Simon Anders

Absolutely savage, I love it.

With all the excitement about AI giving us answers, we often forget that the real trick is to figure out what is the question.

8/ 🤘 For those about to rock (around the Christmas tree), we salute you 🎸🎄: Isabelle Seufert & our team from @dkfz.bsky.social & BioQuant & @akispapantonis.bsky.social, Philipp Mallm, @s-anders.bsky.social & Petros Kolovos labs with support from @spp2202.bsky.social & @mspacealliance.bsky.social.

1/ 🎄 We got our Christmas present today: "Two distinct chromatin modules regulate proinflammatory gene expression" is now published @natcellbio.nature.com doi.org/10.1038/s415.... Our study introduces a scATAC-seq-based framework for genome-wide analysis of gene regulation features.

Screenshot from project 2025 that says By statute or regulation, CDC guidance must be prohibited from taking on a prescriptive character. For example, never again should CDC officials be allowed to say in their official capacity that school children "should be" masked or vaccinated (through a schedule or otherwise) or prohibited from learning in a school building. Such decisions should be left to parents and medical providers. We have learned that when CDC says what people "should" do, it readily becomes a "must" backed by severe punishments, including criminal penalties. CDC should report on the risks and effectiveness of all infectious disease-mitigation measures dispassionately and leave the "should" and "must" policy calls to politically accountable parties. Conflicts of Interest. There was a time when the CDC could not take money

It is utterly catastrophic that RFK Jr. plans to end CDC recommendations for most childhood vaccines.

It’s a betrayal of science, ethics, compassion, and the people of the United States.

And it was also a specific goal of Project 2025 (page 254).

This is the most alarming story I’ve read today. Giving up the fight before it’s started

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

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'

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...

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...

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...

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

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

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...

#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

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.

Fifteen Years

xkcd.com/3172/

Frikkin amazing stuff.

nlmixr2 logo

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

The Euro Bioc 2026 in Turku is official!

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...

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...

this is one of my favourite observations about sample size calculations. (afaik first articulated by Miettinen in 1985)

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!

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...

EXCELLENT graphic on the drain of scientific publishing! zenodo.org/records/1759...

‘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…

‘A new low’: Researchers at Iraqi university must cite colleagues, school journals in papers, @joelving.bsky.social reports

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

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.

When you buy a cutting board from bioinformaticians

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)

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

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 ...

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...

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...

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...