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:…

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…

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

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…

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…

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/…

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 devised a human-mouse mixing experiment to identify RNA-protein contacts that could not have occurred in vivo. We find that many PRC2-RNA contacts are detected even when the RNA and protein are not expressed within the same cells, clearly establishing that there is a problem.

Online Now: Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo dlvr.it/T33rxh

Delighted to see this out. The work deepens our understanding of lncRNAs structure-function relationships, ultimately suggesting that RNAs functional element deriving from SINE may acquire similar folding and function, even without shared ancestor.
doi.org/10.1038/s41467…

Delighted to present our work predicting cell type-specific epigenomic profiles whilst accounting for distal genetic effects. See below for a 🧵 with the details 1/15
biorxiv.org/content/10.110…

Genetic drivers of heterogeneity in type 2 diabetes pathophysiology nature.com/articles/s4158…

Wonderful paper just out nature from Eleftheria Zeggini and co.

Long non-coding RNAs comprise a large part of the genome, yet loss of one copy (haploinsufficiency) of a lncRNA is not known to cause a human disease. Read our preprint to learn how deletions of the lncRNA CHASERR cause a severe neurodevelopmental disorder.medrxiv.org/content/10.110…

Research from HMS, Brigham and Women's Hospital and the Broad Institute, shows how genetic alterations can affect the biology of cells that line the walls of blood vessels to magnify heart disease risk bit.ly/3w6HWx4

Excited to open registration for the symposium 'Frontiers of Implemented Genomic Medicine' hosted by the Novo Nordisk Foundation Center Broad Institute & Maria Rossing fr Rigshospitalet. Such an exciting topic & truly exceptional group of speakers. Please share! broadinstitute.swoogo.com/frontiers2024

Our study is out nature. We identify non-lipid risk pathways for coronary artery disease using pooled CRISPR-interference for 2,285 genes at GWAS loci. With an amazing team we identified the genetic risk pathways for CAD that act in endothelial cells.
nature.com/articles/s4158…