Super excited to get this out. This collab started a few years ago and is the first paper from it. Here, with experimental and computational approaches we: 1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs bsky.app/profile/bior...

New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...

I am thrilled to share a joint work with Melissa Gymrek that spans several years to study what is the impact of promoter proximal short tandem repeats (STRs) on expression by using MPRAs. I am sure you'd enjoy! Awesome effort by @xzhangbsky.bsky.social and the team! www.biorxiv.org/content/10.1...

Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up! www.biorxiv.org/content/10.1... A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)

I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.

Check out MitoScribe in our new preprint led by Linhan Wang: www.biorxiv.org/content/10.1... It's an analog molecular recorder that uses neutral base edits to the mitochondrial genome to store information about historical signaling in a cell. Single cell resolution at scale (see next post)!

Thrilled to share the second half of my PhD work here! We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/) doi.org/10.1101/2025...

happy to say my new department is hiring an associate/full professor: academicjobsonline.org/ajo/jobs/30328 please apply!

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...

Bittersweet to be leaving @docedge.bsky.social after a wonderful postdoc, but excited to share that I'm joining @uoregon.bsky.social next month as an Assistant Professor in the Department of Data Science.

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...

🧪🖥️🧬 It's here!! Our second MPRA, which is totally different from the first. For starters, there's no human sequences anywhere! Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)

I'm excited to announce that I'll be starting a lab at UCSF in the @ihgatucsf.bsky.social and @ucsf-epibiostat.bsky.social in July. We'll work at the intersection of statistical genetics, population genetics, and machine learning.

Flybase lost all of the NIH support overnight - it is a disaster for the community. Please consider donating. I just did! www.philanthropy.cam.ac.uk/give-to-camb...

Excited to share our first anti-aging intervention analysis, led by brilliant Zehao @tommyz626.bsky.social, Alex, and Chloe from our lab at @rockefelleruniv.bsky.social! We identified the aging-associated cell populations that can be rescued by caloric restriction in the mammalian brain!

Postdocs: Human Genetics at Utah will be hosting our annual Rising Stars in Genetics and Genomics Symposium in Sept. Apply here: shorturl.at/wBMg2 There will be sessions on developmental, evolutionary and disease genetics. A chance be invited to SLC to network here and with peers! Please share.

Excited to announce our preprint describing SUPERB-SEQ 🦸, a new method to measure Cas9 edits and their effects on gene expression in single cells. Led by @micklorenzini.bsky.social and @bradbalderson.bsky.social www.biorxiv.org/content/10.1...

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...

We're delighted to share our work on scrambling the human genome using prime editing, repetitive elements, and recombinases in @science.org , led by @jonaskoeppel.bsky.social , @f-raphael.bsky.social , with @proftomellis.bsky.social and George Church. www.science.org/doi/10.1126/...

Now out in @science.org w/ @jshendure.bsky.social we present 'Genome-shuffle-seq': a method to shuffle mammalian genomes and characterize the impact of structural variants (SVs) with single-cell resolution in one experiment. www.science.org/doi/10.1126/...

Our paper “A genome-wide atlas of human cell morphology” is finally out today in @naturemethods.bsky.social ! www.nature.com/articles/s41... (I tweeted about our preprint in 2023 over at the bad place, but deactivated my account, so here we go again!)

Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease? I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵

Hello Bluesky friends! I am a #newPI starting at UC Irvine in April, interested in gene regulation and functional genomics in stem cell models of development (esp neural crest). We are hiring at all levels – please reach out/spread the word! sskimlab.org

Brief PSA for the functional genomics community: if you are profiling complex libraries with >1 internal components (e.g., enhancer+barcodes in MPRAs) delivered via AAVs, be aware that there might be substantial unlinking within your libraries if you packaged as a pool! doi.org/10.1101/2025...

My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful. It’s available on Amazon: tinyurl.com/mx2hewen

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...

Friends and colleagues, I’ve written a book on effective functional genomics study design, which will be available on Amazon in a couple of weeks. Sharing the TOC to spark interest. I hope students and those planning genomics experiments will find it useful! I’ll share updates soon

Now for something a little different: our work on craniofacial development in new born fat tailed dunnarts, a tiny bitey carnivorous marsupial, is now out on eLife, and you can read it and the reviews while we work on the revisions :) elifesciences.org/reviewed-pre...

My thesis work on active machine learning to model regulatory DNA is now out in Cell Systems! We answer the question: When you can synthesize any DNA sequence you want, how do you decide which ones are worth testing? www.sciencedirect.com/science/arti...

Happy New Year! (and first post here 😀) Excited to share the final version of our work where we combine deep mutational scanning, cryo-EM, and molecular dynamics to further resolve the mechanisms of pH sensing in GPCRs. 🧵(1/n) www.cell.com/cell/fulltex...

What do GWAS and rare variant burden tests discover, and why? Do these studies find the most IMPORTANT genes? If not, how DO they rank genes? Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬) www.biorxiv.org/content/10.1...

Specificity, length, and luck: How genes are prioritized by rare and common variant association studies https://www.biorxiv.org/content/10.1101/2024.12.12.628073v1

Aneuploidy is the leading cause of pregnancy loss. In our latest study (www.biorxiv.org/content/10.1...) led by undergrad Angela Yang, we used a simulation framework to infer rates of both meiotic (39-43%) and mitotic errors (1-3% per division) that best explain data from human IVF embryo biopsies.

Excited to see our study on genetic regulation in heterogeneous differentiating cultures out in final form! www.cell.com/cell-genomics/fulltext/S2666-979X(24)00330-6

Friends, We are hiring! My department (Computational Medicine) has an open rank faculty position search this year! I know we are late to the party, but please consider applying! Feel free to ask question here. recruit.apo.ucla.edu/JPF09935

We are now accepting applications for speakers from Native American trainees - if you know of someone who would be a good fit, encourage them to apply! More info in the original thread Apply to be speaker at Full Circle here: forms.gle/dMUtGWvigrNA... PS: We have travel funds available! Plz share!

Our new preprint is out - please share! We asked: How can we make CRISPR knockouts in vivo more efficient? And set up an assay that enables detection of CRISPR cutting with 100s-1000s of sgRNAs over entire chromosome arms in living animals. Grab a ☕ and let’s dive in. 🧵🧪 1/n #CRISPR #geneediting

Biology of Genomes 2025 is coming up: - meeting dates: May 6 - 10, 2025 - abstract deadline: Feb 14, 2025 We hope to see you there for another great meeting with a fantastic speaker lineup! meetings.cshl.edu/meetings.asp...

Excited to share our work @science.org. led by our incredible @tommyz626.bsky.social at @rockefelleruniv.bsky.social! By profiling 21 million single cells across life stages, we reveal aging as distinct, development-like transitions, with dramatic cell population changes in specific time windows!

In a new preprint led by @TheNikhilMilind, we explored a fascinating paradox: For many traits the number of duplications or loss-of-function (LoF) mutations is correlated with phenotype. Curiously, for most traits, the AVERAGE direction of LoFs and Dups is the SAME. Why?

My first post on Blue Sky - moving over ! For all post-docs out there - fantastic opportunity @EMBL. Independent group leader position: Core funding, state-of-the-art core facilities, access to fantastic Ph.D. students, and of course amazing colleagues. Please apply www.embl.org/jobs/positio...

We will be hosting 3rd Full Circle Symposium for Native Biologists hosted at UCSF in April 2025! We aim to build community and provide meaningful opportunities for Native scientists. If you are a Native biologist who is interested plz fill this out to stay up to date: forms.gle/AN7nfkhdB3Fv...

I made a starter pack for those of us interested in or working on T cells. Let me know if you would like to be added or know somebody that should be added. Looking forward to scientific discussions and updates on our favorite immune cell type!

Are you a (or do you know a) recent college graduate who wants to work in human genetics and genomics? Applications are open for the ASHG-NHGRI Post-Baccalaureate Genomics Analyst Fellowship! Great chance to understand how grants and societies work AND get paid. www.ashg.org/careers-lear...

Here are some free/open-source sites for the preparation of scientific illustrations, including icon libraries: bioicons.com, scidraw.io, bioart.niaid.nih.gov, inkscape.org, biogdp.com, reactome.org/icon-lib

Download our database of 492 (!) funding opportunities for EARLY-CAREER FACULTY AND RESEARCHERS. For each entry, we provide link to funder, description, amount, deadline, and eligibility criteria (e.g. citizenship). Download freely here: research.jhu.edu/rdt/funding-...

Interested in Mendelian randomization or GWAS? I thought it could be nice to connect the MR and GWAS community so here is a Starter Pack I'm building! 🧬 #academicsky #genomics #genetics #MR Let me know if you would like to be added or know someone to add. Enjoy and share! go.bsky.app/R19GhDP

Early Career Researchers in Human Genetics Starter Pack! For PhD students, postdocs, and professors to connect with one another! #Academicsky Let me know if you would like to be added 🧬 go.bsky.app/AYgHKYR

I thought it could be nice to connect the community of researchers in human genetics, so here is the Genetics Starter Pack! 🧬 #academicsky Let me know if you would like to be added or know someone to add. Enjoy and share! go.bsky.app/LN2NRuB