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Daniel E. Weeks

@statgendan.bsky.social
767 followers 1.3K following 160 posts

Statistical geneticist. Professor of Human Genetics and Biostatistics at the University of Pittsburgh. Assiduously meticulous.

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Reposted by Daniel E. Weeks
Bat1K Genome Project @bat1kgenomes.bsky.social · 23/09/2026
Where did bats come from?🦇🌍 After decades of debate, the biggest bat genome + fossil study ever done has an answer - and it’s not where anyone expected! 🤩OUR PHASE 1 FLAGSHIP is out today in nature! doi.org/10.1038/s415... A thread 🧵
doi.org
Reference genomes and fossils revise bat family phylogeny and biogeography - Nature
An updated phylogeny of bats is presented, based on new genome assemblies and many ancient fossils and including all known bat families.
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Jacob Tennessen @jacobphd.bsky.social · 29/09/2026
On both the left and right, there is a significant association between genotype (GG / AG / AA) and phenotype (red vs blue). But to odds ratio per allele on the right is more than double that on the left (5.2 vs 2.1), even though visually they don't look all that different.
Hypothetical distribution of genotypes and phenotypes
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Reposted by Daniel E. Weeks
Henrik Bengtsson @henrikbengtsson.bsky.social · 29/09/2026
Heads up. Don't submit to CRAN right now. The CRAN submission system is currently broken, because Windows checks won't complete. If you submit your package will end up in the manual "inspection" queue. You'll see the same on win-builder R devel and R 4.6.1. The R 4.5.3 still works. #RStats
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Pleuni Pennings @pleunipennings.bsky.social · 29/09/2026
I am hiring a postdoc! Are you interested to work on population genetics/ drug resistance/ data? Want to work in Montpellier, France? Fastq files don't scare you? PhD required, start date hopefully Nov 1! (end date Sep 30 2028) Please share! abetterscientist.wordpress.com/2026/09/29/p...
abetterscientist.wordpress.com
Postdoc position on drug resistance evolution in Montpellier, France
I have some exciting news (again!). I got money from the region (Occitanie) to hire a postdoc (and later an engineer / technician) to work on drug resistance evolution in malaria (P. faciparum) and…
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 25/09/2026
Thoughts and prayers for research data managers everywhere. You are not alone. We will get through this together techcommunity.microsoft.com/blog/excelbl...
techcommunity.microsoft.com
Excel now supports multiple values in a single cell | Microsoft Community Hub
Lists, arrays in cells, and nested arrays introduce new ways to store and organize related information, helping you keep data together without sacrificing...
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Reposted by Daniel E. Weeks
BWJones @bwjones.bsky.social · 25/09/2026
Science peeps: Looks like SciENcv updated the digital certificate used to sign Biosketch and Current & Pending documents without notification. The old certificate expires Saturday, September 26, 2026. SciENcv docs before that date may fail validation in eRA Commons delaying or blocking submission.
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Reposted by Daniel E. Weeks
Craig Kaplan @triggerloop.bsky.social · 25/09/2026
It is the case. The Biosketch has a certification so that happens when you generate the document. They updated the current certification to expire Sept 26. So you need new one
Action needed — Regenerate SciENcv documents before upcoming NIH and other federal submissions

The Office of Sponsored Programs (OSP) has become aware of time-sensitive issues affecting SciENcv generated documents.

SciENcv updated the digital certificate used to sign Biosketch and Current & Pending (Other) Support (CPOS) documents without notification. The old certificate expires Saturday, September 26, 2026. Documents downloaded from SciENcv before that date may fail validation in eRA Commons and generate errors that delay or block submission.

This certificate change affects applications and RPPRs to NIH, AHRQ, CDC, NIOSH, FDA, and VA submitted on or after September 26, whether they are submitted in PERIS™ MyFunding/System-to-System, ASSIST, or Grants.gov Workspace. Because SciENcv is also used to prepare Biosketch and CPOS documents for NSF, DOE, NASA, and USDA proposals, investigators with imminent submissions to those agencies are encouraged to regenerate their documents as a precaution.

What to do

Investigators should log back into SciENcv and regenerate their Biosketch and CPOS documents. When 'Download PDF' is selected, SciENcv will prompt the investigator to certify. The new PDFs should replace any older versions in in-progress applications.

October 5 R01 deadline

Any in-progress application that already includes Biosketch or CPOS documents will need those documents regenerated and replaced this coming week.
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Vaughn Cooper @vscooper.micropopbio.org · 25/09/2026
FYI to everyone submitting this October NIH cycle You need to re-certify your ScienCV AFTER Sept 26 (tomorrow) for your application or it may not be accepted. Great timing!
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Max Kozlov @maxkozlov.bsky.social · 25/09/2026
SCOOP: Top researchers at Columbia, Stanford, and others thought they were elected to elite scientific societies alongside Nobel laureates. The catch? The organizations are a sham. I spent the last month diving deep into a massive academic scam spanning continents, for @nature.com
nature.com
Exclusive: Sham scientific societies are misleading star researchers
A Nature investigation reveals a network of organizations that have been building their ranks through deceptive practices.
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Tom Gauld @tomgauld.bsky.social · 24/09/2026
My latest @newscientist.com cartoon. many more here: www.newscientist.com/author/tom-gauld/
Image: A graph with lots of red dots clustered together in a curve. The are all looking upwards at a single red dot wearing sunglasses. 

Caption: Mike was an outlier and would probably be excluded from the study, but all the other data points secretly thought he was really cool.
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Institute for Behavioral Genetics (IBG) @ibg.colorado.edu · 23/09/2026
IBG at CU Boulder is hiring 2-3 tenure-track faculty (junior or senior) in statistical genetics, twin/family designs, and computational work. A chance to help shape IBG for decades. Starts fall 2027. More info: colorado.edu/ibg/. Apply by Oct 15. Please repost!
colorado.edu
Home
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NEJM.org @nejm.org · 23/09/2026
David J. Hunter, MB, BS, FMedSci, and Michael Inouye, PhD, review the ways common genetic variants, polygenic risk scores, and pharmacogenomic genotyping may be useful in the prevention of common diseases and the treatment of common diseases after diagnosis. Full review: nej.md/4Amwv0F
An illustrated diagram from the Review Article "Clinical Uses of Common Genetic Variants Associated with Common Diseases" that shows the levels of human genome analysis and implications for analysis of disease risk and diagnosis.
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John Lovell @jotlovell.bsky.social · 19/05/2026
More details below, tl;dr: We did GWAS on a trait with known single-locus Mendelian inheritance. Depending on the linear reference (top 3 panels), you can get tons of off-target associations. A graph pangenome reference completely resolves this issue (bottom 2 panels) recovering just the single peak
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Jan Broder Engler @jbengler.de · 18/09/2026
In case you ever wondered about the differences between magrittr pipe and base pipe 🤔 This table is taken from a great stackoverflow answer by @GeorgKindermann stackoverflow.com/questions/6763302… #rstats #dataviz #phd
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alex ioannidis @alexgioannidis.bsky.social · 17/09/2026
Fst is a key genetic differentiation metric, but it emphasizes common variants over rare. In IEEE ICASSP out now lab member Margarita Geleta introduces Fq, which can be tuned across the allele freq spectrum. Fst & Shannon differentiation fall out of it as special cases. arxiv.org/abs/2511.03063
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Adam Auton @adamauton.bsky.social · 18/09/2026
What can we learn about a single rare variant? Published today in Science: the 23andMe Research Institute and Dana-Farber studied the EGFR T790M in 10.1M 23andMe research participants. The variant has OR = 25.2 for lung cancer, rising to 61.7 in never-smokers(!). 🧵
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Transactions on Machine Learning Research @tmlrorg.bsky.social · 16/09/2026
Spoilers: all 10 ended up being desk rejected. - 1 paper withdrawn - 1 author was too busy for a call - 1 author no-showed - Authors of 3 papers couldn't answer basic qs - Authors of 3 papers could, but not technical qs - 1 author answered all qs, but paper had a major flaw
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Julia M. Rohrer @dingdingpeng.the100.ci · 14/09/2026
Okay before I do write my screed about cluster analysis, please send me your favorite *positive* examples that illustrate the utility of the method!
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Per Engzell @pengzell.bsky.social · 10/09/2026
The academic process is 10% having ideas and 90% discovering why they won't work
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Ana Martinovici @anamartinovici.bsky.social · 08/09/2026
Workshop done 😀 since I anyway put together a list of resources, I'm going to share it in this thread. So here we go, my top recommendations for how to improve computational reproducibility of your work
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Reposted by Daniel E. Weeks
Marta Grońska-Pęski @gronskapeski.bsky.social · 09/09/2026
Can dietary interventions change how fast genomes accumulate mutations with age? We studied how caloric restriction (CR)—one of the most robust lifespan-extending interventions—affects somatic mutations across the genome in different tissues and cell types in mice.
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Reposted by Daniel E. Weeks
Giacomo Bignardi @giacomobignardi.bsky.social · 09/09/2026
Siblings differ in proportions of genetic ancestry. Wang, Berumen, et al. exploit this (and others) to show within-family genetic ancestry effects on height, T2D, and metabolic traits, but no effects on educational attainment. (EA ancestry associations are environmentally caused or confounded.)
nature.com
Within-family effect of ancestry on complex traits in a Mexican population - Nature
This study uses a within-family design to identify significant ancestry differences in complex traits such as height and type 2 diabetes in a genetically diverse population from Mexico City.
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Ryan Gutenkunst @ryangutenkunst.bsky.social · 09/09/2026
Increasingly powerful methods are enabling increasing complex models of ancient human history to be inferred from population genomic data. In a recent review, I highlight two blind spots in these inferences: limitations of the methods and choices of models to fit. arxiv.org/abs/2608.27591
arxiv.org
Two blind spots in the demographic inference of human origins from genomic data
Ancient DNA and new inference methods have transformed the study of human origins, but consensus has not followed. Evidence increasingly indicates that hominin populations were pervasively structured ...
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Hilary Martin @hilarycmartin.bsky.social · 08/09/2026
Check out this new preprint led by Daniel Malawsky in my group who has developed a very cool new method to infer genetic nurture effects unconfounded by parental assortment (RAVEL) www.biorxiv.org/content/10.6....
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Mitchell Stirling @mitchellst.bsky.social · 07/09/2026
Five years of writing about the last song on albums, and today a peer-reviewed article based on the data is free to read: The cover feature in this month's Significance, the RSS magazine. 2,284 albums, 1953 to 2026 and one question: "Are closing tracks actually different?"
Cover of Significance magazine, September 2026 (volume 23, Issue 5). The masthead features the title "SIGNIFICANCE" in bold red text against a beige background. The left side includes logos for the Royal Statistical Society, the American Statistical Association, and the Statistical Society of Australia.

The central illustration depicts a stylized figure in a blue top holding a large red vinyl record with a white and blue centre directly in front of their face, completely obscuring it. In the bottom right corner, text in red capital letters reads "VINYL ANALYSIS" above the subtitle "WHAT'S HAPPENING WITH ALBUM CLOSING TRACKS?".
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Mike Inouye @mikeinouye.bsky.social · 08/09/2026
📣 New preprint out from the lab! “Enhanced power and transferability for genetics-driven metabolomic biomarker discovery in admixed American cohorts” tackles the important problem that many omics studies still have limited representation of admixed populations www.medrxiv.org/content/10.6...
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Matthew Cobb @matthewcobb.bsky.social · 07/09/2026
I just published a brief account of Jim Watson’s life, aimed at students. It leans heavily on the insights of @nccomfort.bsky.social, whose biography of Watson will be out next year. Free link here: rdcu.be/M91CnnE3N4wa
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Hetan Shah @hetanshah.bsky.social · 07/09/2026
This is very interesting - a blog by a mathematician who was working on a proof of Fermat's Last Theorem on finding out that Anthropic has done it in 11 days. It is interesting because it does not concede the field, but says what it does / doesn't do xenaproject.wordpress.com/2026/09/04/f...
xenaproject.wordpress.com
FLT: Anthropic has beaten me to it
I guess technically it was revealed to the world by a coffee shop in Islington on Insta, but an hour later it was officially announced by Anthropic: one of their internal models, using the prove2.m…
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Ingo Rohlfing @ingorohlfing.bsky.social · 07/09/2026
Scientific datasets are riddled with copy-paste errors www.sciencedetective.org/scientific-d... 18 datasets out of 600 are reported as having serious issues. This is bad enough, but not as bad as the title may suggest. The approach is simple, but powerful and interesting. 1/
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 05/09/2026
Still my slide rule gently weeps. If you are a logarithm and music enjoyer, you might also like www.charlespetzold.com/blog/2026/09...
charlespetzold.com
Can Guitar Frets Perform Multiplication?
I’m sure that some pictures are worth a thousand words, but others trigger a whole lot of puzzlement. Such was the case with the cover of a book I recently bought entitled Calculating with Tones: The ...
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Ted Schwaba @tedmond.bsky.social · 04/09/2026
Some coverage of our Big Five GWAS! (with quotes by @tuckerdrob.bsky.social) After reading the comments section I am now in favor of compulsory psychometrics education.
nytimes.com
Scientists Find More Than 1,000 DNA Variants Linked to Personality Traits (Gift Article)
More than one million genomes helped identify DNA variants linked to extroversion, agreeableness, neuroticism and more. Researchers measured how those traits influenced how people lived.
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Nick Stroustrup @nstroustrup.bsky.social · 05/09/2026
This phenomenon is invisible to standard computational practice. RNA-seq library-size normalization assumes every sample contains equal amounts of mRNA, and rescales libraries to enforce this assumption. 5/22
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Nick Stroustrup @nstroustrup.bsky.social · 05/09/2026
Did you know that the cells of old animals contain much less mRNA than the cells of young ones? Let me share with you some results from an ongoing project in the lab, where we are finding that a progressive depletion of total mRNA abundance is a crucial part of aging 1/22
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Daniel E. Weeks @statgendan.bsky.social · 06/09/2026
“poverty or any other life circumstance that promotes more disease, strongly tends to exacerbate the ill effects of genetic predisposition.”
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MꙬse Allain @mooseallain.bsky.social · 04/09/2026
A playful illustration featuring a poll asking if one likes Venn diagrams, with options to tick a circle for "Yes," "No," and "Ambivalent", the latter illustrated by overlapping circles.
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Discordian (hail Eris, not the app) @serene-chaos.bsky.social · 02/09/2026
> need breaking ...in mathematics, right? Because as a college librarian I see it breaking a lot of things we need intact as thinking beings who can critically evaluate the world, write intelligently about it, and make decisions based on correct facts & cogent analysis.
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Institute for Replication @i4replication.bsky.social · 04/09/2026
🧵 New DP from I4R co-director Lester Lusher, with Sonia Ale, Md Shafiqui Islam, Huda Osman & Jacob Stenstrom (Pitt): "When Samples Shape Significance." What happens when you re-estimate published results using fresh draws of the same data? Some evidence from Google Trends!
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Michel Nivard @michelnivard.bsky.social · 02/09/2026
🚨& 🧵 Our new Nature paper is out! Across 46 cohorts and up to 1.14M people per Big Five trait, we do GWAS and ask how robust, generalizable and consequential the genetic signals underlying personality really are. www.nature.com/articles/s41...
nature.com
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Richard Sever @richardsever.bsky.social · 03/09/2026
You can now update bioRxiv/medRxiv preprints with funding information after the fact. Authors often omit/don't have all funding info when submitting, but funders understandably want it there. This solves the problem without requiring you to submit a whole new paper. openrxiv.org/updating-fun...
openrxiv.org
Updating funder information on preprints - openRxiv
For the past year, bioRxiv and medRxiv authors have been able to include funder information with their preprints. This can be entered in a dedicated field during the submission process, using Research...
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Teun van den Brand @teunbrand.bsky.social · 03/09/2026
Folks, hot off the press here are a few plots about what the new ggarrow update can do: teunbrand.github.io/teunbrand_bl... I'll also tease them below #rstats #ggplot2
Plot where four arrows connect three points. Two points are connected via double arrows pointing in opposite directions.Plot where four arrows connect three points. Arrowheads are one sided/halved. One connection has two arrows in opposite directions, giving the impression of a compound arrow with half-arrowheads at opposite ends.Plot with four arrows connecting three points. The shafts of the arrows are squiggly lines.
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Gordon Hodson @gordonhodsonphd.bsky.social · 03/09/2026
#AcademicSky #PsychSciSky #MetaScience Article worth reading, & sharing w/ your student researchers. Can't get this out of my head: "Bishop’s law: The better designed a study is, the more likely it is to obtain a null result" journals.sagepub.com/doi/10.1177/... Meimoun & @lakens.bsky.social
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The Jackson Laboratory @jax.org · 03/09/2026
A JAX-led study published today in @cellpress.bsky.social of more than 5,000 people is challenging long-held assumptions about cerebral palsy genetics. 🧬🧪
jax.org
Cerebral palsy might be a collection of symptoms, not its own disease
A JAX-led study of more than 5,000 people is challenging long-held assumptions about cerebral palsy genetics.
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Andrew Gelman et al. @statmodeling.bsky.social · 31/08/2026
Do children grow continuously or do they grow in fits and starts? statmodeling.stat.columbia.edu/2026/08/31/f...
statmodeling.stat.columbia.edu
Do children grow continuously or do they grow in fits and starts? | Statistical Modeling, Causal Inference, and Social Science
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Jose Alquicira Hernandez @joseah.bsky.social · 31/08/2026
1/11 We are excited to share Dynema, a new method for ​​efficient genome-wide mapping of reproducible, context-dependent eQTLs at true single-cell resolution w/ @soumya-boston.bsky.social and @aparnanathan biorxiv.org/content/10.6... tldr it finds reproducible eQTLs quickly and accurately!
biorxiv.org
Efficient genome-wide mapping of reproducible, context-dependent eQTLs at single-cell resolution
Single-cell technologies enable linking disease-risk variants to gene regulatory effects in specific cell-state contexts. However, most so called "single-cell eQTL" studies use a "pseudobulking" strat...
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Frank Harrell @f2harrell.bsky.social · 23/08/2026
The gold standard for producing PDF documents (especially books and journal articles) has been LaTeX. @typst.app re-engineered the entire process in an incredibly elegant extensible way. On my MacOS LaTeX (TexLive) takes 9.1GB of disk space. Typst takes 43MB. Not a misprint.
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alex ioannidis @alexgioannidis.bsky.social · 01/09/2026
Gnomix is published! www.nature.com/articles/s41... Still the most accurate & fastest local ancestry inference (LAI) method, bests Flare and others (RecombMix & Orchestra) released since our preprint. Easy to use, github.com/AI-sandbox/g... Use it with our toolkit, snputils.org
nature.com
Scalable high resolution ancestry deconvolution for genomic data - Nature Communications
The authors present Gnomix, a local ancestry framework that delivers leading accuracy across diverse admixed datasets on both whole-genome and array data with high efficiency, together with Gnofix, it...
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Lorenzo Piccoli @lorenzopiccoli.bsky.social · 02/09/2026
This study finds that scientific papers derived from a health and nutrition data set were about four a year between 2014 and 2021. In the first nine months of 2024, there were 190. What changed? The widespread adoption of AI, in not very good ways. www.medrxiv.org/content/10.1...
medrxiv.org
Dramatic increases in redundant publications in the Generative AI era
Background Redundant publication, the practice of submitting the same or substantially overlapping manuscripts multiple times, distorts the scientific record and wastes resources. Since 2022, publicat...
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Erik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026
Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n
nature.com
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
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Rafael Ahlskog @rafaelahlskog.bsky.social · 02/09/2026
Me and @aysuo.bsky.social went to Amsterdam to talk to @michelnivard.bsky.social. Michels stated goal is to get more listens than @dr-appie.bsky.social - can he do it? Stay tuned!
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Helen McCarthy @glider.bsky.social · 29/08/2026
#SomethingBeautiful - the intricate operation of the tiny muscles that enable a dragonfly's flight.
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