New study led by Ning Shen w/ @phruzycki.bsky.social: a genome-wide in vivo CRISPR screen in a retinitis pigmentosa mouse model identifies genes whose loss accelerates photoreceptor death. Overexpressing two, UFD1 and UXT, preserves photoreceptors, retinal function, and vision. 🧵

ChromSMF preprint is out!🚀
tinyurl.com/ChromSMF

We often piece together chromatin regulation layer by layer from separate assays. But this can be limiting!

In @arnaudkr.bsky.social's lab, we developed a method to directly study multiple layers on the same DNA molecule! 🧬

What does this unlock? ⬇️

The main project of my PhD 🧬🔬 is out: we developed single-cell lentiMPRA, a lentivirus-based method to measure enhancer activity and transcriptomes at single-cell resolution. We then applied sc-lentiMPRA to fully synthetic enhancers 🧩...

🔗 doi.org/10.64898/202...

Today marks 4th anniversary of Russia's invasion of Ukraine. Russia is responsible for over 200,000 war crimes, killing over 15,000 civilians and displacing millions. My heart breaks for every Ukrainian. I continue attending rallies and donating hoping one day Ukraine will be free and safe.

Exciting to see it published! I had a lot of fun using AlphaGenome since the preprint. Congratulations!

Europe is stepping up, helping Ukraine for the right moral reasons and helping their mutual economies.

BMP signaling-dependent dorsal-to-ventral gradient of PAX3/7 transcriptional activity revealed by the P34::tk::LacZ reporter. Left: expression patterns of neural progenitor (NP) and interneuron (IN) TF markers in the developing spinal cord. Right: Immunostaining for β-galactosidase (β-gal; red/grey), GFP (blue/grey) and either OLIG3 (green/grey) or pSMAD1/5/9 (green/grey) on transverse sections of E9.0 (bottom) and E9.5 (top) P34::tk::LacZ; Pax3+/GFP spinal cords at brachial level. Black and white panels show magnified views of the boxed region.

How do pleiotropic TFs generate organized diversity in developing tissues? @spinalorga.bsky.social shows that PAX3 & PAX7 organize #SpinalCord by acting as both repressors & pioneer activators, regulated by #morphogens to ensure precise neural subtype specification @plosbiology.org 🧪 plos.io/4qumsla

Cracking the code of the non-coding genome via allele-specific genomics?
Can we link non-coding elements—like lncRNAs and enhancers—to their protein-coding target genes, and in doing so, connect overlapping non-coding disease variants to their protein-coding counterparts?

Promoter-proximal gatekeepers restrict pleiotropic enhancer inputs to achieve tissue specificity Developmental enhancers are central regulatory elements that can activate multiple genes, yet how they selectively regulate one gene over its neighbours remains unclear. Using the Drosophila twist E3 ...

Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one?

Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...

A baby benefits from personalized gene editing in the clinic An infant with an inherited life-threatening metabolic condition has responded to a tailored therapy that uses the gene-editing tool CRISPR to correct a specific mutation.

An infant with an inherited life-threatening metabolic condition has responded to a tailored therapy that uses CRISPR to correct a specific mutation

go.nature.com/3Jmdbuy

Loss of miR-9-2 Causes Cerebral Hemorrhage and Hydrocephalus by Widespread Disruption of Cell-Type-Specific Neurodevelopmental Gene Networks. MIR-9-2 is a broadly and highly expressed microRNA in the developing brain and is frequently deleted in 5q14.3 Microdeletion Syndrome, a rare but severe neurodevelopmental disorder. Despite this, litt...

1/5: How does a presumably redundant microRNA contribute to mammalian brain development and neurodevelopmental disease? Check out our new work led by Dr. Santiago Fregoso now on bioRxiv! www.biorxiv.org/content/10.1... #Neurodev #miRNA #hydrocephalus #Genetics #bioRxiv.

Seattle researchers hit 'breakthrough moment' in understanding SIDS It is one of the most horrific tragedies for a parent: the sudden, unexplained death of a seemingly healthy baby.

Seattle Children’s researchers are making breakthrough discoveries in the quest to prevent #SIDS.
Learn more in this story from KOMO News:

#MedSky

komonews.com/news/local/r...

On Sunday I will cycle 50 km to raise money to support research to prevent blindness. If you can, please sponsor me! fightingblindness.akaraisin.com/ui/MOVEFORSI...

World first: ultra-powerful CRISPR treatment trialled in a person Immune-cell function improved in a teenager whose DNA was altered using prime editing.

The CRISPR family’s most versatile member has made its medical debut: a cutting-edge gene-editing technique known as prime editing has been used to treat a person for the first time

https://go.nature.com/3YNta9V

Today "a milestone in the evolution of personalized therapies for rare & ultra-rare inborn errors of metabolism"
—the 1st human to undergo custom genome editing
—from decades of NIH funded research
www.nejm.org/doi/full/10....
@nejm.org
www.nejm.org/doi/full/10....
www.nytimes.com/2025/05/15/h...

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...

Vilcek Prizes for Creative Promise - Vilcek Foundation The Creative Promise Prizes are awarded to young immigrant professionals who have demonstrated outstanding achievement early in their careers.

If you are immigrant into the US and work in the biomedical sciences (like me) and are still young (not like me), please apply for the Vilcek prizes for Creative Promise founded by an inspiring immigrant couple, Marica and Jan Vilcek.

vilcek.org/prizes/vilce...

🚨 New paper alert! 🚨
We’ve just launched openretina, an open-source framework for collaborative retina modeling across datasets and species.
A 🧵👇 (1/9)

Saying goodbye is hard! So is interpreting non-coding variants in visual disorders! Luckily, that is the gift that Dr. Leah VandenBosch left us with after a very successful postdoc in the Cherry Lab. Check your own favorite retinal regulatory variants here: genome.ucsc.edu/s/CherryLab/...

Whole-genome sequencing analysis identifies rare, large-effect noncoding variants and regulatory regions associated with circulating protein levels Nature Genetics - Rare variant association analysis of plasma proteins using whole-genome sequencing data in 54,306 individuals in the UK Biobank demonstrates that combining both single-variant and...

Excited to finally share that our paper looking at the effect of rare non-coding variants using WGS on circulating protein levels in the UKB has been released in Nature Genetics @naturegenet.bsky.social! We now analyse the full 3,000 circulating proteins in all 50,000 individuals rdcu.be/ea16i

#Neuroskyence students! We're brainstorming ways to support your development over this summer break, esp. given the changes in summer intern programs across our fields. What other opportunities would you like to see?

Some ideas: undergrad-focused webinars, self-paced courses, challenges, etc.

Standing with Ukraine in Seattle

I was touched by the great turnout in Seattle to support #Ukraine. Thank you to the organizers and @adamsmith.house.gov for your speech. We must continue arming Ukraine and defend democracy against Russian invasion. #StandWithUkraine 🇺🇦"

Since 2022, people around the world have stood in solidarity, joining rallies to support Ukraine and refusing to let russia silence the truth. They chose Ukraine’s side, united in the fight for freedom. Join in, speak up, #StandWithUkraine:
uaworldmap.ukrainianworldcongress.org/en?fbclid=PA...

Your city might have separate events, like the one I'll be attending in Seattle, organized by the Ukrainian Association of Washington State

Global Events Where You Can Stand With Ukraine as Russia’s Full-Scale War Hits the Three-Year Mark Global events mark three years since Russia's invasion of Ukraine, showcasing solidarity and raising awareness for ongoing support and resilience.

As Russia's full-scale war hits the three-year mark, it's more important than ever to #StandWithUkraine. I encourage you to raise your voices for peace and justice by attending one of the events organized worldwide.
#RussiaIsATerroristState

Negotiating with the murderous dictator Putin won't lead to anything. He needs to be forced to retreat from Ukraine.

I hope this hastens the fall of Putin's regime

Since Russia's invasion of Ukraine, almost 20,000 Ukrainian children have been kidnapped by Russia. DNA testing might be the only way to one day reconnect them with their families.

I'm sure the Russian government will deny everything similar to MH17 and countless wat crimes they commit in Ukraine.