Prof. Dr. Julien Gagneur
Academic Career and Research Areas
Professor Gagneur’s research focuses on computational models to interpret genomes. To this end, he is developing statistical and machine learning algorithms and works with experimentalists. He is known for the development of RNA-seq and proteomics-based diagnostics of rare diseases (collaboration with Holger Prokisch, TUM) and a range of methodologies and algorithms to model effects of genetic variants on gene expression and phenotypes, including diseases.
Julien Gagneur studied Applied Mathematics at École Centrale Paris and Machine Learning at the École Normale Supérieure de Cachan (France). He received his PhD in Applied Mathematics in 2004 from the École Centrale Paris (France) for his work performed in the Heidelberg-based biotech companies Lion Bioscience and Cellzome AG. Professor Gagneur then joined the Genome Biology department of European Molecular Biology Laboratory (EMBL) in Heidelberg. He assumed a group leader position at the Gene Center of the Ludwig-Maximilians-Universität in Munich in 2012. In 2016, he accepted an appointment as Assistant Professor for Computational Biology at the TUM. Since 2020, he is full professor and holds the chair of Computational Molecular Medicine at the School of CIT with a secondary affiliation at the School of Medicine and Health. He is recipient of an ERC Synergy (EPIC 2024-2031).
Key Publications (all publications)
Hingerl, Martens, et al. scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution. Nature Genetics (2025).
AbstractTomaz da Silva, Karollus, et al. Nucleotide dependency analysis of DNA language models reveals genomic functional elements. Nature Genetics (2025).
AbstractClarke, Holtkamp, et al. Integration of variant annotations using deep set networks boosts rare variant association genetics. Nature Genetics (2024).
AbstractWagner et al. Aberrant splicing prediction across human tissues. Nature Genetics (2023).
AbstractKremer, Bader, at al. Genetic diagnosis of Mendelian disorders via RNA sequencing, Nature communications (2017).
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