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Stefan Schoenfelder

@stefanschoenfelder.bsky.social
884 followers 603 following 185 posts

Enhancers, 3D genome organisation, pluripotent stem cells Babraham Institute and Enhanc3D Genomics

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Reposted by Stefan Schoenfelder
Rada-Iglesias Lab @radaiglesiaslab.bsky.social · 7h
Happy to share that our previous preprint showing that KMT2B controls the enhancer-like activity of LINE-1 elements is now published in @natcomms.nature.com 🎉 Thanks to all co-authors and to @ibbtec.bsky.social @csic.es @univcantabria.bsky.social www.nature.com/articles/s41...
nature.com
KMT2B facilitates long-range gene regulation through LINE1 elements - Nature Communications
The authors demonstrate that KMT2B primarily regulates gene expression through LINE-1 elements with enhancer-like function, rather than by counteracting Polycomb repression, revealing an underapprecia...
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Angelika Feldmann @angelikafeldmann.bsky.social · 14h
Excited to share PostChicago, our lab's new R/Bioconductor package for the analysis of Capture-(Hi)C data downstream of loop calling. We present two of its applications: Meta-profiling of interactions and detection of crosslinking artefacts: www.biorxiv.org/content/10.6...
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Cees Dekker @ceesdekker.bsky.social · 21h
Our latest #CDlab paper on BioRxiv: www.biorxiv.org/content/10.6... Led by 1st author Jaco van der Torre, we report our technique to create long (100 kb) DNA molecules with entirely user-defined sequences. We use this to design motif-depleted DNA sequences for single-molecule experiments.
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Anestis Tsakiridis @tsakiridis.bsky.social · 13h
We welcome fellowship applicants looking to establish their own research group around our cluster’s themes. For stem cell research candidates, feel free to get in touch with me or Matt- I started my group here 10 years ago and can confirm Sheffield is a fantastic place to live and work.
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Itai Yanai @itaiyanai.bsky.social · 10/10/2026
1. CRISPR came from basic research on bacteria. 2. Optogenetics started with a discovery in algae. 3. The GFP protein comes from jellyfish. The biggest breakthroughs all trace to scientists following their curiosity, and this is one huge reason why we must keep funding basic research!
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Mir Lab @mirlab.bsky.social · 09/10/2026
1/ Our paper, “Enhancer binding kinetics explain transcription factor hub formation,” is now published! Here we set out to understand why transcription factors form bright clusters or “hubs” in the nucleus, and whether those hubs actually control gene activity. tinyurl.com/38uf8348
tinyurl.com
Enhancer binding kinetics explain transcription factor hub formation
Transcription factors (TFs) form dynamic, high-concentration clusters, condensates, or hubs, proposed to increase TF binding frequency at target enhancers. However, how enhancer sequence shapes hub pr...
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Jesse Engreitz @jengreitz.bsky.social · 09/10/2026
Systematic mapping of enhancers, silencers, and topological elements using prime editing deletion screens www.biorxiv.org/content/10.6... Check out our preprint on next-generation tech for mapping distal regulatory effects! We’re excited to help set this up - please get in touch Thread 👇
biorxiv.org
Systematic mapping of enhancers, silencers, and topological elements with prime editing deletion screens
Noncoding regulatory elements in the human genome can control gene expression through distinct mechanisms, including acting as enhancers, silencers, or topological elements. However, we lack tools to ...
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Silvia Ramundo @sramundo.bsky.social · 09/10/2026
What I loved most about UCSF (and what I’m trying to cultivate here @vbcscitraining.bsky.social ) is the genuine sense of flat hierarchy. I just found this picture of my son in Bruce Alberts’ office (to be fair, almost any adult or kid would be drawn to that office!). I was a random postdoc, 1/2
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Institute of Genetics and Cancer @uoe-igc.bsky.social · 09/10/2026
IGC is looking for a Research Assistant to work in the @sproullab.bsky.social lab. This role has a particular emphasis on the use of synthetic vector libraries combined with cellular landing pads high throughput sequencing data of variant libraries from mammalian cells. 👇🏽 edin.ac/3VrC4Lw
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Stefan Schoenfelder @stefanschoenfelder.bsky.social · 09/10/2026
She absolutely did! Thank you so much again.
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Stefan Schoenfelder @stefanschoenfelder.bsky.social · 09/10/2026
Thank you so much Selina!
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Reposted by Stefan Schoenfelder
Srinjan Lab @srinjan.bsky.social · 09/10/2026
Interested in mechanobiology, transcription factors and stem cell differentiation? Please check out this postdoc opportunity between my lab @imperiallifesci.bsky.social and the lab of Maxim Molodtsov @mmlab.bsky.social @crick.ac.uk (Deadline: 6 January 2027): www.crick.ac.uk/careers-stud...
crick.ac.uk
Mechanical control of gene expression
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Stefan Schoenfelder @stefanschoenfelder.bsky.social · 09/10/2026
Eugenia’s main body of work has been published recently as a result of a fantastic collaboration with @lancasterlab.bsky.social doi.org/10.1038/s415... Many thanks to Eugenia’s examiners Profs @selinawray.bsky.social and Roger Barker who made the viva such an interesting and fun experience for her
doi.org
Reversible epiblast regionalization determines differentiation potential of human pluripotent stem cells - Nature Biotechnology
The differentiation variability of human pluripotent stem cell lines is diagnosed and corrected.
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Stefan Schoenfelder @stefanschoenfelder.bsky.social · 09/10/2026
Very proud of @eugenia-w.bsky.social who passed her PhD viva yesterday with flying colours - the first PhD from the lab!
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Pravrutha Raman @pravrutharaman.bsky.social · 08/10/2026
Now that we have moved coasts, I am thrilled to share that the ChromEvo (Raman) lab is officially open at UMass Boston 🎉 We ask how CHROMatin EVOlution leads to functional innovation and we are hiring at multiple levels. Read on and share with folks who maybe interested chromevoramanlab.github.io
The logo with a phylogenetic tree, a budding yeast, a fly and a nucleosome that has Raman lab Chrom Evo written in the middle
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Transposon and Cancer Epigenetics Group @deniz-lab.bsky.social · 07/10/2026
Join us to explore whether transposable elements can be harnessed to uncover new immunotherapy targets for childhood AML. A fully funded PhD combining cancer genomics, epigenetics and immunology, with access to unique paediatric AML patient datasets and samples. Join us at Barts Cancer Institute! 👇
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Jean Léon Maître @maitrejl.bsky.social · 06/10/2026
📣Our department is hiring a new group leader!📣 Want to start your team in a vibrant scientific environment in the center of Paris? I was very lucky to do that 10 years ago, reach out if you have any question. Apply by December 18th: jpi-recruitment-curie-umr3215-u934.curie.fr
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Alex de Mendoza @alexdemendoza.bsky.social · 06/10/2026
It's live! The next @embo.org #EvoChromo meeting will take place next year October in St Feliu de Guíxols (Spain), check it out here: meetings.embo.org/event/27-chr.... It's been great to co-organise with @dodonova-sveta.bsky.social @kellervalsecchi.bsky.social @cedricfeschotte.bsky.social & Nick I.
meetings.embo.org
Chromatin evolution from molecules to genomes
Technological advances over the past decade have enabled genome-wide mapping of chromatin organization across diverse organisms at unprecedented resolution. These studies have uncovered both conserve…
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Science Magazine @science.org · 04/10/2026
A species of lungfish found in South America has claimed the title of the animal with the biggest genome sequenced so far. Learn more on #WorldAnimalDay: scim.ag/46OMl6v
This odd fish has 30 times as much DNA as humans—a new record for animals
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Emilia Dimitrova @edimitrova.bsky.social · 02/10/2026
Great session next week! Not to be missed! @paul-villain.bsky.social from our neighbouring lab has a fantastic story
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Rob Klose @robklose.bsky.social · 30/09/2026
Come join us April 2027 for the next instalment of the EMBL Chromatin and Epigenetics meeting. Great invited speakers and lots of talks selected from abstracts! It will be a fantastic meeting (despite the egregious nucleosome images...)
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 29/09/2026
For the last 34 years I have been on the faculty of the UNC-Chapel Hill Department of Biology and have never regretted that decision. This year we are hiring TWO new Assistant Professors in the broad area of Molecular, Cell, Developmental Biology 1/n bio.unc.edu
Front page of the website
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Evgeny Kvon @evgenykvon.bsky.social · 29/09/2026
This is a really cool finding, congrats! It also reminds me of a recent paper from John Lis's lab showing that LTR promoter transcription in the NMU enhancer attenuates its activity: pubmed.ncbi.nlm.nih.gov/42468524/. So it appears to be a broader mechanism?
pubmed.ncbi.nlm.nih.gov
Checking your browser - reCAPTCHA
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Maxim Greenberg @maxvcg.bsky.social · 29/09/2026
Two more days to submit your abstract!!
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 26/09/2026
🧬 Highly related @natgenet.nature.com paper from @binzmit.bsky.social group, using nucleosome-resolution chromatin modeling: Euchromatin forms condensed domains with short active regions on the surface www.nature.com/articles/s41... Congratulations! 🎉
nature.com
Euchromatin forms condensed domains with short active regions on the surface - Nature Genetics
Simulations integrating micro-C and imaging data provide a coherent view of chromatin organization from nucleosomes to clutches to domains, revealing that most regions form compact domains but short r...
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Janina Rinke @jannelrinke.bsky.social · 25/09/2026
Very happy to see this paper out! 🐜🧬🐜🧬🐜🧬🐜 Great team effort from everyone, led by @shaggyschrader.bsky.social 🙏🏼
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Lukas Schrader @shaggyschrader.bsky.social · 25/09/2026
1/ New paper: doi.org/10.1126/scia... 🐜🧬 Ants exploded into >15,000 species just after the dinosaur-killing asteroid hit Earth. We think we've found one catalyst behind that radiation: transposable elements. With @jannelrinke.bsky.social, @esthervandenbos.bsky.social & others not on here. 🧵1/11
A Pseudomyrmex ant walking casually on a drop of honey.
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Marco Trizzino @marcotrizzino.bsky.social · 25/09/2026
Check the latest preprint from my group!
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Rob Klose @robklose.bsky.social · 25/09/2026
I really enjoyed chatting with Stefan at the recent EMBO transcription and chromatin meeting about some of my thoughts on CpG island biology!
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Lorraine Reese @lorraine-reese.bsky.social · 25/09/2026
Synthetic Biology UK 2026, 2-3 Nov, Southampton UK. Sessions will cover protein and enzyme design, genome-scale rewriting, next-generation nucleic acid technologies and the engineering of genetic circuits and cellular control systems. Still time to register! #synbio 🧪 bit.ly/Synthetic_Biology_2026
Biochemical Society Scientific Meeting: Synthetic Biology UK. Hampshire, UK, 2-3 November 2026. Includes image of delegates during a poster session at a previous Synthetic Biology meeting, and Biochemical Society and event logos
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Transposon and Cancer Epigenetics Group @deniz-lab.bsky.social · 24/09/2026
Delighted to share our first preprint of the lab! We introduce TEgment, a new RNA-seq pipeline that classifies TE expression into distinct structural modalities, distinguishing functional TE activity from transcriptional noise! www.biorxiv.org/content/10.6...
biorxiv.org
TEgment dissects transposable element reactivation upon CDK9 inhibition in acute myeloid leukemia
Cyclin-dependent kinase 9 (CDK9) inhibition represents a promising therapeutic strategy in cancers that disrupts RNA polymerase II pause release and collapses oncogenic transcripts. Here, we show that...
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Emma R Andersson @anderssonlab.bsky.social · 23/09/2026
🧬 Preprint! 🧵 Our goal is to genetically manipulate every embryonic germ layer to enable high throughput in vivo studies. We previously showed mouse ectoderm can be targeted by amniotic injection, enabling cell-specific manipulation, lineage tracing, and knockouts. But how to reach mesoderm?
Schematic of method developed and application. At embryonic day 7.5, a lentiviral library carrying unique 30-nucleotide barcodes and a fluorescent reporter is injected into the mouse exocoelomic cavity. An E8 embryo cross-section shows that this cavity is continuous with the intraembryonic coelomic cavity, allowing the virus to reach and barcode mesodermal progenitors, including lateral plate and paraxial mesoderm.
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Cell - a Cell Press journal @cp-cell.bsky.social · 23/09/2026
Now online! Direct cell-to-cell transmission of retrotransposons
dlvr.it
Direct cell-to-cell transmission of retrotransposons
Retrotransposons can infect neighboring cells using a mechanism that relies on a small fusogen-like protein rather than on the envelope protein that is typically required for infection.
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Teif lab @teiflab.bsky.social · 23/09/2026
Zeng et al, 2026. Transcription factors read a second regulatory code in chromatin www.biorxiv.org/content/10.6... "our findings establish that TFs interpret two complementary layers of genomic information: the primary DNA sequence and a second code written into the nucleosome architecture"
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 23/09/2026
🤯
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John Greally @greally.bsky.social · 23/09/2026
Tim Bestor has left us. This obituary captures him well — you always had to be at your intellectual peak with him, while his trainees always spoke highly of their experiences. He made a massive contribution to epigenetics, a giant in our field. www.genetics.cuimc.columbia.edu/news/memoria...
genetics.cuimc.columbia.edu
In memoriam of Professor Timothy H. Bestor
In memoriam: Professor Timothy H. Bestor 1952-2026
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Tien-Chi Huang @tienchihuang.bsky.social · 23/09/2026
www.genetics.cuimc.columbia.edu/news/memoria... such a giant.
genetics.cuimc.columbia.edu
In memoriam of Professor Timothy H. Bestor
In memoriam: Professor Timothy H. Bestor 1952-2026
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Ian McGough 🇪🇺🇮🇪🪰 @ianmcgough.bsky.social · 22/09/2026
Proud to share the labs first preprint! Led by Yeon, whose hard work, dedication and drive have been instrumental in bringing the project to this point. Thank you to everyone involved, especially long-term collaborators Yvonne and Yuguang. #Wnt #WntUK #RASopathy #ERK www.biorxiv.org/content/10.6...
biorxiv.org
GPC6 Lipid Shielding Sustains WNT5A Gradients to Prevent a RASopathy-like Developmental State
Morphogen gradients require ligands to disperse across tissues from their sites of production, yet receptor engagement can consume ligand before it reaches distant cells. This poses a particular chall...
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John Timmer @jtimmer.bsky.social · 22/09/2026
Ok, this "there are two separate brains" thing appears to be making the rounds, and I want to be absolutely clear: this is a press office overhyping some perfectly reasonable science that won't come as a surprise to most developmental biologists.
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Raquel Fueyo @fueyoraquel.bsky.social · 22/09/2026
Want an efficient way to delete cis-regulatory elements in stem cells? 🧬 Our lab just published a methods paper in JoVE's collection on 2D/3D Stem Cell-Based Models of Early Mammalian Development. shorturl.at/QB1xo Thank you @ancheldjs.bsky.social for the invitation to contribute!
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Marc A. Marti-Renom @mamartirenom.bsky.social · 22/09/2026
Join us!! International PhD call 👇🏻👇🏻👇🏻 www.crg.eu/en/content/t...
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Guardian US @us.theguardian.com · 21/09/2026
The “jaw-dropping” El Niño currently heating up the planet has burst through the highest temperature ever recorded for the phenomenon, several months before its expected peak.
A line chart showing temperature anomalies in the Niño 3.4 region of the Pacific Ocean, compared to a 30-year rolling base period since 1982.

A gold line shows temperatures in 1997, a teal line in 2025, and a red line in 2026. The red line surpasses all others reaching 3.07ºC, and at an earlier point (September) than the previous El Niño that reached a comparable range in November 2015.
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Sue Biggins @suebiggins.bsky.social · 21/09/2026
Here it is! @basicsci.fredhutch.org is searching for an associate or senior faculty member!
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Arnaud Krebs @arnaudkr.bsky.social · 21/09/2026
We are recruiting! Wet&Dry either combined or separate. If you are excited about gene regulation, new methods in genomics and AI-based interpretation! Talk to us!
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 21/09/2026
The Hutch does amazing work and you'll have remarkable colleagues
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EMBL @embl.org · 21/09/2026
There is still time to apply for the EMBL International PhD Programme! 📢 Don’t miss this opportunity to receive dedicated mentoring while doing interdisciplinary research. Research groups across EMBL are recruiting now! bit.ly/4x9Edss
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Harmit Singh Malik @harmitmalik.bsky.social · 21/09/2026
Thanks to the generosity of the Bezos Family Foundation, @basicsci.fredhutch.org is excited to announce a new search to recruit a Bezos Family Distinguished Scholar : apply.interfolio.com/193655
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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MwahahahahahadScientist @mads100tist.bsky.social · 24/08/2023
The plot thickens
An X Y axis plot showing dots that get progressively thicker
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paveltomancak.bsky.social @paveltomancak.bsky.social · 20/09/2026
Wow. Amazing, prescient vision of the future of academia by @giorgio.gilest.ro You don’t need to agree, but read and consider.
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Stefan Schoenfelder @stefanschoenfelder.bsky.social · 20/09/2026
The number of MSCA Postdoctoral Fellowship applications in 2026 (21,627) has more than doubled since 2024 (10,360 proposals) and more than tripled since 2022 (7,044). Stating the obvious here but this is not sustainable.
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