Neurons and astrocytes closely coordinate their gene expression, in a program we call “SNAP” – a collaboration that we find to be central in protection from schizophrenia and cognitive aging. nature.com/articles/s4158…

We report a new CRISPR resource, Fragmid, in Cell Genomics today, let by the incomparable Abby McGee. Let's walk through it… cell.com/cell-genomics/…

An Analysis presents a collection of non-coding CRISPRi screens from the ENCODE4 Functional Characterization Centers and establishes experimental guidelines for future screens identifying cis-regulatory elements. Steve Reilly nature.com/articles/s4159…

Our new paper on non-coding CRISPRi screens to functionally characterize enhancers just came out in @NatureMethods ! nature.com/articles/s4159…

Check out this new preprint/white paper from our friends at Entwine bio together with Vijay Ramani and Zaro Lab. We and others have long been interested in sequence-to-function modeling in RNA, especially as it comes to splicing. biorxiv.org/content/10.110…

What a PERFFect day to share our new preprint! With Tsion Abay #BobStickels Meril Takizawa Ronan Chaligne (He/Him) and Ansu Satpathy, we introduce PERFF-seq, a new experimental approach to studying rare cells with scRNA-seq via transcript-specific enrichment. biorxiv.org/content/10.110… 1/n

Published today, our reasons for optimism that success rates in drug discovery can be improved by picking the right targets using human genetics: nature.com/articles/s4158… I break the key findings down panel by panel in this thread: x.com/cureffi/status…

Our paper "A machine readable specification for genomics assays" is now published in Bioinformatics, OUP Bioinformatics. In short, we present a lightweight file format and command-line tool to document the structure of sequencing reads. Coauthored with Xi Chen and Lior Pachter. Paper:

Could not be more delighted to present our work investigating how over 220,000 complex and molecular trait-associated genetic variants affect transcriptional regulation using massively parallel reporter assays! biorxiv.org/content/10.110… See below for a 🧵. 1/n

‼️⚠️Registration Deadline TODAY!⚠️‼️ Register now for the 'From Genetic Discoveries to Gene Function in Human Diseases' Conference to secure your slot and join us in Portugal from 13 - 16 July 2024 #GWAS24☀️🏌️ 🔗➡️bit.ly/4bnHuu6

Cofactors are a crucial part of the gene activation process. Yet, we still don't have a comprehensive understanding of how and why they are used by different genes. Proud to present our attempt to address this key question, now published nature.com/articles/s4158…

Check out ProCapNet by Kelly Cochran, a robust, local sequence context deep learning model of base-resolution transcription initiation profiles (PRO-cap) that provides deep insights into the cis-regulatory code of initiation & more ... biorxiv.org/content/10.110… 1/

Sometimes simple models, proposed years ago, turn out not so bad! This preprint shows that E-P interactions control expression, that cohesin helps mediating these interactions, esp. for distal enhancers (>50kb), see also work from Wendy Bickmore in NSMB. doi.org/10.1101/2024.0…

Do human RNA-binding proteins have modular regulatory domains that downregulate RNA lifetimes? Our preprint Bintu Lab studying this question is now out on bioRxiv, where we indeed identify small domains in RBPs that potently induce RNA degradation! biorxiv.org/content/10.110… (1/9)

Exciting news! Jesse (Jesse Engreitz), Marlene (Stanford BASE), and I have recently received a CIRM grant, and we presumably ranked No. 1 based on the prior year's criteria! I am looking for a talented experimental postdoc to join my team. This position offers close collaboration

I am so excited to share this part of my PhD where we tackle the question: What impact do 3D contacts have on how enhancers regulate their target genes? biorxiv.org/content/10.110… 1/

Our latest preprint: Cohesin-mediated 3D contacts tune enhancer-promoter regulation We put the looping model of enhancer function to the test via enhancer CRISPR screens in a cohesin degron cell line See here 👇

Really excited about work led by Jesse Engreitz and Philine seeking to harmonize two long-standing & potentially contradictory observations: if cohesin is so important to the formation of chromatin loops, why doesn't degrading it have a bigger impact on gene expression?

(1/16) Check out our Simon Gaudin paper tiny.cc/icuazz from the Canzio lab out in Science Magazine today on how tuning local cohesin trajectories enables differential readout of the clustered Protocadherin (Pcdh) locus across different types of neurons.

Excited to share the white paper for the IGVF Consortium, supported by National Human Genome Research Institute Deciphering the impact of genomic variation on function rdcu.be/dSZdm