Simon Anders
@s-anders.bsky.social
physicist, bioinformatics / biostats researcher at University of Heidelberg
Reposted by Simon Anders
ISCO (Innovations in Single-Cell OMICS) will be back in beautiful Barcelona!
🗓️ 28th/29th of May 2026
📍Barcelona Biomedical Research Park @prbb.org (beachfront!)
Keynotes: @bartdeplancke.bsky.social and @bocklab.bsky.social
Submit your abstract and present your research!
www.isco-conference.eu
🗓️ 28th/29th of May 2026
📍Barcelona Biomedical Research Park @prbb.org (beachfront!)
Keynotes: @bartdeplancke.bsky.social and @bocklab.bsky.social
Submit your abstract and present your research!
www.isco-conference.eu
December 5, 2025 at 10:33 AM
ISCO (Innovations in Single-Cell OMICS) will be back in beautiful Barcelona!
🗓️ 28th/29th of May 2026
📍Barcelona Biomedical Research Park @prbb.org (beachfront!)
Keynotes: @bartdeplancke.bsky.social and @bocklab.bsky.social
Submit your abstract and present your research!
www.isco-conference.eu
🗓️ 28th/29th of May 2026
📍Barcelona Biomedical Research Park @prbb.org (beachfront!)
Keynotes: @bartdeplancke.bsky.social and @bocklab.bsky.social
Submit your abstract and present your research!
www.isco-conference.eu
Reposted by Simon Anders
One step in the right direction from @cnrs.fr . Here’s hoping others will follow and we can get some more space for actual science. 🧪 www.cnrs.fr/en/update/cn...
The CNRS is breaking free from the Web of Science
From January 1st 2026, the CNRS will cut access to one of the largest commercial bibliometric databases, Clarivate Analytics'
www.cnrs.fr
December 3, 2025 at 8:07 PM
One step in the right direction from @cnrs.fr . Here’s hoping others will follow and we can get some more space for actual science. 🧪 www.cnrs.fr/en/update/cn...
Reposted by Simon Anders
Happy to see this out now in Cell Genomics: A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines: www.cell.com/cell-genomic...
A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines
Feng et al. present the first genome-scale CRISPR interference perturbation map with
scRNA-seq readout across many genetic backgrounds in human pluripotent cells, pioneering
population-scale CRISPR pe...
www.cell.com
December 3, 2025 at 9:17 AM
Happy to see this out now in Cell Genomics: A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines: www.cell.com/cell-genomic...
Reposted by Simon Anders
Our Ensembl 2026 paper is out!
Learn about 1,900+ new genomes, expanded pangenome support, new regulation interfaces, and what’s coming in our 2026 releases.
doi.org/10.1093/nar/gkaf1239
Learn about 1,900+ new genomes, expanded pangenome support, new regulation interfaces, and what’s coming in our 2026 releases.
doi.org/10.1093/nar/gkaf1239
Ensembl 2026
Abstract. The Ensembl project (https://www.ensembl.org) is a public and open resource providing access to genomes, annotations, high-quality tools, and met
academic.oup.com
November 28, 2025 at 4:30 PM
Our Ensembl 2026 paper is out!
Learn about 1,900+ new genomes, expanded pangenome support, new regulation interfaces, and what’s coming in our 2026 releases.
doi.org/10.1093/nar/gkaf1239
Learn about 1,900+ new genomes, expanded pangenome support, new regulation interfaces, and what’s coming in our 2026 releases.
doi.org/10.1093/nar/gkaf1239
Reposted by Simon Anders
#Postdoc alert! We are looking for motivated individual with experience in computational systems biology to join our NetworkCommons initiative to benchmark and democratise network contextualisation methods across multiple applications. Deadline Dec 17th link here: tinyurl.com/yrrzxa94
Postdoctoral fellow - Petsalaki Group - NetworkCommons
Your group The Petsalaki, Saez-Rodriguez (EMBL-EBI) and Korcsmáros (Imperial College) groups develop cutting-edge computational and AI approaches to unravel cellular signalling and gene regulation fro...
tinyurl.com
November 26, 2025 at 5:05 PM
#Postdoc alert! We are looking for motivated individual with experience in computational systems biology to join our NetworkCommons initiative to benchmark and democratise network contextualisation methods across multiple applications. Deadline Dec 17th link here: tinyurl.com/yrrzxa94
Reposted by Simon Anders
![Comic. Panels up to the 10-year point are grayed out. New panels since the Ten Years comic, which chronicles the first ten years of PERSON 1's journey with cancer: (1) [two people in bed] PERSON 1 (woman): One more chapter? PERSON 2 (man): Don’t we both have to get up early? PERSON 1: Nnnnnggggh PERSON 2: Sure, good point. (2) [many people wearing masks, walking while looking at graphs on their phones] (3) [birds landing on people] PERSON 2 in beanie and scarf: Hah! They like *my* seeds best. PERSON 1 in scarf holding phone with a bird sitting on it: Wait, how do I take a picture of this one? (4) [two people rowing boats with tree landscape] (5) [Person 1 carries overflowing stack of things to Person 2 in bed] PERSON 1: I brought you honey lemon tea, more pillows, a cinnamon roll, Tylenol, another blanket, a– PERSON 2: It was just Appendicitis, I’m really– PERSON 1: *It is my turn to take care of you and I am going to do it right!* (6) [Two people in car] (7) [still in car) PERSON 1: Oh my god. PERSON 2: Oh my god. (8) [car driving] PERSON 1: Pull over! PERSON 2: I am! (9) [both people get out of car] (10) [Large colored panel of aurora borealis over water with both people looking on] (11) [Person 1 sits against tree while Person 2 lies on the ground] PERSON 1: Fifteen years. No sign of the cancer. (12) I *am* having some weird symptoms. Joint pain. Fatigue. I think I’m losing my close-up vision. PERSON 2: Yeah. Me too. (13) PERSON 2: I think we’re getting old. (14) PERSON 1: I guess that’s okay. PERSON 2: It’s all I wanted.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreihwhjblp5lyiwp63ouar7ocfea7evmckytoeo7rkfuoo4gw5rnrra@jpeg)
November 26, 2025 at 10:32 PM
Reposted by Simon Anders
Frikkin amazing stuff.
November 26, 2025 at 8:29 AM
Frikkin amazing stuff.
Reposted by Simon Anders
nlmixr2 is becoming an R Consortium Working Group!
Open-source NLME modeling in R that can compete with commercial pharmacometric tools and support regulatory submissions.
More: r-consortium.org/posts/nlmixr...
#RStats #pharma
Open-source NLME modeling in R that can compete with commercial pharmacometric tools and support regulatory submissions.
More: r-consortium.org/posts/nlmixr...
#RStats #pharma
November 26, 2025 at 6:31 PM
nlmixr2 is becoming an R Consortium Working Group!
Open-source NLME modeling in R that can compete with commercial pharmacometric tools and support regulatory submissions.
More: r-consortium.org/posts/nlmixr...
#RStats #pharma
Open-source NLME modeling in R that can compete with commercial pharmacometric tools and support regulatory submissions.
More: r-consortium.org/posts/nlmixr...
#RStats #pharma
Reposted by Simon Anders
The Euro Bioc 2026 in Turku is official!
November 27, 2025 at 5:06 AM
The Euro Bioc 2026 in Turku is official!
Reposted by Simon Anders
NEW: Postdoc with @epetsalaki.bsky.social @juliosaezrod.bsky.social and Tamas Korcsmáros
Benchmark and integrate state-of-the-art network contextualisation methods, combining large-scale transcriptomics, proteomics, and single-cell data
Apply by 17 Dec
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Benchmark and integrate state-of-the-art network contextualisation methods, combining large-scale transcriptomics, proteomics, and single-cell data
Apply by 17 Dec
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Postdoctoral fellow - Petsalaki Group - NetworkCommons
Your group The Petsalaki, Saez-Rodriguez (EMBL-EBI) and Korcsmáros (Imperial College) groups develop cutting-edge computational and AI approaches to unravel cellular signalling and gene regulation fro...
embl.wd103.myworkdayjobs.com
November 26, 2025 at 11:07 AM
NEW: Postdoc with @epetsalaki.bsky.social @juliosaezrod.bsky.social and Tamas Korcsmáros
Benchmark and integrate state-of-the-art network contextualisation methods, combining large-scale transcriptomics, proteomics, and single-cell data
Apply by 17 Dec
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Benchmark and integrate state-of-the-art network contextualisation methods, combining large-scale transcriptomics, proteomics, and single-cell data
Apply by 17 Dec
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Simon Anders
this is one of my favourite observations about sample size calculations. (afaik first articulated by Miettinen in 1985)
November 25, 2025 at 10:56 AM
this is one of my favourite observations about sample size calculations. (afaik first articulated by Miettinen in 1985)
Reposted by Simon Anders
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
November 21, 2025 at 5:31 PM
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Reposted by Simon Anders
Confidence interval discussion time! The perfect opportunity to repost this blog post answering the question you haven’t dared to ask: www.the100.ci/2024/12/05/w...
November 19, 2025 at 6:47 AM
Confidence interval discussion time! The perfect opportunity to repost this blog post answering the question you haven’t dared to ask: www.the100.ci/2024/12/05/w...
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...