Simon Anders
@s-anders.bsky.social
physicist, bioinformatics / biostats researcher at University of Heidelberg
Reposted by Simon Anders
EXCELLENT graphic on the drain of scientific publishing! zenodo.org/records/1759...
November 15, 2025 at 4:04 AM
EXCELLENT graphic on the drain of scientific publishing! zenodo.org/records/1759...
Reposted by Simon Anders
‘A new low’: Researchers at Iraqi university must cite colleagues, school journals in papers, @joelving.bsky.social reports
‘A new low’: Researchers at Iraqi university must cite colleagues, school journals in papers
Mustansiriyah University At the University of Technology in Baghdad, students must publish papers citing the school’s own journals if they wish to graduate, as we reported earlier this month. But d…
retractionwatch.com
October 27, 2025 at 5:52 PM
‘A new low’: Researchers at Iraqi university must cite colleagues, school journals in papers, @joelving.bsky.social reports
Reposted by Simon Anders
It’s astonishing how many researchers seem to believe that a cluster analysis is such a sensible analysis that it needn’t even be justified through a coherent research question. Just cluster analysis go brrrrr
October 27, 2025 at 3:42 PM
It’s astonishing how many researchers seem to believe that a cluster analysis is such a sensible analysis that it needn’t even be justified through a coherent research question. Just cluster analysis go brrrrr
Reposted by Simon Anders
Nature Communications will publish ~10K papers in 2025 pubmed.ncbi.nlm.nih.gov?term=%22Natu...
That's ~$70M in revenue, while many of the non-profit journals that used to occupy that slot in the journal hierarchy have seen a precipitous decline in submissions in the 15 years it's existed.
That's ~$70M in revenue, while many of the non-profit journals that used to occupy that slot in the journal hierarchy have seen a precipitous decline in submissions in the 15 years it's existed.
October 27, 2025 at 8:38 PM
Nature Communications will publish ~10K papers in 2025 pubmed.ncbi.nlm.nih.gov?term=%22Natu...
That's ~$70M in revenue, while many of the non-profit journals that used to occupy that slot in the journal hierarchy have seen a precipitous decline in submissions in the 15 years it's existed.
That's ~$70M in revenue, while many of the non-profit journals that used to occupy that slot in the journal hierarchy have seen a precipitous decline in submissions in the 15 years it's existed.
Reposted by Simon Anders
When you buy a cutting board from bioinformaticians
October 26, 2025 at 10:56 PM
When you buy a cutting board from bioinformaticians
Reposted by Simon Anders
This is one of my biggest fear with LLMs. They reduce the incentive to create new, non-LLM materials, so we’re going to train on more and more LLM material and reduce the diversity of style/content/topics in the world
(Pic from Wikipedia)
(Pic from Wikipedia)
October 17, 2025 at 7:52 PM
This is one of my biggest fear with LLMs. They reduce the incentive to create new, non-LLM materials, so we’re going to train on more and more LLM material and reduce the diversity of style/content/topics in the world
(Pic from Wikipedia)
(Pic from Wikipedia)
Reposted by Simon Anders
Auszeichnung für Heidelberger Datenwissenschaftlerin: Britta Velten wird für innovative Verfahren für die Analyse von komplexen Datensätzen aus den Lebenswissenschaften mit dem Early Excellence in Science Award ausgezeichnet www.uni-heidelberg.de/de/newsroom/...
#uniheidelberg #lifescience
#uniheidelberg #lifescience
October 16, 2025 at 1:29 PM
Auszeichnung für Heidelberger Datenwissenschaftlerin: Britta Velten wird für innovative Verfahren für die Analyse von komplexen Datensätzen aus den Lebenswissenschaften mit dem Early Excellence in Science Award ausgezeichnet www.uni-heidelberg.de/de/newsroom/...
#uniheidelberg #lifescience
#uniheidelberg #lifescience
Reposted by Simon Anders
Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one?
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Promoter-proximal gatekeepers restrict pleiotropic enhancer inputs to achieve tissue specificity
Developmental enhancers are central regulatory elements that can activate multiple genes, yet how they selectively regulate one gene over its neighbours remains unclear. Using the Drosophila twist E3 ...
www.biorxiv.org
October 16, 2025 at 12:34 PM
Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one?
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Reposted by Simon Anders
Did transposable elements shape brain evolution — and if so, which ones, and in which cell states and lineages? Led by @tyamadat.bsky.social, we explored this question in cerebellum development using sequence-based deep learning models!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 16, 2025 at 10:01 PM
Did transposable elements shape brain evolution — and if so, which ones, and in which cell states and lineages? Led by @tyamadat.bsky.social, we explored this question in cerebellum development using sequence-based deep learning models!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Simon Anders
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...
🧵
@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...
🧵
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...
www.biorxiv.org
October 10, 2025 at 12:50 PM
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...
🧵
@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...
🧵
Reposted by Simon Anders
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...
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...
embl.wd103.myworkdayjobs.com
October 10, 2025 at 7:30 AM
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...
Reposted by Simon Anders
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...
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...
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.
open.substack.com
October 5, 2025 at 1:49 PM
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...
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...
Reposted by Simon Anders
Reposted by Simon Anders
Do NOT be afraid of taking Tylenol.
It is not linked to autism.
Read more here: 🔗 news.immunologic.org/p/the-tyleno...
It is not linked to autism.
Read more here: 🔗 news.immunologic.org/p/the-tyleno...
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.
news.immunologic.org
September 23, 2025 at 11:41 PM
Do NOT be afraid of taking Tylenol.
It is not linked to autism.
Read more here: 🔗 news.immunologic.org/p/the-tyleno...
It is not linked to autism.
Read more here: 🔗 news.immunologic.org/p/the-tyleno...
Reposted by Simon Anders
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.
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…
retractionwatch.com
September 18, 2025 at 7:05 PM
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.
Reposted by Simon Anders
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...
@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...
Viewer
app.smarticle.com
September 17, 2025 at 6:50 PM
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...
@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...
Reposted by Simon Anders
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”
For every uncorrected p value you must add an extra letter to the claim.
“Eating chocolate maaaaaaaaay be associated with lower rates of stroke”
September 16, 2025 at 6:55 PM
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”
For every uncorrected p value you must add an extra letter to the claim.
“Eating chocolate maaaaaaaaay be associated with lower rates of stroke”
Reposted by Simon Anders
Dream job - research software engineer, in one of the most beautiful parts of the world
September 17, 2025 at 1:26 PM
Dream job - research software engineer, in one of the most beautiful parts of the world
Reposted by Simon Anders
Bioinformaticians / computational biologists take note - know where you should take your OS tool chain from and do not introduce backdoors.
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:44 AM
Bioinformaticians / computational biologists take note - know where you should take your OS tool chain from and do not introduce backdoors.
Reposted by Simon Anders
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...
Technical Lead for the "Health + Life Science Alliance Data Space"
jobs.dkfz.de
August 28, 2025 at 9:06 AM
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...
Reposted by Simon Anders
"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."
“Microsoft says U.S. law takes precedence over Canadian data sovereignty”
… or how to lose government contracts all over the world in one easy step. 🖕🏾🖕🏾
www.digitaljournal.com/tech-science...
… or how to lose government contracts all over the world in one easy step. 🖕🏾🖕🏾
www.digitaljournal.com/tech-science...
Microsoft says U.S. law takes precedence over Canadian data sovereignty
Microsoft representative says US CLOUD Act comes before other country's sovereignty.
www.digitaljournal.com
August 23, 2025 at 6:15 AM
"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."
Reposted by Simon Anders
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...
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...
August 22, 2025 at 7:50 PM
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...
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...
Reposted by Simon Anders
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. 🧪👇
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.
www.cell.com
August 7, 2025 at 11:10 AM
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. 🧪👇
Reposted by Simon Anders
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...
www.nature.com/articles/s41...
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...
www.nature.com
August 4, 2025 at 4:07 PM
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...
www.nature.com/articles/s41...
Reposted by Simon Anders
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”
“[elaborate theoretical reasoning] thus, x & y [which are obviously correlated for trivial reasons] should correlate > 0”
July 9, 2025 at 1:17 PM
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”
“[elaborate theoretical reasoning] thus, x & y [which are obviously correlated for trivial reasons] should correlate > 0”