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Reposted by Erik van Nimwegen

David Brückner @davidbrueckner.bsky.social · 9d

Come join us in Basel! @biozentrum.unibas.ch is an amazing place to start your group.

Biozentrum, University of Basel @biozentrum.unibas.ch · 9d

Assistant/Associate Professor in Structural Biology, Biophysics or Biological Imaging

www.biozentrum.unibas.ch/open-positio...

#biozentrum #University #Basel #Professor #Structural #Biology #Biophysics #Biological #Imaging

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Erik van Nimwegen @erikvannimwegen.bsky.social · 9d

Please let us know what you think. And much agreed on Bach and Vermeer (maybe I should give Proust another try).

Erik van Nimwegen @erikvannimwegen.bsky.social · 20d

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 · 20d

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

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Erik van Nimwegen @erikvannimwegen.bsky.social · 21d

and includes accurate error-bars on all estimates.

We believe RealTrace can dramatically enhance the power of time-lapse microscopy data by allowing identification and quantification of far more subtle features in the dynamics than is possible with simple data smoothing approaches. n/n

Erik van Nimwegen @erikvannimwegen.bsky.social · 21d

Surprisingly, protein production rates adapt to their new steady-states far more quickly and with only a minimal transient.

RealTrace can be applied to essentially any time-lapse fluorescence microscopy data and gives accurate estimates of instantaneous growth and volumic GFP production rates, 10/n

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Erik van Nimwegen @erikvannimwegen.bsky.social · 21d

Finally, upon a sudden `downshift' in nutrients, we see very reproducible time-dependent responses across single cells. All cells go almost into growth arrest, then overshoot in growth rate, only to relax to a final growth rate over a time scale of 3 cell cycles. 9/n

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Erik van Nimwegen @erikvannimwegen.bsky.social · 21d

minimum early in the cell cycle and a maximum late in the cell cycle. In contrast, protein production rates show more complex patterns that vary across conditions and across promoters, even across constitutive promoters!
As far as we are aware, no current models can explain these patterns. 8/n

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Erik van Nimwegen @erikvannimwegen.bsky.social · 21d

time, and in slower growth conditions, both the amplitude and duration of these fluctuations increases.

Second, both growth rate and volumic protein production vary systematically across the cell cycle. Interestingly, the variation in growth rate is the same in all conditions, with a 7/n

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Erik van Nimwegen @erikvannimwegen.bsky.social · 21d

We use data from E. coli cells carrying fluorescent reporters of constitutive and ribosomal genes, growing in a microfluidic device in different conditions, to highlight the kind of subtle patterns RealTrace can uncover.
First, instantaneous growth rates vary substantially across cells and 6/n

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Erik van Nimwegen @erikvannimwegen.bsky.social · 21d

RealTrace is very generally applicable, which we demonstrate by applications to data from E. coli cells, mouse embryonic stem cell nuclei (data from the lab of @davidsuter.bsky.social), and entire C. elegans larvae (data from the lab of @betowbin.bsky.social). 5/n

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Erik van Nimwegen @erikvannimwegen.bsky.social · 21d

are correlated on short time scales, all measurement errors are independent. We implemented this idea into a rigorous Bayesian procedure that uses maximum entropy process priors and recursively approximates the non-linear dynamics over short time intervals. 4/n

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Erik van Nimwegen @erikvannimwegen.bsky.social · 21d

We can't fit the data to particular curves because we typically don't know what form the dynamics will take, and local smoothing systematically distorts the true dynamics by replacing it with a time average.

RealTrace solves this challenge using only one assumption: while biological changes 3/n

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Erik van Nimwegen @erikvannimwegen.bsky.social · 21d

Tracking the behavior of single cells using fluorescence time-lapse microscopy is becoming increasingly popular but there is a fundamental challenge in analyzing such data: as biological changes are small on short time scales, much of the true dynamics is hidden under measurement noise. 2/n

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Erik van Nimwegen @erikvannimwegen.bsky.social · 21d

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...

RealTrace: Uncovering biological dynamics hidden under measurement noise in time-lapse microscopy data

One of the most powerful approaches for identifying the mechanisms underlying complex biological phenomena is not just to measure bulk populations, or even take single-cell snapshots, but to directly ...

www.biorxiv.org

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Reposted by Erik van Nimwegen

David Brückner @davidbrueckner.bsky.social · 23d

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!

Biozentrum, University of Basel @biozentrum.unibas.ch · Aug 4

Apply now for the prestigious and independent #BiozentrumPhDFellowships. Great science. Unique rotation-based selection of research group and other incentives. The summer call is open until October 12, 2025. bit.ly/4caiqqX @biozentrum.unibas.ch @unibas.ch #fellowship #PhD#Switzerland

Biozentrum PhD Fellowships

Share your passion for life sciences. If you are talented and highly motivated, want to broaden your horizons and are interested in a wide range of research topics, apply for one of the sought after B...

bit.ly

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Reposted by Erik van Nimwegen

Biozentrum, University of Basel @biozentrum.unibas.ch · Sep 8

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.

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Erik van Nimwegen @erikvannimwegen.bsky.social · Sep 6

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?!

Forbes @forbes.com · Sep 5

Tylenol maker Kenvue denies the connection allegedly made in the report, which is expected to be published by the Department of Health and Human Services this month.

RFK Jr. Report Will Link Autism To Tylenol Use During Pregnancy, Report Says

Tylenol maker Kenvue denies the connection allegedly made in the report, which is expected to be published by the Department of Health and Human Services this month.

www.forbes.com

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Reposted by Erik van Nimwegen

Biozentrum, University of Basel @biozentrum.unibas.ch · Sep 4

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/...

ERC Starting Grant for Physicist David Brückner

How do cells decide which role to take on in the body? Prof. David Brückner from the Biozentrum of the University of Basel is investigating this and similar questions. Over the next five years, a Star...

www.biozentrum.unibas.ch

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Reposted by Erik van Nimwegen

Mihaela Zavolan @mihaelazavolan.bsky.social · Aug 30

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!

Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines

Scientific Data - Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines

rdcu.be

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Erik van Nimwegen @erikvannimwegen.bsky.social · Aug 28

Are you saying that is bad? I already KNOW I'm interested in your lab.. I just used the LLM to help me express it.

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Reposted by Erik van Nimwegen

Biozentrum, University of Basel @biozentrum.unibas.ch · Aug 25

🧪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

Cellular memory: The clever strategy cells use to move through narrow environments

In wound healing, immune response, and cancer metastasis, cells migrate through the body – often squeezing through narrow spaces. Researchers led by Prof. David Brückner at the Biozentrum discovered t...

www.biozentrum.unibas.ch

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Reposted by Erik van Nimwegen

David Brückner @davidbrueckner.bsky.social · Aug 25

🤔 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 actin cortex acts as a mechanical memory of morphology in confined migrating cells - Nature Physics

Cells often navigate through confined spaces. Now it is shown that cells retain a mechanical memory of previous confinement events, which makes them more efficient at migrating through narrow microenv...

www.nature.com

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Reposted by Erik van Nimwegen

Biozentrum, University of Basel @biozentrum.unibas.ch · Aug 26

🧪 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/...

New endowed professorship strengthens climate research at the University of Basel

The University of Basel is setting up a new endowed professorship at the Biozentrum to make fundamental discoveries at the interface between biophysics and climate-relevant environmental biology. This...

www.biozentrum.unibas.ch

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Erik van Nimwegen @erikvannimwegen.bsky.social · Aug 6

I agree many of the unprocessed foods were poorly presented. But I think one can’t conclude from that that it must taste bland. I remember after first coming to the US having birthday pie. Extravagantly colorful and shiny. But it tasted much more bland than the pies I got in Europe.

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Erik van Nimwegen @erikvannimwegen.bsky.social · Aug 6

I feel the thread is vastly exaggerating how much better the processed food looks. In some cases, just based on looks, I would prefer the unprocessed one.
Maybe this study is evidence of imprinting of US citizens on what ‘tasty’ food is supposed to look like.

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