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Research Group Julien Gagneur

Link to website at TUM

Julien Gagneur

Prof. Dr.

Core PI

Computational Molecular Medicine

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

Link to website

Pedro Tomaz da Silva

→ Group Julien Gagneur
 Computational Molecular Medicine

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Johannes Hingerl

→ Group Julien Gagneur
 Computational Molecular Medicine

Link to website

Tilman Hoffbauer

→ Group Julien Gagneur
 Computational Molecular Medicine

Recent News @MCML

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Link to MCML Researchers in Highly-Ranked Journals

02.01.2025

MCML Researchers in Highly-Ranked Journals

164 Papers in 2025 Highlight Scientific Impact

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Link to Pedro Tomaz Da Silva Wins ISBM 2024 Best RegSys Poster Award

21.07.2024

Pedro Tomaz Da Silva Wins ISBM 2024 Best RegSys Poster Award

Our Junior Member Honored for Work on DNA Language Models

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Link to MCML Researchers in Highly-Ranked Journals

02.01.2024

MCML Researchers in Highly-Ranked Journals

96 Papers in 2024 Highlight Scientific Impact

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Link to ERC Synergy Grant for Julien Gagneur

26.10.2023

ERC Synergy Grant for Julien Gagneur

A Chatbot for Gene Regulation

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Publications @MCML

2025

[12] Top Journal
P. T. da Silva • A. Karollus • J. Hingerl • G. S. T. Galindez • N. Wagner • X. Hernandez-Alias • D. Incarnato • J. Gagneur
 Nucleotide dependency analysis of genomic language models detects functional elements.
Nature Genetics 57. Oct. 2025. DOI
[11] Top Journal
J. Hingerl • L. D. Martens • A. Karollus • T. Manz • J. D. Buenrostro • F. J. Theis • J. Gagneur
 scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.
Nature Methods. Oct. 2025. DOI
[10] Top Journal
J. Hingerl • A. Karollus • J. Gagneur
 Flashzoi: An enhanced Borzoi for accelerated genomic analysis.
Bioinformatics 41.9. Sep. 2025. DOI
[9]
B. Szathmári • B. Balint • B. Hegedüs • M. Viragh • Z. Hou • X.-B. Liu • H. Wu • C. Földi • J. Gagneur • J. Promeuschel • Á. Csernetics • L. Nagy
 Orthrus: a Pumilio-family gene involved in fruiting body and dark stipe development in Coprinopsis cinerea.
Frontiers in Fungal Biology 6. Jul. 2025. DOI
[8] Top Journal
D. Di Fraia • A. Marino • J. H. Lee • E. Kelmer Sacramento • M. Baumgart • S. Bagnoli • T. Balla • F. Schalk • S. Kamrad • R. Guan • C. Caterino • C. Giannuzzi • P. T. da Silva • A. K. Sahu • H. Gut • G. Siano • M.  • E. Terzibasi-Tozzini • E. F. Fornasiero • J. Gagneur • C. Englert • K. R. Patil • C. Correia-Melo • D. D. Nedialkova • J. Frydman • A. Cellerino • A. Ori
 Altered translation elongation contributes to key hallmarks of aging in the killifish brain.
Science 389.6759. Jul. 2025. DOI
[7]
P. T. da Silva • A. Karollus • J. Hingerl • G. Galindez • N. Wagner • X. Hernandez-Alias • D. Incarnato • J. Gagneur
 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

[6]
J. Hingerl • A. Karollus • J. Gagneur
 Flashzoi: An enhanced Borzoi model for accelerated genomic analysis.
Preprint (Dec. 2024). DOI
[5] Top Journal
B. Clarke • E. Holtkamp • H. Öztürk • M. Mück • M. Wahlberg • K. Meyer • F. Munzlinger • F. Brechtmann • F. R. Hölzlwimmer • J. Lindner • Z. Chen • J. Gagneur • O. Stegle
 Integration of variant annotations using deep set networks boosts rare variant association testing.
Nature Genetics 56. Sep. 2024. DOI
[4] Top Journal
A. Karollus • J. Hingerl • D. Gankin • M. Grosshauser • K. Klemon • J. Gagneur
 Species-aware DNA language models capture regulatory elements and their evolution.
Genome Biology 35.83. Apr. 2024. DOI
[3] Top Journal
P. T. da Silva • Y. Zhang • E. Theodorakis • L. D. Martens • V. A. Yépez • V. Pelechano • J. Gagneur
 Cellular energy regulates mRNA translation and degradation in a codon-specific manner.
Molecular Systems Biology 20.5. Mar. 2024. DOI
[2]
D. Di Fraia • A. Marino • J. H. Lee • E. Kelmer Sacramento • M. Baumgart • S. Bagnoli • P. T. da Silva • A. K. Sahu • G. Siano • M. Tiessen • E. Terzibasi-Tozzini • J. Gagneur • J. Frydman • A. Cellerino • A. Ori
 Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain.
Preprint (Jan. 2024). DOI

2023

[1]
F. Brechtmann • T. Bechtler • S. Londhe • C. Mertes • J. Gagneur
 Evaluation of input data modality choices on functional gene embeddings.
NAR Genomics and Bioinformatics 5.4. Dec. 2023. DOI

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2024-12-27 - Last modified: 2025-01-02