Jonathan Pritchard
@jkpritch.bsky.social
My lab at Stanford studies human population genetics and complex traits.
Pinned
Jonathan Pritchard
@jkpritch.bsky.social
· Sep 23
Two new chapters from my free online book in human genetics out this weekend!
These complete Part 3 of the book, on human population structure and history:
3.3: Human prehistory [separate thread]
3.4: Ancient DNA: a genetic time capsule [this thread]
web.stanford.edu/group/pritch...
These complete Part 3 of the book, on human population structure and history:
3.3: Human prehistory [separate thread]
3.4: Ancient DNA: a genetic time capsule [this thread]
web.stanford.edu/group/pritch...
Reposted by Jonathan Pritchard
Super excited about our schedule for BAPG at stanford on Dec 6. bapg2025.github.io/bapg2025stan... Amazing talks, a fabulous keynote, a lively poster session. A brilliant and interactive community. What’s not to love? 1/2 @sophiejwalton.bsky.social
BAPG Fall 2025
Bay Area Population Genomics Conference @ Stanford
bapg2025.github.io
November 24, 2025 at 10:54 PM
Super excited about our schedule for BAPG at stanford on Dec 6. bapg2025.github.io/bapg2025stan... Amazing talks, a fabulous keynote, a lively poster session. A brilliant and interactive community. What’s not to love? 1/2 @sophiejwalton.bsky.social
Reposted by Jonathan Pritchard
We have 115 people signed up already for BAPG! Great representation across career stages too. If you want to attend don't forget to sign up. It is free but required. @sophiejwalton.bsky.social and I are looking through the wonderful talk submissions and will announce the talks shortly. Stay tuned!
November 20, 2025 at 6:30 PM
We have 115 people signed up already for BAPG! Great representation across career stages too. If you want to attend don't forget to sign up. It is free but required. @sophiejwalton.bsky.social and I are looking through the wonderful talk submissions and will announce the talks shortly. Stay tuned!
Reposted by Jonathan Pritchard
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 Jonathan Pritchard
Excited to share some new work led by grad student Sophie Walton (w/ @petrovadmitri.bsky.social). We used in vitro gut communities to study how natural selection acts on strains of the same species as they compete within larger communities. Check out Sophie's thread below for details!
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 12, 2025 at 3:43 AM
Excited to share some new work led by grad student Sophie Walton (w/ @petrovadmitri.bsky.social). We used in vitro gut communities to study how natural selection acts on strains of the same species as they compete within larger communities. Check out Sophie's thread below for details!
Reposted by Jonathan Pritchard
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
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 Jonathan Pritchard
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 2:59 AM
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...
Reposted by Jonathan Pritchard
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...
Reposted by Jonathan Pritchard
Proud of the latest edition of my free intro biostats book.
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
Applied Biostatistics
ybrandvain.github.io
October 24, 2025 at 2:33 PM
Proud of the latest edition of my free intro biostats book.
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
Reposted by Jonathan Pritchard
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 Jonathan Pritchard
I'm recruiting a postdoc for my group (based in beautiful Eugene, OR). Please get in touch if you're interested, esp if you'd like to chat at #ASHG25!
We'll primarily work at the intersection of statistical and population genetics, and we also have active projects related to the ethical and social implications of human genetics (ELSI). Please get in touch if that's a combination that sounds interesting to you!
October 15, 2025 at 12:52 PM
I'm recruiting a postdoc for my group (based in beautiful Eugene, OR). Please get in touch if you're interested, esp if you'd like to chat at #ASHG25!
Reposted by Jonathan Pritchard
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 Jonathan Pritchard
Save the date for a new conference exploring genomics for linking polygenic signals to mechanistic insights!
Biology at Scale: From Variants to Cellular Programs & Functions is opening soon for registrations. #BiologyAtScale26
📍 Wellcome Genome Campus, UK
📅 29 June -1 July 2026
👉 bit.ly/4mYud02
Biology at Scale: From Variants to Cellular Programs & Functions is opening soon for registrations. #BiologyAtScale26
📍 Wellcome Genome Campus, UK
📅 29 June -1 July 2026
👉 bit.ly/4mYud02
October 14, 2025 at 10:00 AM
Save the date for a new conference exploring genomics for linking polygenic signals to mechanistic insights!
Biology at Scale: From Variants to Cellular Programs & Functions is opening soon for registrations. #BiologyAtScale26
📍 Wellcome Genome Campus, UK
📅 29 June -1 July 2026
👉 bit.ly/4mYud02
Biology at Scale: From Variants to Cellular Programs & Functions is opening soon for registrations. #BiologyAtScale26
📍 Wellcome Genome Campus, UK
📅 29 June -1 July 2026
👉 bit.ly/4mYud02
Reposted by Jonathan Pritchard
Genetic architectures of #ComplexTraits vary widely. @yuvalsim.bsky.social @jkpritch.bsky.social @gs2747.bsky.social &co show these diffs arise from mutational target size & heritability per site; when controlled for, all tested traits have similar architectures @plosbiology.org 🧪 plos.io/47mZXqT
October 14, 2025 at 12:58 PM
Genetic architectures of #ComplexTraits vary widely. @yuvalsim.bsky.social @jkpritch.bsky.social @gs2747.bsky.social &co show these diffs arise from mutational target size & heritability per site; when controlled for, all tested traits have similar architectures @plosbiology.org 🧪 plos.io/47mZXqT
Reposted by Jonathan Pritchard
Blog post: Ancestry and Education
Indirect, direct, confounded and quasi-causal.
I write about a preprint by Wang et al, in which they look for associations with genetic ancestry in an admixed Mexican population. They found genetic effects for height and Type-II diabetes, but not for education.
Indirect, direct, confounded and quasi-causal.
I write about a preprint by Wang et al, in which they look for associations with genetic ancestry in an admixed Mexican population. They found genetic effects for height and Type-II diabetes, but not for education.
Ancestry and Education
Indirect, direct, confounded and quasi-causal
ericturkheimer.substack.com
October 9, 2025 at 3:45 PM
Blog post: Ancestry and Education
Indirect, direct, confounded and quasi-causal.
I write about a preprint by Wang et al, in which they look for associations with genetic ancestry in an admixed Mexican population. They found genetic effects for height and Type-II diabetes, but not for education.
Indirect, direct, confounded and quasi-causal.
I write about a preprint by Wang et al, in which they look for associations with genetic ancestry in an admixed Mexican population. They found genetic effects for height and Type-II diabetes, but not for education.
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!
Reposted by Jonathan Pritchard
In these dark times, it comes as a rare pleasure to highlight @natanaels.bsky.social & @marcdemanuel.bsky.social's work on germline and somatic mutations in humans. 1/n
www.biorxiv.org/cgi/content/...
www.biorxiv.org/cgi/content/...
Collateral mutagenesis funnels multiple sources of DNA damage into a ubiquitous mutational signature
Mutations reflect the net effects of myriad types of damage, replication errors, and repair mechanisms, and thus are expected to differ across cell types with distinct exposures to mutagens, division ...
www.biorxiv.org
September 2, 2025 at 11:44 AM
In these dark times, it comes as a rare pleasure to highlight @natanaels.bsky.social & @marcdemanuel.bsky.social's work on germline and somatic mutations in humans. 1/n
www.biorxiv.org/cgi/content/...
www.biorxiv.org/cgi/content/...
Reposted by Jonathan Pritchard
🎉scverse conference 2025 Call for Abstracts DEADLINE EXTENDED! 🎉
We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025!
🧵
#scverse #scverse2025 #SingleCell #Conference
We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025!
🧵
#scverse #scverse2025 #SingleCell #Conference
September 1, 2025 at 4:18 PM
🎉scverse conference 2025 Call for Abstracts DEADLINE EXTENDED! 🎉
We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025!
🧵
#scverse #scverse2025 #SingleCell #Conference
We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025!
🧵
#scverse #scverse2025 #SingleCell #Conference
Delighted to share some wonderful work by our recent grad Matthew Aguirre on theoretical models of GRNs, and what eQTL data can teach us about these!
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 9:35 PM
Delighted to share some wonderful work by our recent grad Matthew Aguirre on theoretical models of GRNs, and what eQTL data can teach us about these!
Reposted by Jonathan Pritchard
Excited to share our new preprint for the tskit_arg_visualizer Python package! ARGs can sometimes feel like a black box, so
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.
🔗 arxiv.org/abs/2508.03958
1/6
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.
🔗 arxiv.org/abs/2508.03958
1/6
tskit_arg_visualizer: interactive plotting of ancestral recombination graphs
Summary: Ancestral recombination graphs (ARGs) are a complete representation of the genetic relationships between recombining lineages and are of central importance in population genetics. Recent brea...
arxiv.org
August 19, 2025 at 2:12 PM
Excited to share our new preprint for the tskit_arg_visualizer Python package! ARGs can sometimes feel like a black box, so
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.
🔗 arxiv.org/abs/2508.03958
1/6
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.
🔗 arxiv.org/abs/2508.03958
1/6
Reposted by Jonathan Pritchard
🧠 Meet the keynote speakers for the 2025 scverse conference!
Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai
🧵
@panosroussos.bsky.social
#scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote
Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai
🧵
@panosroussos.bsky.social
#scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote
August 19, 2025 at 3:37 PM
🧠 Meet the keynote speakers for the 2025 scverse conference!
Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai
🧵
@panosroussos.bsky.social
#scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote
Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai
🧵
@panosroussos.bsky.social
#scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote
Reposted by Jonathan Pritchard
Grateful for this terrific commentary by @tomonroe.bsky.social in @jclinical-invest.bsky.social on our paper that is out in final print format today: www.jci.org/articles/vie...
Please check it out: www.jci.org/articles/vie...
Please check it out: www.jci.org/articles/vie...
August 15, 2025 at 7:40 PM
Grateful for this terrific commentary by @tomonroe.bsky.social in @jclinical-invest.bsky.social on our paper that is out in final print format today: www.jci.org/articles/vie...
Please check it out: www.jci.org/articles/vie...
Please check it out: www.jci.org/articles/vie...
Reposted by Jonathan Pritchard
"The molecular evolutionary basis of species formation revisited"
by Molly Schumer (@mollyschumer.bsky.social) & colleagues
"The origin of species has long fascinated biologists, but determining the genes [involved] has only recently become possible in non-model organisms."
shorturl.at/wG0B5
by Molly Schumer (@mollyschumer.bsky.social) & colleagues
"The origin of species has long fascinated biologists, but determining the genes [involved] has only recently become possible in non-model organisms."
shorturl.at/wG0B5
August 13, 2025 at 3:30 PM
"The molecular evolutionary basis of species formation revisited"
by Molly Schumer (@mollyschumer.bsky.social) & colleagues
"The origin of species has long fascinated biologists, but determining the genes [involved] has only recently become possible in non-model organisms."
shorturl.at/wG0B5
by Molly Schumer (@mollyschumer.bsky.social) & colleagues
"The origin of species has long fascinated biologists, but determining the genes [involved] has only recently become possible in non-model organisms."
shorturl.at/wG0B5
Reposted by Jonathan Pritchard
Incredibly proud of this work where we developed a method for understanding the information contained in millions of genomes. Another example of NIH funded research.
📣Online NOW!
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
Estimation of demography and mutation rates from one million haploid genomes
Samples of millions of genomes provide substantial information about recent demography
and mutation, but standard population-genetic methods make assumptions not met in
these data. We introduce DR EVI...
www.cell.com
August 13, 2025 at 2:47 PM
Incredibly proud of this work where we developed a method for understanding the information contained in millions of genomes. Another example of NIH funded research.
Reposted by Jonathan Pritchard
Cool paper, and -- as expected by how similar the titles are -- dovetails nicely with our work (led by Margaret Antonio, Clemens Weiß, Ziyue Gao, and Susanna Sawyer):
elifesciences.org/articles/79714
elifesciences.org/articles/79714
August 8, 2025 at 6:03 PM
Cool paper, and -- as expected by how similar the titles are -- dovetails nicely with our work (led by Margaret Antonio, Clemens Weiß, Ziyue Gao, and Susanna Sawyer):
elifesciences.org/articles/79714
elifesciences.org/articles/79714