Daan de Groot

Have a look at this PhD program in Vienna- most interesting science and the best training program:

From Pankaj’s Mehta group www.biorxiv.org/content/10.6... “Our findings highlight the need for rigorous benchmarking and suggest that the biology of cell identity can be captured by simple linear representations of single cell gene expression data.” 🔥🔥🔥

We‘re looking for a motivated Master student to join our team!

Do you want to optogenetically control metabolic activity to see how metabolism affects patterning and morphogenesis? 💡🧫🧬🔬

Then please apply!
#optogenetics #metabolism #devbio #hESCs

Please RT. Thank you!🙏

this is a **unique** opportunity - Daan de Groot, our new neighbor at @imbavienna.bsky.social , is hiring

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?

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.

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.

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.

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

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!

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

find it remarkable that folks upload the unpublished, confidential work of others to those sites.

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!

Please! No more UMAPs/t-SNEs 👇👇👇

Let us know what you think after reading everything!

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.

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:

Bonsai is out! Finally, we can visually explore high-dimensional data in a distortion-free way. Try it out! It works from scRNA-seq data (bonsai.unibas.ch/bonsai-scout...) up to football statistics (bonsai.unibas.ch/bonsai-scout...). 
Ever wondered why low-dimensional embeddings like t-SNE

New publication! We identify growth coupled sensitivity: a deceivingly simple mechanism that makes E. coli switch to the best sugar. We combined neat theory (due to @erikvannimwegen.bsky.social, and to which I contributed) with clean experiments (due to @thomasjulou.bsky.social and Theo Gervais).

Sparmassnahmen treffen SRF Standort in Basel SRF streicht Formate in den Bereichen Kultur und Wissenschaft. Das wird auch der Standort in Basel zu spüren bekommen. Bei Politiker*innen und in der Bajour-Community lösen die jüngst angekündigten Ma...

Um die grossen Herausforderungen unserer Zeit (KI, Klimawandel, Pandemien, etc) richtig beurteilen zu können, brauchen wir fundierten Wissenschaftsjournalismus.

Es ist ein Fehler, dass #SRF ausgerechnet hier spart.

bajour.ch/a/die-srf-sp...

Quantifying the evolutionary dynamics of structure and content in closely-related E. coli genomes Abstract. Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics

Thrilled to announce that our work (w. with fantastic @neher.io and Liam Shaw) has been published on Molecular Biology and Evolution! 🎉

academic.oup.com/mbe/advance-...

Are you curious about how fast the genome of E.coli evolves structurally (gains, rearrangements...) ? 🧬

A summary thread [1/N]🧵

E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients It is widely believed that due to nutrient limitations in natural environments, bacteria spend most of their life in non-growing states. However, very little is known about how bacteria change their p...

What do bacterial cells do when they run out of nutrients? Although most bacterial studies focus on cells in exponentially growing states, in the wild bacteria likely spend most of their time slowly starving to death. 1/n
www.biorxiv.org/content/10.1...