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Pierre-Paul Axisa

@ppaxisa.bsky.social
240 followers 136 following 328 posts

researcher at CBMR (Copenhagen). Genomics, genetics, compbio, biostats, pun lover. ppaxisa.github.io

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Reposted by Pierre-Paul Axisa
KLAB - finding a cure for GI dysmotility at #HarvardStrong @klab.bsky.social · 24/09/2026
4. Will we in academia wisen up and moderate our language while discussing our science, or will we match the hype-generation of AI cos by getting a bigger loudspeaker to generate more hype? What's at stake is nuance (which already was at risk in academics before advent of AI). (fin)
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laserhedvig @laserhedvig.bsky.social · 21/09/2026
Interdisciplinary research is great and necessary, and also has consistently lower funding success www.nature.com/articles/nat... #academiclabourmarket #academia #research
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In Preparation @inprep.bsky.social · 18/09/2026
inpreparation.substack.com
Regev Daughter Bags Science Fair Win, Edges Baking Soda Volcano With Single-Cell Atlas Of Murine Tumor Microenvironment
SOUTH SAN FRANCISCO, CA—Genentech head of Research and Early Development Aviv Regev confirmed Tuesday that her 12-year-old daughter independently conceived, designed, and executed a 450,000-cell…
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Pierre-Paul Axisa @ppaxisa.bsky.social · 14/09/2026
Damned it got me right in the intrinsically disordered region
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Reposted by Pierre-Paul Axisa
Michael Love @mikelove.bsky.social · 12/09/2026
I wrote a post about how slice_sample() and other slice_* functions work in #tidyomics #Bioconductor tidyomics.github.io/tidyomicsBlo...
tidyomics.github.io
Slicing in tidyomics – tidyomicsBlog
How to use dplyr-style slice operations on omics data objects in the tidyomics project.
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Pierre-Paul Axisa @ppaxisa.bsky.social · 08/09/2026
Since scRNAseq happened I have heard many times "we don’t need large sample sizes, we have SiNgLe cells"
static.klipy.com
That's Not How It Works! That's Not How Any Of This Works!
ALT: That's Not How It Works! That's Not How Any Of This Works!
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Rachael Bay @rachaelabay.bsky.social · 05/09/2026
I have recently noticed a string of vandalism on our floor. These outrageous acts seem to be correlated with visits from a certain corn geneticist @jrossibarra.bsky.social
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Ewan Birney @ewanbirney.bsky.social · 04/09/2026
Two weeks ago the @economist.com had a leader "In praise of designer-ish babies". I wrote a letter to the Editor about this, explaining why the UK system is so confident that this should remain unlawful. The Economist has kindly published a shortened form+ my full letter below lnkd.in/p/ef-n78N8
lnkd.in
Full letter to Economist, response to "In praise of designer-ish babies" | Ewan Birney
Two weeks ago the The Economist published a leader titled "In praise of designer-ish babies". I wrote a letter to the editor in response to this. The Economist was kind enough to publish a shortened f...
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Pierre-Paul Axisa @ppaxisa.bsky.social · 27/08/2026
I am getting dizzy with all the flashy LLM generated diagrams and charts in scientific communication. I want to understand what your research is about, a clear title and an odd box and arrows will do perfectly well. I remember nostalgically my postdoc days where lab meetings were chalk only.
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Reposted by Pierre-Paul Axisa
Erik van Nimwegen @erikvannimwegen.bsky.social · 27/08/2026
Want to explore and understand the structure of your single-cell omics or other high-dimensional data? Try Bonsai! www.nature.com/articles/s41... Check out our tutorial videos with 1. Highlights of the Bonsai-scout exploratory analysis tool: www.youtube.com/watch?v=TE7T...
youtube.com
Bonsai-scout: Highlights
YouTube video by ISMARA: inferring gene regulatory interactions
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Biozentrum, University of Basel @biozentrum.unibas.ch · 21/08/2026
How do you visualize highly complex data without losing important information? Prof. Erik van Nimwegen’s team developed a new tool, Bonsai, that provides a faithful picture of the structure in the data. @erikvannimwegen.bsky.social @unibas.ch @dhdegroot.bsky.social @imbavienna.bsky.social
biozentrum.unibas.ch
Seeing the Unseen: A new tool for exploring complex biological data
Modern biology research can now generate valuable data on an unprecedented scale. But there is one major obstacle: making sense of these complex high-dimensional datasets. Prof. Erik van Nimwegen’s te...
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Reposted by Pierre-Paul Axisa
jp flores (he/him) @jpflores.rbind.io · 19/08/2026
1/7 Prestige sucks. Not because recognition is bad. But because science has spent decades confusing journal prestige with scientific quality. And that shapes what gets published, what gets rewarded, and ultimately what science gets done.
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vincentholst.bsky.social @vincentholst.bsky.social · 14/08/2026
As promised, we now share some details why it took 32 months to get this Matters Arising published, and, since many asked, share some comments on the reply to our critique. All details can be found in this small FAQ vincentholst.github.io/the_curious_.... Below is a summary 🧵
vincentholst.github.io
The Curious Case of the Declining Disruption’s Disappearance
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Dorothy Bishop @deevybee.bsky.social · 21/07/2026
I'm attending online event about a #NIH competition to develop a data-sharing index (S-Index), but am surprised that there aren't more people here (it's hybrid). www.nei.nih.gov/sindex Nice idea for NIH to have a competition for developing a S-index; we've just heard about the winners. 1/n
nei.nih.gov
NIH S-Index Innovation Event | National Eye Institute
Registration: http - July 21, 2026
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Nereide @drnereide.bsky.social · 09/07/2026
9/11 This case shows how, with complex data from large surveys, small errors in distance treatment or distortions can produce apparently significant signals. Science works exactly like this: strong claims are checked and, if necessary, corrected.
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Dr. Jean Fan @jef.works · 16/07/2026
Many of us profs are struggling w/ AI use by students. But a source of frustration I didn't anticipate: AI use by colleagues. Because if I had wanted an AI’s opinion, I too can prompt ChatGPT 🙄 More in my reflection on "Artificial Intelligence among University Professors" jean.fan/2026/07/16/a...
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Cedric Boeckx @cedricboeckx.bsky.social · 08/07/2026
Very good piece by @tuuliel.bsky.social @nevillesanjana.bsky.social @singht.bsky.social & colleagues: “Current challenges in GWAS integration and fine-mapping for variant interpretation” 🧪🧬 www.biorxiv.org/content/10.6...
biorxiv.org
Current challenges in GWAS integration and fine-mapping for variant interpretation
Over the past two decades, genome-wide association studies (GWAS) have identified thousands of trait- and disease-associated loci. However, the mechanistic understanding of these loci remains incomple...
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Reposted by Pierre-Paul Axisa
jp flores (he/him) @jpflores.rbind.io · 03/07/2026
As a Gilliam Fellow, it’s great to see @hhmi-science.bsky.social continue pushing toward evaluating science on its scientific merit rather than the prestige of the journal it’s in. The future of science should be open, accessible, and focused on the quality of the work, not the name on the cover.
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Roope Kaaronen @roopekaaronen.net · 29/06/2026
I've pivoted quite hard, changing fields entirely. Based on my experience: - New field is difficult to publish in (you don't speak the "language") - New work gets cited a lot less (lack of networks) - Hard to find a job/tenure (you lack formal qualifications in new field – huge hurdle!) Cont'd...
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Reposted by Pierre-Paul Axisa
Richard Sever @richardsever.bsky.social · 18/06/2026
"IF is a flawed metric...not an indication of the quality of published research...But, we are not naive. We know IF influences authors' decisions about where to publish". ☝️ The dilemma every journal faces. And that last sentence is a huge understatement. 1/2 journals.biologists.com/dev/article/...
journals.biologists.com
The elephant in the room: impact factor
Summary: This Editorial offers an honest look at impact factor trends in developmental biology, explains how Development serves its community, and makes the case that sustaining developmental biology ...
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Crystal Fleming クリスタル @alwaystheself.bsky.social · 17/06/2026
There's so much to say about this, but what is particularly striking is that the keynote speaker said absolutely nothing about using Claude to write his academic work until I intervened in the Q&A. It appears that he was not going to share this fairly important detail unless asked..
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Pierre-Paul Axisa @ppaxisa.bsky.social · 14/06/2026
UMAPs have become the ultimate get out of jail free card if you want to say whatever fits your narrative. You want to claim no changes: overlay few colors, or way too many colors. You want to claim a change, circle a zone of the plot, scream that there is a difference. No one will bat an eye.
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Reposted by Pierre-Paul Axisa
easystats @easystats.github.io · 11/06/2026
Did you know that you can use the #easystats #rstats {modelbased} package detect missed modeling by adding partial residuals to your plots? Check out the vignette on plotting options that shows you how to check your model: easystats.github.io/modelbased/a...
easystats.github.io
Plotting estimated marginal means
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Pierre-Paul Axisa @ppaxisa.bsky.social · 09/06/2026
Rstudio has a neat feature that when you open a document and some libraries are not installed, there's a banner asking you if you want to install, which triggers a background job installing missing packages. AFAIK this works for CRAN packages. Is there a way to extend it to bioconductor? #rstats
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Carl T. Bergstrom @carlbergstrom.com · 06/06/2026
Let's Streisand-effect these people. Here's the editorial that somehow merited calling the cops. Read and share.
diabetesjournals.org
Misguided Brushes of a Pen Continue to Dismantle and Destroy Biomedical Research in the United States: We Can No Longer Afford Complacency and Fear. We Must All Act Now!
The opinions expressed in this editorial are the personal views of the authors (S.E. Kahn, C.A.M. Anderson, J.B. Buse, and E. Selvin) and do not represent
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Reposted by Pierre-Paul Axisa
Ulrich Atz @ulrichatz.org · 04/06/2026
Did you recently update your #rstats to 4.6? Is your matrix algebra slow? Not #BLAS ting? `sessionInfo()` shows which BLAS library R uses. Switching from reference BLAS to Apple Accelerate is easily a 50x speedup. Let me know if this worked for you. 🚀 uatz.org/blog/2026-06-04-r-blas-macos/ #rstats
uatz.org
The Lurking Dangers of the R Version Update – ulrich atz
After you update on macOS, switch R to Apple’s fast BLAS for a 50x speedup.
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Matthew Kay @mjskay.com · 04/06/2026
The mythology of academia - noble pursuit of knowledge for knowledge's sake etc - is used by administrators to convince academics who think they don't have a real job to do things against their own self interest. The sooner we realize we *are* workers - with employers - the better.
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Reposted by Pierre-Paul Axisa
Clément Canonne @ccanonne.github.io · 03/06/2026
I uploaded a picture of a random root vegetable and asked ChatGPT to identify it. It told me it was a stochastic carrot.
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Pierre-Paul Axisa @ppaxisa.bsky.social · 01/06/2026
SNL’s Tucker Carlson is so good, this has been my mental reaction these last weeks every time I see some non sense research practice
Carlson in SNL saying huh? what are we doing? what’s going on?
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Pierre-Paul Axisa @ppaxisa.bsky.social · 01/06/2026
Also #singlecell RNaseq for sure 🧪🧬💻
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Paola Tellaroli @tellarpao.bsky.social · 29/05/2026
Have a relaxing weekend, everyone who went to Cannes! #stats
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Richard Sever @richardsever.bsky.social · 27/05/2026
Steve Quake quotes Brenner at #cshsymposium2026 : “biology is drowning in a sea of data and starving for knowledge”, arguing that never has this been more apt than now.
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Reposted by Pierre-Paul Axisa
Jay Van Bavel, PhD @jayvanbavel.bsky.social · 26/05/2026
A survey of 2600 Ph.D. students, postdocs, and other researchers in 65 countries found that top three complaints were that supervisors: 1) used dismissive communication 2) provided little feedback 3) ignored team members’ well-being The main thing they wanted was empathy
science.org
Early-career researchers want empathy from their supervisors
Survey of 2600 early-career researchers compiles traits of “ideal supervisor”
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In Preparation @inprep.bsky.social · 26/05/2026
inpreparation.substack.com
ERC Now Requires Rejected Applicants To Grow Oak Tree From Acorn Before Resubmission
BRUSSELS—In an effort to ensure that rejected applicants have undergone “sufficient personal and scientific growth” before resubmitting, the European Research Council announced Tuesday that…
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Pierre-Paul Axisa @ppaxisa.bsky.social · 25/05/2026
When there’s a meeting and the first presenter is full python matplotlib, and the second presenter is full #rstats ggplot viz. I always feel like
static.klipy.com
Zoolander Staring Contest: Ben Stiller & Owen Wilson
ALT: Zoolander Staring Contest: Ben Stiller & Owen Wilson
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easystats @easystats.github.io · 24/05/2026
🚀 Big updates are here! A new round of #rstats #easystats releases is now live on CRAN, featuring major performance boosts and new features for parameters, bayestestR, performance, modelbased, and see. Update via CRAN or grab the latest dev versions with: `easystats::install_latest()`
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Pierre-Paul Axisa @ppaxisa.bsky.social · 22/05/2026
Same if you only use animal models but put the human disease term in the title
static.klipy.com
Fred Armisen: Right To Jail
ALT: Fred Armisen: Right To Jail
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Thomas Yeo @bttyeo.bsky.social · 21/05/2026
In a meta-analysis of 210 biomedical AI studies that statistically compared models under cross-validation, 97% used invalid statistical tests. Here's our new preprint doi.org/10.64898/202... led by @tianchu.bsky.social @hetuli.bsky.social @shaoshiz.bsky.social @nichols.bsky.social 1/N
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Richard Sever @richardsever.bsky.social · 19/05/2026
"a paper today is a Frankensteined-together patchwork of supplementary files that run longer than the manuscript, datasets in repositories...code posted to GitHub without documentation. The paper has been replaced....by a mess" www.thetransmitter.org/from-bench-t...
thetransmitter.org
Is the scientific paper due to be replaced?
AI is pushing scientific publishing to the brink. For neuroscience, the crisis may be an opportunity to finally connect findings across subfields.
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Jeffrey Pullin @jeffreypullin.bsky.social · 18/05/2026
tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:
journals.plos.org
Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation
Author summary Most of the genetic variants associated with complex traits are located outside genes, limiting functional interpretation. Genetic colocalisation helps identify candidate causal genes b...
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Rafael Irizarry @rafalab.bsky.social · 18/05/2026
A flaw in Person-Δ may be overstating progress in single-cell perturbation prediction models. Pearson warned about this in the 19th century: reusing the same controls induces spurious correlation. Split the controls, and much of the claimed prediction power fades: www.biorxiv.org/content/10.6...
biorxiv.org
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Stefano Mangiola @stemang.bsky.social · 08/05/2026
New #tidyomics blog post! 🎉 #tidySummarizedExperiment greatly simplifies your omics workflows, giving tidyverse capabilities. We have improved its performance 30x on large datasets with tens of thousands of samples! tidyomics.github.io/tidyomicsBlo... Plz share! @mpibiochem.bsky.social
tidyomics.github.io
Speeding up tidySummarizedExperiment through query optimisation and the plyxp backend – tidyomicsBlog
Performance optimisation of tidySummarizedExperiment and related benchmark.
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 05/05/2026
The normative fraud that Errington describes is something I've seen my whole career. A biologist once told me, if p is very small, it can't be a false positive. Teams condition on null being false, see anything that makes p small as truth-seeking. These traditions spread bc they get you published.
still from quoted video with caption "It's a norm in the field." Where "it" in context means data fraud.
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Pierre-Paul Axisa @ppaxisa.bsky.social · 05/05/2026
Me every week #rstats
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Crystal Lewis @cghlewis.bsky.social · 01/05/2026
Grad Students, PI, Postdocs
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David Ochoa @d0choa.bsky.social · 01/05/2026
🧬 New preprint: "The Human Pleiotropic Map of GWAS Associations and Therapeutic Implications" Why do some genetically supported drug targets succeed in the clinic while others fail? Across 100,526 GWAS, the same evidence flags constrained gene functions rarely safe to modulate.
The Human Pleiotropic Map of GWAS Associations and Therapeutic Implications
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Luke Pilling @lcpilling.bsky.social · 30/04/2026
GWAS meta-analysed summary statistics for 72 long-term conditions from the GEMINI collaborative updated to v1.1 🌟 The input GWAS are the same but we have fixed several minor issues since the original release v1.0 See our GitHub for links (incl. to Zenodo) github.com/GEMINI-multi...
github.com
GEMINI
GEMINI: Genetic Evaluation of Multimorbidity towards INdividualisation of Interventions - GEMINI
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Mikhail Spivakov @mspivakov.bsky.social · 29/04/2026
I agree. I can see only a very limited number of scenarios in which it is useful and/or helps catch errors/data manipulation. Sharing detailed analysis pipelines and raw data is so much more important for reproducibility.
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Nicola Rennie @nrennie.bsky.social · 29/04/2026
📊 Five #ggplot2 functions I wish I'd known about earlier 📊 I've written a short blog (with examples) of some of the lesser-known {ggplot2} functions and arguments that make it easier to create better charts! Link: nrennie.rbind.io/blog/five-gg... #RStats #DataViz
nrennie.rbind.io
Five ggplot2 functions I wish I’d known about earlier – Nicola Rennie
There are a few small tweaks you can make to your ggplot2 code to improve your charts. However, they’re not often mentioned. So here’s a few functions and arguments I wish I’d known about earlier.
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Pierre-Paul Axisa @ppaxisa.bsky.social · 27/04/2026
Top priority #Copenhagen outing last week-end: scout a French bakery that uses the PROPER terminology. They sell the CHOCOLATINE not the blasphemous "pain au cholocat". Excellent quality too. share.google/u8M0bK5qpkAl...
Ordering board with various items, incrusting chocolatine, brød, mad, kager and other
picture from googlemaps
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