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Erik van Nimwegen

@erikvannimwegen.bsky.social

Gene regulatory networks and genome evolution. How do single cells make up their minds? @NimwegenLab@mstdn.science @NimwegenLab on twitter. Sorry X.

427 Posts1887 Follower259 Folgt
Tami Lieberman@contaminatedsci.bsky.social · last wk.

Two announcements regarding AccuSNV, which calls high precision SNVs across microbial genomes: Version 1.1 is now incredibly easy to install, run, and perform downstream analyses with (see image of typical output!). The manuscript was also published this summer in Genome Research! Links next...

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Mihaela Zavolan@mihaelazavolan.bsky.social · 2w ago

Very interesting indeed, and so many questions to follow up on. As the relative abundances of RNA species don't seem to change, do overall protein concentrations decrease? Rates of cellular processes? Is the number game why expression variability of individual genes seems to increase with age?

Erik van Nimwegen@erikvannimwegen.bsky.social · 2w ago

Very interesting. Unless I’m missing something, this also seems to imply protein production is mRNA limited.

Peter@biotechpedro.bsky.social · 4w ago

I'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 🤩

Erik van Nimwegen@erikvannimwegen.bsky.social · 4w ago

Remember 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/n

Dominic Grün@dominicgrun.bsky.social · 4w ago

Check out the wonderful Bonsai method by @erikvannimwegen.bsky.social and @dhdegroot.bsky.social now published in Nat Biotech! Congrats to all authors!

Erik van Nimwegen@erikvannimwegen.bsky.social · 4w ago

Remember 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/n

Erik van Nimwegen@erikvannimwegen.bsky.social · 4w ago

Remember 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/n

Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology

High-dimensional data are visualized through representation on tree structures.

nature.com

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...

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

How 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.social

Seeing the Unseen: A new tool for exploring complex biological data

Modern 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...

biozentrum.unibas.ch

David Brückner@davidbrueckner.bsky.social · last mo.

If you're looking for a PhD position, or know someone looking checkout our interdisciplinary PhD Fellowship program! We are always looking for talented students with a physics or computational background to join our group to work on the physics of living systems!

Biozentrum, University of Basel@biozentrum.unibas.ch · last mo.

Ready for the next step in your scientific career? Apply now for a fully funded Biozentrum PhD Fellowship and explore a wide range of research fields before choosing your PhD lab. 🧪 Applications for the current call are open until October 18, 2026. More information 👇

Maria Hondele@mariahondele.bsky.social · 2mo ago

🚀 New preprint 🥳 Fantastic work by our recent PhD graduate Daan ! How are mRNPs remodeled as they exit the nucleus? We identify PAIP1 as a factor that promotes exchange of the nuclear poly(A)-binding protein PABPN1 for cytoplasmic PABPC1, coupling mRNA export to cytoplasmic mRNP maturation.

bioRxiv Molecular Biology@biorxiv-molbio.bsky.social · 2mo ago

PAIP1 couples mRNA export to cytoplasmic mRNP remodeling and poly(A) homeostasis https://www.biorxiv.org/content/10.64898/2026.07.31.742013v1

Erik van Nimwegen@erikvannimwegen.bsky.social · 2mo ago

So what if your science uncovers facts that clash with your political preferences? Mother nature doesn't bend to politics. You can pick the questions you study and how, but you don't get to pick reality. And honestly reporting findings, even if you don't like them, that's also being a scientist.

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Erik van Nimwegen@erikvannimwegen.bsky.social · 3mo ago

What do single bacterial cells do when they run out of carbon source? If you missed the preprint, check out the official publication: doi.org/10.1038/s443... If the total bacterial population on earth stays roughly constant, then there must on average be as much death as replication. 1/n

E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients - Molecular Systems Biology

Although in the wild bacteria likely spend most of their time deprived of nutrients and slowly starving to death, very little is known about how bacteria adapt their phenotype to starvation. Here we combine microfluidics with quantitative fluorescence microscopy of transcriptional reporters to comprehensively quantify growth and gene expression at the single-cell level in E. coli during carbon starvation. We find that all cells immediately stop growing upon loss of carbon source and that almost all remain alive for over 30 hours. Furthermore, entry into starvation triggers a dynamic expression program that is remarkably homogeneous across single cells, but highly variable across genes, causing dramatic remodeling of the proteome early in starvation. We further show that, as protein production and the rate of protein degradation both decay approximately exponentially, protein concentrations become essentially ‘frozen’ after the first 5 to 10 hours, setting phenotypes for several days of starvation. Finally, using experiments in which gene expression is inhibited for different periods, we show that protein production in the first 5 hours is crucial for protecting cells from stresses late in starvation.

doi.org

Erik van Nimwegen@erikvannimwegen.bsky.social · 4mo ago

Cool. In random data, it claims to see a signal for what is in fact merely its prior. Just like humans do all the time. Is it perhaps that all it does is regurgitate human behavior from its training data?

Sasha Gusev@sashagusevposts.bsky.social · 4mo ago

I assigned random gender/ethnicity labels to scientific abstracts from the literature and then asked Claude to do a thematic analysis. Claude identified a clinical versus computational split for female/male authors and a DEI focus for Black/URM authors. All in completely random data.

Erik van Nimwegen@erikvannimwegen.bsky.social · 4mo ago

I was planning to write a similar thread. I fear these tools are going to be used mainly for effectively hiding weaknesses in proposals. And reviewers will be using the SAME tools for their review. The endgame of this is that it will become close to impossible to assess the merits of a grant prop. /

Robert Insall@robinsall.bsky.social · 5mo ago

If this is true (I doubt, but possible) it is a catastrophe for science funding process. Last nail in the coffin level. Why? Because funding will remain at 10%. Nobody's going to pull a load of new cash out of the hat. So. At first - grants that use an online tool will have an advantage over ../