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
(Non-identifiability is the equivalent of looking at an equation 'A x B = 20' and claiming you know exactly what value A and B are.)
November 9, 2025 at 9:20 PM
(Non-identifiability is the equivalent of looking at an equation 'A x B = 20' and claiming you know exactly what value A and B are.)
Reposted by Daniel E. Weeks
Theorem of the Day (November 9, 2025) : Netto’s Conjecture (Dixon’s Theorem)
Source : Theorem of the Day / Robin Whitty
pdf : buff.ly/eWQ4C4N
notes : buff.ly/ElCux2H
#mathematics #maths #math #theorem
Source : Theorem of the Day / Robin Whitty
pdf : buff.ly/eWQ4C4N
notes : buff.ly/ElCux2H
#mathematics #maths #math #theorem
November 9, 2025 at 11:00 AM
Theorem of the Day (November 9, 2025) : Netto’s Conjecture (Dixon’s Theorem)
Source : Theorem of the Day / Robin Whitty
pdf : buff.ly/eWQ4C4N
notes : buff.ly/ElCux2H
#mathematics #maths #math #theorem
Source : Theorem of the Day / Robin Whitty
pdf : buff.ly/eWQ4C4N
notes : buff.ly/ElCux2H
#mathematics #maths #math #theorem
“changes in statistical significance are often not themselves statistically significant. … even large changes in significance levels can correspond to small, nonsignificant changes in the underlying quantities.”
www.tandfonline.com/doi/abs/10.1...
#Statistics
www.tandfonline.com/doi/abs/10.1...
#Statistics
The Difference Between “Significant” and “Not Significant” is not Itself Statistically Significant
It is common to summarize statistical comparisons by declarations of statistical significance or nonsignificance. Here we discuss one problem with such declarations, namely that changes in statisti...
www.tandfonline.com
November 9, 2025 at 12:39 PM
“changes in statistical significance are often not themselves statistically significant. … even large changes in significance levels can correspond to small, nonsignificant changes in the underlying quantities.”
www.tandfonline.com/doi/abs/10.1...
#Statistics
www.tandfonline.com/doi/abs/10.1...
#Statistics
Reposted by Daniel E. Weeks
In a field where evidence suggests that a high proportion of papers have serious flaws, a database of "potentially important" papers which appear *not* to have serious flaws might be useful, as well as identifying those that do.
November 9, 2025 at 10:36 AM
In a field where evidence suggests that a high proportion of papers have serious flaws, a database of "potentially important" papers which appear *not* to have serious flaws might be useful, as well as identifying those that do.
In 1982, I was in the Jackson Laboratory Research Training Program. As part of the program, we got to attend the Short Course lectures. At the end of one lecture by a young researcher, this old guy very viciously and aggressively lit into him. Turned out that the nasty old guy was Jim Watson.
November 8, 2025 at 11:57 PM
In 1982, I was in the Jackson Laboratory Research Training Program. As part of the program, we got to attend the Short Course lectures. At the end of one lecture by a young researcher, this old guy very viciously and aggressively lit into him. Turned out that the nasty old guy was Jim Watson.
Reposted by Daniel E. Weeks
A fantastic piece. Fascinating that Watson was another victim of The Bell Curve and became entrenched by his undeserved arrogance and hubris
A Sharon Begley byline, almost 5 years after her death.
Upon hearing the news James Watson had died, a STAT reporter said in our Slack, "I wish I could read what Sharon would have written."
Incredible news: Sharon in fact did pre-write a Watson obit. And it is masterful and excoriating.
🧪🧬🧫
Upon hearing the news James Watson had died, a STAT reporter said in our Slack, "I wish I could read what Sharon would have written."
Incredible news: Sharon in fact did pre-write a Watson obit. And it is masterful and excoriating.
🧪🧬🧫
James Watson, dead at 97, was a scientific legend and a pariah among his peers
James Watson, the co-discoverer of the structure of DNA who died Thursday at 97, was a scientific legend and a pariah among his peers.
www.statnews.com
November 8, 2025 at 10:27 PM
A fantastic piece. Fascinating that Watson was another victim of The Bell Curve and became entrenched by his undeserved arrogance and hubris
Reposted by Daniel E. Weeks
Okay, here are some first reflections on Watson.
Watson's life is a tragedy, really of Shakespearean proportions. He did not, as most bios will tell you, do one great thing when he was young and then collect laurels for it for the next 60 years. His career arc was unlike any in science.
Watson's life is a tragedy, really of Shakespearean proportions. He did not, as most bios will tell you, do one great thing when he was young and then collect laurels for it for the next 60 years. His career arc was unlike any in science.
November 8, 2025 at 11:22 PM
Okay, here are some first reflections on Watson.
Watson's life is a tragedy, really of Shakespearean proportions. He did not, as most bios will tell you, do one great thing when he was young and then collect laurels for it for the next 60 years. His career arc was unlike any in science.
Watson's life is a tragedy, really of Shakespearean proportions. He did not, as most bios will tell you, do one great thing when he was young and then collect laurels for it for the next 60 years. His career arc was unlike any in science.
Reposted by Daniel E. Weeks
Rarely in the entire history of science, has QC been a topic of such passion, importance and impact. If only the French and Americans had adopted such rigor when they messed up the design of that multi billion $ telescope because one was using the metric system, the other the imperial system.
New paper on everyone’s favourite topic, QC!
We show why you should do genotype-level QC on your WGS data
www.biorxiv.org/content/10.1...
Very real quotes about this paper -
“The most exciting, mind-blowing paper of the year!”
“On a par with Fisher 1918”
“I read it every night. Just so beautiful”
We show why you should do genotype-level QC on your WGS data
www.biorxiv.org/content/10.1...
Very real quotes about this paper -
“The most exciting, mind-blowing paper of the year!”
“On a par with Fisher 1918”
“I read it every night. Just so beautiful”
Genotype-level quality control substantially reduces error rates in population-scale whole-genome sequencing
Population-scale whole-genome sequencing data will contain many individual-level genotype errors, even after allele-level quality control (QC). We establish the need for genotype-level QC using UK Bio...
www.biorxiv.org
November 8, 2025 at 3:35 PM
Rarely in the entire history of science, has QC been a topic of such passion, importance and impact. If only the French and Americans had adopted such rigor when they messed up the design of that multi billion $ telescope because one was using the metric system, the other the imperial system.
Reposted by Daniel E. Weeks
New paper on everyone’s favourite topic, QC!
We show why you should do genotype-level QC on your WGS data
www.biorxiv.org/content/10.1...
Very real quotes about this paper -
“The most exciting, mind-blowing paper of the year!”
“On a par with Fisher 1918”
“I read it every night. Just so beautiful”
We show why you should do genotype-level QC on your WGS data
www.biorxiv.org/content/10.1...
Very real quotes about this paper -
“The most exciting, mind-blowing paper of the year!”
“On a par with Fisher 1918”
“I read it every night. Just so beautiful”
Genotype-level quality control substantially reduces error rates in population-scale whole-genome sequencing
Population-scale whole-genome sequencing data will contain many individual-level genotype errors, even after allele-level quality control (QC). We establish the need for genotype-level QC using UK Bio...
www.biorxiv.org
November 8, 2025 at 9:31 AM
New paper on everyone’s favourite topic, QC!
We show why you should do genotype-level QC on your WGS data
www.biorxiv.org/content/10.1...
Very real quotes about this paper -
“The most exciting, mind-blowing paper of the year!”
“On a par with Fisher 1918”
“I read it every night. Just so beautiful”
We show why you should do genotype-level QC on your WGS data
www.biorxiv.org/content/10.1...
Very real quotes about this paper -
“The most exciting, mind-blowing paper of the year!”
“On a par with Fisher 1918”
“I read it every night. Just so beautiful”
Reposted by Daniel E. Weeks
Bluetorial-Jim Watson
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
November 8, 2025 at 1:58 PM
Bluetorial-Jim Watson
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
Reposted by Daniel E. Weeks
Probably the papers I share the most often are @f2harrell.bsky.social 1996 on how to effectively develop multivariate models and @benvancalster.bsky.social 2019 paper on Calibration. Both extremely well written and informative. What are you most shared stats paper? #statistics #statssky #academicsky
November 7, 2025 at 12:12 PM
Probably the papers I share the most often are @f2harrell.bsky.social 1996 on how to effectively develop multivariate models and @benvancalster.bsky.social 2019 paper on Calibration. Both extremely well written and informative. What are you most shared stats paper? #statistics #statssky #academicsky
Reposted by Daniel E. Weeks
✨Hello folks!✨
We're back in your feed with an amazing paper spotlight by @kirahoeffler.bsky.social & colleagues📰🔦
"Optimizing genetic ancestry adjustment in DNA methylation studies: a comparative analysis of approaches"
🔗http://bit.ly/49syndi
Read our overview below!
🧵1/6
We're back in your feed with an amazing paper spotlight by @kirahoeffler.bsky.social & colleagues📰🔦
"Optimizing genetic ancestry adjustment in DNA methylation studies: a comparative analysis of approaches"
🔗http://bit.ly/49syndi
Read our overview below!
🧵1/6
November 1, 2025 at 5:20 PM
✨Hello folks!✨
We're back in your feed with an amazing paper spotlight by @kirahoeffler.bsky.social & colleagues📰🔦
"Optimizing genetic ancestry adjustment in DNA methylation studies: a comparative analysis of approaches"
🔗http://bit.ly/49syndi
Read our overview below!
🧵1/6
We're back in your feed with an amazing paper spotlight by @kirahoeffler.bsky.social & colleagues📰🔦
"Optimizing genetic ancestry adjustment in DNA methylation studies: a comparative analysis of approaches"
🔗http://bit.ly/49syndi
Read our overview below!
🧵1/6
Reposted by Daniel E. Weeks
📈 #TrendingWithImpact:
A new #research paper was #published on September 10, titled “Longitudinal associations of epigenetic aging with cognitive aging in Hispanic/Latino adults from the Hispanic Community Health Study/Study of Latinos.”
🔗 doi.org/10.18632/agi...
#aging #quote #epigenetics
A new #research paper was #published on September 10, titled “Longitudinal associations of epigenetic aging with cognitive aging in Hispanic/Latino adults from the Hispanic Community Health Study/Study of Latinos.”
🔗 doi.org/10.18632/agi...
#aging #quote #epigenetics
November 4, 2025 at 5:43 PM
📈 #TrendingWithImpact:
A new #research paper was #published on September 10, titled “Longitudinal associations of epigenetic aging with cognitive aging in Hispanic/Latino adults from the Hispanic Community Health Study/Study of Latinos.”
🔗 doi.org/10.18632/agi...
#aging #quote #epigenetics
A new #research paper was #published on September 10, titled “Longitudinal associations of epigenetic aging with cognitive aging in Hispanic/Latino adults from the Hispanic Community Health Study/Study of Latinos.”
🔗 doi.org/10.18632/agi...
#aging #quote #epigenetics
Reposted by Daniel E. Weeks
Insights on downstream immunity from blood methylome signatures in children exposed to maternal type 1 diabetes #T1D #Genetics #Epigenetics www.nature.com/articles/s42...
Blood methylome signatures in children exposed to maternal type 1 diabetes are linked to protection against islet autoimmunity - Nature Metabolism
Through an epigenome-wide blood analysis in children of mothers with or without type 1 diabetes, the authors identify epigenetic modifications of type 1 diabetes susceptibility loci through which mate...
www.nature.com
November 6, 2025 at 12:06 PM
Insights on downstream immunity from blood methylome signatures in children exposed to maternal type 1 diabetes #T1D #Genetics #Epigenetics www.nature.com/articles/s42...
Reposted by Daniel E. Weeks
New pre-print out on peer-review milling! Together with @deevybee.bsky.social and M. Angeles Oviedo Garcia.
Enjoy!
doi.org/10.1101/2025...
Enjoy!
doi.org/10.1101/2025...
Gaming the peer review system: a sophisticated review mill in medicine highlights the need to ensure reviewer integrity
Background A review mill is a network of researchers who game the peer review system to apparently boost their citations. Members write generic review reports containing suggestions for citations to t...
doi.org
November 7, 2025 at 10:22 AM
New pre-print out on peer-review milling! Together with @deevybee.bsky.social and M. Angeles Oviedo Garcia.
Enjoy!
doi.org/10.1101/2025...
Enjoy!
doi.org/10.1101/2025...
Reposted by Daniel E. Weeks
If people are using the correct statistics, casual inference and study design, they will quickly realize they don't have the funds to design the study, the time to learn the statistics, or the right data to answer the actual question they are interested in. Then they will never publish or get tenure
November 7, 2025 at 10:44 AM
If people are using the correct statistics, casual inference and study design, they will quickly realize they don't have the funds to design the study, the time to learn the statistics, or the right data to answer the actual question they are interested in. Then they will never publish or get tenure
Reposted by Daniel E. Weeks
Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n
openrxiv.org/enabling-rev...
openrxiv.org/enabling-rev...
Enabling options for review: from training and transparency to author-centered AI tools - openRxiv
Peer review is widely viewed as a critical aspect of biomedical communication. Ideally, it provides authors with feedback so they can improve manuscripts and gives readers, particularly nonspecialists...
openrxiv.org
November 6, 2025 at 2:32 PM
Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n
openrxiv.org/enabling-rev...
openrxiv.org/enabling-rev...
Reposted by Daniel E. Weeks
My prediction is that LLM peer review will slow down science. It will do this for precisely the same reasons that contemporary peer review does and some extra ones. Start by reading @hansonmark.bsky.social thread below, then read on. 🧵
Just tried q.e.d. by @odedrechavi.bsky.social et al. with a few papers including by myself & others where I knew a claim within was flawed based on a misunderstanding of the signal.
1) it was impressive. I see what the hype is about.
2) it hallucinated.
www.qedscience.com
Overly long #SciPub🧵 1/n
1) it was impressive. I see what the hype is about.
2) it hallucinated.
www.qedscience.com
Overly long #SciPub🧵 1/n
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
www.qedscience.com
November 6, 2025 at 9:30 PM
My prediction is that LLM peer review will slow down science. It will do this for precisely the same reasons that contemporary peer review does and some extra ones. Start by reading @hansonmark.bsky.social thread below, then read on. 🧵
Reposted by Daniel E. Weeks
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 Daniel E. Weeks
Now a nice series of papers using genetics to "uncouple" excess adiposity from its adverse metabolic effects. Here for metabolic traits www.nature.com/articles/s42..., here including non metabolic traits elifesciences.org/articles/72452 & here using partitioned PRS www.nature.com/articles/s41...
When more is not worse: Genetic subtypes of obesity challenge conventional risk paradigms
Emerging evidence challenges the view of obesity as a uniform metabolic risk. Spotlighting
the recent Nature Medicine study by Chami et al. this piece discusses how “uncoupling”
adiposity from its car...
www.cell.com
November 7, 2025 at 9:46 AM
Now a nice series of papers using genetics to "uncouple" excess adiposity from its adverse metabolic effects. Here for metabolic traits www.nature.com/articles/s42..., here including non metabolic traits elifesciences.org/articles/72452 & here using partitioned PRS www.nature.com/articles/s41...
Reposted by Daniel E. Weeks
![As of mid 2025, a PubMed search for ‘Mendelian randomization’ in the title or abstract returns around 16,000 results since its first occurrence in 2003. Manual inspection of the hundred or so most recent MR papers in the literature indicates that the large majority of these papers show signs of being low quality, often reporting on relationships of variables that have little justification to be analysed [4], failing to discuss the gene-environment equivalence principle to justify the study design [1], failure to use STROBE-MR reporting guidelines [5, 6], and often with clear methodological errors [7, 8].](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:3zyo4iakhqs47bttjalqgbk7/bafkreiaiycu3ti6dc5d6bo3etj4hvel42ucx2dak3m2u4ygbfd3lmvwe6y@jpeg)
Reposted by Daniel E. Weeks
Great news! We've figured out something for 'trending towards significance' to mean. It's when the significance falls away before you quite finish your now-add-another-control-and-retest process.
"Guys, we _nearly_ got from a bivariate to a defensible analysis with significance intact. Next time!"
"Guys, we _nearly_ got from a bivariate to a defensible analysis with significance intact. Next time!"
Additionally, the practice of presenting a bloated table of regression coefficients and adding one control at a time to show that your per variable remains significant is utter nonsense.
October 25, 2025 at 10:14 PM
Great news! We've figured out something for 'trending towards significance' to mean. It's when the significance falls away before you quite finish your now-add-another-control-and-retest process.
"Guys, we _nearly_ got from a bivariate to a defensible analysis with significance intact. Next time!"
"Guys, we _nearly_ got from a bivariate to a defensible analysis with significance intact. Next time!"
Reposted by Daniel E. Weeks
Did you know (robust) loess fitting can fail if the data is already smooth? I made a notebook that shows the flawed fit (red) along with a possible improvement (blue), using Cleveland's original demonstration curve. #stats
observablehq.com/@xangregg/lo...
observablehq.com/@xangregg/lo...
November 6, 2025 at 5:50 PM
Did you know (robust) loess fitting can fail if the data is already smooth? I made a notebook that shows the flawed fit (red) along with a possible improvement (blue), using Cleveland's original demonstration curve. #stats
observablehq.com/@xangregg/lo...
observablehq.com/@xangregg/lo...
Reposted by Daniel E. Weeks
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 Daniel E. Weeks
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
github.com
November 6, 2025 at 11:25 PM
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.