New preprint. I've been chewing on why bacteria have pangenomes for years. Most species carry a distributed gene pool far larger than any one genome holds. E. coli has ~163,000 rare genes across the species. Each individual cell carries about 5,000. Why? A 🧵👇

Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇

(3/n) We expanded our studies from 2 to 5 cell lines during revisions. Surprisingly, 2 distinct behaviors: U2OS, RPE cells show straight power law MSD with a~0.3 across all time scales. mESCs, RH30 cells do not show power law behavior at all, but steepen over time. Dynamics-->cell specific

Our linker histone H1 paper is featured on the cover of the April 10 issue of #ScienceAdvances. www.science.org/doi/10.1126/... A molecular dynamics simulation of nucleosomes and linker histone H1, with single-H1 trajectories (background). 🎉 Full cover caption: www.science.org/toc/sciadv/1...

Median survival went from 6 months to 13 months. It may not sound like much, but for metastatic pancreatic cancer, this is big, IMO. We finally have something solid to build on in this field.

My first, first author paper is now on #ScienceAdvances ! Linker histone H1 is a liquid-like "glue" condensing chromatin, which revises textbooks! 📖✨ science.org/doi/10.1126/sc… Huge thanks to @kazu-maeshima.bsky.social , for supervision. Amazing collab with @rcollepardo.bsky.social ’s group! 1/

📽️ G&D Tapes 📽️ G&D Author, Tuo Zhang, tells us about their new study showing how embryonic stem cells attain a diapause-like state, and can maintain their pluripotency and metabolic dormancy. Read more here: ➡️ https://genesdev.cshlp.org/content/40/5-6/319.full The Rockefeller University

⚡This Wednesday! 🥁We've got two exciting chromatin talks coming up from @almassalha.bsky.social and @carmeloferrai.bsky.social 🐣If you haven't registered for the series, please register and join us: us06web.zoom.us/webinar/regi...

When gene expression goes wrong, it can cause abnormal cellular growth, cancer, & more. HHMI Investigator Michelle Wang (Cornell University) & collaborators have discovered that nucleosomes—long thought to be obstacles to gene expression—actually help the process work more smoothly. bit.ly/4q9xA6e

A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists! www.nature.com/articles/s41...

Damn this is cool: www.nature.com/articles/s41...

Motivational video for #MigrationMovieMonday. A persistent 4T1 breast cancer cell squeezing itself through a tight constriction despite undergoing repetitive nuclear envelope rupture. Credit: Kristen Nedza @weillinstitute.bsky.social

Pretty neat paper: www.biorxiv.org/content/10.1...

Friday, Nov. 21 @ 12pm CT, Wendy Bickmore, PhD presents the Monthly Seminar on Physical Genomics live on Zoom: "Chromatin Folding And Gene Activation: From The Nucleosome To Transcription Hubs" Registration is free. Join us! tinyurl.com/f9njvnyu #chromatin #genomics #northwestern #biology #dna

We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing: a 🧵 1/n Drain: arxiv.org/abs/2511.04820 Strain: direct.mit.edu/qss/article/... Oligopoly: direct.mit.edu/qss/article/...

umm... was there an update to ChatGPT that turned it belligerent?

A reminder:

Still beta-testing the app that helps people plan science, make it super clear, design their todos, and write a first version of the paper. Feeling overwhelmed by the countless aspects of doing science? Try this (for free): planyourscience.com

New CPGE research in Advanced Science describes a language hidden in the genome, beyond the DNA sequence. The geometric code may help cells “remember” how to create and preserve memories, functioning like a network of living computers. #chromatin #dna www.mccormick.northwestern.edu/news/article...

Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome - Almassalha - Advanced Science - Wiley Online Library advanced.onlinelibrary.wiley.com/doi/10.1002/...

Generative AI sometimes acts as a moving mirror - it reflects my thoughts back to me from different angles to flesh out a picture I've stared at for a long time

Excited to share our paper on dynamics of microcompartments during M-to-G1 is now published in @natsmb.nature.com www.nature.com/articles/s41... Compared to biorxiv, published includes new analysis from James Jusuf and Viraat Goel (from @andersshansen.bsky.social lab) on transcriptional spiking

all discourse aside, there is one machine with consciousness. it's printers. they are alive and conscious and they hate you and they'd take your arm clean off if you let them. never trust a printer.

What an amazing assay. DAF-seq, the evolution of Fiber-seq from the Andrew Stergachis group, using the @pacbio.bsky.social platform: www.biorxiv.org/content/10.1... This will revolutionise our understanding of transcriptional regulation and functional non-coding variants.

Christopher Nolan movies live rent free in my head

Everytime the chart says Billroth all I think about is LoTR

New work from my lab with the Brown lab on how genome folding changes during motor neuron maturation, and how this process goes awry in ALS motor neurons. Led by Dr. Ozgun Uyan. www.biorxiv.org/content/10.1...

I don't really encounter transposable elements (or Arabidopsis) in my clinical day-to-day, but this is awesome: www.science.org/doi/10.1126/...

"AI has generated a genome for the first time" eu.36kr.com/en/p/3472136... www.biorxiv.org/content/10.1...

How do LMNA mutations cause dilated cardiomyopathy (DCM) and other #laminopathies? In our latest preprint (doi.org/10.1101/2024...), led by the amazing Noam Zuela-Sopilniak and Julien Morival, we show that cardiomyocyte-specific lamin A/C depletion causes severe DCM, consistent with other studies.

Bioinformaticians / computational biologists take note - know where you should take your OS tool chain from and do not introduce backdoors.

EpiSci - Hi there! Our review “Mechanotransduction in stem cells” is finally published. With @carstenschulte4.bsky.social we provided a comprehensive picture, that aims to cover the whole mechanotransductive pathway from the cell microenvironment to the nucleus. 1/3 pubmed.ncbi.nlm.nih.gov/38729084/

paper revisions irl

the drosophila genome is weird

New preprint from the lab! Please check it out. 🚨 Have you ever wondered how cells decide when it’s time to divide? So did we! www.biorxiv.org/content/10.1...

🧩 Also highly relevant: a modeling study from Bin Zhang group predicts condensed euchromatin domains with active protrusions. Perfectly complementary to our findings! 3 www.biorxiv.org/content/10.1...

Is euchromatin really “open”? Our new study @bioRxiv suggests otherwise. Using super-resolution imaging @shiori-iida.bsky.social‬ @masaashimazoe.bsky.social reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing. www.biorxiv.org/cgi/content/...

Hot damn, let's goooooo!!! www.biorxiv.org/content/10.1...

That I'm listening to Goo Goo Dolls and coding at 10pm on a Saturday says a lot about my life choices. Shout out to the 4DN and Encode for killer public data

New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards. We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...

Duodenal ulcers. Not even once man

Ballpark, I've likely lost ~3 years of my waking life on 2-factor authentication and verifying I'm a human

paper with @erbash.bsky.social now published in @narjournal.bsky.social academic.oup.com/nar/article/...

Fifty Years of Fractals daily.jstor.org/fifty-years-...

I’m excited to highlight our latest paper, just published in Cell 🎉 We report the existence of a previously uncharacterized signaling pathway that is responsible for activating cell death upon loss of gene expression. 1/n 🧪 www.cell.com/cell/fulltex...