😂

Ever notice that when one gene is disrupted, its orthologs get upregulated? This phenomenon, known as transcriptional adaptation, has been controversial and mysterious - glad to see that we are starting to learn how it works.

Clever use of proteomic data to stress-test TWAS and QTL colocalization methods, revealing a high false sign rate. This hypothesis about high-LD and cross-tissue confounding is particularly interesting:

Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...

If you like larger sample sizes, then do check out our reprocessed and fine mapped cis-eQTLs and cis-sQTLs (leafCutter and MAJIQ!) from the INTERVAL cohort (whole blood, n up to 4,729)! zenodo.org/records/1795... These will be on the eQTL Catalogue FTP soon as well. cc @yosephbarash.bsky.social

Embracing Uncertainty in Life, Science It has been a long time since I wrote a non strictly scientific blog post. The holiday time, often a time of reflection and new resolutions, seems good for getting back to that. But don’t worry, there will be connections to science work as well… 😉 Today’s…

Announcing the 2026 edition of the EMBO workshop on RNA localization and local translation! This meeting will be held June 30 - July 4 near Porto, Portugal. Come for exciting updates in the field from both established investigators and trainees. See the link below for details!

@rnasociety.bsky.social now offers an "undergraduate" category for membership! rnasociety.memberclicks.net/membership #RNA@PUI

The new Enabling Discovery through GEnomics (EDGE) Program page is posted. Please contact us at [email protected] if you have questions. www.nsf.gov/funding/oppo...

New York Times article on science funding with some depressing but familiar curves with interactive graphics. www.nytimes.com/interactive/...

📣📣📣 (one for each new paper from the lab😀): Within ~1 week we had 3 papers published (two in the same day!), each took years... This calls for a quick tweetorial to explain why these may be interesting for you if you are into #RNA processing ( #Splicing #APA #UTR #rG4) with #AI #StatisticalGenetics.

Really cool paper that changed the way I think about what GWAS and Burden tests are doing, and also basically made me pleiotropy-pilled

Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n openrxiv.org/enabling-rev...

As new human assemblies become available on beta.ensembl.org - which human reference genome will you choose? This article explores the question with insights from Ensembl’s own Fergal Martin - www.nature.com/articles/s41... #HumanGenomics #Pangenomes #ReferenceGenomes

And it's a wrap! We just finished a fantastic #RNA #Theraputics meeting in Palermo 🇮🇹😀 And yes, the location was beautiful and the food was 😋 but l want to share a little from the cool things I learned about this week, as they may be interesting for you too...

So excited to see this out in @natgenet.nature.com! An amazing collaboration with @gagneurlab.bsky.social, I am happy I was (a small) part of. Nucleotide dependencies can capture regulatory elements, including #RNA structures! Congrats to the whole team! Check it out: www.nature.com/articles/s41...

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

📣 Attention #RNA #Splicing lovers! How is splicing of exons coordinated??🤔 ➡️ Exon Junction Complex (EJC) coordinates inclusion of blocks of neighboring exons!😯 Cool work by Alexandra Bergfort @karlaneugebauer.bsky.social lab - check it out! (we got to help a bit 😊) genesdev.cshlp.org/content/earl...

Planning your afternoon poster session at #ashg25? Come say hello! This is an amalgamation of our two recent preprints - working with @gregfindlay.bsky.social , @cassimons.bsky.social , @dgmacarthur.bsky.social and many others to study variation across RNU4-2 and describe a new recessive NDD 🧬

After our study on RNU4-2 and RNU5B-1 published in May (Nava et al, Nature Genetics 2025), I am excited to share our new preprint reporting dominant and recessive variants in RNU2-2 as a frequent cause of developmental and epileptic encephalopathy (DEE). 📄 www.medrxiv.org/content/10.1...

Many conserved exons in the heart and brain utilize weak 5 ′ splice sites, yet they are accurately spliced. But how? We show that splicing fidelity is actively enforced through a QKI-U6 checkpoint at the U1→U6 handover in essential cardiac genes during organogenesis. www.biorxiv.org/content/10.1...

📣Abstract deadline is *tomorrow* ! The list of speakers from academia & industry, + dates in Sicily ➡️ you should be on your way to submitting your abstract.... #RNA #therapeutics rnahorizons.com/abstract-sub...

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

If we want to connect genetic variation to disease, we need to move beyond baseline conditions. Our study shows that dynamic, context-specific regulation holds the key to understanding many unexplained GWAS signals. The preprint again: www.biorxiv.org/content/10.1...

Happy to announce our paper comparing embryonic gene expression between C. elegans and C. briggsae, work led by Christopher Large with Rupa Khanal and in collaboration with Junhyong Kim and Bob Waterston. www.science.org/doi/10.1126/...

Very excited to share our new work on gastruloids by the incredible Cat Triandafillou! We mapped gene expression across 26 individual gastruloids at single-cell resolution and discovered some pretty amazing patterns about how these "mini-embryos" organize themselves. www.biorxiv.org/content/10.1...

We are excited to introduce mRNABench, a comprehensive benchmarking suite that we used to evaluate the representational capabilities of 18 families of nucleotide foundation models on mature mRNA specific tasks. Paper: doi.org/10.1101/2025... Code: github.com/morrislab/mR... A 🧵

📣We are happy to announce the release of MAJIQ V3 😊🎉 check out details here #RNA #Splicing #RNASeq biociphers.wordpress.com/2025/06/20/m...

Reminder: Nobel-prize winning PCR (1983), used in basically all genetic tech today, was only possible because of extremophile bacterium discovered in 1964 in Yellowstone funded by a small ~$80k NSF grant with no obvious application at the time. #science 🧪 www.richmondscientific.com/how-a-discov...

🔊 Meet Mathieu Quesnel Vallières @rna-ken.bsky.social : Using transcriptomic analyses to find cancer immunotherapy targets, he’s bringing his expertise to @usherbrooke.bsky.social , supported by D2R’s New Faculty Start-Up program 🔗Learn more: buff.ly/laJgUJ3 #ResearcherSpotlight #RNAResearch

Lux Capital & @wolfejosh.bsky.social are launching the Lux Science Helpline - a $100M commitment to support American scientists whose research is threatened by funding cuts, bureaucratic hurdles, and career roadblocks - that expands our Lux Labs program. www.luxcapital.com/news/our-hel...

Given some recent publications regarding #RNA #Splicing prediction using #DeepLearning we decided to assess some of those claims with surprising findings that have to do more with the target function you chose… biociphers.wordpress.com/2025/04/09/t...

This is high art

To say that I am shocked at this tragic news is an understatement. I got to know Sayan well during my time at Duke; he was deeply knowledgeable about all sorts of things and had a great sense of humor. He was the one and only Bayesian anarchist. www.mis.mpg.de/news/loss-sa...

🏆 Research integrity consultant and image forensics expert @elisabethbik.bsky.social has uncovered fraudulent data in over 7,600 scientific papers and exposed the practices of ‘paper mills’ that produce counterfeit scientific articles. She is honoured with the €200K Individual Award. Congrats!

Hey all! The RNA Society meeting in San Diego features a new session for sharing results on new ways to bring RNA into the curriculum. Get your abstracts in ASAP!

Happy to say our paper with the Whipple lab on snoRNA target profiling with chimeric eCLIP is now out! Great work by co-first authors Joey & Min with the help of a bunch of other folks! genomebiology.biomedcentral.com/articles/10....

A tumultuous 24-ish hours since our preprint was released yesterday. I mentioned that this was a fraught issue and I genuinely do understand that people have mixed feelings about the work. I wanted to take some time to respond to some of the concerns and comments that have 1/

The success of LLMs has inspired their extension to genomics data. A preprints reports that such models lack understanding of genomics and provide minimal utility, even for basic tasks such as sequence classification. www.biorxiv.org/content/10.1...

Massively parallel reporter assays (MPRAs) testing >680,000 sequences combined with machine learning to improve regulatory element & variant effect prediction. Amazing work by @vagar.bsky.social, Fumitaka Inoue, @jshendure.bsky.social and many others as part of ENCODE. www.nature.com/articles/s41...

0/ Essential reading for anyone training or using sequence-function models trained on genomic sequences! 🚨 In our new preprint, we explore the ways homology within genomes can cause leakage when training sequence-based models and ways to prevent it

I'm excited about a meeting on RNA + AI together with @quaidmorris.bsky.social and @hagentilgner.bsky.social in Ascona, Ticino on May 4-8. We have a great line-up of speakers and room for you to present your work. Please join us if you are into RNA & AI. Registration open www.rna-ai.org.

📣 Our 2nd Blog post on improving #sQTL modeling and why it matters #RNASplicing #Genetics #Statistics #QTL biociphers.wordpress.com/2025/01/28/a...

📣 New post re our recent findings/methods dev for #sQTL #RNA #Splicing #RNA-Seq. We think this will be highly useful/impactful for (s)QTL detection/quantification. Hope to get (constructive 😉) feedback and much usage from the community! 😀 biociphers.wordpress.com/2025/01/20/a...

The first preprint of 2025! Together with Matvei, @halfacrocodile.bsky.social, & our amazing team, we are excited to share PARADE: an AI framework for designing mRNA UTRs with enhanced cell-type specificity & stability. www.biorxiv.org/content/10.1...

Our mentor Casey Brown, apart from being an extraordinary scientist, was a brilliant teacher who loved everything genetics. In his honor, some of the world's leading experts came together to create the 'Casey Brown Lecture Series' on human genetics 1/ shorturl.at/eCm7S

Happy New Year everyone. I having pleasing maths to share (courtesy of my 18yo who saw it on insta). 2025 is the only square this century! 🤓