Very proud of this tour de force from two former students, Stephanie Tanis and Leah Simon, with help from a huge team, including @charlesdanko.bsky.social highlighting a novel-overlooked intervention point for male contraception www.pnas.org/doi/10.1073/...

Meiotic prophase I disruption as a strategy for nonhormonal male contraception using small-molecule inhibitor JQ1 | PNAS

Developing safe, reversible, and nonhormonal male contraceptives has been hindered by the lack of defined biological windows that can be transientl...

pnas.org

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...

Resist, eggheads! Universities are not as weak as they have chosen to be.

Opinion: It’s time for public resistance.

arstechnica.com

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...

Genome-wide dynamic nascent transcript profiles reveal that most paused RNA polymerases terminate

We present a simple model for analyzing and interpreting data from kinetic experiments that measure engaged RNA polymerase occupancy. The framework represents the densities of nascent transcripts with...

biorxiv.org

👇🎯 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.

Tom Pepinsky@tompepinsky.com · last yr.

The public really needs to understand this. Every university system in the world rests on public funding, there has never been an alternative model at any time in history. We have universities for literally the same reason that we have roads and armies.

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.

Chris Pickett@chrispickett5.bsky.social · last yr.

This is a simply shameful statement from Columbia. Rolling over in the face of bad faith, unconstitutional attacks by a bully only encourages the bully. When the Trump admin comes for other universities, and they will, I sincerely hope they do the opposite of Columbia.

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...

Accurate de novo transcription unit annotation from run-on and sequencing data

Functional element annotations are critical tools used to provide insight into the molecular processes governing cell development, differentiation, and disease. Run-on and sequencing assays measure th...

biorxiv.org

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 💀

Genomic Foundationless Models: Pretraining Does Not Promise Performance

The success of Large Language Models has inspired the development of Genomic Foundation Models (GFMs) through similar pretraining techniques. However, the relationship between pretraining performance ...

biorxiv.org

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...

Q-rich activation domains: flexible ‘rulers’ for transcription start site selection?

Recent findings broadened the function of RNA polymerase II (Pol II) proximal promoter motifs from quantitative regulators of transcription to important determinants of transcription start site (TSS) position. These motifs are recognized by transcription factors (TFs) that we propose to term ‘ruler’ TFs (rTFs), such as NRF1, NF-Y, YY1, ZNF143, BANP, and members of the SP, ETS, and CRE families, sharing as a common feature a glutamine-rich (Q-rich) effector domain also enriched in valine, isoleucine, and threonine (QVIT-rich). We propose that rTFs guide TSS location by constraining the position of the pre-initiation complex (PIC) during its promoter recognition phase through a specialized, and still enigmatic, class of activation domains.

cell.com

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

Andrea Bernardini@bernardini-andrea.bsky.social · 2y ago

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...

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...

Training deep learning models on personalized genomic sequences improves variant effect prediction

Sequence-to-function models have broad applications in interpreting the molecular impact of genetic variation, yet have been criticized for poor performance in this task. Here we show that training mo...

biorxiv.org

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...

3D Enhancer–promoter networks provide predictive features for gene expression and coregulation in ...

Here, the authors describe 3D hubs as regulatory subunits of gene expression in the three essential lineages of embryogenesis. They develop a computational model that can predict novel enhancers and t...

nature.com

Important thread.

John Greally@greally.bsky.social · 3y ago

Time to roll out an updated version of something I post periodically, why the @NIH needs to change its modular budget and budget cap. The Modular Budget was introduced in 1998 by the@NIH. If you stayed under the ceiling of $250,000, you didn't have to break down your costs.

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. 🧬🔄🧬

bioRxiv Molecular Biology@biorxiv-molbio.bsky.social · 3y ago

ATAC and SAGA histone acetyltransferase modules facilitate transcription factor binding to nucleosomes in an acetylation independent manner https://www.biorxiv.org/content/10.1101/2023.10.27.564358v1

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...