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

Institute of Molecular Biotechnology@imbavienna.bsky.social · 2mo ago

Join 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 · 4mo ago

We 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 · 5mo ago

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

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!🙏

Institute of Molecular Biotechnology@imbavienna.bsky.social · 6mo ago

Apply 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 · 6mo ago

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

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

Institute of Molecular Biotechnology@imbavienna.bsky.social · 6mo ago

Daan 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!

Erik van Nimwegen@erikvannimwegen.bsky.social · 7mo ago

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

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.

Onisillos@onisillos.bsky.social · 8mo ago

Indirect. 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 · 11mo ago

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

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