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Thank you! Any candidates for the positions in your network? Brilliant postdocs who want to develop and maintain large-scale computational tools? Excellent students who want to try their hand at a challenging theoretical biology PhD while living in one of the most beautiful cities in the world?

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For the PhD students, I have many interesting project proposals in mind. Please apply to the Vienna BioCenter PhD Program (lnkd.in/eCDPSGyp) and/or contact me for more information. Especially, if you're ambitious, interested in single-cell decisions, and have a strong computational background.

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The research manager is a unique academic opportunity: lnkd.in/e7NiTvNY. It's long-term and comprises almost all the tasks of a group leader (solving scientific puzzles, mentoring, driving collaborations), while still leaving time to do the actual coding. Really, I'd almost apply myself.

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one of the best places to do it: with various very strong experimental groups working on development and tissue regeneration, we will collaborate with the best! *And I'm looking for people to join me!* In particular, a "computational research manager", 2 PhD students, and maybe some MSc students.

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Big news! At least for me. I'll start building my own research group at the amazing IMBA in Vienna. Starting from single-cell omics data, we will develop computational tools and theoretical models to understand how single cells make decisions, in particular during development. I think that IMBA is

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Daan de Groot @dhdegroot.bsky.social · 13/01/2026

Some time ago, we showed that bacterial adaptation is aided a lot by phenotypes becoming increasingly unstable at slow growth (www.pnas.org/doi/10.1073/...), but we didn't know what caused this phenomenon. Over the last years, others continued the search, and you can now read the results!

pnas.org

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

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Reposted by Daan de Groot

Erik van Nimwegen @erikvannimwegen.bsky.social · 13/01/2026

What are the main sources of gene expression noise in bacteria, and why do slower growing bacteria exhibit more expression noise? TLDR: we found growth-rate fluctuations are a key driver of gene expression noise that increase as average growth rate decreases. www.biorxiv.org/content/10.6... 1/n

biorxiv.org

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Reposted by Daan de Groot

Julius Brennecke @juliusbrennecke.bsky.social · 16/12/2025

find it remarkable that folks upload the unpublished, confidential work of others to those sites.

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Reposted by Daan de Groot

Erik van Nimwegen @erikvannimwegen.bsky.social · 18/09/2025

Are you excited to pursue your own research interests and contribute to our group’s experimental research in the quantitative biology of microbes? We have an opening for a potentially permanent position as research associate. Please repost and notify potential candidates!

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Reposted by Daan de Groot

Carlos Talavera-López @cartalop.bsky.social · 11/05/2025

Please! No more UMAPs/t-SNEs 👇👇👇

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Daan de Groot @dhdegroot.bsky.social · 15/05/2025

Let us know what you think after reading everything!

Daan de Groot @dhdegroot.bsky.social · 15/05/2025

I'm surprised you're the first to make this joke. Congrats

Oh yes, and check out my debut as a failed YouTuber. I'm really much more excited about this than I sound in the video, because look how nice our Bonsai-scout app actually works to explore the data!

Represent the data by a tree structure! That’s the idea that @erikvannimwegen.bsky.social‬ proposed 3 years ago, and what we’ve been working on ever since. It came with many theoretical and computational challenges, but now I’m confident that we’ve created something truly worthwhile.

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and UMAP are so popular, even though everyone agrees they severely mess up your data? It's because there was nothing better, and some data, just demand a visual tool for exploration. Indeed, it’s hard to beat UMAP in the low-dimensional embedding game, unless you just change the game:

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