Arnaud Krebs

Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq - Nature Genetics This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells.

🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China

Congratulations! nice to see this out!

We're growing the VIB.AI Machine Learning Unit, and we're hiring!

📌 Head of the Machine Learning Unit
📌 LLM Engineer

Both roles are based in Leuven, Belgium, at the heart of a thriving research ecosystem.
https://vib.ai/en/opportunities#/job-list
Apply by October 31st.

#Jobalert 🚨: Please RT !
Looking for a #PhD student for exciting project on the interphase between epigenetics and cellular metabolism:
How do (nuclear) metabolic enzymes reguate chromatin function ?
#epigenomics, #epigenetics, #metabolism
www.helmholtz-munich.de/en/ife/job-o...

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...

✨Exciting news: the main story of my PhD is out in Science!

Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.

📖 Read the full story here: www.science.org/doi/10.1126/...

Spectacular work Christine & co! Congrats! Happy to see this out.

Have you ever wondered how the exact location of a gene affects it's activity?

The main story of my PhD deals with exactly that question, and is now published in Science! ✨
www.science.org/doi/10.1126/...

My amazing co-author and friend @mathiaseder.bsky.social summarized the highlights for you

🤞

This feeling usually precedes an emergency call from the kita or school :)

Join EMBL AI!

We have ambitious plans to transform life sciences research through AI.

Interested in using ML/AI to solve complex interdisciplinary challenges?

We’re looking for two senior leaders based at EMBL Heidelberg👇

We're getting started in ~90 minutes!

In addition to watching the seminars, remember you can join us on Discord to chat about transcription and chromatin whenever you want! discord.com/invite/dXqT89r

FEBS Advanced Lecture Course: 6th Danube Conference on Epigenetics The FEBS Advanced Lecture Course: 6th Danube Conference on Epigenetics will take place 19–22 October 2026 in Budapest, Hungary. Here we give a taste of the scientific content, flag some of the speaker...

Do not forget to apply to the FEBS Advanced Lecture Course: 6th Danube Conference on Epigenetics (19–22 October 2026, Budapest, Hungary. Will be a great meeting as always. Check out the site: network.febs.org/posts/febs-a...

Check it out, Chromatin Kids!

Chromatin remodeller does stuff to Transcription Factors!

Functions where it is seldom seen!

Both decreases and increases chromatin accessibility!

How cool is that?

Excited to share another new preprint from our lab in which we developed a cluster-based phasing strategy using long read nano-NOMe-seq data to link distinct CTCF binding states—captured at the single molecule level—to the transcriptional status of genes: biorxiv.org/content/10.1...

Become our colleague at @fmiscience.bsky.social! The FMI is a very special place to start your lab: a vibrant international institute with world-class research groups and facilities, core funding, fantastic trainees, great colleagues😅, and a collegial culture. Get in touch if you're interested!

📢Last chance today! We are looking forward to receiving your applications👇!

Thanks Max

Thanks. Will check after holidays ;-).

Thanks!

Just brilliat work by Kasit and colleagues in @arnaudkr.bsky.social's group @embl.org. This is leveraging the "everyday" length of ONT (20KB) plus exogenous modification to sort out co-occupancy between enhancers and promoters (and inter-enhancer).

Huge thanks to the co-first author @kasitc.bsky.social Also thanks to Rene, Marc Jan, Karine, Kim, and especially @arnaudkr.bsky.social @embl.org @dfg.de.
Finally, Kasit will be presenting the story at the @cshlnews.bsky.social #cshlmoet next week! Please stop by if you are around!

This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇

Epigenome dynamics in early mammalian embryogenesis - Nature Reviews Genetics Upon fertilization and during early mammalian development, major changes in cellular plasticity occur. This is accompanied by large-scale epigenome remodelling, as has been recently highlighted by the...

Our featured article:
Epigenome dynamics in early mammalian embryogenesis by Adam Burton & Maria-Elena Torres-Padilla go.nature.com/45UA8Ob

🎉 Congrats to the poster prize winners at #EMBLSingleMolecule!

🏅 Adam Cawte, University of Oxford, UK
🏅 Masa Shimazoe, National Institute of Genetics, Japan

🧬 Explore their winning abstracts & posters in our latest blog post:

🔗 https://s.embl.org/grg25-01-posters

very cool! Congrats.

Registration is still open for Transcription and Chromatin UK 2025. Join our growing research community in Manchester this September!

Funny how many institutions that self-refer as “leading” have a wait-and-see approach to decision making…

Postdoctoral Research Fellowship in Chromatin Biology and Cancer Epigenetics (283381) | University of Oslo Job title: Postdoctoral Research Fellowship in Chromatin Biology and Cancer Epigenetics (283381), Employer: University of Oslo, Deadline: Wednesday, August 20, 2025

We are hiring! A 3-year postdoc in #Chromatin #Cancer #Epigenetics at University of Oslo, Norway and co-supervised by @amathelier.bsky.social You will be part of @cancelluio.bosky.social. We focus on #Sarcoma #Epigenome #CRISPR and Drug screen studies. Find out more and apply here: shorturl.at/DtLHM

Synthetic engineering demonstrates that synergy among enhancers involves an increase in transcriptionally productive enhancer-gene contacts Enhancers are non-coding cis-regulatory elements that control the expression of distally located genes in a tissue- and time-specific manner. Recent studies indicate that enhancers can differ in their...

Excited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression

www.biorxiv.org/content/10.1...

EMBL is back on hiring faculty! Check out the multiple open positions:

3 PIs- 2 in Heidelberg incl. our Molecular Systems Biology Unit, 1 in Grenoble
1 Head of Unit (Cell Biology & Biophysics, Heidelberg).

Closing deadlines in Sep!
+3 more positions to come out then, stay tuned...
@embl.org