So many emotions right now. I had almost given up hope that this one would get funded. Feeling relief, excitement to do the science, gratitude to everyone on the inside trying to hold NIH together, survivor's guilt. All the things.
Drummond Lab
@drummondlab.bsky.social
The Drummond Lab at UChicago (drummondlab.org). Cell stress, biomolecular condensation of proteins and RNA, chaperones, translation, evolution.
Finally out - our work on high throughput design and characterization of disordered protein sequences 🪱🪱🪱. A long time collaboration with BFFs @alexholehouse.bsky.social and @remenecker.bsky.social, with experimental work led by @trevorbrandt.bsky.social and @karaehunt.bsky.social.
Rational design of disordered proteins for sequence–function investigation - Nature
GOOSE enables the design and testing of thousands of disordered protein region sequences to reveal distinct sequence-to-function relationships.
nature.com
Got the news today that I've been promoted to Full Professor of Biochemistry & Molecular Biology at The University of Chicago. A tremendous honor, one made possible by an incredible group of trainees who I've had the pleasure of working with over the past twenty years. Best is yet to come! 🤓🔬
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...
biorxiv.org
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.
Sequence and chemical specificity define the functional landscape of intrinsically disordered regions - Nature Cell Biology
Langstein-Skora, Schmid, Huth et al. propose that intrinsically disordered region functionality can be driven by the interplay between linear binding motifs and contextual chemical characteristics suc...
nature.com
Alex Holehouse@alexholehouse.bsky.social · 2y agoWe’re pleased to share our substantially updated (more below on that…) version of our manuscript exploring the relationship between conservation in sequence/function for intrinsically disordered regions (IDRs) www.biorxiv.org/content/10.1...
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...
Accurate predictions of disordered protein ensembles with STARLING - Nature
The deep learning model STARLING can generate accurate ensembles of intrinsically disordered regions of proteins using only protein sequence as input.
nature.com
Borna Novak@bornanovak.bsky.social · last yr.Excited to announce the newest member of the flock - STARLING (conSTruction of intrinsicAlly disoRdered proteins ensembles efficientLy vIa multi-dimeNsional Generative models). www.biorxiv.org/content/10.1...
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...
Molecular origins of viscoelasticity in biomolecular condensates
Biomolecular condensates are membraneless organelles that compartmentalize functions in living cells. Formed by the phase separation of biomolecules, condensate
pubs.aip.org
Jerelle Joseph@jerelleaj.bsky.social · 10mo agoIs there a way to directly connect microstructural dynamics of condensates to their mechanical response? In his new pre-print, Pablo presents a “condensate Deborah number” that does just that! www.biorxiv.org/content/10.1...
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...
biorxiv.org
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...
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.
news.cuanschutz.edu
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...
biorxiv.org
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
Nate@nathanieldhess.bsky.social · 7mo agoI am very excited to share our pre-print that was just released on the bioRxiv entitled "Biomolecular Condensates Dictate the Folding Landscape of Proteins" doi.org/10.64898/202... Very grateful for @jerelleaj.bsky.social and the members of the Joseph Group for their support on this project! (1/4)
How titus organizes computational projects: a (very) short presentation. Comments welcome ;)
How titus organizes things - HackMD
tags: bcb298
hackmd.io
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’
(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...
Self-folding laundry
YouTube video by PrakashLab
youtube.com
Faculty position at the department of medicine, University of Chicago. Please share.
Yoav Gilad@ygilad.bsky.social · 8mo ago
🚨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
bioRxivpreprint@biorxivpreprint.bsky.social · 8mo agoOrganelles harbour pH gradients https://www.biorxiv.org/content/10.64898/2025.12.12.694065v1
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...
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...
biorxiv.org
Become a colleague in my department! Applications close in four days, December 15.
Claus Wilke@clauswilke.com · 9mo agoMy 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
Incredible thread
Robert McNees@mcnees.bsky.social · 2y ago"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)
"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)
pubs.aip.org
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...
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...
biorxiv.org
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!
Physics of droplet regulation in biological cells - IOPscience
Physics of droplet regulation in biological cells, Zwicker, David, Paulin, Oliver W, ter Burg, Cathelijne
doi.org
Zwicker Group@zwickergroup.bsky.social · 2y agoWe wrote a review on the "Physics of droplet regulation in biological cells": arxiv.org/abs/2501.13639 Beside the basic #physics of phase separation, we discuss three aspects that separate cellular from traditional droplets:
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/...
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...
science.org
(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...
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...
cell.com