Pierre-Paul Axisa
@ppaxisa.bsky.social
researcher at CBMR (Copenhagen). Genomics, genetics, compbio, biostats, pun lover.
Reposted by Pierre-Paul Axisa
February 12, 2026 at 11:44 AM
Reposted by Pierre-Paul Axisa
I wrote a blog for the Meta-Research Center expressing my infinite frustration about not getting data. What else is new, you might think? Well, I added an extra layer of annoyance directed at the journals who do NOTHING to enforce promised data sharing.
metaresearch.nl/blog/2026/2/...
metaresearch.nl/blog/2026/2/...
Promised Data Unavailable? – I’m Sorry, Ma’am, There’s Nothing We Can Do — Meta-Research Center
This blogpost has been written by Michèle Nuijten. Michèle is an assistant professor of our research group who investigates reproducibility and replicability in psychology. Also, she is the developer ...
metaresearch.nl
February 3, 2026 at 3:03 PM
I wrote a blog for the Meta-Research Center expressing my infinite frustration about not getting data. What else is new, you might think? Well, I added an extra layer of annoyance directed at the journals who do NOTHING to enforce promised data sharing.
metaresearch.nl/blog/2026/2/...
metaresearch.nl/blog/2026/2/...
Reposted by Pierre-Paul Axisa
What does it take to succeed in science? Failure.
Cambridge scientists from @labliston.bsky.social share the self-doubt behind their careers.
Self-Doubt by Adrian Liston from @stcatharines.bsky.social and the Department of Pathology is Out tomorrow 👇
https://bit.ly/4a4tWUE
#Careers #Science
Cambridge scientists from @labliston.bsky.social share the self-doubt behind their careers.
Self-Doubt by Adrian Liston from @stcatharines.bsky.social and the Department of Pathology is Out tomorrow 👇
https://bit.ly/4a4tWUE
#Careers #Science
January 29, 2026 at 2:05 PM
What does it take to succeed in science? Failure.
Cambridge scientists from @labliston.bsky.social share the self-doubt behind their careers.
Self-Doubt by Adrian Liston from @stcatharines.bsky.social and the Department of Pathology is Out tomorrow 👇
https://bit.ly/4a4tWUE
#Careers #Science
Cambridge scientists from @labliston.bsky.social share the self-doubt behind their careers.
Self-Doubt by Adrian Liston from @stcatharines.bsky.social and the Department of Pathology is Out tomorrow 👇
https://bit.ly/4a4tWUE
#Careers #Science
Reposted by Pierre-Paul Axisa
I am deeply offended by boomerplyr (inspired by genzplyr), because I am NOT a boomer (squarely Xennial) and I "get" all the translations bradlindblad.github.io/boomerplyr/ #Rstats
January 20, 2026 at 2:08 PM
I am deeply offended by boomerplyr (inspired by genzplyr), because I am NOT a boomer (squarely Xennial) and I "get" all the translations bradlindblad.github.io/boomerplyr/ #Rstats
Reposted by Pierre-Paul Axisa
every big data paper with a bold story that is impossible to comprehend, evaluate, and independently verify reminds me of DOPRA. i've come to increasingly appreciate small, unassuming papers with humble conclusions that you can track word for word, data point by data point, assumption by assumption.
January 15, 2026 at 5:33 PM
every big data paper with a bold story that is impossible to comprehend, evaluate, and independently verify reminds me of DOPRA. i've come to increasingly appreciate small, unassuming papers with humble conclusions that you can track word for word, data point by data point, assumption by assumption.
Reposted by Pierre-Paul Axisa
New preprint alert: we use sign errors as a test of how well TWAS works.
Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS.
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
High false sign rates in transcriptome-wide association studies
Transcriptome-wide association studies (TWAS) are widely used to identify genes involved in complex traits and to infer the direction of gene effects on traits. However, despite their popularity, it r...
doi.org
January 6, 2026 at 2:48 AM
New preprint alert: we use sign errors as a test of how well TWAS works.
Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
Reposted by Pierre-Paul Axisa
"We also find that approximately half of researchers never publish in a venue with an impact factor above 15, which, under journal-level evaluation regimes, may exclude them from consideration for opportunities. Many of these researchers publish equally influential work"
Most researchers would receive more recognition if assessed by article-level metrics than by journal-level metrics
Are authors fairly judged by assessment of the prestige of the journals in which their work is published? This study compares article level metrics with journal level metrics, finding that the vast ma...
journals.plos.org
December 29, 2025 at 4:40 PM
"We also find that approximately half of researchers never publish in a venue with an impact factor above 15, which, under journal-level evaluation regimes, may exclude them from consideration for opportunities. Many of these researchers publish equally influential work"
Reposted by Pierre-Paul Axisa
Remember: only YOU can prevent the zombie apocalypse
December 6, 2025 at 4:58 PM
Remember: only YOU can prevent the zombie apocalypse
Reposted by Pierre-Paul Axisa
I wrote about missing heritability, "missing environmentality," and why I still think twin studies are interesting and valuable: kathrynpaigeharden.substack.com/p/twins-are-...
Twins Are So Much More Interesting Than Heritability Estimates
On starting places, "missing environmentality," and the Waddington landscape of life
kathrynpaigeharden.substack.com
December 4, 2025 at 7:08 PM
I wrote about missing heritability, "missing environmentality," and why I still think twin studies are interesting and valuable: kathrynpaigeharden.substack.com/p/twins-are-...
Reposted by Pierre-Paul Axisa
Massive single-cell study by Kanai et al (www.medrxiv.org/content/10.1...):
- Once statistical power is high, constrained genes have more (though weaker) eQTLs.
- Chromatin-QTLs near constrained genes have "normal" effect sizes, colocalize more with disease, but exhibit attenuated peak-gene effects.
- Once statistical power is high, constrained genes have more (though weaker) eQTLs.
- Chromatin-QTLs near constrained genes have "normal" effect sizes, colocalize more with disease, but exhibit attenuated peak-gene effects.
November 30, 2025 at 5:06 PM
Massive single-cell study by Kanai et al (www.medrxiv.org/content/10.1...):
- Once statistical power is high, constrained genes have more (though weaker) eQTLs.
- Chromatin-QTLs near constrained genes have "normal" effect sizes, colocalize more with disease, but exhibit attenuated peak-gene effects.
- Once statistical power is high, constrained genes have more (though weaker) eQTLs.
- Chromatin-QTLs near constrained genes have "normal" effect sizes, colocalize more with disease, but exhibit attenuated peak-gene effects.
Reposted by Pierre-Paul Axisa
A thread of directed acyclic graphs (DAGs) that look like record covers... because that's EXACTLY what the world needs
1. Huey Lewis and the News: link.springer.com/chapter/10.1...
1. Huey Lewis and the News: link.springer.com/chapter/10.1...
November 28, 2025 at 11:36 AM
A thread of directed acyclic graphs (DAGs) that look like record covers... because that's EXACTLY what the world needs
1. Huey Lewis and the News: link.springer.com/chapter/10.1...
1. Huey Lewis and the News: link.springer.com/chapter/10.1...
Reposted by Pierre-Paul Axisa
Well, I found the solution Harmit!
November 27, 2025 at 2:08 AM
Well, I found the solution Harmit!
Reposted by Pierre-Paul Axisa
Americans make great biologists because we are forged by the hardest challenge in all of biotech: getting flavor from a turkey
November 27, 2025 at 2:35 PM
Americans make great biologists because we are forged by the hardest challenge in all of biotech: getting flavor from a turkey
Reposted by Pierre-Paul Axisa
I'm a longtime fan of Affinity Designer as an affordable Illustrator-killer for figures, and... it's now free?! www.canva.com/newsroom/new...
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Why we made Affinity free, and how we’ll keep it that way
We’ve made Affinity completely free, empowering professional designers with studio-grade creative software, supported by Canva’s sustainable ecosystem.
www.canva.com
November 18, 2025 at 11:28 PM
I'm a longtime fan of Affinity Designer as an affordable Illustrator-killer for figures, and... it's now free?! www.canva.com/newsroom/new...
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Reposted by Pierre-Paul Axisa
Many journal sites are down. But you know which one is NOT?
That of CSH Protocols!
So, check out the definitive source of technique-related reviews and laboratory protocols in the life sciences.
cshprotocols.cshlp.org
That of CSH Protocols!
So, check out the definitive source of technique-related reviews and laboratory protocols in the life sciences.
cshprotocols.cshlp.org
November 18, 2025 at 3:03 PM
Many journal sites are down. But you know which one is NOT?
That of CSH Protocols!
So, check out the definitive source of technique-related reviews and laboratory protocols in the life sciences.
cshprotocols.cshlp.org
That of CSH Protocols!
So, check out the definitive source of technique-related reviews and laboratory protocols in the life sciences.
cshprotocols.cshlp.org
"it would make sense to adopt some ground rules. In many ways, these would be similar to those adopted by geneticists after the first frenzy of candidate gene associations was found to be a waste of time and money because the area was overwhelmed by nonreplicable false positive results."🙌
We did a thing. 😬
The link between the gut #microbiome and autism is not backed by science, researchers say.
Read the full opinion piece in @cp-neuron.bsky.social: spkl.io/63322AbxpA
@wiringthebrain.bsky.social, @statsepi.bsky.social, & @deevybee.bsky.social
Read the full opinion piece in @cp-neuron.bsky.social: spkl.io/63322AbxpA
@wiringthebrain.bsky.social, @statsepi.bsky.social, & @deevybee.bsky.social
November 13, 2025 at 7:23 PM
"it would make sense to adopt some ground rules. In many ways, these would be similar to those adopted by geneticists after the first frenzy of candidate gene associations was found to be a waste of time and money because the area was overwhelmed by nonreplicable false positive results."🙌
Reposted by Pierre-Paul Axisa
We did a thing. 😬
The link between the gut #microbiome and autism is not backed by science, researchers say.
Read the full opinion piece in @cp-neuron.bsky.social: spkl.io/63322AbxpA
@wiringthebrain.bsky.social, @statsepi.bsky.social, & @deevybee.bsky.social
Read the full opinion piece in @cp-neuron.bsky.social: spkl.io/63322AbxpA
@wiringthebrain.bsky.social, @statsepi.bsky.social, & @deevybee.bsky.social
November 13, 2025 at 5:59 PM
We did a thing. 😬
Reposted by Pierre-Paul Axisa
I've done a lot of work in Python this fall, and it hasn't endeared me to the language at all. Why does stuff have to be so complicated when you're doing it in Python?
blog.genesmindsmachines.com/p/python-is-...
blog.genesmindsmachines.com/p/python-is-...
Python is not a great language for data science. Part 1: The experience
It may be a good language for data science, but it’s not a great one.
blog.genesmindsmachines.com
November 13, 2025 at 4:16 PM
I've done a lot of work in Python this fall, and it hasn't endeared me to the language at all. Why does stuff have to be so complicated when you're doing it in Python?
blog.genesmindsmachines.com/p/python-is-...
blog.genesmindsmachines.com/p/python-is-...
Reposted by Pierre-Paul Axisa
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 Pierre-Paul Axisa
The real question, the one many of us are avoiding, is whether we need some metric to rank publications. Be that JIF, citation count, or something akin to eLife's impact assessment.
And from my recent foray onto the academic job market, the answer is an unequivocal yes. Journals provide this.
And from my recent foray onto the academic job market, the answer is an unequivocal yes. Journals provide this.
November 7, 2025 at 10:24 AM
The real question, the one many of us are avoiding, is whether we need some metric to rank publications. Be that JIF, citation count, or something akin to eLife's impact assessment.
And from my recent foray onto the academic job market, the answer is an unequivocal yes. Journals provide this.
And from my recent foray onto the academic job market, the answer is an unequivocal yes. Journals provide this.
Outlook, can we have a nice email user experience? Or maybe have copilot help us parse through our inbox? Hell no, but I will flag any and all google calendar invites as phishing
November 7, 2025 at 8:33 AM
Outlook, can we have a nice email user experience? Or maybe have copilot help us parse through our inbox? Hell no, but I will flag any and all google calendar invites as phishing
Reposted by Pierre-Paul Axisa
#r2u now contains BioConductor 3.22 released yesterday for Ubuntu 24.04 and 22.04 (for the 500-some packages we cover, details at the site). #Rstats 4.5.2 has been built, we will update the containers in a few days as well.
#r2u. Fast. Easy. Reliable. Pick All Three.
eddelbuettel.github.io/r2u
#r2u. Fast. Easy. Reliable. Pick All Three.
eddelbuettel.github.io/r2u
CRAN as Ubuntu Binaries - r2u
Easy, fast, reliable -- pick all three!
eddelbuettel.github.io
October 31, 2025 at 8:03 PM
#r2u now contains BioConductor 3.22 released yesterday for Ubuntu 24.04 and 22.04 (for the 500-some packages we cover, details at the site). #Rstats 4.5.2 has been built, we will update the containers in a few days as well.
#r2u. Fast. Easy. Reliable. Pick All Three.
eddelbuettel.github.io/r2u
#r2u. Fast. Easy. Reliable. Pick All Three.
eddelbuettel.github.io/r2u
Reposted by Pierre-Paul Axisa
I am very happy to finally share SAFE-LD, a method convert genotypes to an anonymised privacy-preserving version to be used to precisely compute LD. Led by @gdesanctis.bsky.social Claudia Gianbartolomei @sodbo.bsky.social and Davide bolognini.
📄: shorturl.at/BgXqq
Github: shorturl.at/b49Wa
📄: shorturl.at/BgXqq
Github: shorturl.at/b49Wa
SAFE-LD: A novel method for the estimation of linkage disequilibrium from summary statistics
Genome-wide association studies (GWAS) have greatly advanced our understanding of the genetic architecture of complex traits. Downstream analyses of GWAS summary statistics require accurate in-sample ...
www.biorxiv.org
October 21, 2025 at 9:47 AM
I am very happy to finally share SAFE-LD, a method convert genotypes to an anonymised privacy-preserving version to be used to precisely compute LD. Led by @gdesanctis.bsky.social Claudia Gianbartolomei @sodbo.bsky.social and Davide bolognini.
📄: shorturl.at/BgXqq
Github: shorturl.at/b49Wa
📄: shorturl.at/BgXqq
Github: shorturl.at/b49Wa