Pierre-Paul Axisa
@ppaxisa.bsky.social
researcher at CBMR (Copenhagen). Genomics, genetics, compbio, biostats, pun lover.
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
Reposted by Pierre-Paul Axisa
With so many new methods buried in results-focused papers, this thread is my encouragement to groups to also publish separate protocols papers! You'll be pleasantly surprised at the engagement these papers get, and most importantly they provide real impact aiding others in their science.
October 31, 2025 at 9:09 AM
With so many new methods buried in results-focused papers, this thread is my encouragement to groups to also publish separate protocols papers! You'll be pleasantly surprised at the engagement these papers get, and most importantly they provide real impact aiding others in their science.
Reposted by Pierre-Paul Axisa
A small 🧵 encouraging people to publish protocols.
Our #AutoSpectral release has made me reflect on how much the community tends to appreciate protocol papers. People rarely present protocols as their main achievements, but they are often the most impactful work.
www.biorxiv.org/content/10.1...
Our #AutoSpectral release has made me reflect on how much the community tends to appreciate protocol papers. People rarely present protocols as their main achievements, but they are often the most impactful work.
www.biorxiv.org/content/10.1...
AutoSpectral improves spectral flow cytometry accuracy through optimised spectral unmixing and autofluorescence-matching at the cellular level
The advent of spectral flow cytometry has seen a rapid rise in the complexity of flow cytometry experiments, allowing the construction of assays with at least 50 fluorescent parameters. To correctly d...
www.biorxiv.org
October 31, 2025 at 9:09 AM
A small 🧵 encouraging people to publish protocols.
Our #AutoSpectral release has made me reflect on how much the community tends to appreciate protocol papers. People rarely present protocols as their main achievements, but they are often the most impactful work.
www.biorxiv.org/content/10.1...
Our #AutoSpectral release has made me reflect on how much the community tends to appreciate protocol papers. People rarely present protocols as their main achievements, but they are often the most impactful work.
www.biorxiv.org/content/10.1...
PSA: it’s all great if you provide an interactive dashboard to browse the data you painstakingly generated. But please do back up the data on persistent archive like zenodo. It’s too bad we can’t access the database when inevitably the server goes down and you moved onto other projects/institutions
October 31, 2025 at 7:05 PM
PSA: it’s all great if you provide an interactive dashboard to browse the data you painstakingly generated. But please do back up the data on persistent archive like zenodo. It’s too bad we can’t access the database when inevitably the server goes down and you moved onto other projects/institutions
Reposted by Pierre-Paul Axisa
🧬 EuroBioC2026 is coming to Turku, Finland, from June 3–5, 2026!
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
October 29, 2025 at 9:02 AM
🧬 EuroBioC2026 is coming to Turku, Finland, from June 3–5, 2026!
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
Reposted by Pierre-Paul Axisa
I've been asked about this paper (www.nature.com/articles/s41...) enough times that I finally had to read it.
The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.
tl;dr it's glam-slop & everyone involved should be embarrassed
The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.
tl;dr it's glam-slop & everyone involved should be embarrassed
SARS-CoV-2 mRNA vaccines sensitize tumours to immune checkpoint blockade - Nature
mRNA vaccines targeting SARS-CoV-2 also sensitize tumours to immune checkpoint inhibitors.
www.nature.com
October 30, 2025 at 3:35 PM
I've been asked about this paper (www.nature.com/articles/s41...) enough times that I finally had to read it.
The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.
tl;dr it's glam-slop & everyone involved should be embarrassed
The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.
tl;dr it's glam-slop & everyone involved should be embarrassed
#rstats : when you have a path string like "this/is/my/path", is there a formatting shortcut somewhere to quickly split it into a vector like c("this", "is", "my", "path") (even better if with {here} or {this.path})
{lintr} is harassing me for long lines and I ought to do something
{lintr} is harassing me for long lines and I ought to do something
a man in a suit and tie is sitting on a bench and making a funny face .
ALT: a man in a suit and tie is sitting on a bench and making a funny face .
media.tenor.com
October 23, 2025 at 7:04 AM
#rstats : when you have a path string like "this/is/my/path", is there a formatting shortcut somewhere to quickly split it into a vector like c("this", "is", "my", "path") (even better if with {here} or {this.path})
{lintr} is harassing me for long lines and I ought to do something
{lintr} is harassing me for long lines and I ought to do something
Be careful, check your kids’ book, they might contain rogue pseudotime analyses 💻🧬
October 20, 2025 at 6:57 PM
Be careful, check your kids’ book, they might contain rogue pseudotime analyses 💻🧬
Reposted by Pierre-Paul Axisa
💡 Came across this nice tool today:
🎨 qualpal for algorithmically choosing maximally distinct colors under certain restrictions #dataviz
JOSS paper, online tool, R package #rstats
joss.theoj.org/papers/10.21...
🎨 qualpal for algorithmically choosing maximally distinct colors under certain restrictions #dataviz
JOSS paper, online tool, R package #rstats
joss.theoj.org/papers/10.21...
Qualpal: Qualitative Color Palettes for Everyone
Larsson, J., (2025). Qualpal: Qualitative Color Palettes for Everyone. Journal of Open Source Software, 10(114), 8936, https://doi.org/10.21105/joss.08936
joss.theoj.org
October 17, 2025 at 9:12 AM
💡 Came across this nice tool today:
🎨 qualpal for algorithmically choosing maximally distinct colors under certain restrictions #dataviz
JOSS paper, online tool, R package #rstats
joss.theoj.org/papers/10.21...
🎨 qualpal for algorithmically choosing maximally distinct colors under certain restrictions #dataviz
JOSS paper, online tool, R package #rstats
joss.theoj.org/papers/10.21...
Reposted by Pierre-Paul Axisa
Are you going to #ASHG2025 next week in Boston? Interested in getting some mentorship from leading figures in the field (and me)?
Check out our speed mentoring event on Thursday! Sign-ups are online so reserve a spot ASAP.
site.pheedloop.com/event/ASHG25...
Check out our speed mentoring event on Thursday! Sign-ups are online so reserve a spot ASAP.
site.pheedloop.com/event/ASHG25...
PheedLoop
PheedLoop: Hybrid, In-Person & Virtual Event Software
site.pheedloop.com
October 6, 2025 at 3:42 PM
Are you going to #ASHG2025 next week in Boston? Interested in getting some mentorship from leading figures in the field (and me)?
Check out our speed mentoring event on Thursday! Sign-ups are online so reserve a spot ASAP.
site.pheedloop.com/event/ASHG25...
Check out our speed mentoring event on Thursday! Sign-ups are online so reserve a spot ASAP.
site.pheedloop.com/event/ASHG25...
Reposted by Pierre-Paul Axisa
One of the biggest increases in my analysis/coding productivity in recent years is completely embracing git repos 🐧
Coupled with GitHub it is *so easy* to be open, reproducible, efficient, and accountable to myself and colleagues 👨💻
No more chaotic servers wondering which script led to what! 😵💫
Coupled with GitHub it is *so easy* to be open, reproducible, efficient, and accountable to myself and colleagues 👨💻
No more chaotic servers wondering which script led to what! 😵💫
October 3, 2025 at 9:00 AM
One of the biggest increases in my analysis/coding productivity in recent years is completely embracing git repos 🐧
Coupled with GitHub it is *so easy* to be open, reproducible, efficient, and accountable to myself and colleagues 👨💻
No more chaotic servers wondering which script led to what! 😵💫
Coupled with GitHub it is *so easy* to be open, reproducible, efficient, and accountable to myself and colleagues 👨💻
No more chaotic servers wondering which script led to what! 😵💫
Is it me or now Rstudio saves files with .r instead of .R? Same goes for Rmd vs rmd. What is this heresy #rstats? Well I actually don’t know if there is one way that is more correct but
Disappointment Disappointed GIF
ALT: Disappointment Disappointed GIF
media.tenor.com
October 1, 2025 at 6:35 AM
Is it me or now Rstudio saves files with .r instead of .R? Same goes for Rmd vs rmd. What is this heresy #rstats? Well I actually don’t know if there is one way that is more correct but
Reposted by Pierre-Paul Axisa
This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 8:34 AM
This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/
Reposted by Pierre-Paul Axisa
Massive sibling regression study finds that human traits are largely environmentally driven (average heritability = 0.3)
Within-family heritability estimates for behavioural and disease phenotypes from 500,000 sibling pairs of diverse ancestries
Quantification of the direct effect of genetic variation on human behavioural traits is important for understanding between-individual variation in socio-economic and health outcomes but estimates of ...
www.medrxiv.org
September 20, 2025 at 6:19 PM
Massive sibling regression study finds that human traits are largely environmentally driven (average heritability = 0.3)