Reposted by Daan de GrootPeter @biotechpedro.bsky.social · 21/08/2026I'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 🤩 0102
Reposted by Daan de GrootErik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026Remember 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/nnature.comBonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature BiotechnologyHigh-dimensional data are visualized through representation on tree structures. 110446
Reposted by Daan de GrootBiozentrum, University of Basel @biozentrum.unibas.ch · 21/08/2026How 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.socialbiozentrum.unibas.chSeeing the Unseen: A new tool for exploring complex biological dataModern 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... 0258
Reposted by Daan de GrootInstitute of Molecular Biotechnology @imbavienna.bsky.social · 12/08/2026We 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. 152
Reposted by Daan de GrootKristina Stapornwongkul @kstapornwongkul.bsky.social · 27/05/2026You'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.atdevstem.pages.ist.ac.atDevelopment and Stem Cells Regional Meeting 1137
Daan de Groot @dhdegroot.bsky.social · 28/03/2026We'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! 064
Reposted by Daan de GrootVienna BioCenter Scientific Training @vbcscitraining.bsky.social · 23/03/2026Our 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 0106
Reposted by Daan de GrootEva Hörmanseder @evahoermanseder.bsky.social · 03/03/2026Have a look at this PhD program in Vienna- most interesting science and the best training program: 014
Reposted by Daan de GrootPaul Francois @pfrancois.bsky.social · 17/02/2026From 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 0126
Reposted by Daan de GrootKristina Stapornwongkul @kstapornwongkul.bsky.social · 17/02/2026We‘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!🙏 03839
Reposted by Daan de GrootAnton Goloborodko @golobor.bsky.social · 27/01/2026this is a **unique** opportunity - Daan de Groot, our new neighbor at @imbavienna.bsky.social , is hiring 032
Daan de Groot @dhdegroot.bsky.social · 27/01/2026Big 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 islnkd.inLinkedInThis link will take you to a page that’s not on LinkedIn 2187
Daan de Groot @dhdegroot.bsky.social · 13/01/2026Some 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.orgPNASProceedings 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... 041
Reposted by Daan de GrootErik van Nimwegen @erikvannimwegen.bsky.social · 13/01/2026What 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/nbiorxiv.org 12711
Reposted by Daan de GrootJulius Brennecke @juliusbrennecke.bsky.social · 16/12/2025find it remarkable that folks upload the unpublished, confidential work of others to those sites. 33313
Reposted by Daan de GrootErik van Nimwegen @erikvannimwegen.bsky.social · 18/09/2025Are 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! 0412
Reposted by Daan de GrootCarlos Talavera-López @cartalop.bsky.social · 11/05/2025Please! No more UMAPs/t-SNEs 👇👇👇 021
Daan de Groot @dhdegroot.bsky.social · 09/05/2025Oh 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! 010
Daan de Groot @dhdegroot.bsky.social · 09/05/2025Bonsai 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-SNEbonsai.unibas.chFirst 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. 24614
Daan de Groot @dhdegroot.bsky.social · 04/05/2025New 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). 1318
Reposted by Daan de GrootRichard Neher @neher.io · 09/02/2025Um 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...bajour.chSparmassnahmen treffen SRF Standort in BaselSRF 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... 0187
Reposted by Daan de GrootMarco Molari @mmolari.bsky.social · 06/01/2025Thrilled 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.comQuantifying the evolutionary dynamics of structure and content in closely-related E. coli genomesAbstract. Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics 56124
Reposted by Daan de GrootErik van Nimwegen @erikvannimwegen.bsky.social · 15/01/2025What 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...biorxiv.orgE. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrientsIt 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... 213567