Daan de Groot
@dhdegroot.bsky.social
Group leader at IMBA at Vienna BioCenter. How do single cells decide what to become? What to do? When? Where? https://www.oeaw.ac.at/imba/groups/daan-de-groot
Update to @golobor.bsky.social message: distortion-free Bonsai trees >> umaps > quick trees Picture shows realistic simulated scRNA-seq data and how well Bonsai represents its structure, while another tree-representation does not. It shows that a tree is not all you need. You actually have to
Anton Goloborodko@golobor.bsky.social · 2mo agotrees >> umaps
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 🤩
Erik van Nimwegen@erikvannimwegen.bsky.social · 2mo agoRemember 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
trees >> umaps
Erik van Nimwegen@erikvannimwegen.bsky.social · 2mo agoRemember 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
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
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
nature.com
Erik van Nimwegen@erikvannimwegen.bsky.social · last yr.Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...
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
Seeing the Unseen: A new tool for exploring complex biological data
Modern biology research can now generate valuable data on an unprecedented scale. But there is one major obstacle: making sense of these complex high-dimensional datasets. Prof. Erik van Nimwegen’s te...
biozentrum.unibas.ch
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
Development and Stem Cells Regional Meeting
devstem.pages.ist.ac.at
Institute of Molecular Biotechnology@imbavienna.bsky.social · 5mo agoJoin us on June 18 at ISTA for a day dedicated to developmental and stem cell biology, with talks, poster sessions, flash talks, and opportunities to connect across the Vienna life science community. More. 👇
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!
Institute of Molecular Biotechnology@imbavienna.bsky.social · 7mo agoWe are #hiring! Join the de Groot lab as a PhD student in Computational Biology & Theoretical Modeling. Deadline: April 15. How to apply. 👇
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:
Vienna BioCenter Scientific Training@vbcscitraining.bsky.social · 7mo agoThe Vienna BioCenter PhD program in Molecular BioSciences will offer 25+ fully-funded positions in the Spring Call which is now open. Check the vacancies in this call: www.vbcphd.at Institute of Molecular Biotechnology, Max Perutz Labs Vienna, IMP, Gregor Mendel Institute of Molecular Plant Biology
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.” 🔥🔥🔥
biorxiv.org
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!🙏
Institute of Molecular Biotechnology@imbavienna.bsky.social · 8mo agoApply to the Master’s project position at IMBA: https://www.oeaw.ac.at/imba/career-education/open-positions/pos2607-masters-project #research #jobs #europe #biology
this is a **unique** opportunity - Daan de Groot, our new neighbor at @imbavienna.bsky.social , is hiring
Daan de Groot@dhdegroot.bsky.social · 9mo agoBig 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
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
This link will take you to a page that’s not on LinkedIn
lnkd.in
Institute of Molecular Biotechnology@imbavienna.bsky.social · 9mo agoDaan de Groot is joining IMBA as group leader, and he is hiring now! https://imba.science/3M9sfxg The de Groot Lab will study how cells make fate decisions during embryonic development, a research area with broad implications for both fundamental biology and biomedical applications. Welcome to
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
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...
pnas.org
Erik van Nimwegen@erikvannimwegen.bsky.social · 9mo agoWhat 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
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
find it remarkable that folks upload the unpublished, confidential work of others to those sites.
Onisillos@onisillos.bsky.social · 10mo agoIndirect. Prompt. Injection. www.nature.com/articles/d41...
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!
Biozentrum, University of Basel@biozentrum.unibas.ch · last yr.Research Associate (100%) Starting from 1 November 2025 or as per agreement Group @erikvannimwegen.bsky.social @biozentrum.unibas.ch @unibas.ch www.biozentrum.unibas.ch/open-positio... #job #research #biology #microbiology #science #basel #recruiting #career
Please! No more UMAPs/t-SNEs 👇👇👇
Erik van Nimwegen@erikvannimwegen.bsky.social · last yr.Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...
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!
Erik van Nimwegen@erikvannimwegen.bsky.social · last yr.Bonsai-scout allows different layouts, zooming in and out on areas, visualizing gene expression or annotations on the tree, finding 'clusters' (well-separated clades), and finding marker genes that distinguish any pair of clades. Check out our tutorial videos! www.youtube.com/watch?v=TE7T...
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
First select a node by clicking in the tree, then click the below buttons to indicate if that node is the ancestor or a downstream node of the subtree.
bonsai.unibas.ch
Erik van Nimwegen@erikvannimwegen.bsky.social · last yr.Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...
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).
Erik van Nimwegen@erikvannimwegen.bsky.social · last yr.The most profound insights are often also the most simple: growth-rate, by setting the dilution rate of intra-cellular molecules, controls the sensitivity of gene regulatory circuits. In retrospect it seems crazy that this effect seems to have been overlooked so far. www.science.org/doi/10.1126/...
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...
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...
bajour.ch
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]🧵
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
academic.oup.com
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...
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...
biorxiv.org