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Schubeler Lab @schubelerlab.bsky.social · 20d

Congrats Francesca !

FMI science @fmiscience.bsky.social · 21d

This year’s Ed Fischer Prize goes to Francesca Masoni (@schubelerlab.bsky.social) for her PhD on chromatin organization—revealing how the ISWI chromatin remodeler subcomplex NURF positions nucleosomes to safeguard genomic boundaries & gene regulation. Read more at www.fmi.ch/news-events/...

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FMI science @fmiscience.bsky.social · Aug 28

Our Open Day for Novartis was a great success! 🎉 Many @novartis.bsky.social colleagues joined us today to explore our science, meet our researchers & enjoy food trucks. Huge thanks to all volunteers and everyone who stopped by — here’s to more connections and collaborations!

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Schubeler Lab @schubelerlab.bsky.social · Aug 27

Iconic!

FMI science @fmiscience.bsky.social · Aug 27

A little piece of our history has a new home! The iconic logo that graced the old FMI building on the Rosental campus is now in the lobby of our new home on the Novartis campus, just across the river in Basel. A symbol of our journey and memories 🫶🧬

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Alexandra Bendel @alexbendel.bsky.social · Aug 25

I am happy to finally share this preprint of my PhD project in @guillaumediss.bsky.social lab at the FMI in Basel.
We used ddPCA to map the genetic architecture of the entire human bZIP interaction network.

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

Thanks to all our co-authors for the great collaboration!

The genetic architecture of the human bZIP family

Generative biology holds the promise to transform our ability to design and understand living systems by creating novel proteins, pathways, and organisms with tailored functions that address challenge...

www.biorxiv.org

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Schubeler Lab @schubelerlab.bsky.social · Aug 26

We all look forward to the Batki lab at FMI !!!!

Julia Batki @juliabatki.bsky.social · Aug 25

I am excited to share that I will join the Friedrich Miescher Institute @fmiscience.bsky.social in Basel as a group leader, starting my lab in March 2026 🎉

We will explore cell fate regulation during organogenesis, with a focus on how cell elimination underlies the emergence of functional tissues.

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Schubeler Lab @schubelerlab.bsky.social · Aug 12

Using this definition leads to the observed continuum of chromatin sensitivities across TFs.
Thanks to all authors and all the helpful input from lab members and members of the computational biology platform. Looking forward to feedback.

Schubeler Lab @schubelerlab.bsky.social · Aug 12

The framework quantifies chromatin sensitivity as the degree to which binding is determined by the motif sequence, i.e. the motif affinity, versus the flanking sequence around the motif, likely indicating the presence of additional motifs bound by other TFs.

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Schubeler Lab @schubelerlab.bsky.social · Aug 12

To circumvent this problem, we developed a deep-learning-based framework which assesses chromatin sensitivity via an evaluation of predicted binding at a balanced set of in silico sequence constructs.

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Schubeler Lab @schubelerlab.bsky.social · Aug 12

However, as we show, genomic motifs are biased in terms of their occurrence relative to chromatin features, making it difficult to quantitatively assess chromatin sensitivity from binding profiles at genomic motifs.

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Schubeler Lab @schubelerlab.bsky.social · Aug 12

We started by characterizing TF binding at genomic motifs and found a large variety in binding behaviours, indicating both differential sensitivity to chromatin for different TFs and a general dependence of chromatin sensitivity on motif affinity.

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Schubeler Lab @schubelerlab.bsky.social · Aug 12

Key finding is that chromatin sensitivity is not binary, but a continuum across TFs, clearly arguing against a purely hierarchical model involving chromatin-insensitive TFs (pioneers) that open the chromatin for other chromatin-sensitive TFs to bind.

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Schubeler Lab @schubelerlab.bsky.social · Aug 12

Excited to share our latest preprint. www.biorxiv.org/content/10.1.... Lead by Lukas, we investigated multiple ways of assessing a TF's sensitivity to chromatin based on genome-wide binding profiles. The developed methods allowed us to quantify chromatin sensitivity across tested TFs.

A novel deep learning-based framework reveals a continuum of chromatin sensitivities across transcription factors

The genome-wide binding of many transcription factors (TFs) depends not only on the presence of their recognition motifs, but also on the surrounding chromatin context. This raises the question of how...

www.biorxiv.org

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Schubeler Lab @schubelerlab.bsky.social · Aug 7

Demonstrates how a combination of opportunistic binding and context-specific chromatin-opening underpin TF specificity, driving differentiation trajectories.

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Schubeler Lab @schubelerlab.bsky.social · Aug 7

Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....

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Schubeler Lab @schubelerlab.bsky.social · Dec 16

Great colleagues in a vibrant and supportive community. We are looking forward to your application !!!

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FMI science @fmiscience.bsky.social · Dec 10

What a night! The FMI year-end party had it all: an inspiring speech from our director, a delicious dinner buffet, a hilarious meme contest, and our traditional cake showdown. Here's to a fantastic 2025 ahead! 🥂🎉

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Schubeler Lab @schubelerlab.bsky.social · Dec 4

congrats Pia. Well deserved

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