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Johannes Stein

@jmstein.bsky.social
1.3K followers 626 following 41 posts

Group Leader at Max Planck Institute for Molecular Genetics Studying genome organization with quantitative super-resolution microscopy www.molgen.mpg.de/stein-lab

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Reposted by Johannes Stein
Fena Ochs @fenaochs.bsky.social · 25/09/2026
Happy to share our new software SIMworks out today in Nature Protocols (1/3) SIMworks is a software suite built on our previous tools SIMCheck, Chromagnon, ChaiN and SIMinspector and enables data augmentation, quantitative processing and analysis. Link to publication: www.nature.com/articles/s41...
nature.com
SIMworks—an integrated software suite for quality-controlled augmented quantitative structured illumination microscopy
Nature Protocols - SIMworks is an integrated software suite for quality-controlled augmented quantitative structured illumination microscopy (SIM), enabling both new learners and experienced users...
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Fena Ochs @fenaochs.bsky.social · 10/09/2026
My lab at the Center for Gene Expression (CGEN), University of Copenhagen is looking for a motivated Postdoc interested in cohesin biology, 3D chromatin, and super-resolution microscopy. 📩 Please email your CV and letter of intent to fena.ochs(at)sund.ku.dk.
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Gabrijela Dumbović @gabrijelad.bsky.social · 09/09/2026
Incredibly happy to share the first publication from our lab, now published in Nature Cell Biology! 🎉 How do cells coordinate RNA processing with nuclear organization and the cell cycle? www.nature.com/articles/s41...
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Karsten Rippe @karsten-rippe.bsky.social · 09/09/2026
🧬 1/ HP1α marks silenced heterochromatin, but how does it repress, and what happens when transcription is switched on? On mouse fibroblast chromocenters, HP1α stays bound, its barrier is local, and the domain reorganizes nanodomain by nanodomain. 👉 @cp-molcell.bsky.social doi.org/10.1016/j.mo...
Schematic of the two experimental systems. Left, activators recruited to chromocenters of wild-type and Suv39h dn mouse fibroblasts, with DAPI and anti-HP1α images showing HP1α enrichment and loss. Right, the U2OS 2-6-3 reporter array with an activator recruited alone or together with HP1α.
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 08/09/2026
Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @natgenet.nature.com reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation🚧 🔗 www.nature.com/articles/s41... (1/2)
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mareikejordan.bsky.social @mareikejordan.bsky.social · 04/09/2026
Check out our preprint on the structural mechanisms of how LEM2 and ESCRTs seal the nuclear envelope. Awesome collaboration with @karenpalacior.bsky.social who brought my structures to life 💃🔬❄️🌀 @hummerlab.bsky.social www.biorxiv.org/content/10.6...
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Rada-Iglesias Lab @radaiglesiaslab.bsky.social · 01/09/2026
Have you ever wondered why developmental genes are often regulated by enhancers located at long distances? In this @natgenet.nature.com perspective, we speculate that long-range enhancer positioning may provide regulatory properties essential for proper gene expression www.nature.com/articles/s41...
nature.com
Mechanisms and functional implications of long-range enhancer-dependent gene regulation - Nature Genetics
Development depends on gene regulation by enhancers across long genomic distances. This Perspective discusses mechanisms enabling long-range enhancer–promoter communication and the potential advantage...
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Marc A. Marti-Renom @mamartirenom.bsky.social · 08/08/2026
🚨the latest from the lab! 😃👇🏻 www.science.org/doi/10.1126/...
science.org
3D genome organization in tissue regeneration involves long-range chromatin loops
Chromosome conformation analysis in Drosophila wing discs reveals the requirement of specific meta-loops during regeneration.
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Simon Gaudin @simongaudin.bsky.social · 02/08/2026
Now out from Bintu lab: compaction following transient KRAB recruitment tracks long-term epigenetic memory. But K9me3 decays after KRAB release and is replaced by DNA methylation. Does compaction help maintain K9me3, or slow its loss enough to facilitate the handoff to DNAme? tinyurl.com/ycay4mrh
tinyurl.com
Single-cell chromatin state transitions during epigenetic memory formation
Large-scale chromatin compaction quantitatively predicts the percentage of cells with durable epigenetic memory of gene silencing.
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Anders Sejr Hansen @andersshansen.bsky.social · 14/07/2026
@mileshuseyin.bsky.social and the lab have put together a comprehensive protocol for genome-wide Micro-C and for Region-Capture Micro-C in @natprot.nature.com : www.nature.com/articles/s41... See also the GitHub for a user-friendly end-to-end computational pipeline: github.com/ahansenlab/M...
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Tjian + Darzacq Lab, UC Berkeley @tjiandarzacq.bsky.social · 02/06/2026
Out now in Science! Our study challenges long-standing assumptions about transcription factor specificity in eukaryotes. Novel single-molecule measurements of TF behavior in living cells reveal an independence of locus-specific binding from DNA sequence recognition.🧵 www.science.org/doi/10.1126/...
science.org
Unstructured transcription factor interactions enable emergent specificity
How intrinsically disordered regions (IDRs) shape chromatin binding and nuclear organization of transcription factors (TFs) remains unclear. We used proximity-assisted photoactivation (PAPA), a single...
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Tugce Aktas @aktast.bsky.social · 26/05/2026
Today, it was Lisa's turn to defend her PhD thesis and she did an absolutely fantastic job 😍 Especially going into full structure of the RNA Pol2 catalytic core and explaining the mutants. It was an outstanding discussion! I am really proud of her performance today 🥹
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Aydan Bulut-Karslioglu @bulutkarslioglu.bsky.social · 03/05/2026
Very excited to share our newest findings! A very long team effort pursued by multiple team members -to frantically reproduce everything over and over-, we show mTOR-Polycomb synergy at promoters of developmental master regulator TFs in ESCs prior to their expression. www.biorxiv.org/content/10.6...
biorxiv.org
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Stefan Niekamp @niekamp.bsky.social · 25/04/2026
Excited to share our latest work in Molecular Cell: www.cell.com/molecular-ce... We show that PRC1 condensates exclude SWI/SNF from chromatin, revealing a physical mechanism for how opposing regulators compete to control gene expression. Huge thanks to all collaborators and mentors!
cell.com
Mutual antagonism between PRC1 condensates and SWI/SNF in chromatin regulation
Niekamp et al. show that biomolecular condensates formed by Polycomb repressive complexes can physically restrict access of the activating remodeler SWI/SNF to chromatin. Establishing this barrier dep...
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Max Planck Institute for Molecular Genetics @molgen.mpg.de · 22/04/2026
Johannes Stein's new lab at the MPIMG will use microscopy to study the organization of the genome at a molecular level. We talked to him about how, despite being a trained physicist, he ended up in biology, the potential of his research and the power of interdisciplinary teams. @jmstein.bsky.social
molgen.mpg.de
A nanoscopic look at gene regulation
Johannes Stein joined the MPIMG in 2025. His lab will use state-of-the-art microscopy techniques to examine the organisation of the genome at a molecular level. We talked to him about how, despite bei...
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Devin Schweppe @dschweppe.bsky.social · 07/04/2026
The next iteration of O-MAP targeting genomic loci is now at eLife!! DNA O-MAP enables proximity labeling at specific DNA loci took a ton of work from many lab members and collaborators, so it's really exciting to wrap up this paper with @oligopain.bsky.social! elifesciences.org/articles/102...
elifesciences.org
DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci
DNA O-MAP enables proximity labeling at specific genomic loci in fixed cells using programmable oligonucleotides, revealing locus-proximal proteomes and chromatin interactions without genetic modifica...
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Mark Bates @wmarkbates.bsky.social · 31/03/2026
Delighted to share our preprint describing COMET, a new approach to drift correction for #SMLM, which performs exceptionally well in practice. Check out the benchmarking results compared to other methods! :) Thanks to @lreinkensmeier.bsky.social for a superb effort. www.biorxiv.org/cgi/content/...
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Florian Schueder @florianschueder.bsky.social · 26/03/2026
Please check out our newest work on fluorogenic speed imager probes, in which we combine the strengths of speed-optimized imagers and fluorogenic imagers. #SuperResolution #DNAPAINT #microscopy www.biorxiv.org/content/10.6...
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André Nadler @nadlerlab.bsky.social · 23/03/2026
It’s incredibly hard to study lipids in biological membranes on the nanoscale. You need near-perfect information on both membrane ultrastructure and lipid density. Lipid-CLEM, now out in @natcellbio.nature.com brought to you by @mathilda95.bsky.social changes that: www.nature.com/articles/s41...
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Tugce Aktas @aktast.bsky.social · 25/02/2026
Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social doi.org/10.1016/j.ce... Read the thread👇 for the highlights of our findings.
doi.org
Redirecting
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Marc A. Marti-Renom @mamartirenom.bsky.social · 24/02/2026
🚨 We’re happy to announce (finally!) the publication of METALoci, in collaboration with @dariloops.bsky.social and heroes: @jrotwitguez.bsky.social & @imotagom.bsky.social. METALoci integrates #3DGenome and #Epigenetics data into a unified framework we believe is very useful! Here 👉🏻 rdcu.be/e5sm2
rdcu.be
Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs
Nature Structural & Molecular Biology - METALoci, a new three-dimensional genome computational tool, reveals a major rewiring of regulatory interactions during sex determination. By combining...
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Technische Universität München @tum.de · 24/02/2026
Get to know Thomas Schlichthärle, our newly appointed professor of #AI-guided #ProteinDesign, in the latest NewIn episode. He wants to use custom-designed #proteins to advance the development of new #medicines: go.tum.de/484027 #HightechAgendaBayern ▶️ youtu.be/G-pt28HJpA8 📹& 📷ProLehre
go.tum.de
Designing proteins for targeted cell activation
Prof. Thomas Schlichthärle spricht über seine Arbeit als Professor für AI-guided Protein Design.
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Reposted by Johannes Stein
Netherlands Cancer Institute @nkinl.bsky.social · 20/02/2026
We;re hiring Junior Group Leaders! 🔬✨ We’re looking for researchers in immunology, chemical biology, AI in biology, or protein design to launch their own independent groups in our collaborative, international environment. www.nki.nl/news-events/...
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Sjors Scheres @sjorsscheres.bsky.social · 16/02/2026
Please spread the word: the Structural Studies Division @mrclmb.bsky.social is looking for a new tenure-track, independent group leader with an exciting plan in any area of Structural (Molecular & Cell) biology, in discovery biology and/or methods development. 🥳 mrc.tal.net/vx/mobile-0/...
mrc.tal.net
Research Group Leader Tenure Track - Structural Studies - LMB 2775 - Medical Research Council
Location: Cambridge. Vacancy: Research Group Leader Tenure Track - Structural Studies - LMB 2775. Closing Date: 16/03/2026, 23:55
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Talley Lambert @talley.codes · 16/02/2026
Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package: - fully bootstrapped Java setup (just pip install) - lazy, repeatably-indexable Array object - fully spec-compliant OME-Zarr group obj. - xarray/dask exports github.com/imaging-form... v0.0.rc1 on PyPI
github.com
GitHub - imaging-formats/bffile: Modern Bio-Formats wrapper with clean lazy Python API
Modern Bio-Formats wrapper with clean lazy Python API - imaging-formats/bffile
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Rita Mateus @ritamateus.bsky.social · 05/02/2026
New paper alert!🤩Super proud that our story led by superstar postdocs @liujinghui.bsky.social and @nerlielisa.bsky.social is finally out! We found how electrical signals are key for promoting organ regenerative growth!!! A thread 🧵https://www.science.org/doi/10.1126/sciadv.aec0687
science.org
Injury-induced electrochemical coupling triggers organ growth
Organ repair and growth rely on coupling tissue-wide membrane depolarization with intracellular proliferative signaling.
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Niko Dalheimer @niko-dalheimer.bsky.social · 05/02/2026
I’m excited to share my first-author paper, with co-first author @rongqinxiaoxiao.bsky.social, now out in @nature.com. We developed a live-cell single-particle tracking platform to see how TRiC & prefoldin engage proteins during co- and post-translational folding. 1/9 www.nature.com/articles/s41...
nature.com
Single-molecule dynamics of the TRiC chaperonin system in vivo - Nature
Single-particle tracking experiments in intact cells reveal dynamic co- and post-translational interactions of the TRiC–PFD chaperonin complex with client proteins during in vivo protein folding.
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Achilles Kapanidis @achilleskap.bsky.social · 30/01/2026
Great to see our Science Review on emerging multiplexed single-molecule methods that use libraries to link sequence to dynamics. A fun collaborative writing project! From sequence to function: Bridging single-molecule kinetics and molecular diversity | Science www.science.org/doi/10.1126/...
science.org
From sequence to function: Bridging single-molecule kinetics and molecular diversity
Biological function is fundamentally determined by nucleic acid and protein sequence. Beyond encoding genetic information, nucleic acids also display complex physicochemical parameters that shape stru...
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Max Planck Institute of Biochemistry @mpibiochem.bsky.social · 28/01/2026
Formation & function of #MembranelessOrganelles! #CryoET structures of #proteasome storage granules inside cells! Read our paper @cp-cell.bsky.social! ❕Publication: doi.org/10.1016/j.ce... ❕Press Release: www.biochem.mpg.de/en/pressroom @uoftmedicine.bsky.social @erc.europa.eu #UPSmeetMet
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Enhanced Genomics @enhancedgenomics.bsky.social · 06/01/2026
Join our virtual seminar! @sedonamurphy.bsky.social presents cutting-edge research on 3D genome organisation & epigenetic memory in development, moderated by @stefanschoenfelder.bsky.social 📅 Jan 8, 4pm UK 💻 Zoom Register: us02web.zoom.us/webinar/regi... #3DGenome #Epigenetics #ChromatinBiology
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Fena Ochs @fenaochs.bsky.social · 02/01/2026
Happy to share our new review on 3D chromatin organisation by cohesin with you. It was a great pleasure to review recent advances and future prospects with @danielgerlich.bsky.social.
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Fena Ochs @fenaochs.bsky.social · 02/01/2026
We are looking for a Postdoc at the Center for Gene Expression in Copenhagen. Deadline for applications is the 11th of January. If you are interested in 3D chromatin, SMC complexes, and super-resolution microscopy, join us. www.nature.com/naturecareer...
nature.com
Postdocs at Center for Gene Expression in Department of Cellular and Molecular Medicine - Copenhagen, Hovedstaden (DK) job with University of Copenhagen | 12849488
We are looking for 2 or more highly motivated postdocs interested in ribosome biology, 3D chromatin organisation, or regulation of protein turnove...
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Nature Biotechnology @natbiotech.nature.com · 30/12/2025
An ultra-rapid 3D immunostaining protocol can uniformly label organ-scale tissues go.nature.com/40wig8l rdcu.be/eUK9R
go.nature.com
Uniform volumetric single-cell processing for organ-scale molecular phenotyping - Nature Biotechnology
An ultra-rapid 3D immunostaining protocol can uniformly label organ-scale tissues.
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Job Dekker @jobdekker.bsky.social · 22/12/2025
Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm! www.nature.com/articles/s41...
nature.com
Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm - Nature Cell Biology
Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through the cytoplasm.
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Max Planck Institute for Molecular Genetics @molgen.mpg.de · 11/12/2025
🧬 Are you interested in synthetic biology, CRISPR-Cas9 genome editing and cutting-edge genomics? Apply by 07.01.2026 to join Stefan Mundlos’ lab @stemundi.bsky.social at the MPIMG. #IMPRS-BAC #gradschool! @nataliabenetti.bsky.social 👉 www.molgen.mpg.de/5124667/Mund...
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Rohit V. Pappu @rohitpappu68.bsky.social · 19/12/2025
Nuclear speckle associated RRM-containing proteins are block copolymers. They make size-limited, ordered microphases, tens of nm in size comprising tens of molecules. Speckles are likely clusters or emulsions of distinct microphases and not macrophases www.sciencedirect.com/science/arti...
sciencedirect.com
Nuclear speckle proteins form intrinsic and MALAT1-dependent microphases
Pre-mRNA processing components in nuclear speckles encompass one or more folded RNA recognition motifs (RRMs) and disordered regions with specific seq…
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Johannes Stein @jmstein.bsky.social · 19/12/2025
Very happy to share the published version of our study on the benefits of sodium sulfite + trolox (SST) as oxygen scavenger for #DNA-PAINT - now out in Small! Thanks to the reviewers for helpful comments and again congrats, Becky, on your PhD's first paper!! tinyurl.com/54m2pt9c
onlinelibrary.wiley.com
A Simple, Ultrastable, and Cost‐Effective Oxygen‐Scavenging System for Long‐Term DNA‐PAINT Imaging
A simple, enzyme-free, and cost-effective oxygen scavenging system enhances DNA-PAINT super-resolution microscopy by increasing photostability, minimizing docking strand degradation, and enabling fas...
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Yamuna Krishnan @krishnanyamuna.bsky.social · 17/12/2025
Organelles do NOT have a single uniform pH. And if you think they must, because “protons diffuse fast,” this paper is for you. A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
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Oli Clarke @olibclarke.bsky.social · 11/12/2025
🤯
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Claudia Matthaeus @cmatthaeus.bsky.social · 11/12/2025
💥I am excited to present our first research paper from the lab about caveolae lipid trafficking 🎉 Led by my fantastic PhD candidate @estherocket.bsky.social Here we looked into caveolae mediated dietary lipid uptake and how this process is mechanistically facilitated 👇 1/n
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MPI for Biology Tübingen & Friedrich Miescher Laboratory @mpi-bio-fml.bsky.social · 09/12/2025
Here's another exciting doctoral project led by Research Group Leader Beatrice Ramm at the Friedrich Miescher Laboratory. Check the list of other available projects on our website: lnkd.in/gEMXNQY6 The application portal is open so apply now! #PhD #IMPRS #graduateprogram #maxplanck
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Rita Strack @ritastrack.bsky.social · 08/12/2025
Janelia is hiring! "Invent new imaging methods, molecular tools, or protein chemistry approaches" www.janelia.org/content/lead...
janelia.org
Lead a lab at Janelia
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Institut Pasteur | 130 years of biomedical research @pasteur.fr · 08/12/2025
🔬 Call to create junior research groups at the Institut Pasteur Focus: Infectious diseases, host-microbe interactions, vaccines Special interest: AI methodologies 📅 Deadline: Feb 9, 2026 👥 2-12 years post-PhD Apply now 📝 research.pasteur.fr/en/call/crea... #JobOpportunity #Research
research.pasteur.fr
Creation of new junior research groups at the Institut Pasteur - Call for applications 2026 - Research
The Institut Pasteur is launching an international call to recruit new junior research group leaders leveraging cutting-edge transdisciplinary approaches to exploring infectious diseases, host-microbe...
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Federico Teloni @fedeteloni.bsky.social · 04/12/2025
I am happy to share that my postdoctoral work in the @gerlichlab.bsky.social at @imbavienna.bsky.social is finally out 🎉! Our study reveals how cohesin guides focused and accurate homology search. Read more 👉 www.science.org/doi/10.1126/... Follow along for key insights and updates! 🧵
science.org
Cohesin guides homology search during DNA repair using loops and sister chromatid linkages
Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, and defective repair underlies diseases such as cancer. Homologous recombination uses an intact homologous sequenc...
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Heilemann Lab @heilemannlab.bsky.social · 28/11/2025
We developed a 'smart STED microscope' to detect rare objects/events in cells, and unraveled the 3D morphology of a nuclear membraneless organelle (paraspeckle). Amazing collaboration with Sjoerd Stallinga, Bernd Rieger (TU Delft) and @mixmue.bsky.social 🙏 (1/3) www.nature.com/articles/s41...
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Benoit Bruneau @benoitbruneau.bsky.social · 27/11/2025
Bah, who needs cohesin if you're at the right place (near). Grover once taught us the difference between near and far (my favourite Sesame Street piece), and now amazing work from @elphegenoralab.bsky.social led by @karissalhansen.bsky.social shows us how: www.science.org/doi/10.1126/...
science.org
Synergy between regulatory elements can render cohesin dispensable for distal enhancer function
Enhancers are critical genetic elements controlling transcription from promoters, yet how they convey regulatory information across large genomic distances remains unclear. Here, we engineer pluripote...
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Max Planck Institute for Molecular Genetics @molgen.mpg.de · 27/11/2025
Want to analyze the role of endogenous retroviruses in early human development or investigate their regulation in pluripotency and early development for your PhD? Join the lab of @fueyoraquel.bsky.social via the IMPRS-BAC #gradschool! 👉 www.molgen.mpg.de/5094682/Fuey...
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Max Planck Institute for Molecular Genetics @molgen.mpg.de · 25/11/2025
🔬 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...
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Yvonne Stahl @yvonnestahl.bsky.social · 19/11/2025
A great opportunity to join our newly established imaging centre in Frankfurt as engineer/technician. If you love light microscopy, please apply! Please share!
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