Research Group Julien Gagneur
Julien Gagneur
Prof. Dr.
Principal Investigator
Julien Gagneur
is Assistant Professor for Computational Biology at TU Munich.
His research focuses on delineating the genetic basis of gene regulation and its implication in diseases. To this end, he is developing statistical and machine learning algorithms and works with experimentalists to design novel experimental approaches. His group is also developing strategies to pinpoint the cause of genetic disorders by integrating data from genetics and ‘multiomics’ disciplines such as transcriptomics and proteomics.
Team members @MCML
PhD Students
Pedro Tomaz da Silva
→ Group Julien Gagneur
Computational Molecular Medicine
Johannes Hingerl
→ Group Julien Gagneur
Computational Molecular Medicine
Tilman Hoffbauer
→ Group Julien Gagneur
Computational Molecular Medicine
Alexander Karollus
→ Group Julien Gagneur
Computational Molecular Medicine
Recent News @MCML
Publications @MCML
2025
Nucleotide dependency analysis of genomic language models detects functional elements.
Nature Genetics 57. Oct. 2025. DOI
scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.
Nature Methods. Oct. 2025. DOI
Flashzoi: An enhanced Borzoi for accelerated genomic analysis.
Bioinformatics 41.9. Sep. 2025. DOI
Altered translation elongation contributes to key hallmarks of aging in the killifish brain.
Science 389.6759. Jul. 2025. DOI
Nucleotide dependency analysis of DNA language models reveals genomic functional elements.
CSHL 2025 - 5th Cold Spring Harbor conference on Probabilistic Modeling in Genomics. Cold Spring Harbor Laboratory, New York, USA, Mar 05-08, 2025. DOI URL
2024
Flashzoi: An enhanced Borzoi model for accelerated genomic analysis.
Preprint (Dec. 2024). DOI
Integration of variant annotations using deep set networks boosts rare variant association testing.
Nature Genetics 56. Sep. 2024. DOI
Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain.
Preprint (Jan. 2024). DOI
2023
Evaluation of input data modality choices on functional gene embeddings.
NAR Genomics and Bioinformatics 5.4. Dec. 2023. DOI
Species-aware DNA language models capture regulatory elements and their evolution.
Genome Biology 35.83. Apr. 2023. DOI
Cellular energy regulates mRNA translation and degradation in a codon-specific manner.
Preprint (Apr. 2023). DOI
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