Absolutely outstanding op ed piece on the importance of US universities standing firm in this moment. Also covers the various tools at their disposal to do so. arstechnica.com/culture/2025...

Our latest work indicates that termination of paused RNA polymerase is its most likely fate, while attempting to reconcile disparate estimates of relative rates and pause residency times from previous studies: www.biorxiv.org/content/10.1...

👇🎯 The public isn't going to understand this, unless the presidents of R1 universities around the country <loudly> & <collectively> get out into the public square & start explaining this & calling out the existential threat to the entire 🇺🇸 university system. The silence is deafening right now.

The admin plans to pick off universities 1-by-1. Instead, we have to come together. Universities need to stand together, fight in court, and take our case to the public by explaining the importance of what we do.

Yikes. That Trump economy is really starting to shine.

Slava Ukraini! 🇺🇦

Accurate de novo transcription unit annotation from run-on and sequencing data @charlesdanko.bsky.social www.biorxiv.org/content/10.1...

My hot take: Universities and medical centers need to get *MUCH* better at outreach and explaining the benefits of funding independent research to the public.

www.biorxiv.org/content/10.1... Another genomic FM benchmark 💀

I wanted to write briefly about a very pleasant experience we recently had coordinating and collaborating closely on competing publications with 2 other teams. 1/

We wrote an opinion article inspired by the recent exciting reports on the sequence determinants of TSS selection + old observations on TFs activation domains. More posts on this soon! Q-rich activation domains: flexible ‘rulers’ for transcription start site selection? www.cell.com/trends/genet...

Brief thread on our opinion article "Q-rich activation domains: flexible ‘rulers’ for transcription start site selection?". Transcription people are surely aware of the important reports on the DNA sequence determinants of start site (TSS) selection in the human genome that came out this year. 1/15

Latest from our lab: Training sequence-to-function models using matched genome sequence and functional data improves performance in variant interpretation tasks. Congrats to Adam He and Nathan Palamuttam on getting this out. www.biorxiv.org/content/10.1...

RNA polymerases reshape chromatin and coordinate transcription on individual fibers www.biorxiv.org/content/10.1...

I just sent my congressman a strong letter supporting Ukraine aid. Please consider doing the same!

Beautiful work from Effie Apostolou' lab. www.nature.com/articles/s41...

Important thread.

Let's say is clearly: $474K is what the modular budget cap would be if it kept pace with inflation over 25 years.    If you're sticking to $250K these days, how much is that equivalent to in 1998 dollars? About $132,000.

Antisemitic threats are disgusting. I am heartbroken to hear about this happening in our community. www.cnn.com/2023/10/29/u...

New preprint by Sonny Arora and Jianyu Yang in our lab, in collab with Frank Pugh & lab, Minoru Ko, and Tomohiko Akiyama. We started with a simple question: are all Fox TFs pioneer factors? We investigated with the help of ChIP-exo and neural networks. 1/n www.biorxiv.org/content/10.1...

This looks very interesting. 🧬🔄🧬

Interesting new preprint from Corri Sept & Martin Aryee et al. combines MNase HiChIP for CTCF with new FactorFinder algorithm to profile 3D interactions conditional on CTCF being bound. Nice insights in loop extrusion from the perspective of CTCF-anchored cohesin www.biorxiv.org/content/10.1...

Fellow Ithaca: Our congressman Marc Molinaro is considering voting for Speaker Jordan. Consider sending a letter stating how you feel about this. Contact here: molinaro.house.gov/contact/ Afair, Our district is no longer safe red. Molinaro will have to win a wider swath of us to keep his seat.

Happy to share our latest preprint -- we built an integrated compendium of all publicly available human gut microbiome 16S data (~168,000 samples) and used it to explore patterns of microbiome variation around the world www.biorxiv.org/content/10.1...

new paper from the Luger Lab Parpers - collaboration with Dan LaBarbera's group at CU AMC Center for Drug Discovery, and funded by an ABNexus grant that should foster collaborations between CU Anschuetz and Boulder. i think it did just that! Congrats team Parp! www.sciencedirect.com/science/arti...

Fellow Ithaca: Our congressman Marc Molinaro is considering voting for Speaker Jordan. Consider sending a letter stating how you feel about this. Contact here: molinaro.house.gov/contact/ Afair, Our district is no longer safe red. Molinaro will have to win a wider swath of us to keep his seat.

New evidence for a higher-order chromatin organization in which distant TADs form large domains. www.cell.com/cell/fulltex...

finally our manuscript describing the weird and wonderful binding mode of a bacterial histone is online. www.nature.com/articles/s41...

Colors getting close to peak.

Hi Bluesky - happy to be here!!

@charlesdanko.bsky.social thanks for making me almost as cool as you!!

New faculty position in Gene Regulation at Penn State! Come join the fantastic collaborative environment in the Center for Eukaryotic Gene Regulation ( www.cegr.psu.edu )! Review of applications starts Nov. 1st 🧪🧬🔄🖥️ psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...

CC gene regulation community. 🔄🧬🔄 bsky.app/profile/char...

cBAF genomic targeting relies on the IDR. Looks like a very nice paper that begins to work out some of the amino acids involved. www.cell.com/cell/fulltex...

What's the over/ under on this pushing back the Oct 5 NIH deadline?!

I had an RNA joke, but it was degraded.

New preprint with Cerda-Smith, Hutchinson, Eyler, Wood et. al combining high-res Region Capture Micro-C (RCMC) with CRISPRa screens to identify functional enhancers of tumor supressor, PTEN, revealing separation between structural and functional elements: www.biorxiv.org/content/10.1...

Hi Bluesky. I'm very excited to be here!