Stefan Schoenfelder
@stefanschoenfelder.bsky.social
Enhancers, 3D genome organisation, pluripotent stem cells
Babraham Institute and Enhanc3D Genomics
Babraham Institute and Enhanc3D Genomics
Pinned
Non-canonical enhancers control gene expression and cell fate in human pluripotent stem cells
Enhancers are key gene regulatory elements that ensure the precise spatiotemporal execution of developmental gene expression programmes. However recent findings indicate that approaches to identify en...
www.biorxiv.org
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
www.biorxiv.org/content/10.1...
🧵 below
Reposted by Stefan Schoenfelder
www.nature.com/articles/s41...
Progressive coevolution of the yeast centromere and kinetochore
🤩
@helsenjana.bsky.social @gautamdey.bsky.social
Progressive coevolution of the yeast centromere and kinetochore
🤩
@helsenjana.bsky.social @gautamdey.bsky.social
Progressive coevolution of the yeast centromere and kinetochore - Nature
Thousands of centromeres were identified and tracked across two major fungal clades, showing that new centromeres spread progressively and that the kinetochore acts as a filter to determine which new ...
www.nature.com
November 27, 2025 at 6:22 PM
www.nature.com/articles/s41...
Progressive coevolution of the yeast centromere and kinetochore
🤩
@helsenjana.bsky.social @gautamdey.bsky.social
Progressive coevolution of the yeast centromere and kinetochore
🤩
@helsenjana.bsky.social @gautamdey.bsky.social
Reposted by Stefan Schoenfelder
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/...
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...
www.science.org
November 27, 2025 at 7:10 PM
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/...
Reposted by Stefan Schoenfelder
📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
November 27, 2025 at 1:17 PM
📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
Reposted by Stefan Schoenfelder
Rapid compensatory evolution within a multiprotein complex preserves telomere integrity www.science.org/doi/10.1126/... @levine-lab.bsky.social very cool work
Rapid compensatory evolution within a multiprotein complex preserves telomere integrity
Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such comp...
www.science.org
November 27, 2025 at 8:43 PM
Rapid compensatory evolution within a multiprotein complex preserves telomere integrity www.science.org/doi/10.1126/... @levine-lab.bsky.social very cool work
Reposted by Stefan Schoenfelder
🚨Post open in our lab! Come work on some cool themes involving metabolism, chromatin, early development 🤓. Pls RT
Join @mpercharde.bsky.social Lab at the MRC LMS! We have an 18mo postdoc position to cover a couple of projects (maternity leave and paper revisions). The projects are focussed on chromatin in early mouse embryos and metabolism in mouse embryonic stem cells and pluripotency.
November 27, 2025 at 2:26 PM
🚨Post open in our lab! Come work on some cool themes involving metabolism, chromatin, early development 🤓. Pls RT
Reposted by Stefan Schoenfelder
Join @mpercharde.bsky.social Lab at the MRC LMS! We have an 18mo postdoc position to cover a couple of projects (maternity leave and paper revisions). The projects are focussed on chromatin in early mouse embryos and metabolism in mouse embryonic stem cells and pluripotency.
November 27, 2025 at 2:18 PM
Join @mpercharde.bsky.social Lab at the MRC LMS! We have an 18mo postdoc position to cover a couple of projects (maternity leave and paper revisions). The projects are focussed on chromatin in early mouse embryos and metabolism in mouse embryonic stem cells and pluripotency.
Reposted by Stefan Schoenfelder
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...
Join the lab of @fueyoraquel.bsky.social via the IMPRS-BAC #gradschool!
👉 www.molgen.mpg.de/5094682/Fuey...
November 27, 2025 at 2:06 PM
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...
Join the lab of @fueyoraquel.bsky.social via the IMPRS-BAC #gradschool!
👉 www.molgen.mpg.de/5094682/Fuey...
Reposted by Stefan Schoenfelder
Looking for some Thanksgiving reading? 🦃🦃🦃
🚨Check out our new preprint on CRISPore-seq!🚨
Combining pooled CRISPR perturbations with single-cell sequencing has been tremendously powerful... but we are missing a lot with current approaches like Perturb-seq and ECCITE-seq.
🚨Check out our new preprint on CRISPore-seq!🚨
Combining pooled CRISPR perturbations with single-cell sequencing has been tremendously powerful... but we are missing a lot with current approaches like Perturb-seq and ECCITE-seq.
November 27, 2025 at 11:40 AM
Looking for some Thanksgiving reading? 🦃🦃🦃
🚨Check out our new preprint on CRISPore-seq!🚨
Combining pooled CRISPR perturbations with single-cell sequencing has been tremendously powerful... but we are missing a lot with current approaches like Perturb-seq and ECCITE-seq.
🚨Check out our new preprint on CRISPore-seq!🚨
Combining pooled CRISPR perturbations with single-cell sequencing has been tremendously powerful... but we are missing a lot with current approaches like Perturb-seq and ECCITE-seq.
Reposted by Stefan Schoenfelder
Outstanding PhD fellowship call OPEN for excellent students.
lacaixafoundation.org/en/doctoral-...
This is for students incoming from outside Spain. And it is VERY well supported (ie at European levels).
If you’re interested in doing a PhD in our lab @irbbarcelona.org, reach out!!!!
lacaixafoundation.org/en/doctoral-...
This is for students incoming from outside Spain. And it is VERY well supported (ie at European levels).
If you’re interested in doing a PhD in our lab @irbbarcelona.org, reach out!!!!
Doctoral INPhINIT fellowships - Incoming Call 2026
We grant 30 fellowships for researchers of any nationality who wish to pursue a doctorate in a STEM discipline at research centres of excellence in Spain or Portugal.
www.google.com
November 26, 2025 at 7:43 AM
Outstanding PhD fellowship call OPEN for excellent students.
lacaixafoundation.org/en/doctoral-...
This is for students incoming from outside Spain. And it is VERY well supported (ie at European levels).
If you’re interested in doing a PhD in our lab @irbbarcelona.org, reach out!!!!
lacaixafoundation.org/en/doctoral-...
This is for students incoming from outside Spain. And it is VERY well supported (ie at European levels).
If you’re interested in doing a PhD in our lab @irbbarcelona.org, reach out!!!!
Reposted by Stefan Schoenfelder
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our a...
www.biorxiv.org
November 19, 2025 at 8:57 PM
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Reposted by Stefan Schoenfelder
Cool project with a couple of great supervisors!
I'm looking for top-notch candidate for a fully-funded PhD working on role of somatic mutations in ageing immune decline. Ideal for wet-lab or quantitative candidates. Fantastic collaboration with Prof Martin Taylor in Edinburgh THE UK expert in mutations.
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
www.findaphd.com
November 24, 2025 at 9:24 AM
Cool project with a couple of great supervisors!
Reposted by Stefan Schoenfelder
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
RNA polymerase II coordinates histone deacetylation at active promoters
Transcription initiation limits histone acetylation and H2AZ incorporation at promoters.
www.science.org
February 12, 2025 at 9:21 PM
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
Reposted by Stefan Schoenfelder
Programmable initiation of mRNA translation by trans-RNA - @cornelluniversity.bsky.social @iecb.bsky.social go.nature.com/3K7SEdO
Programmable initiation of mRNA translation by trans-RNA - Nature Biotechnology
Translation can be initiated from a specific start codon using trans-RNA.
go.nature.com
November 21, 2025 at 2:44 PM
Programmable initiation of mRNA translation by trans-RNA - @cornelluniversity.bsky.social @iecb.bsky.social go.nature.com/3K7SEdO
Reposted by Stefan Schoenfelder
Excited to share our new study, led by @dellaVolpe_L, now out in @natcellbio.nature.com! Blocking #ferroptosis enhances human 🩸 stem cell expansion, with implications for transplantation and gene therapy. www.nature.com/articles/s41...
November 18, 2025 at 5:49 PM
Excited to share our new study, led by @dellaVolpe_L, now out in @natcellbio.nature.com! Blocking #ferroptosis enhances human 🩸 stem cell expansion, with implications for transplantation and gene therapy. www.nature.com/articles/s41...
Reposted by Stefan Schoenfelder
Today in @nature.com, in work led by @adititm.bsky.social, we report the ability to prompt Evo to generate functional de novo genes.
You shall know a gene by the company it keeps!
You shall know a gene by the company it keeps!
November 19, 2025 at 4:24 PM
Today in @nature.com, in work led by @adititm.bsky.social, we report the ability to prompt Evo to generate functional de novo genes.
You shall know a gene by the company it keeps!
You shall know a gene by the company it keeps!
Reposted by Stefan Schoenfelder
It's always special when you find your own paper in the table of contents of the journal 😍
"The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube" -> Now out in its final form
www.cell.com/developmenta...
"The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube" -> Now out in its final form
www.cell.com/developmenta...
November 18, 2025 at 4:11 PM
It's always special when you find your own paper in the table of contents of the journal 😍
"The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube" -> Now out in its final form
www.cell.com/developmenta...
"The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube" -> Now out in its final form
www.cell.com/developmenta...
Reposted by Stefan Schoenfelder
Our new preprint is online! Viruses, bacteria and parasites use effector proteins to evade immunity and rewire host cell pathways. Together with @AlexanderStark8, we wondered if we could systematically map what these effectors, regardless of their origin, do in human cells. 1/8
www.biorxiv.org
November 18, 2025 at 3:57 PM
Our new preprint is online! Viruses, bacteria and parasites use effector proteins to evade immunity and rewire host cell pathways. Together with @AlexanderStark8, we wondered if we could systematically map what these effectors, regardless of their origin, do in human cells. 1/8
Reposted by Stefan Schoenfelder
Major new direction in the lab: hacking human cell biology with pathogen effectors (eORFs) - amazing collaboration with @miketilapia.bsky.social lab. Huge congrats to first authors Tomas & He & all co-authors! Check out the pre-print on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...
www.biorxiv.org
November 18, 2025 at 2:51 PM
Major new direction in the lab: hacking human cell biology with pathogen effectors (eORFs) - amazing collaboration with @miketilapia.bsky.social lab. Huge congrats to first authors Tomas & He & all co-authors! Check out the pre-print on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...
Reposted by Stefan Schoenfelder
IMPRS-BAC #gradschool: Our new groupleader @sedonamurphy.bsky.social has an open PhD project in her lab. Topic: Spatial feedback between epigenetic regulation and chromatin regulation. Apply by Jan 7, 2026!
👉 www.molgen.mpg.de/5091778/Murp...
👉 www.molgen.mpg.de/5091778/Murp...
November 18, 2025 at 4:05 PM
IMPRS-BAC #gradschool: Our new groupleader @sedonamurphy.bsky.social has an open PhD project in her lab. Topic: Spatial feedback between epigenetic regulation and chromatin regulation. Apply by Jan 7, 2026!
👉 www.molgen.mpg.de/5091778/Murp...
👉 www.molgen.mpg.de/5091778/Murp...
💯 %👇
Great PhD opportunity in a top lab!
Great PhD opportunity in a top lab!
🚨Reposts appreciated‼️If I had read this PhD offer five years ago, I wouldn’t have hesitated for a second to apply 😉
Passionate about gene regulation, chromatin, and developmental biology? Just contact @radaiglesiaslab.bsky.social at @ibbtec.bsky.social 🧬✨
#PhD #3DGenome
Passionate about gene regulation, chromatin, and developmental biology? Just contact @radaiglesiaslab.bsky.social at @ibbtec.bsky.social 🧬✨
#PhD #3DGenome
November 17, 2025 at 10:03 AM
💯 %👇
Great PhD opportunity in a top lab!
Great PhD opportunity in a top lab!
Reposted by Stefan Schoenfelder
Excited to share I’ve received a #SSMF #Consolidator grant!
📣 Recruiting a #postdoc to study #cancer #neuroscience #3Dgenomics #multiomics #singlecellomics
🔬How neural inputs shape #3Dgenome and #cellplasticity in #glioblastoma #GBM
Interested? Apply now 👇
rb.gy/m7xz7b
📣 Recruiting a #postdoc to study #cancer #neuroscience #3Dgenomics #multiomics #singlecellomics
🔬How neural inputs shape #3Dgenome and #cellplasticity in #glioblastoma #GBM
Interested? Apply now 👇
rb.gy/m7xz7b
Postdoctoral Researcher in "Cancer Neuroscience: the impact of neural activity on 3D genome organization and cellular plasticity in glioblastoma”
rb.gy
November 14, 2025 at 11:00 AM
Excited to share I’ve received a #SSMF #Consolidator grant!
📣 Recruiting a #postdoc to study #cancer #neuroscience #3Dgenomics #multiomics #singlecellomics
🔬How neural inputs shape #3Dgenome and #cellplasticity in #glioblastoma #GBM
Interested? Apply now 👇
rb.gy/m7xz7b
📣 Recruiting a #postdoc to study #cancer #neuroscience #3Dgenomics #multiomics #singlecellomics
🔬How neural inputs shape #3Dgenome and #cellplasticity in #glioblastoma #GBM
Interested? Apply now 👇
rb.gy/m7xz7b
Reposted by Stefan Schoenfelder
☕ @katerinakraft.bsky.social @sedonamurphy.bsky.social @mattjones.bsky.social et al. identify extrachromosomal DNA(ecDNA)-interacting elements (EIEs) enriched for #TransposableElements in #ColorectalCancer. EIE 14 integrated within ecDNA acts as an enhancer to promote cancer fitness.
bit.ly/49iFC7C
bit.ly/49iFC7C
Enhancer activation from transposable elements in extrachromosomal DNA - Nature Cell Biology
Kraft, Murphy, Jones et al. identify extrachromosomal DNA (ecDNA)-interacting elements (EIEs) enriched for transposable elements within ecDNA in colorectal cancer cells. They show that EIE 14 integrat...
bit.ly
November 16, 2025 at 8:29 AM
☕ @katerinakraft.bsky.social @sedonamurphy.bsky.social @mattjones.bsky.social et al. identify extrachromosomal DNA(ecDNA)-interacting elements (EIEs) enriched for #TransposableElements in #ColorectalCancer. EIE 14 integrated within ecDNA acts as an enhancer to promote cancer fitness.
bit.ly/49iFC7C
bit.ly/49iFC7C
Reposted by Stefan Schoenfelder
🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)
November 11, 2025 at 12:52 PM
🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)
Reposted by Stefan Schoenfelder
Wonderful to see the beautiful preprint from Sabate et al now published - TADs are also dynamic structures in human cells, with remarkably similar parameters between mESCs and HCT116 cells
www.nature.com/articles/s41...
www.nature.com/articles/s41...
November 15, 2025 at 5:24 PM
Wonderful to see the beautiful preprint from Sabate et al now published - TADs are also dynamic structures in human cells, with remarkably similar parameters between mESCs and HCT116 cells
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Stefan Schoenfelder
Many exciting opportunities for a PhD in Life Sciences in CRG, Barcelona. If you are interested in Genomics of Diabetes check out the offer for a fully funded fellowship in our lab - we will consider candidates with experimental or computational backgrounds.
Please spread the word!
Please spread the word!
Are you looking for a PhD? Join us in Barcelona! You'll dive into a community of >100 PhD students from 30 countries exploring the frontiers of biology. You can also join an online workshop on 6 November (15:00 CET) to learn how to find the right lab for you.
More info: www.crg.eu/en/content/t...
More info: www.crg.eu/en/content/t...
October 23, 2025 at 9:09 AM
Many exciting opportunities for a PhD in Life Sciences in CRG, Barcelona. If you are interested in Genomics of Diabetes check out the offer for a fully funded fellowship in our lab - we will consider candidates with experimental or computational backgrounds.
Please spread the word!
Please spread the word!