What happened to the super-enhancer communities of 4-5 SEs, detected at 700 nm contact threshold, that correlate with higher transcription output? Here the preprint I am referring to…I kinda really liked the preprint message, so I’m a little curious 🧐 www.biorxiv.org/content/10.1...

Wonderful visit to @samwilken.bsky.social lab at Uni Mainz today, discussing joint projects within @centersyngen.bsky.social and science in general. Got to snap a whiteboard selfie, but missed our postdocs Abishek Ghadai & Marcel Piepers in the photo…also thanks Huan (spelling?) for the lab tour 🙏

Did you look at TRX scale? We only landed upon that concept due to a great referee comment, and the results connecting two-letter sequence composition with evolutionary age were (to us) absolutely astonishing! www.sciencedirect.com/science/arti...

A week in the life of Hilbert lab, in four photos. Academic work felt great this week, and I hope the photos can show it. Description and details for each photo below.

A periodic reminder for all of our convenience: “The data are not good or bad. The data are the data.” “Data is king.” “Without data, all theory is crap.” 3 sentences I learned from 3 supervisors AKA the reason it’s worth spending 1/3 of my time and 2/3 of our budget on keeping a wet lab running.

Still trying to figure out what should be my take-away from these directly juxtaposed posts on AI and robotics in Shenzhen and Karlsruhe on my LinkedIn timeline…there’s a lot contained in here, but I don’t even exactly know what.

Automated image analysis confirms that "Stem Cell Differentiation Disperses Transcriptional Clusters via a Conserved Surface-Condensate Trajectory" in zebrafish embryos with great similarity to mESC, fruit fly testes, and a block copolymer-based simulation model.

The zebrafish embryo is a great model of stem cell processes: zygotic genome activation and germ layer specification, within a single work day! Similar to mouse embryonic stem cells, we find transcriptional clusters undergo massive, global shifts. advanced.onlinelibrary.wiley.com/doi/10.1002/...

In our new Advanced Science article, super-res imaging and cluster shape analysis show "Stem Cell Differentiation Disperses Transcriptional Clusters via a Conserved Surface-Condensate Trajectory". Besides mESC, we also have zebrafish, fruit flies & simulations to show the process is conserved!

Did you know that stem cells have unusually large transcription clusters, which disappear upon differentiation? Yes? You paid attention in 2018! In 2026, we show you that this process proceeds via massive, global shifts in transcriptional control. advanced.onlinelibrary.wiley.com/doi/10.1002/...

We see in three model systems (including fruit fly testes) and in block copolymer simulations that "Stem Cell Differentiation Disperses Transcriptional Clusters via a Conserved Surface-Condensate Trajectory". Here, we use a differentiation coordinate to trace cluster number, control state & shape.

If you see this image and think "ha, fly testis!", you know your stuff. If you also know how transcription clusters form and disperse during sperm precursor formation, maybe don't read our new Advanced Science paper, out today 😉 advanced.onlinelibrary.wiley.com/doi/10.1002/...

And, as a more conventional graphical abstract format, showing the same key steps in the coarse-graining and network analysis process.

New preprint by our predoc Aaron Gadzekpo "Bayesian optimisation and graph-based rheology enable sequence-dependent modelling of DNA materials" Coarse-graining realistic DNA nanostars provides hydrogel network connectivity and mechanics www.biorxiv.org/content/10.6... @centersyngen.bsky.social

May the sun shine on all labs as it did on Modic and our Hilbert lab groups during our joint outing today 🌞 The photo reminds me how much we grew recently, we were even still missing several members! Most of all, the man Miha @paraspeckle.bsky.social himself, but we ate a lot of 🍕 for you.

Got great news on a manuscript this week, extensive and long-term developed story forthcoming soon, ultimately placed in a wonderful journal. Cannot be specific, but also cannot contain myself. So here’s a weird non-factory image I generated with chatGPT, with no relation to the project at all ;-)

Completed the annual Karlsruhe running event “Badische Meile”, shaved 5 minutes off my time from last year (run distance 8,888 km). This year, @kit.edu provided shirts for participating employees and students, I’ve seen *many* green shirts in the crowd. Reminder of the role we play in this city!

Selected photos from Boys Day last Thursday. We welcomed 7 young bright minds to our lab. They learned about options to study biology, train as lab technicians, and connections with physics, maths, materials and computer science. Offered by Iliya Stoev and our Hilbert Lab members via Center SynGen.

Astra mortemque praestare gradatim

Keep on hating AI, but the new Copilot in MatLab just *explained an error*: structured, accurate, complete with troubleshooting and fix-walk-through, pertaining to a *MatLab-external library". It actually teaches! Chapeau @mathworks.bsky.social! Of course, hat tip to @openmicroscopy.org

Received this nice Easter present for our lab today. Happy Easter and good luck to all colleagues and collaborators :-) 🥚🐟🧬

Some work life impressions of the week: Huge-a&& KIT logo downtown, our new slogan #scienceforimpact (I like it) Friday evening Campus North institute sunset panorama Drosophila testes imaging for revisions with @erhardtlab.bsky.social lab, samples looking great! #FluorescenceFriday #latergram

The online viewer? 👌 Here’s lft1 and lft2 at 50% epiboly, looks great! Too bad dome or sphere isn’t available…

An extra goodie, where we I tried to see whether Pol II clusters (cyan) are placed in pockets of low chromatin content, connecting via low-chromatin channels to NPC-rich export patches. I suppose both is the case.

For #FluorescenceFriday, I am sharing a first glimpse at Mona Wellhäusser's @mofrawe.bsky.social new nuclei expansion microscopy. Stained are bulk protein, bulk DNA, and nuclear pore complexes (NPC). Expansion is supposed to be 16x, in all three dimensions. Imaged with @visitech.bsky.social iSIM.

Arrived at @nvastenhouw.bsky.social lab today for a short visit. I had to stop on my approach to Génopode building @unil.bsky.social and take a photo. This just isn’t fair! 😠

For anyone at @dpgphysik.bsky.social Condensed Matter Spring Meeting: Our PhD student Aaron Gadzekpo is presenting Wednesday morning on one of the major recent areas of work in our group: “Multiscale Approaches to Phase Behaviour and Mechanical Properties of Synthetic DNA Networks”

Monday: new Postdoc arrives at the lab Friday: first own experiment, DNA nanostar condensates clearly visible, even in in vitro transcription buffer Welcome on board, Dr. Marcel Piepers! Stay tuned! PS Marcel is co-supervised w Ralf Reussner, tasked w ground work for www.sfb1608.kit.edu @kit.edu

Apparently, we made the (additional) cover of the January issue of Annals of the NY Academy of Sciences with our artistic representation of surface condensates on a chromatin strand. I hope you appreciate the subtle use of a modified Hilbert curve? nyaspubs.onlinelibrary.wiley.com/doi/10.1111/...