Daan de Groot

I've used it to re analyse my neutrophil single cell proteomics data. The representation was excellent and made much biological sense. Mature neutrophils sit close together. Immature branch off. NETing populations are far off. Its great ill keep using Bonsai! Great tool!

Hey, I heard about Bonsai, but now I heard there is another method called MILK that also visualizes scRNA-seq on trees. And it is much faster! Should I just use that then? A tree is a tree, right? TLDR: No. #methodsmatter Not even close. On realistic synthetic data MILK performs worse than UMAP.

I've tried Bonsai in various datasets through the web server. It has always added some insights to my understanding of the data. Totally recommended, especially seeing the new additions 🤩

trees >> umaps

Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n

How do you visualize highly complex data without losing important information? Prof. Erik van Nimwegen’s team developed a new tool, Bonsai, that provides a faithful picture of the structure in the data. @erikvannimwegen.bsky.social @unibas.ch @dhdegroot.bsky.social @imbavienna.bsky.social

We are hiring! Join the de Groot Lab as a Master's Student / Research Intern in Computational Biology and Theoretical Modeling to develop a Bayesian method for comparing single-cell datasets by explicitly modeling measurement noise to bring out true biological variability.

You're a devbio and stem cell enthusiast in Vienna? Come meet the community at #DevStem26 @istaresearch.bsky.social on June 16th! Only 3 days left to register & submit your abstract! Free registration 👇 devstem.pages.ist.ac.at

We're looking for people with a solid computational background (Math, Physics, Computer science, Computational Biology, etcetera) to dive into biology! Come study the physical principles of cell-fate decisions using Bayesian data analysis and biophysical modeling!

Our Spring PhD call is OPEN. English is the program language and open to all nationalities. 30+ fully funded positions & diverse life science subjects. 👉 www.vbcphd.at Apply now! Institute of Molecular Biotechnology, Max Perutz Labs Vienna, IMP, Gregor Mendel Institute of Molecular Plant Biology

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

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 👇👇👇

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!

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).

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...

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]🧵

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...