Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. nature.com/articles/s4158…

Single-cell RNA sequencing is biased (and more so if you count more molecules). But biases aren't just arbitrary artifacts; they reveal something non-obvious about the technology and chemistry of sequencing, and we can learn a lot by using physical models. Read to find out more!

Our ChromBPNet preprint out! Huge congrats to Anusri Pampari! This was quite a slog for both of us but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Link in the next tweet. Bluetorial coming soon .. 1/

Tonight I found out that the NSF math postdoctoral fellowship I applied for is being deleted because it does not comply with Trump’s executive orders on DEI in the federal government. I’m going to answer some FAQs and share some thoughts about this ordeal in this thread 1/n

longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/longc…

This is really exciting work and it is prob of interest to many of my biology-adjacent followers. The paper itself is very readable for people not doing LLM stuff and it has many nice interactive diagrams. It's just amazing to see the algorithms that LLMs learn

Very excited to finally see this out! 🦠🧬 Huge thanks to all of my amazing co-authors! Lior Pachter Delaney Sullivan Maria Carilli Kristján Eldjárn Alexander Viloria Winnett and Tara Chari Original thread about this work: x.com/neuroluebbert/… Free access link to the paper: rdcu.be/eiIWC

Synthetic biology could enable new types of programmable therapeutics. Our new preprint introduces synthetic protein circuits that selectively trigger cell death in Ras-mutant cancer cells, with interesting advantages compared to existing approaches. biorxiv.org/content/10.110…

I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/rep…

This a really exciting leap forward for genomic sequence to activity gene regulation models. It is a genuine improvement over pretty much all SOTA models spanning a wide range of regulatory, transcriptional and post-transcriptional processes. 1/

This week in academia, a not so short🧵... 1. Staff reductions and other cost cutting measures coming to Brown University highereddive.com/news/brown-uni…

My lab’s 5-year NIH R01 grant, awarded to study gene therapy for hearing loss, was abruptly terminated. I want to share how this action has been incredibly harmful and disruptive, not just to my lab, but to the scientific process itself. 1/15

Absolutely awful 😢. WTF NIH 🤬?

Even if the awful NIH grant terminations eventually get overturned, a lot of damage has already been done. The human cost has already been paid. Scientific progress has already been delayed. Horrible. NIH do better.

News: NIH to crack down on excessive publisher fees for publicly funded research bit.ly/4nCdIbl

Nature research paper: Mapping and engineering RNA-driven architecture of the multiphase nucleolus go.nature.com/4luDEUy

Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In Cell, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment. sciencedirect.com/science/articl…

Anyone knows adam?

Congrats Jimmy K. Guo and team!

Nature research paper: Lithium deficiency and the onset of Alzheimer’s disease go.nature.com/4mwBvbr