been that many editors do not have the confidence/expertise to do so (but some do). a) Thank goodness for preprints, b) I review with the expectation that the paper will be published.

“It’s too easy to be swamped by a short-term political and social environment.” Neil Shubin tells “Babbage” why he remains optimistic about science in America

More pictures of the brilliance that is (lab manager) Aida de la Cruz with her creation.

Our photoswitchable HaloTag is out in Angewandte Chemie @angewandtechemie.bsky.social ! We now also show that this system can be used to control emitter density in SMLM. Congrats to Franzi, Bego, and our amazing collaborators. Check it out: onlinelibrary.wiley.com/doi/full/10....

Why do complex traits differ in their genetic architecture? In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits. Thread: journals.plos.org/plosbiology/...

At this point, I'm just writing grants as a matter of personal artistic expression. I don't expect anything to come of it.

Thoughts from our own Tom Rapoport on the role of basic science in curing disease. magazine.hms.harvard.edu/articles/rev...

NIH Study Sections are on hold...again. drugmonkey.wordpress.com/2025/10/13/n...

My HPLC was definitely overlooked www.nature.com/articles/d41...

AI in biology: "I read about some new computational method...get excited because it’s exactly what I need...I try the method...Most of the time things don’t work...I have seen this play out so many times my default assumption is nothing is going to work" blog.genesmindsmachines.com/p/we-still-c...

"Lacking even any particularly useful theory of emergence, and confronted with the obvious wild variety of emergent phenomena, it seems likely that predictive theories of biology are unknowably far off" via @dadrummond.art open.substack.com/pub/clauswil...

Today my @nytimes.com colleagues and I are launching a new series called Lost Science. We interview US scientists who can no longer discover something new about our world, thanks to this year‘s cuts. Here is my first interview with a scientist who studied bees and fires. Gift link: nyti.ms/3IWXbiE

Very insightful reconsideration what Stress Granules might actually be good for! Going back to the fundamentals & questions arising from Susan Lindquist's and Nancy Kedersha's work. Amazing talk & scholarship by @drummondlab.bsky.social! youtu.be/caAPToh8v0Q

Humbled to announce that we received a New Innovator award. I thank the NIH’s civil servants for their hard work during a stressful funding cycle. I thank the leadership (and chair, Marc Diamond) at UTSW for betting on my lab’s high risk, high reward research. www.utsouthwestern.edu/newsroom/art...

Reposting, submit soon!

The most important paper in evolutionary biology I'd never heard of: 1/ www.sciencedirect.com/science/arti...

UChicago Microbiology is searching for tenured or tenure-track faculty working in host-pathogens interactions, viral and bacterial pathogenesis, and emerging infectious diseases. Come join our vibrant Department! microbiology.uchicago.edu Apply here apply.interfolio.com/174404