Schubeler Lab

Congrats Francesca !

18.09.2025 11:32 — 👍 1    🔁 0    💬 0    📌 0

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!

28.08.2025 13:08 — 👍 7    🔁 2    💬 0    📌 0

Iconic!

27.08.2025 10:50 — 👍 4    🔁 0    💬 0    📌 0

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...

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!

25.08.2025 15:29 — 👍 32    🔁 13    💬 1    📌 2

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

26.08.2025 18:36 — 👍 2    🔁 0    💬 1    📌 0

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.

12.08.2025 08:32 — 👍 0    🔁 0    💬 0    📌 0

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.

12.08.2025 08:32 — 👍 0    🔁 0    💬 1    📌 0

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.

12.08.2025 08:32 — 👍 1    🔁 0    💬 1    📌 0

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.

12.08.2025 08:32 — 👍 0    🔁 0    💬 1    📌 0

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.

12.08.2025 08:32 — 👍 0    🔁 0    💬 1    📌 0

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.

12.08.2025 08:32 — 👍 2    🔁 0    💬 1    📌 0

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...

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.

12.08.2025 08:32 — 👍 43    🔁 12    💬 1    📌 0

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

07.08.2025 16:20 — 👍 7    🔁 0    💬 0    📌 0

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....

07.08.2025 16:20 — 👍 114    🔁 49    💬 2    📌 3

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

16.12.2024 13:09 — 👍 2    🔁 0    💬 0    📌 0

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! 🥂🎉

10.12.2024 17:05 — 👍 8    🔁 1    💬 0    📌 0

congrats Pia. Well deserved

04.12.2024 22:19 — 👍 1    🔁 0    💬 1    📌 0