Alu-mediated RNA duplexes are associated with widespread exon skipping across primate transcriptomes - Genome Biology Alternative splicing patterns have diverged rapidly during vertebrate evolution. By integrating genome-wide predictions of stable RNA duplexes, alternative splicing profiles, and proximity ligation-de...

link.springer.com/article/10.1...

Ryan Gosling from the Nice Guys saying “I don’t think I can die”

UConn

Poster for “Stand Up for Science — National Day of Action.” A stylized red-and-blue illustration of the Statue of Liberty holding up a torch appears on the left. Bold text reads: “Take back our science, health, and democracy!” Event details: March 7, 2026, New York City, NY, at Washington Square Park, 12:00pm. Footer text invites viewers to visit standupforscience.net/march7 to register, volunteer, or donate.

I'd say be there or be square, but if you're there, you're in the square! Puns aside -- there will be a
@standupforscience.bsky.social rally in NYC! Plz repost!

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social
doi.org/10.1016/j.ce...
Read the thread👇 for the highlights of our findings.

He made beer that’s also a vaccine. Now controversy is brewing An NIH scientist’s maverick approach reveals legal, ethical, moral, scientific and social challenges to developing potentially life-saving vaccines.

Well. It's certainly not boring over in vaccine world.

SAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the
@simonsfoundation.org. Details to follow. Please RT.

KATMAP infers splicing factor activity and regulatory targets from knockdown data - Nature Biotechnology A biophysical model uses knockdown or overexpression data to infer splicing factor activity.

KATMAP infers splicing factor activity and regulatory targets from knockdown data - @daspliceisright.bsky.social go.nature.com/47ycrMJ

a 3d rendering of a colorful dna molecule with a black background ALT: a 3d rendering of a colorful dna molecule with a black background

Happy #RNA Day everyone!!! 🎉🎉🎉

#AUG1st #RNASky

Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox - Nature Communications The majority of human genes can produce multiple isoforms, but studying their functional relevance requires tools to target specific isoforms. Here, the authors develop a CRISPR-based exon-exon juncti...

Excited for this to be out officially! It was a great team effort and has a lot of useful tidbits for studying isoform function. www.nature.com/articles/s41...

A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function - Nature Biotechnology RNA-binding motifs in eukaryotic proteins are presented in a comprehensive resource.

A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function go.nature.com/4mc1SmQ

Predicting the translation efficiency of messenger RNA in mammalian cells Nature Biotechnology - A deep convolutional neural network model predicts the influence of the full-length mRNA sequence on translation efficiency.

Very excited that our most significant work, a collaboration w/ Dr. Can Cenik at UT Austin on translational gene regulation, was finally published in Nature Biotechnology in a dual set of studies:

Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l

Love RNA biology and care about reproducibility? I’m co-editing a @bio-protocol.bsky.social special issue with @marionhogg.bsky.social & Renate Weizbauer —focusing open access and transparent RNA detection protocols.
Submit yours today - en.bio-protocol.org/content17
#OpenScience #ReproRNAbiology

Perplexity as a Metric for Isoform Diversity in the Human Transcriptome Long-read sequencing (LRS) has revealed a far greater diversity of RNA isoforms than earlier technologies, increasing the critical need to determine which, and how many, isoforms per gene are biologic...

New work from the lab trying to wrap our heads around the massive complexity of the human transcriptome revealed by long-read RNA-seq! Fun collab with Gloria Sheynkman. www.biorxiv.org/content/10.1...

Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇
www.biorxiv.org/content/10.1...

Eastern phoebe on a hiking trail post.

Birb on a sign

Had that for the first time last week... it's spreading...

Leveraging functional annotations to map rare variants associated with Alzheimer's disease with gruyere The increasing availability of whole-genome sequencing (WGS) has begun to elucidate the contribution of rare variants (RVs), both coding and non-coding, to complex disease. Multiple RV association tes...

Excited to share our first foray into (noncoding) rare variant association testing: a probabilistic model that learns functional annotation importance and finds associations missed by existing methods. Anjali did a fantastic job with model assessment and scaling! www.medrxiv.org/content/10.1...

Finally I'm in a top percentile of scientists!

Looks like a pleco (Hypostomus plecostomus) to me. Although I'm not sure I'm exactly a fish person per se 😅.

If we post enough complementary Heng Li memes, he'll surely join.

Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes RNA-binding proteins (RBPs) are key regulators of gene expression. Here, we introduce EuPRI (Eukaryotic Protein-RNA Interactions) — a freely available resource of RNA motifs for 34,736 RBPs from 690 e...

New preprint alert! EuPRI has everything:

* New binding data (174 RBPs)
* New motifs (34,000 RBPs)
* New ML for inferring motifs from protein sequence (JPLE)
* Evolution of RBP motifs across eukaryotes
* 12 Plant RBPs assigned PTR function. Stay tuned for more

www.biorxiv.org/content/10.1...

We're recruiting postdocs! Join our lab at 
@scilifelab.bsky.social and KTH in Stockholm to work on functional genomics at the experimental and/or computational intersection of CRISPR/scRNA-seq/genetics approaches. Close links to our team at NY Genome Center. 1/

For those in the NY area, SAVE THE DATE (& register) for a Symposium on Human Genetics at Columbia University: Oct 10-11 2024. Talks will also be streamed.

You got the kind of hedgehog that can be so smooth, yeah
Give me your heart, make it real, or else forget about it

Grinch on motorcycle pointing.

Train going by with "The Polar Express" written on the side of it.

Grinch on motorcycle.

Gotta love a surprise Grinch on a motorcycle and Polar Express while wandering around town.

It's an RNase burner account.

Codon optimality modulates protein output by tuning translation initiation bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Spurred on by ribosome profiling and other cool methods, translation elongation has grown into a whole field with new surprises all the time (and new relevance for vaccine mRNAs!). Here’s our latest on why synonymous codons aren’t all the same. (Thread) www.biorxiv.org/content/10.1...

Genetic determinants of blood gene expression and splicing and their contribution to molecular pheno... medRxiv - The Preprint Server for Health Sciences

Very excited to share the first manuscript out of my PhD presenting our analysis into the genetic architecture of gene expression and splicing using blood RNA-seq of 4,732 blood donors from the INTERVAL study. (1/7)