Hakhamanesh Mostafavi
@hakha.bsky.social
Assistant Professor at NYU Langone. Genetics, evolution and biology of complex traits and diseases.
Pinned
Hakhamanesh Mostafavi
@hakha.bsky.social
· Jul 25
I'm thrilled that my lab at NYU is now supported by an NIH MIRA grant! I'm looking to hire 1-2 senior lab members (outstanding postdoc candidates or experienced staff scientists) with expertise in computational or statistical methods in human genetics or genomics. Please share!
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.
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...
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.
www.nature.com
November 7, 2025 at 6:33 PM
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.
Reposted by Hakhamanesh Mostafavi
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:
We describe a critical concept that we call *specificity*.
Led by Jeff Spence and Hakhamanesh Mostafavi:
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...
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.
www.nature.com
November 7, 2025 at 4:08 AM
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:
We describe a critical concept that we call *specificity*.
Led by Jeff Spence and Hakhamanesh Mostafavi:
Reposted by Hakhamanesh Mostafavi
How does life evolve to adapt to modern cities?
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Ancient origin of an urban underground mosquito
Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...
www.science.org
October 25, 2025 at 4:46 AM
How does life evolve to adapt to modern cities?
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Reposted by Hakhamanesh Mostafavi
Why do complex traits differ in their genetic architecture?
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
Simple scaling laws control the genetic architectures of human complex traits
Genome-wide association studies have revealed that the genetic architectures of complex traits vary widely. This study shows that differences in architectures of highly polygenic traits arise mainly f...
journals.plos.org
October 24, 2025 at 1:51 AM
Why do complex traits differ in their genetic architecture?
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
I’ll be attending #ASHG25! I’m currently hiring for (i) a Senior Research Scientist or (ii) a Postdoc position in my lab. If you’re interested, please reach out to arrange a time to meet and discuss.
October 13, 2025 at 11:19 PM
I’ll be attending #ASHG25! I’m currently hiring for (i) a Senior Research Scientist or (ii) a Postdoc position in my lab. If you’re interested, please reach out to arrange a time to meet and discuss.
Reposted by Hakhamanesh Mostafavi
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.
August 6, 2025 at 5:18 PM
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.
Reposted by Hakhamanesh Mostafavi
The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs:
probgen2026.github.io
Please help spread the news.
probgen2026.github.io
Please help spread the news.
Home - ProbGen 2026
Your Site Description
probgen2026.github.io
June 6, 2025 at 5:52 PM
The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs:
probgen2026.github.io
Please help spread the news.
probgen2026.github.io
Please help spread the news.
I'm thrilled that my lab at NYU is now supported by an NIH MIRA grant! I'm looking to hire 1-2 senior lab members (outstanding postdoc candidates or experienced staff scientists) with expertise in computational or statistical methods in human genetics or genomics. Please share!
July 25, 2025 at 8:29 PM
I'm thrilled that my lab at NYU is now supported by an NIH MIRA grant! I'm looking to hire 1-2 senior lab members (outstanding postdoc candidates or experienced staff scientists) with expertise in computational or statistical methods in human genetics or genomics. Please share!
A brief musical note: I’m very excited to share that my brilliant wife, a pianist and composer, has just released her debut album featuring works by Iranian women composers, including one of her own. Here is the link in case you’d like to take a listen: www.navonarecords.com/catalog/nv67...
Nahoft – Navona Records
Drawing its name from a melodic motif found in Iranian music, NAHOFT is the culmination of pianist Ava Nazar’s collaboration with the Iranian Female Composers Association, showcasing six woman compose...
www.navonarecords.com
July 21, 2025 at 2:55 AM
A brief musical note: I’m very excited to share that my brilliant wife, a pianist and composer, has just released her debut album featuring works by Iranian women composers, including one of her own. Here is the link in case you’d like to take a listen: www.navonarecords.com/catalog/nv67...
Reposted by Hakhamanesh Mostafavi
Staff scientist position (computational):
I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
July 7, 2025 at 3:27 PM
Staff scientist position (computational):
I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
It was fun writing this short piece on the omnigenic model. Sharing it here, though it's a painful time as my family, along with millions of others, is at risk in Iran and the region.
New online! Making sense of the polygenicity of complex traits
Making sense of the polygenicity of complex traits
Nature Reviews Genetics, Published online: 16 June 2025; doi:10.1038/s41576-025-00866-7Hakhamanesh Mostafavi recalls a landmark paper by Boyle et al. on the omnigenic model, which proposed that complex traits are influenced by thousands of genes across the genome, including many that are only indirectly related to a trait through regulatory networks.
www.nature.com
June 17, 2025 at 3:15 PM
It was fun writing this short piece on the omnigenic model. Sharing it here, though it's a painful time as my family, along with millions of others, is at risk in Iran and the region.
Reposted by Hakhamanesh Mostafavi
Thanks to everybody who chimed in!
I arrived at the conclusion that (1) there's a lot of interesting stuff about interactions and (2) the figure I was looking for does not exist.
So, I made it myself! Here's a simple illustration of how to control for confounding in interactions:>
I arrived at the conclusion that (1) there's a lot of interesting stuff about interactions and (2) the figure I was looking for does not exist.
So, I made it myself! Here's a simple illustration of how to control for confounding in interactions:>
May 11, 2025 at 5:34 AM
Thanks to everybody who chimed in!
I arrived at the conclusion that (1) there's a lot of interesting stuff about interactions and (2) the figure I was looking for does not exist.
So, I made it myself! Here's a simple illustration of how to control for confounding in interactions:>
I arrived at the conclusion that (1) there's a lot of interesting stuff about interactions and (2) the figure I was looking for does not exist.
So, I made it myself! Here's a simple illustration of how to control for confounding in interactions:>
Reposted by Hakhamanesh Mostafavi
Amidst all the terrible and terrifying news, so lovely to hear of
@jkpritch.bsky.social's election to the National Academy of Sciences. Congratulations!
@jkpritch.bsky.social's election to the National Academy of Sciences. Congratulations!
April 29, 2025 at 8:52 PM
Amidst all the terrible and terrifying news, so lovely to hear of
@jkpritch.bsky.social's election to the National Academy of Sciences. Congratulations!
@jkpritch.bsky.social's election to the National Academy of Sciences. Congratulations!
I've been singing with the Bronx County Chorus since 2015. It's a beautiful, intergenerational community bringing free music to the Bronx since the 1930s. With grants shrinking, they now need support to keep going. If you can, please consider helping: www.gofundme.com/f/support-th...
Donate to Support the Longest Running Community Chorus in the Bronx!, organized by Denise Wharton
Keep the Bronx Singing – Support the Bronx County Chorus!
… Denise Wharton needs your support for Support the Longest Running Community Chorus in the Bronx!
www.gofundme.com
April 28, 2025 at 2:24 PM
I've been singing with the Bronx County Chorus since 2015. It's a beautiful, intergenerational community bringing free music to the Bronx since the 1930s. With grants shrinking, they now need support to keep going. If you can, please consider helping: www.gofundme.com/f/support-th...
Reposted by Hakhamanesh Mostafavi
Posting on behalf of Shamil Sunyaev: Eimear(Vice Chair) and I (Chair) are organizing the 2025 Gordon Research Conference (GRC) on Human Genetics and Genomics, which will be held on July 6-11, 2025 in beautiful University of Southern Maine, Portland, Maine.
2025 Human Genetics and Genomics Conference GRC
The 2025 Gordon Research Conference on Human Genetics and Genomics will be held in Portland, Maine. Apply today to reserve your spot.
www.grc.org
April 24, 2025 at 2:31 PM
Posting on behalf of Shamil Sunyaev: Eimear(Vice Chair) and I (Chair) are organizing the 2025 Gordon Research Conference (GRC) on Human Genetics and Genomics, which will be held on July 6-11, 2025 in beautiful University of Southern Maine, Portland, Maine.
Reposted by Hakhamanesh Mostafavi
A really nice paper by @drghawkes.bsky.social et al. argues that rare and common genetic associations converge on the same genes.
While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6)
www.biorxiv.org/content/10.1...
While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6)
www.biorxiv.org/content/10.1...
Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations
Genetic association studies have mostly focussed on common variants from genotyping arrays or rare protein-coding variants from exome sequencing. Here, we used whole-genome sequence (WGS) data in 672,...
www.biorxiv.org
March 28, 2025 at 1:22 AM
A really nice paper by @drghawkes.bsky.social et al. argues that rare and common genetic associations converge on the same genes.
While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6)
www.biorxiv.org/content/10.1...
While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6)
www.biorxiv.org/content/10.1...
Reposted by Hakhamanesh Mostafavi
One month to go until the CSHL Biology of Genomes abstract deadline! My all-time fav meeting, and one of the few covering genomics broadly. We have a ✨🤩 lineup of speakers, but it's the abstract talks & posters that really make the meeting - send us your best work! meetings.cshl.edu/meetings.asp...
January 14, 2025 at 1:57 PM
One month to go until the CSHL Biology of Genomes abstract deadline! My all-time fav meeting, and one of the few covering genomics broadly. We have a ✨🤩 lineup of speakers, but it's the abstract talks & posters that really make the meeting - send us your best work! meetings.cshl.edu/meetings.asp...
Reposted by Hakhamanesh Mostafavi
Think of a polygenic score you care about. Are direct genetic effects driving variation among people in this predictor? Or perhaps other, confounding factors? We at the @arbelharpak.bsky.social & @docedge.bsky.social Labs developed a method to tackle this question. [1/n]
A Litmus Test for Confounding in Polygenic Scores
Polygenic scores (PGSs) are being rapidly adopted for trait prediction in the clinic and beyond. PGSs are often thought of as capturing the direct genetic effect of one's genotype on their phenotype. ...
www.biorxiv.org
February 4, 2025 at 6:04 PM
Think of a polygenic score you care about. Are direct genetic effects driving variation among people in this predictor? Or perhaps other, confounding factors? We at the @arbelharpak.bsky.social & @docedge.bsky.social Labs developed a method to tackle this question. [1/n]
Reposted by Hakhamanesh Mostafavi
The distribution of highly deleterious variants across human ancestry groups https://www.biorxiv.org/content/10.1101/2025.01.31.635988v1
February 1, 2025 at 11:32 AM
The distribution of highly deleterious variants across human ancestry groups https://www.biorxiv.org/content/10.1101/2025.01.31.635988v1
Reposted by Hakhamanesh Mostafavi
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!)
(I tweeted about our preprint in 2023 over at the bad place, but deactivated my account, so here we go again!)
A genome-wide atlas of human cell morphology - Nature Methods
An optical pooled cell profiling platform (PERISCOPE) based on Cell Painting and optical sequencing of molecular barcodes was used to develop the first unbiased genome-wide morphology-based perturbati...
www.nature.com
January 27, 2025 at 6:23 PM
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!)
(I tweeted about our preprint in 2023 over at the bad place, but deactivated my account, so here we go again!)
Reposted by Hakhamanesh Mostafavi
How population stratification makes environments look like genes. A short 🧵:
January 20, 2025 at 7:09 PM
How population stratification makes environments look like genes. A short 🧵:
Reposted by Hakhamanesh Mostafavi
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 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
January 26, 2025 at 12:13 AM
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 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
Reposted by Hakhamanesh Mostafavi
Very excited about this new work from our lab! Explainer thread coming soon
@minetoota.bsky.social
@minetoota.bsky.social
Causal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq https://www.biorxiv.org/content/10.1101/2025.01.22.634424v1
January 24, 2025 at 4:45 PM
Very excited about this new work from our lab! Explainer thread coming soon
@minetoota.bsky.social
@minetoota.bsky.social
Reposted by Hakhamanesh Mostafavi
I am excited to share the first first-author paper of my PhD describing work with Changde Cheng, Mark Kirkpatrick and @arbelharpak.bsky.social has been published at AJHG! We ask if sex-differential gene expression drives sex-differential selection in humans. (1/14)
www.cell.com/ajhg/fulltex...
www.cell.com/ajhg/fulltex...
No evidence for sex-differential transcriptomes driving genome-wide sex-differential natural selection
We assess the evidence for a genome-wide relationship between sex differences in gene
expression and sex differences in natural selection. We develop an improved model
for testing this association but...
www.cell.com
January 14, 2025 at 10:35 PM
I am excited to share the first first-author paper of my PhD describing work with Changde Cheng, Mark Kirkpatrick and @arbelharpak.bsky.social has been published at AJHG! We ask if sex-differential gene expression drives sex-differential selection in humans. (1/14)
www.cell.com/ajhg/fulltex...
www.cell.com/ajhg/fulltex...
Reposted by Hakhamanesh Mostafavi
Our daughter's wonderful teacher and her family lost everything in the Eaton fire. If you can spare a few dollars to help out, I would be grateful www.gofundme.com/f/help-the-l...
Donate to Help the Lim Family rebuild after the Altadena Eaton Fire, organized by roy yoo
On Wednesday, January 7th, the devastating Eaton fire in Altadena, C… roy yoo needs your support for Help the Lim Family rebuild after the Altadena Eaton Fire
www.gofundme.com
January 10, 2025 at 6:40 AM
Our daughter's wonderful teacher and her family lost everything in the Eaton fire. If you can spare a few dollars to help out, I would be grateful www.gofundme.com/f/help-the-l...