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
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!
Reposted by Stefan Schoenfelder
The countdown is on! One week left for early birds to get their tickets to the Frontiers in Stem Cell Innovation conference 🎟️
📅 5–6 February 2026
📍 Cambridge, UK
Hosted by The Babraham Institute and Newcastle University.
Register now www.eventbrite.co.uk/e/frontiers-...
📅 5–6 February 2026
📍 Cambridge, UK
Hosted by The Babraham Institute and Newcastle University.
Register now www.eventbrite.co.uk/e/frontiers-...
Frontiers in Stem Cell Innovation 2026
Join leading academics and industry professionals exploring cutting-edge stem cell technologies and disease modelling for drug discovery
www.eventbrite.co.uk
November 14, 2025 at 4:44 PM
The countdown is on! One week left for early birds to get their tickets to the Frontiers in Stem Cell Innovation conference 🎟️
📅 5–6 February 2026
📍 Cambridge, UK
Hosted by The Babraham Institute and Newcastle University.
Register now www.eventbrite.co.uk/e/frontiers-...
📅 5–6 February 2026
📍 Cambridge, UK
Hosted by The Babraham Institute and Newcastle University.
Register now www.eventbrite.co.uk/e/frontiers-...
Reposted by Stefan Schoenfelder
In this episode we talked with @andersshansen.bsky.social from MIT about his work on the impact of 3D genome structures on gene expression and advanced techniques like Region Capture Micro-C for mapping genome organisation. #podcast #epigenetics
Listen here: activemotif.com/podcasts-and...
Listen here: activemotif.com/podcasts-and...
November 14, 2025 at 8:01 AM
In this episode we talked with @andersshansen.bsky.social from MIT about his work on the impact of 3D genome structures on gene expression and advanced techniques like Region Capture Micro-C for mapping genome organisation. #podcast #epigenetics
Listen here: activemotif.com/podcasts-and...
Listen here: activemotif.com/podcasts-and...
Reposted by Stefan Schoenfelder
🧬 Our co-founder @stefanschoenfelder.bsky.social & John Skidmore just published in The Scientist on unlocking the "dark genome" for drug discovery. 95% of disease variants hide here—untapped potential for new therapeutics.
Read more: www.the-scientist.com/illuminating...
#Biotech
Read more: www.the-scientist.com/illuminating...
#Biotech
November 13, 2025 at 2:32 PM
🧬 Our co-founder @stefanschoenfelder.bsky.social & John Skidmore just published in The Scientist on unlocking the "dark genome" for drug discovery. 95% of disease variants hide here—untapped potential for new therapeutics.
Read more: www.the-scientist.com/illuminating...
#Biotech
Read more: www.the-scientist.com/illuminating...
#Biotech
I really enjoyed writing this Innovation Spotlight for The Scientist with John Skidmore (CSO at the ALBORADA Drug Discovery Institute) on the huge potential of 3D genomics to enable and supercharge therapeutic discoveries.
www.the-scientist.com/illuminating...
www.the-scientist.com/illuminating...
Illuminating the Dark Genome to Accelerate Novel Therapeutic Discoveries
Advances in 3D genomics and multiomics are enabling scientists to uncover disease mechanisms hidden in the human genome's noncoding regions.
www.the-scientist.com
November 13, 2025 at 6:34 PM
I really enjoyed writing this Innovation Spotlight for The Scientist with John Skidmore (CSO at the ALBORADA Drug Discovery Institute) on the huge potential of 3D genomics to enable and supercharge therapeutic discoveries.
www.the-scientist.com/illuminating...
www.the-scientist.com/illuminating...
Very excited to host @efapostolou29.bsky.social for her talk on "Building, predicting and targeting 3D regulatory networks in development and cancer" in @enhancedgenomics.bsky.social's
seminar series "The 3D Regulatory Genome".
📅 13 November 2025 (today!)
⏰ 4 pm GMT
Please join: lnkd.in/eEKe4Z7H
seminar series "The 3D Regulatory Genome".
📅 13 November 2025 (today!)
⏰ 4 pm GMT
Please join: lnkd.in/eEKe4Z7H
November 13, 2025 at 12:32 PM
Very excited to host @efapostolou29.bsky.social for her talk on "Building, predicting and targeting 3D regulatory networks in development and cancer" in @enhancedgenomics.bsky.social's
seminar series "The 3D Regulatory Genome".
📅 13 November 2025 (today!)
⏰ 4 pm GMT
Please join: lnkd.in/eEKe4Z7H
seminar series "The 3D Regulatory Genome".
📅 13 November 2025 (today!)
⏰ 4 pm GMT
Please join: lnkd.in/eEKe4Z7H
Reposted by Stefan Schoenfelder
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A
Insertion of an invading retrovirus regulates a novel color trait in swordtail fish
For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable wi...
shorturl.at
November 12, 2025 at 8:34 PM
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A
Reposted by Stefan Schoenfelder
🌍Open call: Junior Group Leader positions!
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
November 10, 2025 at 1:26 PM
🌍Open call: Junior Group Leader positions!
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
Reposted by Stefan Schoenfelder
📣 Paper alert!
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
November 10, 2025 at 11:11 AM
📣 Paper alert!
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...