thinking a lot about this cartoon this week...

WHY DID I AGREE TO THOSE REVIEWS??

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...

Yes Alex! This is such a beautiful idea and result. Congratulations on having it done-done. Instant classic.

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 🧵

CU Anschutz Recruits National Leader to Launch Functional Personalized Medicine Initiative CU Anschutz welcomes Alice Soragni to launch a Functional Personalized Medicine Initiative using rapid tumor organoid testing to guide treatment decisions.

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 things - HackMD tags: bcb298

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

Painted portrait of Isaac Newton, who is looking slightly to his left. He has a long, wolffish face with a pale complexion and red lips. Newton’s hair is shoulder length and graying - the painting was made when he was 46 years old. He wears a dark coat and white shirt with a frilly collar.

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

Self-folding laundry YouTube video by PrakashLab

(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

No molecular evidence for Muller's ratchet in mitochondrial genomes Muller's ratchet predicts that non-recombining genomes can accumulate deleterious mutations, though molecular evidence for it is rare. Previous studies have tried to detect ratchet-like behavior in mi...

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)

The discovery and patterns of the underlying long-standing mild-effect mutator alleles in S. cerevisiae populations Most mutations are neutral or deleterious, and mutator alleles that increase the mutation rate of an organism are considered rare and short-lived. Here, we report a genomic signature consistent with t...

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!

Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

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/...

Incredible work—congrats Josh and the whole team! What a way to begin! 🤩

Disparate leukemia mutations converge on nuclear phase-separated condensates Mutant NPM1 and various leukemia oncofusions form biophysically indistingishable nuclear condensates, termed C-bodies, which orchestrate leukemogenic gene expression. These findings consolidate divers...

(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.