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.

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

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...

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...

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

#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

Fifteen Years xkcd.com/3172/

Frikkin amazing stuff.

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!

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, @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

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...

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... 🧵

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...

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...

Do NOT be afraid of taking Tylenol. It is not linked to autism. Read more here: 🔗 news.immunologic.org/p/the-tyleno...

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.

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...

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. 🧪👇

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”

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 :)

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...