Monod fits biophysically motivated models to single-cell transcriptomics data, providing insights into gene expression dynamics. @goringennady @lpachter @mariacarilli @johnjvastola https://t.co/zx27cbPvZS

Reference-based variant detection with varseek https://t.co/M3Yo1bpAT5

In a new work with @Josephmrich and Conrad Oakes we tackle the problem of how to best organize alluvial plots. We formalize two optimization problems and develop a solution for them based on the neighbornet algorithm, implemented in the program wompwomp: https://t.co/njQRkjYHNh

Nature research paper: Lithium deficiency and the onset of Alzheimer’s disease https://t.co/weLUUh1BAS

Anyone knows adam?

Congrats @jimmykguo and team!

Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In @CellCellPress, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment. https://t.co/Zs2Rn35D3s

Nature research paper: Mapping and engineering RNA-driven architecture of the multiphase nucleolus https://t.co/9iAiDD6f2g

News: NIH to crack down on excessive publisher fees for publicly funded research https://t.co/vzCCoumf5S

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.

Absolutely awful 😢. WTF @NIH 🤬?

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

This week in academia, a not so short🧵... 1. Staff reductions and other cost cutting measures coming to Brown University

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/

I wrote a review of a recent paper on false discovery and multiple testing correction.

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. https://t.co/R9kDsrftJK

Very excited to finally see this out! 🦠🧬 Huge thanks to all of my amazing co-authors! @lpachter @DelaneyKSull Maria Carilli @kreldjarn @alex_winnett and Tara Chari Original thread about this work: https://t.co/c0m9jfZ3Fk Free access link to the paper:

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

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.

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