Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies” shorturl.at/H3Qww This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon. Bluetorial below.

Been working on a really strange retron bacterial immune system, here's the preprint: www.biorxiv.org/content/10.1... Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.

Most neurodevelopmental disorders are caused by having 1 functional gene copy. Using SCN2A, we show that upregulating the functional copy rescues neuronal phenotypes. Amazing work with @neurobender.bsky.social led by Serena Tamura, Andrew Nelson, Perry Spratt & others. www.nature.com/articles/s41...

We are excited to inform you about the annual UCSF IHG Genotech Symposium, taking place on 9/22. The goal of this symposium is to foster collaboration and cross-fertilization between industry and academia in genetics and genomics. Hope to see you there! genotech.ucsf.edu/home

New preprint with @gfudenberg.bsky.social We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding. This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇 www.biorxiv.org/content/10.1...

Neomers are short 16bp sequences missing in our genome. Cancer causes mutations, leading to their appearance, making them a great diagnostic tool from cell-free DNA. Amazing work by Ilias Georgakopoulos-Soares, Ofer Yizhar-Barnea, Ioannis Mouratidis, Martin Hemberg... www.nature.com/articles/s43...

Our protocol on growing adipocytes or adipose organoids for Adipose Manipulation Transplantation (AMT), by the amazing Kelly An and Yusuke Ito, is out in Bio-Protocol. Hoping it will be helpful in the adoption of this therapeutic technology for various conditions. bio-protocol.org/en/bpdetail?...

📣 We are recruiting! Please share!! Are you a bioinformatician / computational scientist who wants to apply your skills to understanding regulatory biology and improving rare disease diagnosis and treatment? 🧠 💻 🧬 🩺 We have two roles available 👇 🧵 1/4

To all post-docs: The Genome Biology dept ‪@embl.org has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Given two genomes, can you tell who’s taller or more prone to a disease? How confident can you be? A fresh take on phenotypic inference, now out: rdcu.be/exW4f See thread🧵👇:

Join us for our @ihgatucsf.bsky.social Genotech Symposium on September 22nd 9-6pm at our Mission Bay campus! We have a great lineup of speakers and registration is free. genotech.ucsf.edu

Lentivirus massively parallel reporter assays integrate & enrich for specific sequences in the genome. We utilize this to test their epigenetic modifications & open chromatin alongside their regulatory activity. Amazing work by Zicong Zhang, Fumitaka Inoue & others. www.biorxiv.org/content/10.1...

Capture C identifies promoter interacting sequences. MPRA tests sequences for regulatory activity. Here, we combined them both to test sequences with their target promoter. Amazing work by @colinearnould.bsky.social, Pia Keukeleire, Martin Kircher and many others. www.biorxiv.org/content/10.1...

Comparison between a neuronal massively parallel reporter assay for 50,000 sequences and 20,000 variants with mouse enhancer assays provide complimentary information. Great work by Michael Kosicki, Dianne Laboy Cintrón, Len Pennacchio, Martin Kircher lab & many others. www.nature.com/articles/s41...

Massively parallel jumping assay (MPJA) enables to test the jumping potential of thousands of transposons. Analysis of >160,000 Alu haplotypes identified transposition-asssociated domains. Amazing work by Navneet Matharu, Jingjing Zhao, Martin Kircher and many others. www.nature.com/articles/s41...

MPRAbase (mprabase.ucsf.edu) , a customized database for massively parallel reporter assays (MPRAs) to easily find and download MPRA data. Amazing work by Jingjing Zhao, Fotis Baltoumas, Georgios Pavlopoulos, @vagar.bsky.social, ilias Georgakopoulos-Soares & others. genome.cshlp.org/content/earl...

One of the toughest parts of the field of massively parallel reporter assays to measure >~thousands of elements is that there are hundreds of pubs using them, but no central repo to easily locate the results....until now! Great collab w/ Jingjing Zhao, Ilias G-S, and @nadavahituv.bsky.social!!

Was a lot of fun doing this podcast! Thanks @thermofishersci.bsky.social team! speaking-of-mol-bio.simplecast.com/episodes/fro...

I could not be more excited to have our lab's first story online where we report our discovery that HDACs ~reverse~ their activity to ADD acyl groups to lysine! We found this for our favorite ketone body, BHB, but this pathway controls other lysine modifications too!🧵 www.nature.com/articles/s41...

Nice story about our adipose manipulation transplantation (AMT) cancer therapy written by Edward Winstead at NCI. www.cancer.gov/news-events/...

Looking forward to this symopium in honor of Ray White. There is still time to register.

#ResearchHighlight 🚨 @nadavahituv.bsky.social#ResearchHighlight&Co developed a new therapeutic approach, adipose manipulation transplantation (AMT), in which engineered adipocytes are used to outcompete tumours for lipids and glucose to suppress cancer progression. 👀 ⬇️

Looking for a new director for our Genetic Counseling Program at UCSF. Job ad below and feel free to contact me directly with any questions. sjobs.brassring.com/TGnewUI/Sear...

Looking forward to this meeting!

Tumors need a lot of nutrients to grow. By engineering and implanting fat cells to outcompete cancers for nutrients we can suppress them. Novel cancer therapy called Adipose Manipulation Transplantation (AMT). AMAZING work led by and dedicated to Hai Nguyen. www.nature.com/articles/s41...

Beware! AAV libraries prone to length & homology dependent chimerism! Our latest preprint, from the brilliant @jblalanne.bsky.social‬, was a true surprise as related phenomena are textbook for lentivirus (highly relevant to HIV & Perturb-seq) yet to our reading not known for AAV tinyurl.com/5amc562a

Super excited to announce our latest work. On a personal note, it's not an exaggeration to say that blood, sweat, and tears got us to the finish line on this: working w/ an outstanding global team of scientists in Germany, Japan, Russia, and USA responding in >100 pages of complex reviewer comments.

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...

Extremely excited to see that our work on how fruit bats can eat so much sugar without getting diabetes is one of the seven on this list! www.smithsonianmag.com/innovation/s...

The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics