Lectures and seminars Seminar by Prof. Julien Gagneur, Technical University of Munich

Abstract:

I will present a series of recent sequence-based computational models of gene regulation. Reporting on our results on DNA language models, I will present Species-aware DNA language modeling, which learns from genomes of species at large phylogenetic distances capturing the evolution of the regulatory code [1], and nucleotide-dependency maps [2], a technique for interpretation of DNA language model which helps to reveal a broad spectrum of functional genomic elements from enhancer and promoter organization to RNA structures. Moving to supervised modeling, I will present scooby, a model predicting expression at single-cell resolution from half a megabase-scale sequence context [3]. Finally, with rare disease diagnostic applications in mind, I will present AbExp, a model predicting which rare variants cause extreme gene expression aberration across human tissues [4]. 

References:

1. Karollus, Hingerl, Gankin, et al. Species-aware DNA language models capture regulatory elements and their evolution. Genome Biology, 2024. https://doi.org/10.1186/s13059-024-03221-x
2. da Silva, Karollus et al. Nucleotide dependency analysis of DNA language models reveals genomic functional elements. bioRxiv, 2024. https://doi.org/10.1101/2024.07.27.605418
3. Martens, Hingerl, et al. in preparation
4. Hölzlwimmer, et al. Aberrant expression prediction across human tissues. bioRxiv, 2023. https://www.biorxiv.org/content/10.1101/2023.12.04.569414v1 

Biosketch and collaboration interests:

Julien Gagneur holds the chair of Computational Molecular Medicine at the Technical University of Munich. His research goal is an improved understanding of the genetic basis of gene regulation and its implication in diseases. He is known for his contributions to the development of machine learning models of the regulatory code (see talk abstract) and multi-omics approaches for the diagnostics of rare diseases (OUTRIDER, FRASER, DROP).

During his visit at SciLifeLab and the Karolinska Institute, Julien would enjoy meeting with bioinformatics colleagues but also potential wet lab collaborators, be on gene regulatory questions (human or multi-species, from transcription, splicing, all the way to protein abundance) or medical, especially rare diseases. 

Lab website: https://www.cs.cit.tum.de/cmm/home/
 

Host: Vicent Pelechano