Daniel E. Weeks
@statgendan.bsky.social
Statistical geneticist. Professor of Human Genetics and Biostatistics at the University of Pittsburgh. Assiduously meticulous.
Reposted by Daniel E. Weeks
PRSformer: Disease Prediction from Million-Scale Individual Genotypes [new]
Deep learning w/ neighborhood attention predicts disease from million-scale genotype data by learning genetic interactions.
Deep learning w/ neighborhood attention predicts disease from million-scale genotype data by learning genetic interactions.
October 27, 2025 at 7:22 PM
PRSformer: Disease Prediction from Million-Scale Individual Genotypes [new]
Deep learning w/ neighborhood attention predicts disease from million-scale genotype data by learning genetic interactions.
Deep learning w/ neighborhood attention predicts disease from million-scale genotype data by learning genetic interactions.
Reposted by Daniel E. Weeks
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...
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...
www.medrxiv.org
November 24, 2025 at 5:13 PM
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...
A thread... 🧵
www.medrxiv.org/content/10.1...
Reposted by Daniel E. Weeks
Blog post: A Missing Heritability Update. Three legs and other problems. I follow up on the recent excellent post on the subject by @sashagusevposts.bsky.social. ericturkheimer.substack.com/p/missing-he...
Missing Heritability Revisited
Following up on Sasha
ericturkheimer.substack.com
November 25, 2025 at 3:04 PM
Blog post: A Missing Heritability Update. Three legs and other problems. I follow up on the recent excellent post on the subject by @sashagusevposts.bsky.social. ericturkheimer.substack.com/p/missing-he...
Reposted by Daniel E. Weeks
this is one of my favourite observations about sample size calculations. (afaik first articulated by Miettinen in 1985)
November 25, 2025 at 10:56 AM
this is one of my favourite observations about sample size calculations. (afaik first articulated by Miettinen in 1985)
Reposted by Daniel E. Weeks
Out now in @natgenet.nature.com, our Comment analyzing uses of the Human Genome Diversity Project (HGDP), a controversial dataset in human genomics research. A 🧵
rdcu.be/eRu65
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rdcu.be/eRu65
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November 25, 2025 at 4:57 AM
Out now in @natgenet.nature.com, our Comment analyzing uses of the Human Genome Diversity Project (HGDP), a controversial dataset in human genomics research. A 🧵
rdcu.be/eRu65
1/
rdcu.be/eRu65
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Reposted by Daniel E. Weeks
New paper “Proteome-wide model for human disease genetics” is now live at Nature Genetics: rdcu.be/eRu7K
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
November 24, 2025 at 2:53 PM
New paper “Proteome-wide model for human disease genetics” is now live at Nature Genetics: rdcu.be/eRu7K
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
Reposted by Daniel E. Weeks
The INCEPTION is organizing its Annual Symposium. This year is about GWAS & beyond! We're happy to have @bpasaniuc.bsky.social, @caina89.bsky.social, Iuliana Ionita-Laza , Sriram Sankararaman, and others, who will talk about tools for understanding the genetic determinants of complex diseases
INCEPTION Symposium 2025 - Research
INCEPTION symposium 2025 - Focus on GWAS: paving the way for the future of genetics.
research.pasteur.fr
November 24, 2025 at 7:05 AM
The INCEPTION is organizing its Annual Symposium. This year is about GWAS & beyond! We're happy to have @bpasaniuc.bsky.social, @caina89.bsky.social, Iuliana Ionita-Laza , Sriram Sankararaman, and others, who will talk about tools for understanding the genetic determinants of complex diseases
Reposted by Daniel E. Weeks
Incredible story of tracking down the real human behind AI slop stories, by @nickhunebrown.bsky.social
"I was embarrassed. I had been naively operating with a pre-ChatGPT mindset, still assuming a pitch’s ideas and prose were actually connected to the person who sent it"
Stunning investigation of how slop merchants are getting work into established media outlets
thelocal.to/investigatin...
Stunning investigation of how slop merchants are getting work into established media outlets
thelocal.to/investigatin...
November 24, 2025 at 3:24 AM
Incredible story of tracking down the real human behind AI slop stories, by @nickhunebrown.bsky.social
Reposted by Daniel E. Weeks
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 21, 2025 at 10:34 PM
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
Reposted by Daniel E. Weeks
Interesting answers, and striking that I never asked myself that question until now.
A question for scientists (construed as broadly as you like) of BlueSky: What makes something data?
(Question inspired by a talk I listened to this morning, and of course I have thoughts, but I wanted to throw this out there first.)
(Question inspired by a talk I listened to this morning, and of course I have thoughts, but I wanted to throw this out there first.)
November 22, 2025 at 8:18 AM
Interesting answers, and striking that I never asked myself that question until now.
Reposted by Daniel E. Weeks
#rstats Please welcome Jarl, a new R linter.
Jarl is a CLI tool with extensions in VS Code, Positron, and Zed. It can check thousands of lines of R code in milliseconds.
Jarl provides several output formats, a Github Actions workflow, and more.
Blog post: www.etiennebacher.com/posts/2025-1...
Jarl is a CLI tool with extensions in VS Code, Positron, and Zed. It can check thousands of lines of R code in milliseconds.
Jarl provides several output formats, a Github Actions workflow, and more.
Blog post: www.etiennebacher.com/posts/2025-1...
November 20, 2025 at 4:50 PM
#rstats Please welcome Jarl, a new R linter.
Jarl is a CLI tool with extensions in VS Code, Positron, and Zed. It can check thousands of lines of R code in milliseconds.
Jarl provides several output formats, a Github Actions workflow, and more.
Blog post: www.etiennebacher.com/posts/2025-1...
Jarl is a CLI tool with extensions in VS Code, Positron, and Zed. It can check thousands of lines of R code in milliseconds.
Jarl provides several output formats, a Github Actions workflow, and more.
Blog post: www.etiennebacher.com/posts/2025-1...
Reposted by Daniel E. Weeks
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
biorxiv.org
November 12, 2025 at 9:26 PM
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Reposted by Daniel E. Weeks
Aaah! New preprint from the Sethuraman Lab has dropped! Tamsen and I have been working on this for a while, and we can’t wait for your feedback. Short thread on our swanky new polyploid genome simulator, DemographiKs, and its functionality.
Hidden in Plain Sight. How Ks histogram dynamics can reveal and obscure ancient whole genome duplications. https://www.biorxiv.org/content/10.1101/2025.11.19.689290v1
November 20, 2025 at 1:11 PM
Aaah! New preprint from the Sethuraman Lab has dropped! Tamsen and I have been working on this for a while, and we can’t wait for your feedback. Short thread on our swanky new polyploid genome simulator, DemographiKs, and its functionality.
Reposted by Daniel E. Weeks
The results of the study were published in Nature Genetics: @natgenet.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Genome-wide association analyses identify distinct genetic architectures for early-onset and late-onset depression - Nature Genetics
Genome-wide association analyses leveraging Nordic biobanks with longitudinal health registries identify differences in the genetic architectures of early-onset and late-onset major depressive disorde...
www.nature.com
November 20, 2025 at 1:01 PM
The results of the study were published in Nature Genetics: @natgenet.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Daniel E. Weeks
@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...
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.
www.nature.com
November 19, 2025 at 6:43 PM
@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...
www.nature.com/articles/d41...
Reposted by Daniel E. Weeks
Researchers publish paper about the promise and perils of post-publication peer review (e.g. Pubpeer). Turns out the paper has several hallucinated citations, which are pointed out on... Pubpeer.
Commenters have also spotted that the last author (and EIC of the journal) has 11 retractions. 🤷♂️
Commenters have also spotted that the last author (and EIC of the journal) has 11 retractions. 🤷♂️
PubPeer - An expert criticism on post-publication peer review platform...
There are comments on PubPeer for publication: An expert criticism on post-publication peer review platforms: the case of pubpeer (2025)
pubpeer.com
November 18, 2025 at 6:19 PM
Researchers publish paper about the promise and perils of post-publication peer review (e.g. Pubpeer). Turns out the paper has several hallucinated citations, which are pointed out on... Pubpeer.
Commenters have also spotted that the last author (and EIC of the journal) has 11 retractions. 🤷♂️
Commenters have also spotted that the last author (and EIC of the journal) has 11 retractions. 🤷♂️
Reposted by Daniel E. Weeks
Advances in genomics are giving exciting new perspectives on biology of speech, language & reading. My latest peer-reviewed paper is a tutorial, guiding readers from different backgrounds through the history of the field, current state-of-the-art, & where we’re heading. A taster in this thread.🧪
1/n
1/n
Genomic Investigations of Spoken and Written Language Abilities: A Guide to Advances in Approaches, Technologies, and Discovery
Purpose: The aim of this tutorial is to show how the rise of molecular technologies
and analytical methods in human genetics yields exciting new ...
pubs.asha.org
November 17, 2025 at 5:54 PM
Advances in genomics are giving exciting new perspectives on biology of speech, language & reading. My latest peer-reviewed paper is a tutorial, guiding readers from different backgrounds through the history of the field, current state-of-the-art, & where we’re heading. A taster in this thread.🧪
1/n
1/n
Reposted by Daniel E. Weeks
OK.
DOES THIS WESTERN BLOT LOOK MORE LIKE A FISH OR A SHOE.
DOES THIS WESTERN BLOT LOOK MORE LIKE A FISH OR A SHOE.
November 19, 2025 at 5:44 AM
OK.
DOES THIS WESTERN BLOT LOOK MORE LIKE A FISH OR A SHOE.
DOES THIS WESTERN BLOT LOOK MORE LIKE A FISH OR A SHOE.
Reposted by Daniel E. Weeks
This is another example of why I think default priors are generally inappropriate for professional work. They're still great for teaching, though.
The default prior for the intercept in both {rstanarm} and {brms} are very wide.
Counterintuitively - being on the logit scale, this is actually translates to a **strong** prior that p(y=1) is near 1 or near 0.
Always check your priors!
#rstats
Counterintuitively - being on the logit scale, this is actually translates to a **strong** prior that p(y=1) is near 1 or near 0.
Always check your priors!
#rstats
November 18, 2025 at 3:44 PM
This is another example of why I think default priors are generally inappropriate for professional work. They're still great for teaching, though.
Reposted by Daniel E. Weeks
Nice thread about why CI won't help to solve the p-value problem
This is an education problem, not a tool problem; and we don't want people simply moving from thinking p-values are magic to thinking confidence intervals are.
Next: Geoff Cumming @thenewstats.bsky.social with 'Statistical significance and p values: The researcher’s heroin'
* p values are highly unrealiable - don't trust them, don't use them!
www.thenewstatistics.com
tiny.cc/osfsigroulette
#IRICSydney
* p values are highly unrealiable - don't trust them, don't use them!
www.thenewstatistics.com
tiny.cc/osfsigroulette
#IRICSydney
November 19, 2025 at 9:24 AM
Nice thread about why CI won't help to solve the p-value problem
Reposted by Daniel E. Weeks
Nice to see all these confidence intervals. I use Wilson as a default but should be using Bayes. Challenge: figure out why “exact” confidence intervals are not recommended.
For people trying to teach themselves more about statistics, go read about these different approaches and try to make sense of why they don't exactly agree. What are they doing differently? Use wikipedia. Look up new terms along the way.
My #rstats cheat code for today is the binom.confint function in the binom package that will spit out *12* different ways of calculating a CI for a proportion.
Also, this is why you use R for statistics...
(and of course the correct CI method is bayes 😎)
Also, this is why you use R for statistics...
(and of course the correct CI method is bayes 😎)
November 16, 2025 at 12:32 PM
Nice to see all these confidence intervals. I use Wilson as a default but should be using Bayes. Challenge: figure out why “exact” confidence intervals are not recommended.
Reposted by Daniel E. Weeks
relatedly, your images, text, and especially graphs/figures can almost always be bigger than you're making them
one thing I force myself to do is never present multi-panel figures in talks. just put each panel on its own slide then it will be huge. it's hard to read graphs from far away!
eg:
one thing I force myself to do is never present multi-panel figures in talks. just put each panel on its own slide then it will be huge. it's hard to read graphs from far away!
eg:
November 17, 2025 at 4:42 AM
relatedly, your images, text, and especially graphs/figures can almost always be bigger than you're making them
one thing I force myself to do is never present multi-panel figures in talks. just put each panel on its own slide then it will be huge. it's hard to read graphs from far away!
eg:
one thing I force myself to do is never present multi-panel figures in talks. just put each panel on its own slide then it will be huge. it's hard to read graphs from far away!
eg:
Reposted by Daniel E. Weeks
Hello bluesky community!
I'm hiring a postdoc to do machine learning in population genetics.
Starting to build up a lab at Indiana University Bloomington where I just started a faculty position.
Apply with the below link: indiana.peopleadmin.com/postings/30325
I'm hiring a postdoc to do machine learning in population genetics.
Starting to build up a lab at Indiana University Bloomington where I just started a faculty position.
Apply with the below link: indiana.peopleadmin.com/postings/30325
Postdoctoral Research Fellow
The department of Biology is a large, unified department with strong undergraduate degrees, nationally-ranked graduate programs, and world-class research spanning the breadth of biological questions a...
indiana.peopleadmin.com
August 11, 2025 at 11:51 AM
Hello bluesky community!
I'm hiring a postdoc to do machine learning in population genetics.
Starting to build up a lab at Indiana University Bloomington where I just started a faculty position.
Apply with the below link: indiana.peopleadmin.com/postings/30325
I'm hiring a postdoc to do machine learning in population genetics.
Starting to build up a lab at Indiana University Bloomington where I just started a faculty position.
Apply with the below link: indiana.peopleadmin.com/postings/30325
Reposted by Daniel E. Weeks
I recently discovered Conventional Comments (conventionalcomments.org) for providing a pseudo-standard set of labels for feedback and just tried it for an article review and it was really helpful to specify issues vs. thoughts vs. suggestions, etc. Hopefully it's helpful for the authors too!
November 17, 2025 at 3:52 PM
I recently discovered Conventional Comments (conventionalcomments.org) for providing a pseudo-standard set of labels for feedback and just tried it for an article review and it was really helpful to specify issues vs. thoughts vs. suggestions, etc. Hopefully it's helpful for the authors too!
Reposted by Daniel E. Weeks
Thrilled to finally share the magnum opus of my PhD that focuses on the genetic basis of evolutionary change! Specifically, we know we can map the genetic basis of a trait, but can we tell which genes will underlie the trait shift when it evolves? doi.org/10.1101/2025...
High-resolution mapping of a rapidly evolving complex trait reveals genotype-phenotype stability and an unpredictable genetic architecture of adaptation
The extent to which adaptation can be predicted, particularly for traits with complex genetic bases, is unknown. Here, we leveraged a model complex trait, model species, and high-powered longitudinal ...
doi.org
November 18, 2025 at 12:15 AM
Thrilled to finally share the magnum opus of my PhD that focuses on the genetic basis of evolutionary change! Specifically, we know we can map the genetic basis of a trait, but can we tell which genes will underlie the trait shift when it evolves? doi.org/10.1101/2025...