Stefan Schoenfelder
Enhancers, 3D genome organisation, pluripotent stem cells
Babraham Institute and Enhanc3D Genomics
- Reposted by Stefan SchoenfelderWant to interpret DNA sequence-to-function models to understand the underlying molecular mechanisms? Then this is a must read!
- Reposted by Stefan SchoenfelderVery excited to share our new Molecular Cell paper on missense mutations in Polycomb genes and how they can disrupt chromatin regulation to drive neurodevelopmental disorders. A huge thank you to everyone involved, and to our amazing collaborators! www.cell.com/molecular-ce...
- Reposted by Stefan SchoenfelderOur new preprint on SMCHD1! We’ve shown SMCHD1’s ATPase activity is critical for function in vivo, and excitingly a new DNA binding domain neighbouring the ATPase domain activates the enzymatic function, which is important for normal chromatin binding. urldefense.com/v3/__https:/...
- Reposted by Stefan SchoenfelderFinal version of our paper now published. elifesciences.org/articles/109... Take homes: CHD4/NuRD directly limits transcription factor residence times. At active enhancers this keeps them working efficiently. At inactive enhancers it prevents TFs from getting a foothold and causing activation. 1/n
- Reposted by Stefan SchoenfelderTerrific paper on a new chromosomal compartment where extensive loop extrusion isolates domains from other such domains
- How do compartmentalization & loop extrusion organize eukaryotic genomes beyond classical model organisms? Hi-C analysis of silkworm chromosomes by Drinnenberg, Muller, Mirny et al reveals new combination of these mechanisms, and a new, secluded “S” compartment link.springer.com/article/10.1...
- Reposted by Stefan SchoenfelderHow do compartmentalization & loop extrusion organize eukaryotic genomes beyond classical model organisms? Hi-C analysis of silkworm chromosomes by Drinnenberg, Muller, Mirny et al reveals new combination of these mechanisms, and a new, secluded “S” compartment link.springer.com/article/10.1...
- Reposted by Stefan SchoenfelderNew study led by Prof. Daniel Munoz-Espin in collaboration with Prof. James Brenton's and our lab 🚨🚨🚨 www.nature.com/articles/s43...
- Reposted by Stefan SchoenfelderSelf-Doubt, the new book from @labliston.bsky.social, explores the uncertainty researchers face in their careers. Several scientists share their stories, including Tombi Makuyana, a postdoc in the LMB’s PNAC Division. Read more about the book here: www.cam.ac.uk/stories/camb... #LMBNews
- Reposted by Stefan SchoenfelderI think Ian Chapman's focus throughout this process has been excessively PI-centred and ignores early career researchers and training. A big funding pause doesn't cause them to worry about their jobs. It causes them to lose their jobs. And to be unable to get new ones. Their careers will be ended.
- Reposted by Stefan SchoenfelderDuring germline epigenetic reprogramming, Polycomb must be restricted in the gametes to ensure proper genome regulation in the fertilized embryo. 2 must-read papers assess what happens when Ezhip (Polycomb antagonist) is lost. They come to highly similar conclusions and should be read in tandem 1/4
- Reposted by Stefan Schoenfelder🚨 1/ Preprint Alert! Sex determination outcome is conserved across vertebrates (i.e. generating 2 compatible sexes) ♀️♂️ But are the cell types and gene programs behind them conserved too? 🧬 Spoiler: not really 👀 Find out in our new preprint ⬇️ www.biorxiv.org/content/10.6...
- Reposted by Stefan Schoenfelder"AI is rapidly populating medical records with synthetic content, creating a feedback loop [that] drives a rapid erosion of pathological variability and diagnostic reliability...this renders AI generated documentation clinically useless after just two generations" www.medrxiv.org/content/10.6...
- Reposted by Stefan SchoenfelderCheck out our new findings showing BRD4's role in preventing the premature activation of developmental transcription factors via #Polycomb, providing new mechanistic insights into the pathogenesis of neurodevelopmental disorder #CdLS #NDDs, #chromatinopathies www.biorxiv.org/content/10.6...
- Reposted by Stefan SchoenfelderNew preprint from the lab! We dig into the regulatory roles of TEs in the mouse placenta, with some surprising findings. Led by the awesome @smamante.bsky.social. Particular kudos to him for navigating the many twists and turns of the project.
- Reposted by Stefan SchoenfelderBoth MRC and BBSRC responsive modes now withdrawn until further notice. Existing applications unlikely to succeed (late 2025 round expecting 1-5% success rate). Listen, I get that UKRI wants to pivot. But killing both at once is devastating. Let's hope at least one opens by summer... #AcademicSky
- Reposted by Stefan SchoenfelderAt a time when the UK should be capitalising on its global reputation as a great place to do science, this is an enormous own goal. I am so sorry for all those who jobs are going to be impacted.
- Both MRC and BBSRC responsive modes now withdrawn until further notice. Existing applications unlikely to succeed (late 2025 round expecting 1-5% success rate). Listen, I get that UKRI wants to pivot. But killing both at once is devastating. Let's hope at least one opens by summer... #AcademicSky
- Reposted by Stefan SchoenfelderSeconded!
- For anyone interested in the history of molecular biology, I cannot recommend Judson's The Eighth Day of Creation highly enough. One of the great book on the history of science. I have two copies because a actually wore out the first one (paperback) www.cshlpress.com/default.tpl?...
- Reposted by Stefan Schoenfelderexcellent thread
- I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵 www.nature.com/articles/s41...
- Reposted by Stefan SchoenfelderThe pause of future funding is awful. But the retrospective culling of already submitted grants is horrific. How many wasted hours for those of us who have grants submitted? What about the post docs who have been given hope their position might be extended who should have been job hunting?
- Reposted by Stefan SchoenfelderReally, we need to decide as a society whether we value science, the training of scientists. Because it's feeling very much like we, collectively, don't. If we (our government) claims to, then it needs to invest in science. Otherwise it had better give us notice to find somewhere that does.
- Reposted by Stefan SchoenfelderThe MRC has asked each of its grant review boards to recommend no more than 3 applications for funding, RPN has heard from multiple sources Normally, boards recommend an average of 12-13 bids, so the success rate this year will be tiny This affects applicant-led calls which closed in 2025...
- Reposted by Stefan SchoenfelderThat would be catastrophic
- MRC instructs grant review boards to slash funding rates. Boards asked to recommend just three applications for funding, as BBSRC also suspends calls. www.researchprofessionalnews.com/rr-news-uk-r...
- Reposted by Stefan SchoenfelderI've started my own lab 🎉 PhD/postdoc positions available - reach out if curious about cerebellum evo-devo and autism spectrum disorders. We’re based at Uni Tartu, Institute of Genomics (home to Estonian Biobank), and funded by @simonsfoundation.org @embo.org, and the Estonian Research Council.
- Reposted by Stefan SchoenfelderJoin us at the Evolutionary Biology Centre at Uppsala University. We’re searching for an Assistant Professor in Biology. www.uu.se/en/about-uu/...
- Reposted by Stefan SchoenfelderJust out @natrevimmunol.nature.com RNA-binding proteins and ribonucleoproteins as determinants of immunity www.nature.com/articles/s41... gives our perspective on this growing area of research. Special thanks to the editor Alexandra, for streamlining the manuscript.
- Reposted by Stefan Schoenfelder#FragileNuclesome is back tomorrow! Join us to hear about exciting talks from: - @au-ho-yu.bsky.social in @robklose.bsky.social's group about transcriptional control by SET1/MLL complexes - @gcloner.bsky.social at @epicypher.bsky.social about the histone PTM landscape of the immune system
- 🥁 #FragileNucleosome is back on Jan 28! We are very excited to host @au-ho-yu.bsky.social and @gcloner.bsky.social as our first speakers of 2026! 📋Please don't forget to register for our 2026 seminar series: us06web.zoom.us/webinar/regi...
- Very excited for @livcracknell.bsky.social and @eugenia-w.bsky.social to represent our lab at the Keystone Symposia Meeting "iPSCs: Progress, Opportunities and Challenges" in Kyoto, Japan www.keystonesymposia.org/conferences/...
- If you're attending the meeting in person or remotely, please check out @eugenia-w.bsky.social's poster and talk (both on January 27th) on "A novel method to restore full differentiation potential in human Pluripotent Stem Cell lines by epigenetic chromatin resetting" (poster number 1023)...
- ...and @livcracknell.bsky.social 's poster (number 2005) on "Dynamic erosion and de novo formation of bivalent chromatin domains during human macrophage specification and stimulation" on January 28th.
- Reposted by Stefan SchoenfelderHave you wondered how the rules of chromatin folding have evolved? Well, this task is not easy to formalize. But here is our take on it: train species-specific DNA-to-chromatin encoder, apply to DNA of unseen species, and build chromatin rules-based tree of life. Have a look: doi.org/10.1093/nar/...
- Reposted by Stefan SchoenfelderI had the privilege to meet artist Mary Griffiths. Mary got inspired by Hi-C maps and over zooms we spoke about Hi-C maps, patterns and drawings. Mary’s Hi-C inspired art has been exhibited eg the Royal Academy. We wrote this piece about this art-science collaboration pubs.aip.org/aip/bpr/arti...
- Reposted by Stefan Schoenfelder📣 Please spread: we’re hiring a Lab Manager! It is a critical position in our new lab. As our lab moves to Barcelona and joins the @crg.eu, we’re looking for a Lab Manager to help build the lab and set the lab atmosphere. 🔗 Apply here 👉 recruitment.crg.eu/content/jobs...
- Reposted by Stefan Schoenfelder🚨Postdoc opportunity🚨Our lab at MRC-LMB Cambridge is recruting a postdoc to study transcription-coupled splicing using cryoEM and endogenous isolation! 🔬 🧬 Please feel free to get in touch directly #postdoc #cryoEM #biochemistry #splicing Apply here by 11 Feb www.nature.com/naturecareer...
- Reposted by Stefan SchoenfelderTurns out that if you use a broom to scratch yourself everyone thinks you're a weirdo but if a cow does it they end up in the cover of Current Biology
- Reposted by Stefan Schoenfelder🔔 New paper alert 🔔 www.nature.com/articles/s41... Some regions in the genome replicate early and some late, but the why and how remain poorly understood. DNA replication and 3D genome organization appear linked, raising the question if one may regulate the other? (1/n)
- Reposted by Stefan SchoenfelderPreprint alert: Jiangyuan Liu developed a new workflow for chromatin loop calling across Hi-C datasets, e.g., during differentiation. Most loops are shared between datasets/cell states. Important work for all interested in chromatin loops and how to identify them! www.biorxiv.org/content/10.6...
- Reposted by Stefan SchoenfelderIf you are looking to build your lab, take a listen to these interviews on @lonelypipette.bsky.social! www.buzzsprout.com/1356877/epis...
- Reposted by Stefan SchoenfelderNew preprint on technologies to scale up CRISPR screens. We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells. We also introduce an approach for cloning lentiviral libraries with billions of elements.
- Reposted by Stefan SchoenfelderWhat can we learn from comparing ~2,000 fungal genomes? Find out about: 🍄evolutionary transitions 🍄lifestyles 🍄genome dynamics 🍄sampling gaps 🍄efforts to uncover the remaining fungal dark matter New review by @jgi.doe.gov's Stephen Mondo and Igor Grigoriev www.nature.com/articles/s41...
- Reposted by Stefan Schoenfelder⚠️ The final work of two former PhD students Till @tschwammle.bsky.social and Verena @verenamutzel.bsky.social is out! ➡️⬅️ They dissect how memory can arise from antisense transcription using mathematical modelling 💻, genomics 🧬 and synthetic biology ⚒️! link.springer.com/article/10.1...
- Reposted by Stefan Schoenfelder"We need to ask ourselves, on both sides of the Atlantic, if we want to live in a world where democracy is recast as weakness, truth as opinion and justice as an option." Perfectly summed up by the secretary general of the Council of Europe. (gift article) www.nytimes.com/2026/01/19/o...
- Thank you @auersperga.bsky.social and Veronika for this perfect timeline cleanse.
- Our new paper (with @biotay.bsky.social) is out and on the cover story of @currentbiology.bsky.social !!!! Veronika, a Carinthian mountain cow flexibly uses a “multi-purpose tool” to scratch herself. A video and more information will follow in the comments. www.cell.com/current-biol...
- Reposted by Stefan SchoenfelderHappy New Year all. I know it's been a draining and difficult year for science in general, but wanted to share some good news: our intrabody paper has now been published in Science Advances with lots of additional data. www.science.org/doi/10.1126/...
- Reposted by Stefan SchoenfelderThrilled to share our latest work: Fine-tuning BACH2 dosage balances stemness and effector function to enhance antitumor T cell therapy - now online in Nature Immunology. Led by Alberto Conti, Alex Evans and Teresa von Linde in the lab. www.nature.com/articles/s41...
- Reposted by Stefan Schoenfelder
There is a special Current Opinion in Genetics & Development issue about genome architecture and expression and it looks great including reviews by @lennarthilbert.bsky.social @yghavi.bsky.social and @wbickmor.bsky.social www.sciencedirect.com/special-issu... - Reposted by Stefan SchoenfelderThe Vlaming lab continues to grow! It's an exciting time in the Vlaming lab: we've just had our 2nd PhD student join, and the 3rd is joining in February. Now, we're looking to recruit a postdoc!
- Reposted by Stefan SchoenfelderThe total NSF budget was 9 billion. I doubt they spend 89% of it on quail.
- Reposted by Stefan Schoenfelder"RNAPII clusters reflect local accumulations of transcriptionally engaged polymerases and do not form through higher-order mechanisms such as phase separation" 😬 www.biorxiv.org/content/10.1... by the @mirlab.bsky.social
- Reposted by Stefan SchoenfelderTF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread
- Reposted by Stefan SchoenfelderLooking forward to this meeting. Early bird registration encouraged!!
- Early bird registration deadline of our joint meeting in Potsdam between March 10-13, 2026 - “Joint international meeting of the German @gfeev.bsky.social, Dutch (DSDB), and #SEBD for #DevBio “Development & Regeneration” is approaching fast. Please apply before the 15th of January!
- Reposted by Stefan SchoenfelderNovel compact CRISPR systems unlock easier delivery and more applications... epigenome editing anyone 👀 Very happy to be involved in work to rationally engineer enhanced Cme2 - an ultra-high fidelity & compact Cas, delivered in vivo in a single AAV (with gRNA) www.biorxiv.org/content/10.6...
- Reposted by Stefan SchoenfelderOur work on #RegulatoryTrajectories is out today in Nat. Comms: www.nature.com/articles/s41... Led by @raquelrouco.bsky.social, this study establishes a new framework to study how enhancer landscapes act sequentially at developmental loci and are silenced to shape gene expression patterns. (1/n)
- Reposted by Stefan SchoenfelderDid you ever wonder how gene expression, once activated, it's maintained for a precise period of time before being decommissioned? Happy to present the final version of our manuscript on the discovery of regulatory trajectories, just published in Nat. Comms: www.nature.com/articles/s41... 1/14
- Our work on #RegulatoryTrajectories is out today in Nat. Comms: www.nature.com/articles/s41... Led by @raquelrouco.bsky.social, this study establishes a new framework to study how enhancer landscapes act sequentially at developmental loci and are silenced to shape gene expression patterns. (1/n)
- Reposted by Stefan SchoenfelderWe’re hiring! @jcellsci.bsky.social is looking for a Reviews Editor to join the team. This is a fantastic opportunity for someone who loves #cellbiology and wants to stay connected with the field. A great chance to work for an organisation that believes in helping the community! Details below👇
- Journal of Cell Science @jcellsci.bsky.social is recruiting an enthusiastic and motivated Reviews Editor. An exciting opportunity for a talented scientific editor to make a contribution to an important journal in the field of #cellbiology. Deadline 2 Feb. More at: www.biologists.com/about-us/wor...
