@karsten-rippe.bsky.social rocking down memory lane and along single cell genomics data in Day 2 of the @spp2202.bsky.social Closing Retreat in Goettingen!

The Closing Scientific Retreat of @spp2202.bsky.social is under way in Goettingen with Gerd Blobel delivering the first Keynote lecture on LDB11-mediated looping of chromatin.

OFERTA DE EMPLEO (por favor difundir): Ofrecemos un contrato predoctoral de 4 años asociado a nuestro proyecto PID2024-157249OB-I00. El objetivo del proyecto es evaluar un nuevo mecanismo patológico según el cual la competición entre promotores puede llegar a ocasionar enfermedades congénitas 👇

Happy to share our latest publication, in which we show that the arrangement of nucleosomes around CTCF sites contributes to higher-order organisation of chromatin into TADs: www.embopress.org/doi/full/10....

The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project! If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further! rdcu.be/eLiT5

Only two days left to apply for the open tenure track professorship in Computational Biology here in @uni-goettingen.de uni-goettingen.de/en/700631.html

Science-peripheral post (ignore unless you read in Greek or French): I was surprised and truly honored to receive the Aix-Marseille Metropolitain for the French translation of my novel ‘The last bear of the woods’ (Kichli 2023)—a great thanks to my translators M. Volkich and H. Zervas.

We are thrilled to announce that our NEW Large Language Model will be released on 11.18.25.

Just half a day in and it’s been a blast, with really incredible talks here on Giessen!

Congrats to my friends in the Boettiger lab for this really beautiful live imaging work. A big leap forward in understanding the dynamic side of genome organization. www.science.org/doi/10.1126/...

New preprint is up, led by former postdoc Braulio Bonilla. We know these remodelers regulate nucleosome positions and occupancy, but do they have a role in regulating higher order chromatin structure? We take a peek for BAF and INO80C. www.biorxiv.org/content/10.1...

Very interesting new @wbickmor.bsky.social commentary on the mechanistic mystery that is very distal enhancer-promoter interactions www.nature.com/articles/s41...

My lab @mpi-muenster.bsky.social is looking for a computational biologist with a passion for imaging and spatial biology. A staff scientist position with long-term perspective! Apply and spread the word 🙏 jobs.mpi-muenster.mpg.de/jobposting/0...

On behalf of @ckadoch.bsky.social and myself, we are pleased to present our upcoming @KeystoneSymposia, #KSEpigenetics26 Epigenetics and Gene Regulation in Health and Disease, March 2-5, in Geneva, Switzerland. keysym.us/KSEpigenetic...

In our latest preprinted work, Yajie and Kostas combine computational analysis with precision KO of single variant U1 snRNA genes in human iPSCs to find pronounced deregulation of both gene expression and splicing that seem to affect the cell cycle and the differentiation potency of stem cells. 1/n

Most read, I hear! Here is your chance to read what @mariekeoudelaar.bsky.social and I had in mind when writing this together.

This is an incredible mechanistic dissection by the @kurianlab.bsky.social and Van Nostrand labs linking splicing choice to cardiac development!

Soon at a Goettingen amphitheater near us! Do join, folks! Leo always has very cool data to share.

Excited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression www.biorxiv.org/content/10.1...

Pleased to see this study out, combining experimental work from our lab at the @cbitoulouse.bsky.social, in particular by @nathaliebastie.bsky.social and @beckof.bsky.social, and from Laura Chaptal and @alengronne.bsky.social at IGH Montpellier @cnrs.fr @cnrsbiologie.bsky.social Congrats to all!

Check out this exciting meeting and register! Fantastic line-up of speakers on cell biology of the nucleus and a great venue 🔥

If I wasn’t this old, I would definitely apply.

How do enhancer-gene contacts relate to transcription activation? In mouse embryonic stem cells, a combo of STED, oligoFISH & RNA FISH shows that 3% of Dppa3 alleles transcribe. For these, enhancers and promoters come closer (panel E). Stumberger ... Leonhardt & Harz www.biorxiv.org/content/10.1...

Be there or be square!

Freshly launched! 🚀 Check out the new CRC 1678 website 🌐 👉 crc1678.uni-koeln.de

Fantastic opportunity to launch your research group following the @embl.org model in a great environment with a solid startup package and access to state-of-the-art resources. Join us at the @ncmbm.bsky.social, part of the @nordicembl.bsky.social, at @uio.no Feel free to reach out if you have Qs.

Thank you, Evgeny! I am delighted that we have a top line up of speakers confirmed for 'The 3D Regulatory Genome' for 2025: @andersshansen.bsky.social July 3rd 2025 @mariekeoudelaar.bsky.social September 4th 2025 @axelvisel.bsky.social October 2nd 2025 @efapostolou29.bsky.social November 6th 2025

🧬 New in Bioinformatics! We’re excited to share StripePy - a Python application for fast, robust detection of architectural stripes in Hi-C & Micro-C data. 🔗 Read the paper 👉 doi.org/10.1093/bioi... #3DGenomics #Bioinformatics #HiC #cool #hic @robomics.bsky.social @rea191.bsky.social

How to represent genomes in 3D? In this paper (and video), we propose Geometric Diagrams of Genomes (GDG)—a visual grammar that aims at emulating the effect ribbon diagrams (Richardson et al 1981) had in protein structural biology. Time will tell.😅 👉🏼 genomebiology.biomedcentral.com/articles/10....

This is a piece that I and @karsten-rippe.bsky.social discussing a lot, and a topic that is very close to my heart. The editors @naturerevgenet.bsky.social gave us the stage to do so, and the final version of our review is now available under this link: rdcu.be/erP1u A short thread follows 1/n

Textbooks: “Enhancers are just a bunch of TFBSs” But how do they REALLY work? New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social A 🧵 (1/n) Free access link: rdcu.be/erD22

Hear, hear! Since last week, I have the honor of serving as a Scout for the Henriette Herz program of the Humboldt Foundation. 1/n

Mario Nicodemi kicking off SIBBM2025 with an elegant talk on phase transitions in 3D genome folding in front a wall-to-wall full house in Naples.

Here’s the thing: the 2025 German Pathology Congress is kicking off in a huge room with a non-pathologist as first speaker. Let’s see how Hi-C in cancer fairs today :-)

Delighted & excited to share our latest preprint on non-canonical enhancers in human pluripotent stem cells, the result of a fantastic and fun collaboration with @guenesdoganlab.bsky.social‬: www.biorxiv.org/content/10.1... 🧵 below

Extensive differences observed in 3D genome structure between homologous heterozygous chromosomes revealed by Genome Architecture Mapping #GAM in the @apombo1.bsky.social lab ➡️ www.embopress.org/doi/full/10....

You want to apply #ATACseq in your emerging model organism, but you don't know where to start? Is #ATACseq the best method for my research questions? Search no more! We got you covered with our new review: doi.org/10.1002/jez.... Excellent collaboration with @gevol.bsky.social

1/ New preprint! How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites? www.biorxiv.org/content/10.1... #TranscriptionFactors #IDPs #SingleMolecule #Biophysics

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭 Check out our paper - fresh off the press!!! We find widespread functional conservation of enhancers in absence of sequence homology Including: a bioinformatic tool to map sequence-diverged enhancers! rdcu.be/enVDN github.com/tobiaszehnde...

Always an emotional moment when one of your trainees graduates. Here, Dr. Adi Mackay (Danieli), 10th PhD from our lab, after an impeccable defense and a well-deserved "summa cum laude" distinction. ...paper will hopefully follow soon and it will become very clear why the distinction was awarded.

Very happy to see that the work by Magdalena Karpinska from @mariekeoudelaar.bsky.social's lab at @mpi-nat.bsky.social is now out in NSMB! Mariano Barbieri from my lab contributed modeling that (we think) nicely explain CTCF contribution to multiway E-P interactions. www.nature.com/articles/s41...

Today, in a few hours. Tune in!

This week — mark your calendars!

I very much look forward to @mosterwalder.bsky.social's talk on "Functional architecture of cardiac TF regulatory landscapes in control of mammalian heart development" in 'The 3D Regulatory Genome', @enhancedgenomics.bsky.social's virtual seminar series. Join us at: us02web.zoom.us/webinar/regi...

Looking for a PhD in sunny Barcelona? ☀️🔬 Our team is hiring a PhD student for the @hologen.bsky.social project! 📅 Deadline: Apr 20 ⚠️ READ THE MOBILITY RULE FOR THIS POSITION 🔁 Please, spread the word All the info here 👉 www.cnag.eu/jobs/phd-stu... #PhDlife #Genomics #HoloGen #Barcelona

A few days left to apply for exciting PhD and Postdoc opportunities in wonderful Copenhagen and join our efforts in understanding Epigenetic Cell Memory.

Tomorrow — for anyone in the Frankfurt area that might be interested in 3D genome folding, cell aging and splicing.

@mariekeoudelaar.bsky.social and I had quite some fun putting this together, so we would be happy for it to be read any feedback from readers!

Do you have an exciting story about #enhancers or #enhanceropathies?. Then submit your abstract to the @embo.org workshop on "Enhancer mechanics and Enhanceropathies" in Denmark before is too late: the deadline for abstract submissions is in two weeks (March 17th)! meetings.embo.org/event/25-enh...