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erikvannimwegen.bsky.social
Erik van Nimwegen
@erikvannimwegen.bsky.social
1.8K followers 250 following 310 posts
Gene regulatory networks and genome evolution. How do single cells make up their minds?
@NimwegenLab@mstdn.science
@NimwegenLab on twitter. Sorry X.
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Reposted by Erik van Nimwegen
biozentrum.unibas.ch
Apply for our Master of Science in Physics of Life – training in cutting-edge research at the interface of physics, mathematics, engineering and life sciences. Scholarships available. Application deadline: 30 November. More: www.biozentrum.unibas.ch/education/de...
@biozentrum.unibas.ch @unibas.ch
October 17, 2025 at 9:22 AM
Reposted by Erik van Nimwegen
davidbrueckner.bsky.social
Come join us in Basel! @biozentrum.unibas.ch is an amazing place to start your group.
September 29, 2025 at 6:35 PM
erikvannimwegen.bsky.social
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!
September 18, 2025 at 9:26 AM
erikvannimwegen.bsky.social
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
September 17, 2025 at 2:19 PM
Reposted by Erik van Nimwegen
davidbrueckner.bsky.social
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!
September 15, 2025 at 10:04 AM
Reposted by Erik van Nimwegen
biozentrum.unibas.ch
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.
September 8, 2025 at 9:13 AM
erikvannimwegen.bsky.social
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?!
September 6, 2025 at 4:47 PM
Reposted by Erik van Nimwegen
biozentrum.unibas.ch
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
September 4, 2025 at 10:13 AM
Reposted by Erik van Nimwegen
mihaelazavolan.bsky.social
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
August 30, 2025 at 11:40 AM
Reposted by Erik van Nimwegen
biozentrum.unibas.ch
🧪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
August 25, 2025 at 10:04 AM
Reposted by Erik van Nimwegen
davidbrueckner.bsky.social
🤔 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
August 25, 2025 at 9:49 AM
Reposted by Erik van Nimwegen
biozentrum.unibas.ch
🧪 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
August 26, 2025 at 7:10 AM
Reposted by Erik van Nimwegen
biozentrum.unibas.ch
🧪 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/...
Rapid fluctuations drive complex gene regulation in bacteria
Bacteria respond to environmental factors such as antibiotics by inducing regulatory proteins that switch their target genes on or off. Researchers led by Prof. Erik van Nimwegen have discovered that ...
www.biozentrum.unibas.ch
July 30, 2025 at 4:08 PM
erikvannimwegen.bsky.social
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...
Different Bacterial Genes Have Different Turn-Ons
Not all genes respond in the same way to regulation by the same molecule—a property that might enable cells to produce complex genetic responses.
physics.aps.org
July 18, 2025 at 9:30 PM
erikvannimwegen.bsky.social
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...
PRX Life on X: "Different target genes controlled by the same regulator respond to DNA damage with highly distinct expression responses when fluctuations in transcription factor levels match the timescale of their binding and unbindingfrom DNA. Read the paper: https://t.co/HVwQL3pj1l https://t.co/qVSsqzrTah" / X
Different target genes controlled by the same regulator respond to DNA damage with highly distinct expression responses when fluctuations in transcription factor levels match the timescale of their binding and unbindingfrom DNA. Read the paper: https://t.co/HVwQL3pj1l https://t.co/qVSsqzrTah
x.com
July 18, 2025 at 9:17 PM
Reposted by Erik van Nimwegen
contaminatedsci.bsky.social
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...
June 30, 2025 at 12:26 PM
Reposted by Erik van Nimwegen
elife.bsky.social
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
June 6, 2025 at 8:21 AM
Reposted by Erik van Nimwegen
melaniemitchell.bsky.social
Amazing account of ChatGPT's sycophancy and confabulation on steroids.

amandaguinzburg.substack.com/p/diabolus-e...
Diabolus Ex Machina
This Is Not An Essay
amandaguinzburg.substack.com
June 4, 2025 at 3:02 AM
Reposted by Erik van Nimwegen
contaminatedsci.bsky.social
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/...
The microbiome of the human facial skin is unique compared to that of other hominids | mSystems
Understanding how and why human skin bacteria differ from our closest animal relatives provides crucial insights into human evolution and health. While we have known that human facial skin hosts disti...
journals.asm.org
May 30, 2025 at 12:14 PM
erikvannimwegen.bsky.social
Truly inmates running the asylum.
cryptogenomicon.bsky.social Sean Eddy @cryptogenomicon.bsky.social · May 22
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
May 28, 2025 at 4:58 PM
Reposted by Erik van Nimwegen
markowenmartin.bsky.social
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.
May 24, 2025 at 11:31 PM
Reposted by Erik van Nimwegen
molinalab.bsky.social
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
May 19, 2025 at 6:55 PM
Reposted by Erik van Nimwegen
slavov-n.bsky.social
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
May 10, 2025 at 2:08 PM
Reposted by Erik van Nimwegen
dhdegroot.bsky.social
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
Reposted by Erik van Nimwegen
slavovlab.bsky.social
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.
May 9, 2025 at 11:07 AM