Nikhil Milind
@nikhilmilind.dev
PhD Candidate in the Pritchard Lab at Stanford University. Interested in statistical and population genetics.
https://nikhilmilind.dev/
https://nikhilmilind.dev/
Pinned
Nikhil Milind
@nikhilmilind.dev
· Nov 12
For many traits there is a correlation between the number of duplications or loss-of-function (LoF) mutations someone carries, and their phenotype. Curiously, for most traits, these effects are aligned in the SAME direction. Why?
Reposted by Nikhil Milind
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
Apply - Interfolio
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apply.interfolio.com
November 14, 2025 at 3:51 PM
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
Reposted by Nikhil Milind
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.
@simonsfoundation.org. Details to follow. Please RT.
November 14, 2025 at 5:05 PM
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.
@simonsfoundation.org. Details to follow. Please RT.
Reposted by Nikhil Milind
An empirical approach to evaluating the prevalence of long-lived balancing selection in humans--and important limitations. Work by @hannahmm.bsky.social
November 11, 2025 at 7:14 PM
An empirical approach to evaluating the prevalence of long-lived balancing selection in humans--and important limitations. Work by @hannahmm.bsky.social
Reposted by Nikhil Milind
Happy to see this paper from my time with @spicybotrytis.bsky.social out in @theplantcell.bsky.social!
Amanda, a fantastic PhD student with Dan, led this "phylo-functional" work & uncovered complex duplication & loss of a glucosinolate gene across the Brassicaceae affecting enantiomeric specificity
Amanda, a fantastic PhD student with Dan, led this "phylo-functional" work & uncovered complex duplication & loss of a glucosinolate gene across the Brassicaceae affecting enantiomeric specificity
Convergence and constraint in glucosinolate evolution across the Brassicaceae
Studying a glucosinolate enzyme across the Brassicaceae shows evolution of plant specialized metabolism involves independent gene losses, distal duplicatio
academic.oup.com
November 13, 2025 at 4:01 PM
Happy to see this paper from my time with @spicybotrytis.bsky.social out in @theplantcell.bsky.social!
Amanda, a fantastic PhD student with Dan, led this "phylo-functional" work & uncovered complex duplication & loss of a glucosinolate gene across the Brassicaceae affecting enantiomeric specificity
Amanda, a fantastic PhD student with Dan, led this "phylo-functional" work & uncovered complex duplication & loss of a glucosinolate gene across the Brassicaceae affecting enantiomeric specificity
Reposted by Nikhil Milind
Really cool paper that changed the way I think about what GWAS and Burden tests are doing, and also basically made me pleiotropy-pilled
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 12:17 AM
Really cool paper that changed the way I think about what GWAS and Burden tests are doing, and also basically made me pleiotropy-pilled
Reposted by Nikhil Milind
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 Nikhil Milind
If GWAS and burden tests are ranking genes differently then how exactly are they doing that ranking?
More fundamentally, how SHOULD we rank genes?
We propose two possible criteria: trait IMPORTANCE and trait SPECIFICITY.
5/n
More fundamentally, how SHOULD we rank genes?
We propose two possible criteria: trait IMPORTANCE and trait SPECIFICITY.
5/n
November 7, 2025 at 12:05 AM
If GWAS and burden tests are ranking genes differently then how exactly are they doing that ranking?
More fundamentally, how SHOULD we rank genes?
We propose two possible criteria: trait IMPORTANCE and trait SPECIFICITY.
5/n
More fundamentally, how SHOULD we rank genes?
We propose two possible criteria: trait IMPORTANCE and trait SPECIFICITY.
5/n
Reposted by Nikhil Milind
One of the coolest papers I’ve read. Changed the way I think about GWAS and burden testing.
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 12:37 AM
One of the coolest papers I’ve read. Changed the way I think about GWAS and burden testing.
Exciting work by Jeff and Hakhamanesh is now published!
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 12:16 AM
Exciting work by Jeff and Hakhamanesh is now published!
Reposted by Nikhil Milind
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 12:05 AM
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...
Reposted by Nikhil Milind
reminder that my (wonderful, diverse, interdisciplinary) department at the University of Oregon is seeking applications for an Associate/Full Professor of Data Science -- deadline 10/31 and only cover letter/CV needed to apply
academicjobsonline.org/ajo/jobs/30328
academicjobsonline.org/ajo/jobs/30328
University of Oregon, Department of Data Science
Job #AJO30328, 535565 Associate or Full Professor of Data Science, Department of Data Science, University of Oregon, Eugene, Oregon, US
academicjobsonline.org
October 22, 2025 at 6:55 PM
reminder that my (wonderful, diverse, interdisciplinary) department at the University of Oregon is seeking applications for an Associate/Full Professor of Data Science -- deadline 10/31 and only cover letter/CV needed to apply
academicjobsonline.org/ajo/jobs/30328
academicjobsonline.org/ajo/jobs/30328
Reposted by Nikhil Milind
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/...
Reposted by Nikhil Milind
For population genetics and evolutionary biology folks in the Bay Area: the next BAPG will be hosted by Stanford CEHG and the Petrov lab at Stanford on 12/6.
Registration is free but required. The deadline for talk submission is Nov. 16. Hope to see you soon! Pls RT!
docs.google.com/forms/d/e/1F...
Registration is free but required. The deadline for talk submission is Nov. 16. Hope to see you soon! Pls RT!
docs.google.com/forms/d/e/1F...
docs.google.com
October 20, 2025 at 10:42 PM
For population genetics and evolutionary biology folks in the Bay Area: the next BAPG will be hosted by Stanford CEHG and the Petrov lab at Stanford on 12/6.
Registration is free but required. The deadline for talk submission is Nov. 16. Hope to see you soon! Pls RT!
docs.google.com/forms/d/e/1F...
Registration is free but required. The deadline for talk submission is Nov. 16. Hope to see you soon! Pls RT!
docs.google.com/forms/d/e/1F...
Reposted by Nikhil Milind
Have you noticed plane turbulence is getting worse?
It’s not your imagination. It’s climate change.
It’s not your imagination. It’s climate change.
Our new study finds that the upper atmosphere is becoming more sheared and less stratified because of climate change. Both these changes are making the air less stable and more conducive to turbulence.
Published in the November issue of Journal of the Atmospheric Sciences.
doi.org/10.1175/JAS-...
Published in the November issue of Journal of the Atmospheric Sciences.
doi.org/10.1175/JAS-...
October 26, 2025 at 5:11 PM
Have you noticed plane turbulence is getting worse?
It’s not your imagination. It’s climate change.
It’s not your imagination. It’s climate change.
Reposted by Nikhil Milind
We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT
October 15, 2025 at 3:53 PM
We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT
Reposted by Nikhil Milind
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 Nikhil Milind
En route to Boston for #ASHG25 #ASHG2025!
👉 I'll be presenting a poster on our new work on genome-wide perturb-seq screens in primary human T cells (5049W, Wed 2.30pm)
👉 you can hear me talk about it at the Industry Education session presented by Ultima Genomics (Thu 3pm) [1/2]
👉 I'll be presenting a poster on our new work on genome-wide perturb-seq screens in primary human T cells (5049W, Wed 2.30pm)
👉 you can hear me talk about it at the Industry Education session presented by Ultima Genomics (Thu 3pm) [1/2]
October 13, 2025 at 11:19 PM
Reposted by Nikhil Milind
I want to try something again at #ASHG25 this year: I'll block some time on Thursday and Friday afternoons to meet with trainees who would be interested to chat on any topic.
I did this last year and it was great to meet a whole bunch of new people, at all career stages!
I did this last year and it was great to meet a whole bunch of new people, at all career stages!
October 6, 2025 at 11:14 PM
I want to try something again at #ASHG25 this year: I'll block some time on Thursday and Friday afternoons to meet with trainees who would be interested to chat on any topic.
I did this last year and it was great to meet a whole bunch of new people, at all career stages!
I did this last year and it was great to meet a whole bunch of new people, at all career stages!
Excited to be presenting part of my thesis at VESS! I’ll be discussing work from my recent pre-print on gene dosage response curves. Drop by if you’ve been curious but haven’t had a chance to read it yet!
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
October 10, 2025 at 4:50 PM
Excited to be presenting part of my thesis at VESS! I’ll be discussing work from my recent pre-print on gene dosage response curves. Drop by if you’ve been curious but haven’t had a chance to read it yet!
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Nikhil Milind
Reposted by Nikhil Milind
Reposted by Nikhil Milind
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
Reposted by Nikhil Milind
SINGER, our ARG inference method, is finally published and freely available online:
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes - Nature Genetics
SINGER is a method for creating ancestral recombination graphs to understand the genealogical history of genomes. The method has increased speed, and thus scalability, without sacrificing accuracy.
doi.org
September 11, 2025 at 3:50 AM
SINGER, our ARG inference method, is finally published and freely available online:
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
Reposted by Nikhil Milind
Why do males and females often differ in traits?
The expected answer: selection.
But our new paper in GENETICS shows that genetic drift alone can generate sexual dimorphism — even when male & female optima are the same
The expected answer: selection.
But our new paper in GENETICS shows that genetic drift alone can generate sexual dimorphism — even when male & female optima are the same
August 23, 2025 at 11:12 PM
Why do males and females often differ in traits?
The expected answer: selection.
But our new paper in GENETICS shows that genetic drift alone can generate sexual dimorphism — even when male & female optima are the same
The expected answer: selection.
But our new paper in GENETICS shows that genetic drift alone can generate sexual dimorphism — even when male & female optima are the same
Reposted by Nikhil Milind
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...
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...
August 22, 2025 at 7:50 PM
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...
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...