Simon Anders

Induction of menstruation in mice reveals the regulation of menstrual shedding During menstruation, an inner layer of the endometrium is selectively shed, while an outer, progenitor-containing layer is preserved to support repeated regeneration. Progress in understanding this co...

I’m thrilled to share my postdoc work and the first paper from the McKinley Lab! 🎉
@karalmckinley.bsky.social
We built the first transgenic model of menstruation in mice.
We used it to uncover how the endometrium organizes and sheds during menstruation. 🧪
www.biorxiv.org/content/10.1...
🧵

Staff Scientist About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...

I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

RFK Jr's third Tylenol-autism study is just run-of-the-mill bad research I’m reading through RFK Jr’s supposed evidence that Tylenol causes autism and it’s not looking good for his conclusions.

My review of the third autism-Tylenol study RFK Jr mentioned is out now.

If you weighed in on "what proportion of kids have neurodevelopmental disorders" yesterday, this paper is why I asked the question. Most of you will be very surprised by their answer!

open.substack.com/pub/epiellie...

A gray and a tan bunny lie on a blanket, gazing at a scenic sunset over hills.

The Tylenol–Autism Pseudoscience Pipeline How false testimony about Tylenol and autism failed in court, was repackaged as “peer-reviewed” junk science, and is now driving Trump’s dangerous medical advice.

Do NOT be afraid of taking Tylenol.

It is not linked to autism.

Read more here: 🔗 news.immunologic.org/p/the-tyleno...

Publisher investigating DNA contamination paper that authors say CDC vaccine committee will consider The publisher Taylor & Francis is investigating concerns raised on PubPeer about a paper claiming to find DNA contamination in COVID-19 vaccines beyond regulators’ recommended amounts.  Th…

The move comes as the U.S. body tasked with making recommendations for vaccine use is scheduled to consider the safety of COVID-19 shots, and two of the study’s authors say their findings will be discussed.

Niedersächs. Ärzteblatt: Warum ist die #Psychologisierung so gefährlich?

@geschom.bsky.social: Die Gefahr ist einmal, dass die Hypothese, es könnte eine somatoforme oder funktionelle Störung sein, nicht falsifizierbar ist […]

Ganzer Artikel mit ganzen Antworten:
app.smarticle.com/html5/DsLS6i...

Proposal for how to fix family wise error rates.

For every uncorrected p value you must add an extra letter to the claim.

“Eating chocolate maaaaaaaaay be associated with lower rates of stroke”

Dream job - research software engineer, in one of the most beautiful parts of the world

Bioinformaticians / computational biologists take note - know where you should take your OS tool chain from and do not introduce backdoors.

Technical Lead for the "Health + Life Science Alliance Data Space"

You are passionate about making data accessible? The Heidelberg Mannheim life science builds a data space - a major step for bridging basic science and translation. Two of more jobs to come. Technical lead and cloud engineer jobs.dkfz.de/en/jobs/1680... jobs.dkfz.de/en/jobs/1680...

"if the United States were to issue a legal request to Microsoft for the data of a French citizen hosted in the EU, Microsoft would comply regardless of French or EU law."

Thrilled to share the second half of my PhD work here!

We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)

doi.org/10.1101/2025...

Notes from Beethoven’s genome Wesseldijk et al. compare the genomic information collected from Ludwig van Beethoven with population-based datasets used to quantify musical achievement.

If someone you know buys into claims about "genetic optimization" of embryos using polygenic scores of cognition, just send them our 2024 paper on Beethoven & musicality. We wrote it to help communicate limits of individual-level genetic predictions & complexity of links between DNA & behaviour. 🧪👇

Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines - Nature Methods The analysis presented in this Brief Communication shows that, despite their complexity, current deep learning models do not outperform linear baselines in predicting gene perturbation effects, thus e...

An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social

www.nature.com/articles/s41...

Will never get over the fact that some with only a faint idea of what an informative test would look like think hypothesis tests are the only valid mode of doing science

“[elaborate theoretical reasoning] thus, x & y [which are obviously correlated for trivial reasons] should correlate > 0”

Powerful CRISPR system inserts whole gene into human DNA ‘Directed’ evolution in the laboratory creates an editing tool that outperforms classic CRISPR systems.

www.nature.com/articles/d41...
Coverage of our collaboration with the Liu group..
' “This is crazy directed evolution!” - Makoto Saito'

Abstract submissions are now open for the European Bioconductor Conference (EuroBioC2025), 17-19 September 2025 in Barcelona.
This event will bring together the Bioconductor community in Europe to advance bioinformatics, data science, and open-source software.

eurobioc2025.bioconductor.org

Registrations are now open! Follow the link at
csama2025.bioconductor.eu/registration...

Post-doc positions in biomedical research available in Heidelberg: www.health-life-sciences.de/opportunitie...

(This is a funding scheme for joint projects of research group at University, University Hospital, EMBL and/or DKFZ).

This is the result of my brief postdoc with Simon Anders in the last 6 months and grew out of an intriguing reviewer comment for the LEMUR paper with @wkhuber.bsky.social :)

Beeswarm plot of the double perturbation predictions. The Additive model outperforms GEARS, scGPT, and scFoundation by a large margin

Line plot of the accuracy of the predictions that are most different from the additive model. The No Change model outperforms GEARS, scGPT, and scFoundation.

Beeswarm plot of the single perturbation predictions. The linear model perform as good as GEARS, scGPT, and scFoundation.

There's a lot of excitement about foundation models and their ability to learn biology 🧬💻

But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress.

www.biorxiv.org/content/10.1...