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Christof Gebhardt

@gebhardtlab.bsky.social
163 followers 209 following 18 posts

Physics at Ulm University | live-cell/organism single-molecule microscopy | super-resolution microscopy | gene regulation | chromatin architecture | embryo development

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Reposted by Christof Gebhardt
Elzo de Wit lab @ NKI @dewitlab.bsky.social · 01/07/2025
(1/n) Excited to present the latest work from the de Wit lab, where we identify and characterise loop extrusion-mediated fountains in mammalian genomes using acute depletion of 3D genome regulators: doi.org/10.1093/nar/.... A Bluetorial🧵:
doi.org
Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers
Abstract. Interphase chromosomes are mainly shaped by loop extrusion and compartmentalisation mechanisms. However, their temporal component and cause-effec
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Christof Gebhardt @gebhardtlab.bsky.social · 27/06/2025
The review on live-cell SMT that I contribute to the jmolbiol.bsky.social special issue ‚Imaging of the central dogma‘ is now online as pre-proof: www.sciencedirect.com/science/arti...
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Reposted by Christof Gebhardt
Akis (Argyris) Papantonis @akispapantonis.bsky.social · 19/06/2025
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
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Reposted by Christof Gebhardt
Di Jiang @dijiang319.bsky.social · 29/05/2025
@science.org Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation | Science www.science.org/doi/10.1126/... @jbuenrostro.bsky.social @eboyden3.bsky.social + al @broadinstitute.org @harvard.edu #ExIGS #Chromatin #Lamin #Progeria #Aging #ExpansionMicroscopy
science.org
Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation
Microscopy and genomics are used to characterize cell function, but approaches to connect the two types of information are lacking, particularly at subnuclear resolution. Here, we describe expansion i...
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Reposted by Christof Gebhardt
Wendy Bickmore @wbickmor.bsky.social · 30/05/2025
Great to see this published @genesdev.bsky.social. Evidence that enhancers can activate a bystander gene in an adjacent TAD, and that cohesin facilitates this. @uoe-igc.bsky.social. pubmed.ncbi.nlm.nih.gov/40436628/
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Reposted by Christof Gebhardt
matteomazzocca.bsky.social @matteomazzocca.bsky.social · 14/05/2025
1/ Super excited to share my first preprint from @andersshansen.bsky.social Lab! We used MINFLUX to track chromatin (H2B-Halo and Fbn2 locus) at an unprecedented 200 μs, then combined it with SPT to span μs-minutes (H2B) or SPT & Super-Res Live-Cell Imaging (SRLCI) to span μs-hours (Fbn2)
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Reposted by Christof Gebhardt
David Suter @davidsuter.bsky.social · 12/03/2025
📣 New preprint from the lab – Massive work entirely driven by super-talented @simsakong.bsky.social , jointly betw. @beatfierz.bsky.social lab and mine – combining in vitro and in vivo TF single molecule imaging www.biorxiv.org/content/10.1...
biorxiv.org
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Christof Gebhardt @gebhardtlab.bsky.social · 12/03/2025
Intriguing mechanism to balance production and degradation rates of proteins
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Reposted by Christof Gebhardt
Arnaud Krebs @arnaudkr.bsky.social · 21/02/2025
Program is out for our first EMBL #singlemolecule gene regulation meeting! Check out the dedicated panel sessions on single molecule genomics, single molecule imaging and theory where we would like to brainstorm the future of the field: Registration is open! 👇 www.embl.org/about/info/c...
embl.org
Gene regulation: one molecule at a time
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Christof Gebhardt @gebhardtlab.bsky.social · 21/02/2025
Single molecules, in living zebrafish embryos, during hour-long period of development: Jonas' work on binding kinetics of cohesin and CTCF around ZGA now online. Great collab with labs of @lucagiorgetti.bsky.social @akispapantonis.bsky.social doi.org/10.1038/s414...
doi.org
Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis - Nature Communications
Using single-molecule tracking of cohesin and CTCF during zebrafish embryogenesis, the molecular kinetics underlying chromatin architecture formation was revealed and gradual emergence of chromatin st...
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Reposted by Christof Gebhardt
Carsen Stringer @computingnature.bsky.social · 12/02/2025
#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...
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Reposted by Christof Gebhardt
Kazuhiro Maeshima @kazu-maeshima.bsky.social · 20/02/2025
Our new review on how the #chromatin domain is formed in the cell is now available @Curr Opin Struct Biol.📄✨ We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation. 📥 Free-download link: authors.elsevier.com/a/1keGn,LqAr...
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Reposted by Christof Gebhardt
Constantin Pape @cppape.bsky.social · 12/02/2025
After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool. www.nature.com/articles/s41...
Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.
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Reposted by Christof Gebhardt
David Suter @davidsuter.bsky.social · 13/02/2025
Big thanks to all people involved @armelletollenaere.bsky.social , Enes Ugur, Susanna Dalla-Longa, Cédric Deluz, Devin Assenheimer, @gebhardtlab.bsky.social , and Heinrich Leonhardt And thanks ChatGPT for haikuing the abstract
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Reposted by Christof Gebhardt
Mir Lab @mirlab.bsky.social · 12/02/2025
1/n Excited to share our new preprint! Using live imaging in Drosophila embryos, we show that RNA Pol II clusters switch from sites of initiation to elongation during zygotic genome activation and that they are stably associated with an active gene: www.biorxiv.org/content/10.1...
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Christof Gebhardt @gebhardtlab.bsky.social · 12/02/2025
Great work and very useful developments!
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Reposted by Christof Gebhardt
bioRxiv Developmental Biology @biorxiv-devbio.bsky.social · 09/02/2025
Measuring morphogen transport over multiple spatial scales in live zebrafish embryos www.biorxiv.org/content/10.1101/202…
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Christof Gebhardt @gebhardtlab.bsky.social · 02/02/2025
Happy to share Duyen's and Philipp's work on effective binding energy landscape and affinity of RBPJ obtained in vivo by on- and off-rate measurements is now published. Great collaboration with labs of Franz Oswald and Tilman Borggrefe doi.org/10.1038/s414...
doi.org
Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding - Nature Communications
Transcription factor binding to DNA is vital for gene regulation. Here, the authors determine the kinetics of DNA binding for RBPJ in living cells. They find that the binding is kinetically rather tha...
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Reposted by Christof Gebhardt
Teif lab @teiflab.bsky.social · 01/02/2025
Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells www.biorxiv.org/content/10.1... ▶️40-fold flanking sequence effect on TF binding ▶️Motif recognition beats kinetics ▶️Minutes-long residence times ▶️Models of TF-nucleosome competiton
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