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
How do single cells decide what to become? What to do? When? Where?
https://www.oeaw.ac.at/imba/groups/daan-de-groot
Pinned
Daan de Groot
@dhdegroot.bsky.social
· Jan 27
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
Reposted by Daan de Groot
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 🤩
Totally recommended, especially seeing the new additions 🤩
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
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
August 21, 2026 at 11:12 AM
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 🤩
Totally recommended, especially seeing the new additions 🤩
Reposted by Daan de Groot
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
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
August 24, 2026 at 9:20 AM
trees >> umaps
Reposted by Daan de Groot
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
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
August 21, 2026 at 11:01 AM
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
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
Reposted by Daan de Groot
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...
www.biozentrum.unibas.ch
August 21, 2026 at 9:26 AM
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
Reposted by Daan de Groot
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.
August 12, 2026 at 1:47 PM
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.
Reposted by Daan de Groot
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
Only 3 days left to register & submit your abstract!
Free registration 👇
devstem.pages.ist.ac.at
May 27, 2026 at 2:42 PM
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
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!
We are #hiring! Join the de Groot lab as a PhD student in Computational Biology & Theoretical Modeling. Deadline: April 15. How to apply. 👇
March 28, 2026 at 9:33 AM
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!
Reposted by Daan de Groot
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
Apply now!
Institute of Molecular Biotechnology, Max Perutz Labs Vienna, IMP, Gregor Mendel Institute of Molecular Plant Biology
March 23, 2026 at 2:55 PM
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
Apply now!
Institute of Molecular Biotechnology, Max Perutz Labs Vienna, IMP, Gregor Mendel Institute of Molecular Plant Biology
Reposted by Daan de Groot
Have a look at this PhD program in Vienna- most interesting science and the best training program:
The 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
Institute of Molecular Biotechnology, Max Perutz Labs Vienna, IMP, Gregor Mendel Institute of Molecular Plant Biology
March 3, 2026 at 10:18 AM
Have a look at this PhD program in Vienna- most interesting science and the best training program:
Reposted by Daan de Groot
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.” 🔥🔥🔥
www.biorxiv.org
February 17, 2026 at 11:21 PM
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.” 🔥🔥🔥
Reposted by Daan de Groot
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!🙏
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!🙏
February 17, 2026 at 6:21 PM
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!🙏
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!🙏
Reposted by Daan de Groot
this is a **unique** opportunity - Daan de Groot, our new neighbor at @imbavienna.bsky.social , is hiring
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
January 27, 2026 at 2:56 PM
this is a **unique** opportunity - Daan de Groot, our new neighbor at @imbavienna.bsky.social , is hiring
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
January 27, 2026 at 1:44 PM
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!
January 13, 2026 at 1:11 PM
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!
Reposted by Daan de Groot
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
www.biorxiv.org/content/10.6...
1/n
www.biorxiv.org
January 13, 2026 at 12:47 PM
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
www.biorxiv.org/content/10.6...
1/n
Reposted by Daan de Groot
find it remarkable that folks upload the unpublished, confidential work of others to those sites.
December 16, 2025 at 3:46 PM
find it remarkable that folks upload the unpublished, confidential work of others to those sites.
Reposted by Daan de Groot
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 repost and notify potential candidates!
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
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
September 18, 2025 at 9:26 AM
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 repost and notify potential candidates!
Reposted by Daan de Groot
Please! No more UMAPs/t-SNEs 👇👇👇
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...
I'm so excited about this!
www.biorxiv.org/content/10.1...
Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data
Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...
www.biorxiv.org
May 11, 2025 at 8:36 PM
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!
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...
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-scout: Highlights
YouTube video by ISMARA: inferring gene regulatory interactions
www.youtube.com
May 9, 2025 at 12:00 PM
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!
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
May 9, 2025 at 11:55 AM
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).
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/...
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/...
Growth rate controls the sensitivity of gene regulatory circuits
Through the simple effect of dilution rate, regulatory circuits systematically change their sensitivity with growth rate.
www.science.org
May 4, 2025 at 7:48 AM
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).
Reposted by Daan de Groot
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...
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
February 9, 2025 at 8:54 PM
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...
Es ist ein Fehler, dass #SRF ausgerechnet hier spart.
bajour.ch/a/die-srf-sp...
Reposted by Daan de Groot
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]🧵
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
January 6, 2025 at 5:12 PM
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]🧵
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]🧵
Reposted by Daan de Groot
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...
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...
www.biorxiv.org
January 15, 2025 at 11:12 AM
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...
www.biorxiv.org/content/10.1...