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...
Hakhamanesh Mostafavi
@hakha.bsky.social
Assistant Professor at NYU Langone. Genetics, evolution and biology of complex traits and diseases.
I’m looking to hire one or two postdocs - possible projects include pop gen theory, methods development, and human evolutionary inference. Please share, and email if you are interested. More info: evoldir.net/brian/evoldi...
evoldir.net
Happy to have the chance to share this commentary by @will-milligan.bsky.social & me: rdcu.be/fldBs.
Adaptation: by giant leaps or many tiny steps?
Nature Reviews Genetics - In this Comment, the authors argue that understanding the genetic basis of adaptation requires considering the genetic architecture and ecological properties of traits...
rdcu.be
I'm excited to share that our work studying gene dosage response curves (GDRCs) is now out in Cell Genomics (@cellpress.bsky.social). www.cell.com/cell-genomic... [1/n]
Buffering of gene dosage response curves for human complex traits
Milind et al. explore why loss-of-function variants and duplications tend to have average effects in the same direction on 94 complex traits. Using gene dosage response curves (GDRCs), they gather evi...
cell.com
Happy to share that this is now out in Cell Genomics and a featured paper for Multi-Journal Submission from @cellpress.bsky.social — many thanks to the editorial team + our reviewers! Short recap + some further thoughts on the paper ⬇️ [1/7] www.cell.com/cell-genomic...
Matthew Aguirre@aguirre404.bsky.social · 12mo agoThrilled 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...
Great work from Sheel Chandra and Ziyue Gao: “Overall, our findings reveal that the base composition at polymorphic sites is strongly shaped by the interaction between demographic history, mutation bias, and gBGC, and does not represent stable, genome-wide trends.”
bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 3mo agoInterpreting GC content differences across populations at polymorphic sites https://www.biorxiv.org/content/10.64898/2026.05.16.725686v1
Happy to highlight new findings by Vanesa Getseva and Lin Poyraz about the sources of variation in germline mutation rates among humans: www.biorxiv.org/content/10.6... Joint work with Anastasia Stolyarova and @ipsitaagarwal.bsky.social. 1/n
A sibling study of variation in parental mutation rates
People are born with variable numbers of de novo germline mutations (DNMs), depending primarily on the ages of their parents. To explore additional causes, we developed an approach to call DNMs from nucleotide differences between siblings in genomic regions inherited identical by descent from both parents. Applying it to whole genome sequences from 28,985 sibling pairs of diverse genetic ancestries present in the UK Biobank and All of Us datasets, as well as 2,330 trios, we identified >800K autosomal DNMs and characterized mutation phenotypes in 27,645 sets of parents. We found subtle shifts in the mutation spectrum but no differences in total DNM rates among genetic ancestry groups, or between smokers and non-smokers. Testing for associations between parental mutation phenotypes and their burden of loss-of-function and deleterious missense variants in a set of 180 DNA repair and maintenance genes, we discovered that disruptions in REV1 and LIG1 increase germline mutation rates, and thus that rare mutator alleles segregate in population cohorts. ### Competing Interest Statement The authors have declared no competing interest. NIH, R35 GM083098
biorxiv.org
I am hiring a popgen postdoc! Looking for a creative scientist to join us at USC to investigate recessive variation and complex traits in model or non-model species. The project is funded by a multi-year NIH grant, contract can be renewed. Job add & details 👇🏽 usccareers.usc.edu/job/los-ange...
The program for the 2026 New York Population Genetics meeting, hosted by at the @simonsfoundation.org on March 9th 2026, is now up: events.simonsfoundation.org/event/7c91dd....
NY Population Genetics meeting
events.simonsfoundation.org
Registration for the 2026 NY Area Population Genetics meeting is now open, at events.simonsfoundation.org/e0mEoL?rt=8k.... Registration is free but required; if you are submitting an abstract, note that the deadline is *January 30th*.
Home - NY Population Genetics meeting
events.simonsfoundation.org
Molly Przeworski@mollyprz.bsky.social · 9mo agoSAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the @simonsfoundation.org. Details to follow. Please RT.
I'm just delighted to announce our new preprint on genome-scale perturb-seq in CD4+ T cells. We learned both general lessons about the power of perturb-seq, and specific lessons about T cell biology. Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Emma Dann@emmamarydann.bsky.social · 7mo agoTogether 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
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
New preprint alert: we use sign errors as a test of how well TWAS works. Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
Nikhil Milind@nikhilmilind.dev · 7mo agoHow well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time! doi.org/10.64898/202... 1/n
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time! doi.org/10.64898/202... 1/n
High false sign rates in transcriptome-wide association studies
Transcriptome-wide association studies (TWAS) are widely used to identify genes involved in complex traits and to infer the direction of gene effects on traits. However, despite their popularity, it r...
doi.org
I guess the preprint came out in 2024 but it was published this year so I'll say this paper from @jeffspence.github.io and @hakha.bsky.social which is probably the paper that pleiotropy-pilled me the most. Really got me to think about what GWAS means 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
Dmitri Petrov@petrovadmitri.bsky.social · 8mo agoAll right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.
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 agoLooking 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
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult. Our latest work on causal models for this is out yesterday: www.nature.com/articles/s41... A short🧵:
Causal modelling of gene effects from regulators to programs to traits - Nature
Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.
nature.com
After time in the Bay Area, I’ve started a new role as Lecturer in the Department of Allergy and Rheumatology at the University of Tokyo. We’re the group of clinicians who see patients with autoimmune diseases, while researching new treatments and patient stratification. (continued)
Thank you Alex! Excited to see our paper published in @nature.com ! Huge thanks to @jeffspence.github.io , @tkyzeng.bsky.social , @emmamarydann.bsky.social, @nikhilmilind.dev, @marsonlab.bsky.social, @jkpritch.bsky.social, and all the members of the Pritchard and Marson labs for your enormous help!
Causal modelling of gene effects from regulators to programs to traits
Nature - Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.
rdcu.be
Marson Lab@marsonlab.bsky.social · 8mo agoOur latest collaboration with @jkpritch.bsky.social – led by joint post-doc Mineto Ota – is in @nature.com today: www.nature.com/articles/s41...
As promised, a longer thread on what I consider to be some of the most interesting and important contributions of this paper (1/10)
Roshni Patel@roshnipatel.bsky.social · 8mo agoHere, we show that the genetic relatedness matrix (GRM) can be used to control this type of genetic confounding. (Though our model has not been explicitly described in prior literature, we show that it is the basis for existing methods to control genetic confounding... but more on that later.) (4/6)
It was a total pleasure to work with @roshnipatel.bsky.social on this, who really led the charge in all respects. Anyone interested in learning about the intersection of population genetics and statistical genetics should check out her new lab in Oregon!
Roshni Patel@roshnipatel.bsky.social · 8mo agoExcited to share work from my postdoc with @docedge.bsky.social and collaborators Matt Pennell and @jgschraiber.bsky.social, newly out over the weekend: www.biorxiv.org/content/10.1... (1/6)
Excited to share a preprint of my PhD project looking at interactions between SNPs and polygenic scores in the UK Biobank! A thread... 🧵 www.medrxiv.org/content/10.1...
Interactions with polygenic background impact quantitative traits in the UK Biobank
Association studies have linked many genetic variants to a variety of phenotypes but under-standing the biological mechanisms underlying these signals remains a major challenge. Since genes operate wi...
medrxiv.org
#OnThisDay in 1859, Charles Darwin's On the Origin of Species was first published. Much of the original manuscript was used as scrap paper by Darwin's children. On the back of this painting of a house is an original manuscript page from Origin! #CambridgeUniversityLibrary (DAR 185)
@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪 www.nature.com/articles/d41...
How do genetic association studies rank genes?
Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology.
nature.com
SAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the @simonsfoundation.org. Details to follow. Please RT.
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
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An empirical approach to evaluating the prevalence of long-lived balancing selection in humans--and important limitations. Work by @hannahmm.bsky.social
Hannah Munby (@hannahmm.bsky.social)
PhD candidate @ Biological Sciences, Columbia
hannahmm.bsky.social
bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 9mo agoRevisiting the evidence for long-lived balancing selection in humans. https://www.biorxiv.org/content/10.1101/2025.11.10.687682v1
Very excited for our paper in @nature.com on what genes association studies discover and why. It was a privilege to work closely with @jeffspence.github.io, @jkpritch.bsky.social, and our collaborators.
Jeff Spence@jeffspence.github.io · 9mo agoHow 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...
Excited to share our latest work on the factors that determine what genes we find (and don't find!) in GWAS and burden tests. We describe a critical concept that we call *specificity*. Led by Jeff Spence and Hakhamanesh Mostafavi:
Jeff Spence@jeffspence.github.io · 9mo agoHow 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...