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!

What novel biological dynamics might be hiding under the measurement noise of your time-lapse fluorescence microscopy data? Try our new RealTrace tool to find out! Fantastic work by Bjoern Kscheschinski and others. Tweetorial follows. 1/n www.biorxiv.org/content/10.1...

We're looking for highly motivated candidates for PhD positions in the physics of living systems. Our group uses theoretical physics to understand how cells collectively self-organize. If you're interested, get in touch & check out the Biozentrum PhD Fellowship program, deadline October 12th!

Join us for an exciting #BiozentrumDiscovery lecture! Prof. Tami Lieberman from @mit.edu will speak about the dynamic selective landscape of human microbiomes. Her lab studies microbial evolution in real time, with a focus on mutations occurring within individual human microbiomes.

Anybody taking bets on how obvious the cherry-picking/p-hacking is going to turn out to be to obtain this supposed association? I'm personally going with: mind-blowingly glaringly obvious. Like 'My mouth is wide open but I still cannot breathe at the stupidity of it' obvious. But hey, who knows?!

Why do some cells become neurons and others muscle? Physicist Prof. David Brückner @davidbrueckner.bsky.social @biozentrum.unibas.ch @unibas.ch receives a prestigious #ERCStartingGrant to uncover how cells make life-shaping decisions. @erc.europa.eu www.biozentrum.unibas.ch/news/detail/...

Hey there, #mRNAtranslation buffs! Our latest multi-faceted dataset from liver cancer cell lines is out in #ScientificData: RNA-seq, ribosome run-off/ribo-seq, polysome-seq, pSILAC. rdcu.be/eC86H. Great team effort spearheaded by Asier Gonzalez Sevine and Niels Schlusser. Happy data crunching!

🧪How do cells navigate the body? David Brückner @davidbrueckner.bsky.social & researchers @umons.bsky.social discovered that cells retain a “memory” of their past shapes, allowing them migrate more efficiently–crucial for immune response & metastasis. @unibas.ch @natphys.nature.com ow.ly/SSzX50WLg3t

🤔 Can migrating cells 'remember' their past trajectories? In collab w/ @sgabriele.bsky.social & @kyohalie.bsky.social, we address this question: Confined cells undergo geometry-sensitive morphology switches, and these switches depend on the past migration history! www.nature.com/articles/s41...

🧪 The University of Basel is setting up a new endowed professorship in #ClimateBiophysics at the @biozentrum.unibas.ch, funded by the Georg H. Endress Foundation. This new professorship strengthens climate research @unibas.ch. www.biozentrum.unibas.ch/news/detail/...

🧪 Gene regulation in bacteria: The team led by @erikvannimwegen.bsky.social discovered that environmental stimuli cause rapid fluctuations in the concentration of regulatory proteins, leading different target genes to respond differently to the same stimulus. www.biozentrum.unibas.ch/news/detail/...

Because of a lack of separation of the time scales for TF binding/unbinding and fluctuations in active TF levels, non-equilibrium gene regulation may be common in bacteria. Check out this nice piece by ‪@philipcball.bsky.social‬ on our new publication in PRX Life. physics.aps.org/articles/v18...

Levels of active TFs can fluctuate on the same time scale as individual binding and unbinding events to the DNA, causing 'non-equilibrium' gene regulatory responses. We believe this may be pervasive in bacterial gene regulation. Check out our new work in PRX Life: x.com/PRX_Life/sta...

Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...

Not all persister bacteria are dormant! 🦠 Single-cell imaging of over a million #EColi shows that many antibiotic-resistant persisters were actively growing before drug exposure. Persistence appears to be more dynamic than once thought. buff.ly/04T4L1k

Amazing account of ChatGPT's sycophancy and confabulation on steroids. amandaguinzburg.substack.com/p/diabolus-e...

Our work on the facial skin microbiome of non-human primates is out in mSystems! We show there is no close relative of Cutibacterium on the faces of gorillas and chimps at the Lincoln Park Zoo, furthering the mysterious origin of the dominant human skin colonizer. journals.asm.org/doi/10.1128/...

Truly inmates running the asylum.

One problem we face today is how few people understand the science that helps us all. Some scientists are able to explain the importance of their work. @baym.lol of Harvard University is one of them. Science is for everyone, and benefits us all more than most people know.

Time for a short thread! We developed HiddenFoot, a biophysics-inspired approach to decode single-molecule footprinting data and infer TF, nucleosome, and RNA Pol II binding profiles on individual DNA molecules. One molecule at a time! www.biorxiv.org/content/10.1... 1/6

Gene regulatory interactions are assumed to be finely tuned. Yet, making (strong) promoters from random DNA sequences is remarkably easy ! De novo evolved promoters in E. coli exhibit low noise by default. 1/2

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

An alternative to tSNE & UMAP for more accurate data visualization: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data. The trees are constructed to accurately represent true distances between the objects in the high-dimensional space.

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...

Bacteria have a simple yet potent mechanism that controls their sensitivity to environmental stimuli. A new study by researchers led by @erikvannimwegen.bsky.social @biozentrum.unibas.ch shows: the slower cells grow, the more sensitively they respond to their environment.

The slower cells grow, the more sensitively they respond to their environment! A new study by @erikvannimwegen.bsky.social reveals that the responsiveness of cells is directly linked to their growth rate. @ScienceMagazine #ecoli #cell #science #research www.biozentrum.unibas.ch/news/detail/...

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).

Surreal!

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/...

Are there any examples of people announcing a publication without noting what a long and hard journey it was? Any examples of people saying: Getting this published was like a walk in the park? Cause I'm feeling getting a paper published is f-ing torture every single time these days.

And here it is, the completed BASEL collection finally published as early access in @plosbiology.org - see the thread for more details. 🤗🧬🎣

The former ambassador to Denmark for the United States, Rufus Gifford, posted this video on his Facebook account: Ht: @hpsc24.bsky.social

Applications for our Master in Physics of Life @biozentrum.unibas.ch are open! Specifically designed for students with physics/math/engineering/compsci background, this is a great opportunity to step into the world of living systems from a physics perspective Please RT and share!

Apply now for our international Master of Science in Physics of Life @biozentrum.unibas.ch @unibasel.ch! Scholarships available. More information: www.biozentrum.unibas.ch/education/de... #Master #Students #Research #Physics #Mathematics #ComputerScience #Engineering #Basel #Switzerland

"ls -lt | more" is one of my best friends ever.

Useful reminder that 1. It is unacceptable that we haven't clarified the origin of a pandemic that killed >10^7 people, and 2. Remaining in denial about how we were actively mislead by a small group of scientists with a conflict of interest will badly backfire on science. tinyurl.com/mrrxva3y

🚨New preprint alert!!! We show using #Celegans that mothers control the #ribosome levels of their offspring depending on their diet. Pioneered by fantastic Sigma Pradhan (not yet on 🟦). #worms biorxiv.org/content/10.1.... 🧵

Biozentrum (Basel, Switzerland) is an amazing research community. Not a problem if you speak only English.

Great idea. To add to this list, my institute @biozentrum.unibas.ch has a wonderful international PhD fellowship program: www.biozentrum.unibas.ch/phd/internat... Students do rotations and choose their PhD lab. Also great for students with quantitative background.

Wolfgang! @wkhuber.bsky.social Read my slow analysis manifesto and join the slow analysis movement. Let's make data analysis healthy again!

Couldn’t agree more with this. There is a sea of crap out there because people care only about pubs not finding useful new truth. Got lucky to get into a position in CH early enough that I can still do long hard meaningful projects with lower output rate. But it’s coming under pressure everywhere.

Nee NRC, dit is geen onderhandeling over het beëindigen van de oorlog. Het land dat Rusland is binnengevallen, en waar de oorlog plaatsvindt, zit niet eens aan tafel. Dit is een onderhandeling over hoe het slachtoffer Oekraïne tussen Rusland en de VS te verdelen. www.nrc.nl/nieuws/2025/...

The AI hype is really getting people to lose their mind. www.theguardian.com/technology/2... Let me give some comments on the abstract of the paper in question. Let's go one sentence at a time.

I have one open PhD position. Maybe one of the last PhD positions in the lab as I'm planning changes in what we do and how we will do it some five years from now. I'm offering freedom (pun intended), respect, an interesting project, and a good full time contract w. health insurance.

What? Milley has indeed said things to cross Trump. But Fauci? I don't remember Fauci explicitly criticizing Trump. He in fact seems to have managed remarkably well avoiding getting into arguments with Trump. Sorry, I don't buy this pardon is about fear for Trump revenge. apnews.com/article/bide...

And don't miss the "skeetorial" by @erikvannimwegen.bsky.social: bsky.app/profile/erik...

Interesting research here! A lot of the system on ISS are populated by bacteria that can spend a LONG time in stasis in low nutrient environments.

This is such a cool set of findings. I've always been curious about that switch from exponential growth to stationary and death phase in 🦠. This is a good look into that switch at the individual cell level. 🧪

@kostchristian.bsky.social this might be relevant for your starvation experiments to induce selective cell death in clusters