Teif lab
@teiflab.bsky.social
Teif lab at the University of Essex. We work on gene regulation in chromatin and applications to liquid biopsies, using approaches of genomics, biophysics, bioinformatics & AI. Our focus is nucleosomics, TF binding, CTCF, cfDNA. https://generegulation.org
Reposted by Teif lab
I'm guest-editing a collection on "Enhancer-promoter interactions" at Genome Biology. Please send us your exciting stories!
link.springer.com/collections/...
link.springer.com/collections/...
Enhancer-promoter interactions
Genome Biology is calling for submissions to our Collection on enhancer-promoter interactions.
Enhancer–promoter interactions are central to the regulation ...
link.springer.com
November 25, 2025 at 10:55 AM
I'm guest-editing a collection on "Enhancer-promoter interactions" at Genome Biology. Please send us your exciting stories!
link.springer.com/collections/...
link.springer.com/collections/...
Maansson et al., 2025. Liquid biopsy epigenetics: establishing a molecular profile based on cell-free DNA [review] febs.onlinelibrary.wiley.com/doi/full/10....
November 24, 2025 at 11:24 AM
Maansson et al., 2025. Liquid biopsy epigenetics: establishing a molecular profile based on cell-free DNA [review] febs.onlinelibrary.wiley.com/doi/full/10....
Some refs on nucleosome-mediated cooperativity in TF binding:
▶️Concept suggested by Polach & Widom, 1996: www.sciencedirect.com/science/arti...
▶️Our first single-bp resolution model, 2010: www.cell.com/biophysj/ful...
▶️Its application to TFs at enhancers, 2011: iopscience.iop.org/article/10.1...
▶️Concept suggested by Polach & Widom, 1996: www.sciencedirect.com/science/arti...
▶️Our first single-bp resolution model, 2010: www.cell.com/biophysj/ful...
▶️Its application to TFs at enhancers, 2011: iopscience.iop.org/article/10.1...
November 24, 2025 at 10:21 AM
Some refs on nucleosome-mediated cooperativity in TF binding:
▶️Concept suggested by Polach & Widom, 1996: www.sciencedirect.com/science/arti...
▶️Our first single-bp resolution model, 2010: www.cell.com/biophysj/ful...
▶️Its application to TFs at enhancers, 2011: iopscience.iop.org/article/10.1...
▶️Concept suggested by Polach & Widom, 1996: www.sciencedirect.com/science/arti...
▶️Our first single-bp resolution model, 2010: www.cell.com/biophysj/ful...
▶️Its application to TFs at enhancers, 2011: iopscience.iop.org/article/10.1...
Reposted by Teif lab
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!)
Circular DNA has a ticket to ride chromosomes www.nature.com/articles/d41...
Circular DNA has a ticket to ride chromosomes
How circular extrachromosomal DNA is inherited during cell division is a puzzle. Key sequences enabling this DNA to journey with chromosomes have been identified.
www.nature.com
November 23, 2025 at 4:36 PM
Circular DNA has a ticket to ride chromosomes www.nature.com/articles/d41...
A new £2.5 million Government-funded laboratory is set to open at the University of Essex to train workplace-ready scientists for the NHS and the life-sciences sector www.essex.ac.uk/news/2025/11...
Essex to train workplace-ready NHS scientists in new lab | University of Essex
www.essex.ac.uk
November 19, 2025 at 4:47 PM
A new £2.5 million Government-funded laboratory is set to open at the University of Essex to train workplace-ready scientists for the NHS and the life-sciences sector www.essex.ac.uk/news/2025/11...
Congratulations to Amishasingh Beeharry for successfully passing the MSD viva! You are the best, Amisha! Thank you very much to the examiners, Abdenour Soufi and Toni Marco!
November 18, 2025 at 4:20 PM
Congratulations to Amishasingh Beeharry for successfully passing the MSD viva! You are the best, Amisha! Thank you very much to the examiners, Abdenour Soufi and Toni Marco!
Reposted by Teif lab
Finally, we propose a model in which chromatin is self-organising based on histone acetylation and nucleosome depletion. We hypothesise that active cis-regulatory elements may contact one another at or above a layer of acetylated nucleosomes.
November 5, 2025 at 5:20 PM
Finally, we propose a model in which chromatin is self-organising based on histone acetylation and nucleosome depletion. We hypothesise that active cis-regulatory elements may contact one another at or above a layer of acetylated nucleosomes.
Reposted by Teif lab
Spread the word! There is a professor position opening at our University @upcite.bsky.social. There are several possible (great) labs to join, but if you are interested in DNA methylation and epigenetics in mammals, don't hesitate to contact me directly!
#JobOffer
💼 Un poste susceptible d’être vacant de Professeur en stabilité des génomes devrait s’ouvrir pour la rentrée 2026 au sein de l’Institut Jacques Monod
➡️ Informations concernant ce poste et la procédure de candidature 🔗 www.ijm.fr/poste-de-pro...
💼 Un poste susceptible d’être vacant de Professeur en stabilité des génomes devrait s’ouvrir pour la rentrée 2026 au sein de l’Institut Jacques Monod
➡️ Informations concernant ce poste et la procédure de candidature 🔗 www.ijm.fr/poste-de-pro...
October 28, 2025 at 1:51 PM
Spread the word! There is a professor position opening at our University @upcite.bsky.social. There are several possible (great) labs to join, but if you are interested in DNA methylation and epigenetics in mammals, don't hesitate to contact me directly!
Since 2020, we were running a practical introducing year 2 students to a hypothetical situation requiring to diagnose a patient placed in ICU based on real-time analysis of cfDNA. This new paper shows that it works in actual ICU at a bedside-relevant sequencing depth www.nature.com/articles/s41...
Nanopore sequencing enables tissue-of-origin and pathogen detection in plasma cell-free DNA from critically ill patients - Cell Death Discovery
Cell Death Discovery - Nanopore sequencing enables tissue-of-origin and pathogen detection in plasma cell-free DNA from critically ill patients
www.nature.com
October 27, 2025 at 9:29 AM
Since 2020, we were running a practical introducing year 2 students to a hypothetical situation requiring to diagnose a patient placed in ICU based on real-time analysis of cfDNA. This new paper shows that it works in actual ICU at a bedside-relevant sequencing depth www.nature.com/articles/s41...
Reposted by Teif lab
Do we need LLMs to predict epigenomes from DNA—or is biophysics enough? 🧬
IceQream (IQ) is a biophysics-based framework that predicts epigenomes with SOTA-level accuracy—and is fully explainable.
@NatureComms: www.nature.com/articles/s41...
Thread 🧵👇
1/
IceQream (IQ) is a biophysics-based framework that predicts epigenomes with SOTA-level accuracy—and is fully explainable.
@NatureComms: www.nature.com/articles/s41...
Thread 🧵👇
1/
October 17, 2025 at 8:31 AM
Do we need LLMs to predict epigenomes from DNA—or is biophysics enough? 🧬
IceQream (IQ) is a biophysics-based framework that predicts epigenomes with SOTA-level accuracy—and is fully explainable.
@NatureComms: www.nature.com/articles/s41...
Thread 🧵👇
1/
IceQream (IQ) is a biophysics-based framework that predicts epigenomes with SOTA-level accuracy—and is fully explainable.
@NatureComms: www.nature.com/articles/s41...
Thread 🧵👇
1/
Bercovich et al., 2025. IceQream: Quantitative chromosome accessibility analysis using physical TF models www.nature.com/articles/s41...
▶️spatially integrates sequences and localises them relative to the target locus
▶️infers effective TF concentrations
▶️supplements with pairwise TF interactions
▶️spatially integrates sequences and localises them relative to the target locus
▶️infers effective TF concentrations
▶️supplements with pairwise TF interactions
October 26, 2025 at 2:25 PM
Bercovich et al., 2025. IceQream: Quantitative chromosome accessibility analysis using physical TF models www.nature.com/articles/s41...
▶️spatially integrates sequences and localises them relative to the target locus
▶️infers effective TF concentrations
▶️supplements with pairwise TF interactions
▶️spatially integrates sequences and localises them relative to the target locus
▶️infers effective TF concentrations
▶️supplements with pairwise TF interactions
We lack clear guidelines for AI use by our students. My attempt:
Encouraged (when used responsibly):
✅Exploration, brainstorming and troubleshooting
✅Controlled software development and debugging
Discouraged (in most cases):
🚫Writing or "improving" academic texts
🚫Creating academic illustrations
Encouraged (when used responsibly):
✅Exploration, brainstorming and troubleshooting
✅Controlled software development and debugging
Discouraged (in most cases):
🚫Writing or "improving" academic texts
🚫Creating academic illustrations
October 26, 2025 at 10:41 AM
We lack clear guidelines for AI use by our students. My attempt:
Encouraged (when used responsibly):
✅Exploration, brainstorming and troubleshooting
✅Controlled software development and debugging
Discouraged (in most cases):
🚫Writing or "improving" academic texts
🚫Creating academic illustrations
Encouraged (when used responsibly):
✅Exploration, brainstorming and troubleshooting
✅Controlled software development and debugging
Discouraged (in most cases):
🚫Writing or "improving" academic texts
🚫Creating academic illustrations
Reposted by Teif lab
we are recruiting a postdoc with interest in using genomics and molecular biology to study transcription factors. We have an R35 to fund the project/salary.
October 15, 2025 at 4:00 PM
we are recruiting a postdoc with interest in using genomics and molecular biology to study transcription factors. We have an R35 to fund the project/salary.
Reposted by Teif lab
BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)
October 15, 2025 at 12:22 PM
BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)
Just received a notification that our university is renegotiating #openaccess agreements with the “big five” publishers (Springer, Elsevier, etc), and it is highly likely that we will lose some of these agreements. If we do, this will be a big problem since we do not have budgets to pay OA fees
October 15, 2025 at 8:48 AM
Just received a notification that our university is renegotiating #openaccess agreements with the “big five” publishers (Springer, Elsevier, etc), and it is highly likely that we will lose some of these agreements. If we do, this will be a big problem since we do not have budgets to pay OA fees
Reposted by Teif lab
Remember this paper "Low overlap
of transcription factor DNA binding and regulatory targets" ? (www.nature.com/articles/s41...)
well, well, well 🍿
⬇️
www.biorxiv.org/content/10.1...
of transcription factor DNA binding and regulatory targets" ? (www.nature.com/articles/s41...)
well, well, well 🍿
⬇️
www.biorxiv.org/content/10.1...
On the overlap of transcription factor binding and regulatory targets: functional and regulatory coherence of top-bound targets is masked by weakly bound ones
A recent study that systematically mapped genomic bindings and regulatory effects of transcription factors (TFs) reported a surprisingly low overlap between TF binding and regulatory targets in Saccha...
www.biorxiv.org
October 14, 2025 at 12:00 PM
Remember this paper "Low overlap
of transcription factor DNA binding and regulatory targets" ? (www.nature.com/articles/s41...)
well, well, well 🍿
⬇️
www.biorxiv.org/content/10.1...
of transcription factor DNA binding and regulatory targets" ? (www.nature.com/articles/s41...)
well, well, well 🍿
⬇️
www.biorxiv.org/content/10.1...
Reposted by Teif lab
Sequencing advice sought:
Anyone have any experience of Element AVITI sequencing for methylation profiling by WGBS or EM-sequencing?
Useful to know what other people's experience is as local facility have one and cheaper than Illumina for short read sequencing.
Please share 🙏
#epigenetics
Anyone have any experience of Element AVITI sequencing for methylation profiling by WGBS or EM-sequencing?
Useful to know what other people's experience is as local facility have one and cheaper than Illumina for short read sequencing.
Please share 🙏
#epigenetics
October 8, 2025 at 9:41 AM
Sequencing advice sought:
Anyone have any experience of Element AVITI sequencing for methylation profiling by WGBS or EM-sequencing?
Useful to know what other people's experience is as local facility have one and cheaper than Illumina for short read sequencing.
Please share 🙏
#epigenetics
Anyone have any experience of Element AVITI sequencing for methylation profiling by WGBS or EM-sequencing?
Useful to know what other people's experience is as local facility have one and cheaper than Illumina for short read sequencing.
Please share 🙏
#epigenetics
Reposted by Teif lab
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
October 7, 2025 at 3:24 PM
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
Interesting paper from Gernot Längst & Co. They calculated nucleosome repeat length in Plasmodium falciparum, the malaria-causing parasite, and showed that it follows a smooth continuous function of time (the numbers on the X axis below are hours post-invasion) www.biorxiv.org/content/10.1...
October 4, 2025 at 7:01 PM
Interesting paper from Gernot Längst & Co. They calculated nucleosome repeat length in Plasmodium falciparum, the malaria-causing parasite, and showed that it follows a smooth continuous function of time (the numbers on the X axis below are hours post-invasion) www.biorxiv.org/content/10.1...
Reposted by Teif lab
Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells.
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency
In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associate...
www.biorxiv.org
October 3, 2025 at 3:09 PM
Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells.
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
Polletti et al, 2025. Control of myeloid lineage fidelity and response to stimuli by ISWI-enforced nucleosome phasing www.cell.com/immunity/abs...
▶️PU.1 can form strongly phased nucleosome arrays similar to CTCF
▶️PU.1 can form strongly phased nucleosome arrays similar to CTCF
September 28, 2025 at 1:29 PM
Polletti et al, 2025. Control of myeloid lineage fidelity and response to stimuli by ISWI-enforced nucleosome phasing www.cell.com/immunity/abs...
▶️PU.1 can form strongly phased nucleosome arrays similar to CTCF
▶️PU.1 can form strongly phased nucleosome arrays similar to CTCF