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
🧬 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/...
Reposted by Stefan Schoenfelder
In light of the recent news, I did a thread a couple of years ago about some #classicpaper in #molecularbiology
I kept a record if anyone is interested
⬇️
aninfinityofhypotheses.wordpress.com/2018/09/28/c...
I kept a record if anyone is interested
⬇️
aninfinityofhypotheses.wordpress.com/2018/09/28/c...
#Classicpaper
Recently I started a Twitter thread highlighting a couple of seminal discoveries in molecular biology going back in the 40’s 50’s #classicpaper. I received many positive feedback and the thread was…
aninfinityofhypotheses.wordpress.com
November 9, 2025 at 7:22 PM
In light of the recent news, I did a thread a couple of years ago about some #classicpaper in #molecularbiology
I kept a record if anyone is interested
⬇️
aninfinityofhypotheses.wordpress.com/2018/09/28/c...
I kept a record if anyone is interested
⬇️
aninfinityofhypotheses.wordpress.com/2018/09/28/c...
Reposted by Stefan Schoenfelder
🧬 Interested in dissecting dose-dependent transcriptional regulation through epigenome editing and synthetic biology for your PhD? Apply by 07.01.2026 to join the lab of @eddaschulz.bsky.social @molgen.mpg.de & #IMPRS-BAC #gradschool.
👉 www.molgen.mpg.de/5099133/schu...
👉 www.molgen.mpg.de/5099133/schu...
November 4, 2025 at 11:19 AM
🧬 Interested in dissecting dose-dependent transcriptional regulation through epigenome editing and synthetic biology for your PhD? Apply by 07.01.2026 to join the lab of @eddaschulz.bsky.social @molgen.mpg.de & #IMPRS-BAC #gradschool.
👉 www.molgen.mpg.de/5099133/schu...
👉 www.molgen.mpg.de/5099133/schu...
Reposted by Stefan Schoenfelder
To mark the death of James Watson, please read this 2023 piece about Rosalind Franklin's role in the discovery of the double helix
www.nature.com/articles/d41...
www.nature.com/articles/d41...
What Rosalind Franklin truly contributed to the discovery of DNA’s structure
Franklin was no victim in how the DNA double helix was solved. An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player.
www.nature.com
November 8, 2025 at 10:52 AM
To mark the death of James Watson, please read this 2023 piece about Rosalind Franklin's role in the discovery of the double helix
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted by Stefan Schoenfelder
tinyurl.com/GenGenFaculty
GenGen is hiring group leaders! If you want to generate data at scale to train the next generation of AI models to make molecular biology predictive and programmable, we want to hear from you.
GenGen is hiring group leaders! If you want to generate data at scale to train the next generation of AI models to make molecular biology predictive and programmable, we want to hear from you.
Group Leader - Generative Biology and AI
Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...
tinyurl.com
November 7, 2025 at 9:37 AM
tinyurl.com/GenGenFaculty
GenGen is hiring group leaders! If you want to generate data at scale to train the next generation of AI models to make molecular biology predictive and programmable, we want to hear from you.
GenGen is hiring group leaders! If you want to generate data at scale to train the next generation of AI models to make molecular biology predictive and programmable, we want to hear from you.
Reposted by Stefan Schoenfelder
𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n
Repair of DNA double-strand breaks leaves heritable impairment to genome function
Upon DNA breakage, a genomic locus undergoes alterations in three-dimensional chromatin architecture to facilitate signaling and repair. Although cells possess mechanisms to repair damaged DNA, it is ...
tinyurl.com
November 6, 2025 at 11:05 PM
𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n
Reposted by Stefan Schoenfelder
We recently reported that promoter competition can contribute to the robust insulation of gene regulatory domains (www.nature.com/articles/s41...).
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇
November 6, 2025 at 6:37 PM
We recently reported that promoter competition can contribute to the robust insulation of gene regulatory domains (www.nature.com/articles/s41...).
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇
Reposted by Stefan Schoenfelder
Lots of exciting PhD projects available through @swbiodtp.bsky.social
If you are interested in our project using stem cells, CRISPR and genomics, please get in touch. Informal inquiries encouraged
Project:
www.swbio.ac.uk/files/2025/1...
If you are interested in our project using stem cells, CRISPR and genomics, please get in touch. Informal inquiries encouraged
Project:
www.swbio.ac.uk/files/2025/1...
November 6, 2025 at 3:34 PM
Lots of exciting PhD projects available through @swbiodtp.bsky.social
If you are interested in our project using stem cells, CRISPR and genomics, please get in touch. Informal inquiries encouraged
Project:
www.swbio.ac.uk/files/2025/1...
If you are interested in our project using stem cells, CRISPR and genomics, please get in touch. Informal inquiries encouraged
Project:
www.swbio.ac.uk/files/2025/1...
Reposted by Stefan Schoenfelder
Please repost - Multiple PhDs available
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
November 5, 2025 at 9:18 AM
Please repost - Multiple PhDs available
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
Reposted by Stefan Schoenfelder
And we have another open position, this time with a focus on Genome Biology! Join a great community in Vienna to bring your research to the next level!
📢 Open Call! The Max Perutz Labs invite applications for a Tenure-Track Professorship in Genome Biology. We are particularly interested in researchers investigating the molecular and biophysical mechanisms underlying genome function and regulation. More details ➡️ tinyurl.com/3t7vvdct
November 6, 2025 at 4:35 AM
And we have another open position, this time with a focus on Genome Biology! Join a great community in Vienna to bring your research to the next level!
Reposted by Stefan Schoenfelder
Don't miss the chance to attend the annual virtual meeting on the advances in Nuclear Topology and 3D chromatin Architecture in Cancer organized by @janeskok @iannisaifantis1 @artsinyc and Melnick. The registration is FREE (see barcode) and the speaker lineup SPECTACULAR.
November 5, 2025 at 3:06 PM
Don't miss the chance to attend the annual virtual meeting on the advances in Nuclear Topology and 3D chromatin Architecture in Cancer organized by @janeskok @iannisaifantis1 @artsinyc and Melnick. The registration is FREE (see barcode) and the speaker lineup SPECTACULAR.
Reposted by Stefan Schoenfelder
New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome.
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
Generating long deletions across the genome with pooled paired prime editing screens
Engineered deletions are a powerful probe for studying genome architecture, function, and regulation. Yet, the lack of effective methods to create them in large numbers and at multi-kilobase scale has...
biorxiv.org
November 5, 2025 at 2:17 PM
New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome.
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
Reposted by Stefan Schoenfelder
🚀 𝗣𝗼𝘀𝘁𝗱𝗼𝗰 𝗢𝗽𝗲𝗻𝗶𝗻𝗴
We’re recruiting an ERC-funded Postdoctoral Researcher to explore how 3D gene regulatory networks evolved during human and primate brain development, using cutting-edge single-cell multiomics, organoid models, and CRISPR screens.
👉 Apply by Nov 30 | www.bonevlab.com/join
We’re recruiting an ERC-funded Postdoctoral Researcher to explore how 3D gene regulatory networks evolved during human and primate brain development, using cutting-edge single-cell multiomics, organoid models, and CRISPR screens.
👉 Apply by Nov 30 | www.bonevlab.com/join
November 5, 2025 at 2:03 PM
🚀 𝗣𝗼𝘀𝘁𝗱𝗼𝗰 𝗢𝗽𝗲𝗻𝗶𝗻𝗴
We’re recruiting an ERC-funded Postdoctoral Researcher to explore how 3D gene regulatory networks evolved during human and primate brain development, using cutting-edge single-cell multiomics, organoid models, and CRISPR screens.
👉 Apply by Nov 30 | www.bonevlab.com/join
We’re recruiting an ERC-funded Postdoctoral Researcher to explore how 3D gene regulatory networks evolved during human and primate brain development, using cutting-edge single-cell multiomics, organoid models, and CRISPR screens.
👉 Apply by Nov 30 | www.bonevlab.com/join
Reposted by Stefan Schoenfelder
Our latest paper on comparative analysis of HiChIP data is now online! HiChIP is one of the most useful/practical assays to profile 3D genome organization and chromatin loops but has its challenges in the data analysis especially when it comes to comparative analysis.
November 4, 2025 at 10:58 PM
Our latest paper on comparative analysis of HiChIP data is now online! HiChIP is one of the most useful/practical assays to profile 3D genome organization and chromatin loops but has its challenges in the data analysis especially when it comes to comparative analysis.
Reposted by Stefan Schoenfelder
Our source code, utility scripts and links to processed data and results are all available on our lab's GitHub: lnkd.in/g7EdGYuu
Hope you enjoy reading it and reach out if you have any questions or feedback!
Big thanks to Cell Reports Methods and their editorial team for the efficient review
Hope you enjoy reading it and reach out if you have any questions or feedback!
Big thanks to Cell Reports Methods and their editorial team for the efficient review
November 4, 2025 at 10:58 PM
Our source code, utility scripts and links to processed data and results are all available on our lab's GitHub: lnkd.in/g7EdGYuu
Hope you enjoy reading it and reach out if you have any questions or feedback!
Big thanks to Cell Reports Methods and their editorial team for the efficient review
Hope you enjoy reading it and reach out if you have any questions or feedback!
Big thanks to Cell Reports Methods and their editorial team for the efficient review
Reposted by Stefan Schoenfelder
Europe's MSCA postdoctoral fellowships are now attracting many researchers who would have gone to the US. So the payline has dropped below 10% (~1,600 fellowships to 17k applicants). Super tough situation. One more reason to double the next Horizon budget, as proposed by the EU Commission.
Applications for MCSA are up 64%! 50% now come from outside the EU. Trump effect?
The European Research market just got a hell of a lot more crowded.
EU should turn on the tap
marie-sklodowska-curie-actions.ec.europa.eu/news/msca-po...
The European Research market just got a hell of a lot more crowded.
EU should turn on the tap
marie-sklodowska-curie-actions.ec.europa.eu/news/msca-po...
MSCA Postdoctoral Fellowships 2025 receives record number of 17,058 proposals
This year’s annual MSCA Postdoctoral Fellowships call has attracted considerable interest from the research community with 17,058 proposals submitted.
marie-sklodowska-curie-actions.ec.europa.eu
November 3, 2025 at 8:24 AM
Europe's MSCA postdoctoral fellowships are now attracting many researchers who would have gone to the US. So the payline has dropped below 10% (~1,600 fellowships to 17k applicants). Super tough situation. One more reason to double the next Horizon budget, as proposed by the EU Commission.
Reposted by Stefan Schoenfelder
Paul Nurse describing the main job of a PI
(From ‘The Thinking Game’, 2024)
(From ‘The Thinking Game’, 2024)
October 31, 2025 at 8:45 AM
Paul Nurse describing the main job of a PI
(From ‘The Thinking Game’, 2024)
(From ‘The Thinking Game’, 2024)
🚨 Exciting conference for stem cell aficionados!
‘Frontiers in Stem Cell Innovation’ will bring together experts in stem cell biology from academia & industry to discuss key developments as well as challenges in regenerative medicine and disease modelling.
fisci2026.eventbrite.co.uk
Please repost 🙏
‘Frontiers in Stem Cell Innovation’ will bring together experts in stem cell biology from academia & industry to discuss key developments as well as challenges in regenerative medicine and disease modelling.
fisci2026.eventbrite.co.uk
Please repost 🙏
Frontiers in Stem Cell Innovation 2026
Join leading academics and industry professionals exploring cutting-edge stem cell technologies and disease modelling for drug discovery
FISCI2026.eventbrite.co.uk
November 1, 2025 at 8:56 PM
🚨 Exciting conference for stem cell aficionados!
‘Frontiers in Stem Cell Innovation’ will bring together experts in stem cell biology from academia & industry to discuss key developments as well as challenges in regenerative medicine and disease modelling.
fisci2026.eventbrite.co.uk
Please repost 🙏
‘Frontiers in Stem Cell Innovation’ will bring together experts in stem cell biology from academia & industry to discuss key developments as well as challenges in regenerative medicine and disease modelling.
fisci2026.eventbrite.co.uk
Please repost 🙏
Reposted by Stefan Schoenfelder
📢 Open Call! The Max Perutz Labs invite applications for a Full Professorship in Integrative Structure Biology with a focus on in situ structural biology using cryo-electron tomography (cryo-ET) and related methods. More details ➡️ tinyurl.com/brswbymu
October 31, 2025 at 9:25 AM
Reposted by Stefan Schoenfelder
This is such an interesting paper. Why? Because the binding of transcription factor (TF) proteins to DNA governs how our genes are turned on/off/up/down, & so is the primary issue for how our genes work in development and how our cells respond to just about anything.🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Multiple overlapping binding sites determine transcription factor occupancy - Nature
A new method enables comprehensive screening and identification of low-affinity DNA binding sites for transcription factors, and reveals that nucleotides flanking high-affinity binding sites create ov...
www.nature.com
October 30, 2025 at 11:04 PM
This is such an interesting paper. Why? Because the binding of transcription factor (TF) proteins to DNA governs how our genes are turned on/off/up/down, & so is the primary issue for how our genes work in development and how our cells respond to just about anything.🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...