Jeff Spence
@jeffspence.github.io
assistant professor at ucsf interested in genetics, statistics, etc…
jeffspence.github.io
jeffspence.github.io
Pinned
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
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 Jeff Spence
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
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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 Jeff Spence
Yes! And also we have an exciting announcement - we are so lucky to have the privilege of having Brenna Henn give the keynote. hennlab.ucdavis.edu
November 13, 2025 at 8:37 PM
Yes! And also we have an exciting announcement - we are so lucky to have the privilege of having Brenna Henn give the keynote. hennlab.ucdavis.edu
Reposted by Jeff Spence
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A
Insertion of an invading retrovirus regulates a novel color trait in swordtail fish
For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable wi...
shorturl.at
November 12, 2025 at 8:34 PM
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A
Reposted by Jeff Spence
First time on Bsky and first big announcement!
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
Estimation and mapping of the missing heritability of human phenotypes - Nature
WGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 co...
www.nature.com
November 12, 2025 at 5:57 PM
First time on Bsky and first big announcement!
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
Reposted by Jeff Spence
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 Jeff Spence
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:15 PM
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jeff Spence
New preprint by Hannah Munby and @mollyprz.bsky.social:
“Revisiting the evidence for long-lived balancing selection in humans” 🧪🧬
www.biorxiv.org/content/10.1...
“Revisiting the evidence for long-lived balancing selection in humans” 🧪🧬
www.biorxiv.org/content/10.1...
Revisiting the evidence for long-lived balancing selection in humans.
Balancing selection maintains variation in a population longer than expected under neutrality. In humans, there are dozens of tentative candidate loci for balancing selection, but only a handful of we...
www.biorxiv.org
November 11, 2025 at 1:06 PM
New preprint by Hannah Munby and @mollyprz.bsky.social:
“Revisiting the evidence for long-lived balancing selection in humans” 🧪🧬
www.biorxiv.org/content/10.1...
“Revisiting the evidence for long-lived balancing selection in humans” 🧪🧬
www.biorxiv.org/content/10.1...
Reposted by Jeff Spence
Introducing Nona! 🧬 @suragnair.bsky.social 's brilliant idea to unify siloed genomic AI. Nona learns jointly from DNA seq + functional data, enabling new ways of modeling genomic data!
November 10, 2025 at 9:03 PM
Introducing Nona! 🧬 @suragnair.bsky.social 's brilliant idea to unify siloed genomic AI. Nona learns jointly from DNA seq + functional data, enabling new ways of modeling genomic data!
Reposted by Jeff Spence
Nature research paper: Specificity, length and luck drive gene rankings in association studies
go.nature.com/47Fsqax
go.nature.com/47Fsqax
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
go.nature.com
November 10, 2025 at 11:36 AM
Nature research paper: Specificity, length and luck drive gene rankings in association studies
go.nature.com/47Fsqax
go.nature.com/47Fsqax
Reposted by Jeff Spence
I'm on the academic job market!
I design and analyze probabilistic machine-learning methods---motivated by real-world scientific constraints, and developed in collaboration with scientists in biology, chemistry, and physics.
A few highlights of my research areas are:
I design and analyze probabilistic machine-learning methods---motivated by real-world scientific constraints, and developed in collaboration with scientists in biology, chemistry, and physics.
A few highlights of my research areas are:
November 7, 2025 at 2:47 PM
I'm on the academic job market!
I design and analyze probabilistic machine-learning methods---motivated by real-world scientific constraints, and developed in collaboration with scientists in biology, chemistry, and physics.
A few highlights of my research areas are:
I design and analyze probabilistic machine-learning methods---motivated by real-world scientific constraints, and developed in collaboration with scientists in biology, chemistry, and physics.
A few highlights of my research areas are:
Reposted by Jeff Spence
¿Hiciste tu doctorado en México? ¿Quieres hacer un postdoc en California? ¿Te interesa la genética evolutiva? ¡Checa esta beca y mándame un mensaje! alianzamx.universityofcalifornia.edu/research-and...
Postdoctoral Research Fellowships - University of California Alianza MX
Submitting an Application Current Fellows 2025 Cohort Additional Information Humberger Toggle Menu Interested in applying for a Postdoctoral Research Fellowship? Eligibility The program seeks applican...
alianzamx.universityofcalifornia.edu
November 7, 2025 at 10:47 PM
¿Hiciste tu doctorado en México? ¿Quieres hacer un postdoc en California? ¿Te interesa la genética evolutiva? ¡Checa esta beca y mándame un mensaje! alianzamx.universityofcalifornia.edu/research-and...
Reposted by Jeff Spence
Our new manuscript, led by Emily Corrigan, examines inhibitory neuron diversity across approximately 160 million years of evolutionary divergence, as part of BRAIN Initiative Cell Atlas Network (BICAN) developing brain atlas package: www.nature.com/articles/s41...
Conservation and alteration of mammalian striatal interneurons - Nature
An analysis of cell-type diversity in brain samples from a variety of mammalian species, both during development and in adult animals, reveals that the TAC3 initial class of striatal interneurons is c...
www.nature.com
November 7, 2025 at 6:06 PM
Our new manuscript, led by Emily Corrigan, examines inhibitory neuron diversity across approximately 160 million years of evolutionary divergence, as part of BRAIN Initiative Cell Atlas Network (BICAN) developing brain atlas package: www.nature.com/articles/s41...
Reposted by Jeff Spence
Exciting new study led by @ekerdoncuff.bsky.social and @meaghanmarohn.bsky.social on the evolution of Lactase Persistence in South Asia.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes
Lactase persistence (LP), the ability to digest lactose from milk into adulthood, is a classic example of natural selection in humans. Multiple mutations upstream of the LCT gene are associated with L...
www.biorxiv.org
November 7, 2025 at 2:33 PM
Exciting new study led by @ekerdoncuff.bsky.social and @meaghanmarohn.bsky.social on the evolution of Lactase Persistence in South Asia.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jeff Spence
Super interesting thread and paper
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 5:29 AM
Super interesting thread and paper
Reposted by Jeff Spence
Outstanding work by @jeffspence.github.io @hakha.bsky.social
@jkpritch.bsky.social & colleagues
“Specificity, length and luck drive gene rankings in association studies”, out in @nature.com
🧪🧬
👇
@jkpritch.bsky.social & colleagues
“Specificity, length and luck drive gene rankings in association studies”, out in @nature.com
🧪🧬
👇
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 6:59 AM
Outstanding work by @jeffspence.github.io @hakha.bsky.social
@jkpritch.bsky.social & colleagues
“Specificity, length and luck drive gene rankings in association studies”, out in @nature.com
🧪🧬
👇
@jkpritch.bsky.social & colleagues
“Specificity, length and luck drive gene rankings in association studies”, out in @nature.com
🧪🧬
👇
Reposted by Jeff Spence
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 Jeff Spence
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 Jeff Spence
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.
Reposted by Jeff Spence
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 Jeff Spence
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
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 Jeff Spence
How is functional variation at large-effect loci maintained in natural populations, even as environments change? In a paper led by @mkarag.bsky.social, we tracked known pesticide resistant alleles in outdoor 𝘋. 𝘮𝘦𝘭𝘢𝘯𝘰𝘨𝘢𝘴𝘵𝘦𝘳 cages & inferred selection and dominance from temporal sequencing data.
November 6, 2025 at 9:51 PM
How is functional variation at large-effect loci maintained in natural populations, even as environments change? In a paper led by @mkarag.bsky.social, we tracked known pesticide resistant alleles in outdoor 𝘋. 𝘮𝘦𝘭𝘢𝘯𝘰𝘨𝘢𝘴𝘵𝘦𝘳 cages & inferred selection and dominance from temporal sequencing data.
Reposted by Jeff Spence
Let’s talk about rare variant association tests - we have a new method that helps you discover more with the same data! It’s called *FlexRV* to signal our approach: “flexibly modeling rare variant pathogenicity improves gene discovery for complex traits”. www.biorxiv.org/content/10.1...
Flexibly Modeling Rare Variant Pathogenicity Improves Gene Discovery for Complex Traits
Rare variant burden tests can directly identify genes that influence complex traits, but their power is limited by our ability to separate functional from benign alleles. We introduce FlexRV, an appro...
www.biorxiv.org
November 5, 2025 at 10:29 PM
Let’s talk about rare variant association tests - we have a new method that helps you discover more with the same data! It’s called *FlexRV* to signal our approach: “flexibly modeling rare variant pathogenicity improves gene discovery for complex traits”. www.biorxiv.org/content/10.1...
Reposted by Jeff Spence
Excited to help host the 54th European Mathematical Genetics Meeting in Davos, Switzerland, next spring!
Speakers include @timfrayling.bsky.social, @marylynritchie.bsky.social, Dr. Joelle Mbatchou and Dr. Eleonora Porcu
Travel grants available - register here: emgm2026.sciencesconf.org?lang=en
Speakers include @timfrayling.bsky.social, @marylynritchie.bsky.social, Dr. Joelle Mbatchou and Dr. Eleonora Porcu
Travel grants available - register here: emgm2026.sciencesconf.org?lang=en
November 4, 2025 at 2:05 PM
Excited to help host the 54th European Mathematical Genetics Meeting in Davos, Switzerland, next spring!
Speakers include @timfrayling.bsky.social, @marylynritchie.bsky.social, Dr. Joelle Mbatchou and Dr. Eleonora Porcu
Travel grants available - register here: emgm2026.sciencesconf.org?lang=en
Speakers include @timfrayling.bsky.social, @marylynritchie.bsky.social, Dr. Joelle Mbatchou and Dr. Eleonora Porcu
Travel grants available - register here: emgm2026.sciencesconf.org?lang=en
Reposted by Jeff Spence
Everything Jeff said except since we're hosting at Stanford it's pronounced BAP-G bsky.app/profile/jros...
Bay Area Pop Gen conference Dec 6! One of my favorite conferences. Registration is free! Only controversy is how to pronounce BAPG (bap-guh is the right answer). docs.google.com/forms/d/e/1F...
Registration for BAPG 2025, Stanford Dec 6 2025
docs.google.com
November 2, 2025 at 4:43 PM
Everything Jeff said except since we're hosting at Stanford it's pronounced BAP-G bsky.app/profile/jros...