Job opening: I'm looking for a lab tech primarily supporting ongoing projects and running computational analyses for the lab. Apply here and reach out with questions! utah.peopleadmin.com/postings/205...

For the last 5 years, my lab has focused on developing mutational scanning methods and learning how to answer specific questions in protein biology. @matthewkhoward.bsky.social and I wrote a review on experimental decisions and future directions for our nascent field! doi.org/10.1146/annu...

Mechanistic Mutational Scanning to Uncover the Secret Life of Proteins

Deep mutational scanning (DMS) has emerged as a transformative tool for dissecting individual protein function and broader cell biology. DMS methods enable comprehensive interrogation of sequence–func...

annualreviews.org

What if an embryo made immune cells before it finished building the tissue they usually come from? In our new preprint, we show that annual killifish embryos specify neutrophils before germ layers are fully resolved. www.biorxiv.org/content/10.6... Huge thanks to my PI, @ohnolog.bsky.social ! 🧵

Early immune cell development precedes gastrulation in annual killifish

During embryogenesis, cell types arise in a predictable order because developmental regulators act sequentially. But how evolutionary changes in morphogenesis reshape the signaling environments that a...

biorxiv.org

Delighted to share our lab's latest (w/ inimitable @genophoria.bsky.social) in final form at @nature.com. Enormous lift by Sean Wang, @palindromephd.bsky.social & @martyyang.bsky.social to address extensive & constructive reviewer comments & see this through. (1/n) www.nature.com/articles/s41...

Pervasive and programmed nucleosome distortion on single chromatin fibres - Nature

An analytical pipeline called Iteratively Defined Lengths of Inaccessibility (IDLI) maps the genome-wide occupancy of a range of nucleosome types and shows that most nucleosomes exhibit programmed ‘di...

nature.com

We’re hiring a Junior Specialist in the Calderon Lab. Great fit for someone thinking about grad school who wants hands-on experience in functional genomics (MPRA, single-cell), contribute to ongoing projects, and grow into more independent work over time. Apply by 4/24: aprecruit.ucsf.edu/JPF06010

Junior Specialist- Calderon Lab

University of California, San Francisco is hiring. Apply now!

aprecruit.ucsf.edu

New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth. www.biorxiv.org/content/10.6...

New paper alert 🚀 Our organism-wide single-cell ATAC-seq atlas of mammalian aging is now out in @science.org, led by our fantastic graduate student Ziyu Lu from @rockefeller.edu! www.science.org/doi/10.1126/...

Over a year ago, along with Gary Churchill at Jackson Labs, we explored the impact of dietary restriction on lifespan in one of the largest studies using 960 female Diversity Outbred mice. Caloric restriction and intermittent fasting both extended lifespan proportionally to the level of restriction.

Happy to share that our review on mammalian genome writing with Jack Atwater, Ran Brosh, Jef Boeke, @jshendure.bsky.social and Matt Maurano is now out in @cellpress.bsky.social! www.sciencedirect.com/science/arti...

Mammalian genome writing: Unlocking new length scales for genome engineering

The ability to design and engineer mammalian genomes across arbitrary length scales would transform biology and medicine. Such capabilities would enab…

sciencedirect.com

Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk. First authors: @saracarioscia.bsky.social & @aabiddanda.github.io

Common variation in meiosis genes shapes human recombination and aneuploidy - Nature

Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...

nature.com

Three years ago, we showed ~70% of lifespan variation in yeast traces to rDNA copy number. Ribosomal DNA, encoded as 5S and 45S subunits in hundreds of copies, vary substantially across humans. Does this copy number variation, and sequence variation within these paralogs, matter for humans?

Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025

Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits

Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...

tinyurl.com

My lab is recruiting postdocs in AI/ML for genetics & genomics through the Malone Postdoctoral Fellows program. Apply by Jan 30! Lots of other great labs across the Malone Center as well.

JHU Malone Center for Engineering in Healthcare@jhumceh.bsky.social · 8mo ago

Looking for a postdoc opportunity in computational & engineering applications in medicine & health care? Apply to the Malone Fellows Program and work with mentors in genomics, AI/data science, robotics, human-computer interaction, augmented/virtual reality, & more. Deadline coming up: Jan 31, 2025

Open faculty position (Assistant or Associate) in UW Medical Genetics. As you might expect, faculty often end up also interacting with Genome Sciences, so we're hoping for some great prospects! Note the clinical requirements for the position. apply.interfolio.com/176466

My lab at UCSF is recruiting postdoc candidates interested in CRISPR synthetic biology and functional genomics approaches to study and engineer tissue injury responses! hsiunglab.org

Super cool paper from Sheel Chandra + Ziyue Gao. kmer context matters a lot for mutability of both methylated and unmethylated CpGs. But!! the effect of kmer context on unmethylated CpGs is basically independent of the effect of kmer context on methylated CpGs! www.biorxiv.org/content/10.1...

Sequence context and methylation interact to shape germline mutation rate variation at CpG sites

A prominent example of sequence context-dependent mutation rate variation is the elevated transition rate at CpG sites, which is largely attributed to cytosine methylation. CpGs with different flankin...

biorxiv.org

My center at NYU SoM is hiring an Assistant/Associate Professor in human genetics and genomics. It's a wonderful place to do science. Please apply or pass along. apply.interfolio.com/177375

Our work developing a parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording is now out @natbiotech.nature.com

Nature Biotechnology@natbiotech.nature.com · 9mo ago

A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - @jshendure.bsky.social @troymcdiarmid.bsky.social @uwgenome.bsky.social go.nature.com/49eTPCu

🚀 Very excited to share the first major work from my PhD!! We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬 www.biorxiv.org/content/10.1...

How do GWAS and rare variant burden tests rank gene signals? In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck! 🧬🧪🧵 www.nature.com/articles/s41...

Specificity, length and luck drive gene rankings in association studies - Nature

Genetic association tests prioritize candidate genes based on different criteria.

nature.com

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.

Thrilled to share I’ve started my lab at Dartmouth’s Geisel School of Medicine! We focus on mapping cellular trajectories & TF networks in development and Mendelian disorders, exploring new therapies. Join us—postdocs, grads, and scientists welcome! sites.dartmouth.edu/qiulab/

🚨PhD opportunity at the intersection of computation & biology! 🖥️🧬🧪 Ready to tackle complex biological problems with cutting-edge tools? The BMI PhD program @UCSF trains future leaders in comp bio, bioinformatics, & data science. 📢 Info session: 11/6 @ 1 PM PT bmi.ucsf.edu/admissions Learn more👇

Building community! Finishing undergrad (or just finished) and interested in gaining research experience before applying to PhD programs and also want to be part of a group that cares about you? Join our next matchmaking event!! Jan 30th 9am - 1pm PT propelscholars.org/matchmaking-...

UCSF PROPEL@ucsf-propel.bsky.social · 10mo ago

Pumpkins, networking, and good vibes 🎃✨ Join us Oct 30 (4–6 PM) at Mission Hall MH1407 for our Fall Networking Event! 📍RSVP with the Partiful link!

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...

bioRxiv Genetics@biorxiv-genetic.bsky.social · 10mo ago

Cell villages and Dirichlet modeling map human cell fitness genetics https://www.biorxiv.org/content/10.1101/2025.09.26.678880v1

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)

The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers

DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...

biorxiv.org

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