Huge congrats to Justas who now is Doctor Ritmejeris after defending his excellent PhD thesis 'Nanopore sequencing of peptides - terminal conjugation and PTM detection' today!!

I’m very pleased to share our work looking at what controls condensin II cell-cycle dependant activity; a great collaboration with @eugenekimlab.bsky.social, @damlatetiker.bsky.social, Kyle Muir and Kumiko Samejima
www.biorxiv.org/content/10.6...

Latest #CDlab paper on nanopore protein sequencing now published in JACS: pubs.acs.org/doi/full/10....

Here, Justas Ritmejeris, Xiuqi Chen, collaborator Bauke Albada, and me developed a conjugation chemistry strategy for nanopore sequencing of natural peptides!

🚨New paper out! In our @MolCellNews paper, we solve a piece of the puzzle of how our genome folds. We found the two specific molecular "brakes" in the CTCF protein that stop DNA loop extrusion. One of the final pieces of my PhD!
tinyurl.com/29uuc5by

Excited to share our latest fully in-house paper! 🎉
We show how cohesin integrates loop extrusion with sister tethering to guide the homology search during DNA repair.

Huge congratulations to all authors, and to @fedeteloni.bsky.social for leading this work 👏
We’re excited to see his next steps!

🔬 Hot #PhD topic: Single-molecule fluorescence and super-resolution microscopy! Use quantitative nanoscale imaging to map nuclear organization. Apply by Jan 7 to join Johannes Stein’s Lab @jmstein.bsky.social & #IMPRS-BAC #gradschool!

👉 www.molgen.mpg.de/5098010/stei...

I am thrilled with the news that our ERC Synergy proposal GeneMotors was granted!!

This prestigious grant allows Leonid Mirny (MIT), Wendy Bickmore (Edinburgh), Benjamin Rowland (NKI) and me to study the DNA-looping SMC motors proteins that control our chromosomes in the next 6 years

Soon available in my group: 1 PhD position to investigate prokaryotic histones. See our recent work that highlights the existence and diversity of prokaryotic histones (e.g. Schwab et al., TIBS, 2025; Schwab et al., Nat Comm, 2024; Hu et al., Nucl Acids Res, 2024). Please DM for informal enquiries.

Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...

Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇

H-NS mediated compaction of DNA visualised by atomic force microscopy Abstract. The Escherichia coli H-NS protein is a nucleoid-associated protein involved in gene regulation and DNA compaction. To get more insight into the m

Time flies .. it is today 25 years ago that we published our studies that revealed that bacterial H-NS is a DNA bridging protein:
academic.oup.com/nar/article/... @narjournal.bsky.social

NIPBL dosage shapes genome folding by tuning the rate of cohesin loop extrusion Cohesin loop extrusion is a major driver of chromosome folding, but how its dynamics are controlled to shape the genome remains elusive. Here we disentangle the contributions of the cohesin cofactors ...

New preprint with @gfudenberg.bsky.social

We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding.

This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇

www.biorxiv.org/content/10.1...

WORK!

I currently have 5 (!) open positions for postdocs/PhD students in our CDlab for projects:

- Nanopore protein sequencing
- Archaeal CDV cell division
- Microfluidics for synthetic cells
- Nuclear Pore Complex
- Origami mimics of peroxisomes

Please apply! ceesdekkerlab.nl/come-join-us/

RT=👍

📣 New paper alert! Just out in Cell Reports! pubmed.ncbi.nlm.nih.gov/40644298/
Thrilled to share that we have discovered a brand-new anti-phage defense system! Bacteria have evolved various defense strategies (CRISPR etc) to counter phage attacks. We found a new one - fascinating and dramatic
⚔️🦠❄️🔬

3 more weeks to apply!

🧬 Fully funded PhD opportunity! 🧬

We are looking for a curious and motivated candidate to join our new team in Utrecht. Our goal is to develop biomimetic mechanisms for protein folding using DNA origami.

More info:
🔗 www.uu.nl/en/organisat...
🗓️ Deadline: 15.08

💥 We have 3 positions open in my lab in Basel, Switzerland🇨🇭:
#nanopores #smFRET #biomolecular #dynamics #singleMolecules

We’re looking for talented & ambitious new colleagues enthusiastic about biomolecular dynamics & single-molecule tech.

Please share broadly, thank you!🤝

schmid.chemie.unibas.ch

Since December 2020, I’ve been building visualize-it.github.io as part of my science communication and outreach efforts. It features 45 interactive visualizations from math, physics, computer science, and complex systems.

If you find it interesting, please repost it!
#science #scicomm #education

We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
1/

Here's a new very exciting paper from our #CDlab: www.cell.com/cell-reports...

In an exemplary in vitro/in vivo study, 1st authors ‪@btanalikwu.bsky.social‬ & Alice Deshayes showed that dense linear protein arrays (e.g. telomeres) do stop loop-extruding SMCs!

Great collaboration with Marcand lab.

Latest #CDlab paper out now in Nucleus: www.tandfonline.com/doi/epdf/10....

This short article sketches the state of the art of the field that studies the structure and dynamic gating mechanism of the nuclear pore complex

(1/n) Thread @matteomazzocca.bsky.social @domenicnarducci.bsky.social Simon Grosse-Holz @jessematthias.bsky.social preprint

Q: how does chromatin move?

Using MINFLUX, SPT & SRLCI, we track chromatin dynamics across 7 orders of magnitude in time to provide answers www.biorxiv.org/content/10.1...

Measurements of molecular size and shape on a chip Size and shape are critical discriminators between molecular species and states. We describe a microchip-based high-throughput imaging approach offering rapid and precise determination of molecular pr...

An amazing new enabling technology. Measurements of molecular size and shape on a chip. Couldn't be prouder of our friend Madhavi Krishnan of @ox.ac.uk this was and is one among the must fun collaborations I ever had. www.science.org/doi/10.1126/...

Very excited to present our latest work: SPINNA, an analysis framework and software package for single-protein resolution data! 🖥️🤩

We can directly quantify stoichiometry and oligomerization from super-res (DNA-PAINT, RESI) images!! 🧬🎨

(1/n) New preprint from @claricehongky.bsky.social
Fan Fang Varshini Ramanathan in collab w Jie Liu.

Q: How do we get ultra-high-res 3D genome maps?

A: New deep learning model, Cleopatra.

Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.

Latest #CDlab paper on @biorxivpreprint.bsky.social:
Lipid flip flop regulates the shape of growing and dividing synthetic cells
www.biorxiv.org/content/10.1...

Here, postdoc Rafa Lira studied GUV growth by SUV fusions to show that lipid flip flop is key for low curvature stress and symmetric buds

Rules of Engagement YouTube video by Johan Gibcus

Earnshaw, Goloborodko, Dekker & Mirny labs are excited to present our latest work, "Rules of engagement for condensins and cohesins guide mitotic chromosome formation" - now accepted!!
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...

Huge congrats to you Cees! 😀

Wow, I feel greatly honored by being awarded the 2026 Biochemical Society Award for Significant Breakthrough or Achievement, as was just announced!

www.biochemistry.org/about-us/new...

It is wonderful that the Biochemical Society honors our contributions to single-molecule biophysics in this way!

PDB101: Irina Bezsonova Gallery PDB-101: Training, Outreach, and Education portal of RCSB PDB

You can download my protein structure-inspired artwork from pdb webpage:

pdb101.rcsb.org/sci-art/bezs...

@rcsbpdb.bsky.social
@pdbeurope.bsky.social
#sciart

Latest #CDlab paper online in @labonachip.rsc.org: pubs.rsc.org/en/content/a...

Here, 1st authors Alex Joesaar & Martin Holub developed a microfluidics platform to extract and study full length megabase-size genomes in microfluidic chambers (where they are protected against shearing by flow)!