Julien Gagneur | Helmholtz Munich

Portrait of Prof. Dr. Julien Gagneur, Research Group Leader

Research Group Leader, Computational Health Center

julien.gagneur@helmholtz-munich.de

“We develop algorithms to interpret genomes for biology and medicine.”

I trained as an applied mathematician at École Centrale Paris and École Normale Supérieure de Cachan, graduating in 2000, and completed my PhD in 2004 through a collaboration between Cellzome in Heidelberg and École Centrale Paris. I then spent seven years as a staff scientist in the Genome Biology Unit at EMBL, where I developed a lasting taste for interdisciplinary science and a fascination with genetics and gene regulation. In 2012, I started my own research group at the Gene Center of LMU Munich, before joining the Technical University of Munich a few years later. Since 2020, I have held the Chair of Computational Molecular Medicine at TUM and also lead a research group at Helmholtz Munich in the Computational Health Center.

We work on deciphering genomes because causality is fundamental in biology and medicine: inherited genomic sequence can cause phenotypes, including disease, but cannot be their consequence. Our lab develops and adapts statistical learning methods, including AI, to address this challenge. We are particularly known for our contributions to sequence-to-function models, neural networks that take genomic sequence as input and predict molecular consequences, including which RNAs and proteins cells produce, when, where, and in what amounts.

I am proud that our research bridges fundamental biology and clinical application. It ranges from uncovering the genetic determinants of the kinetics of regulatory processes such as splicing to developing methods now used worldwide to analyse transcriptomes and proteomes in rare disease, helping clinicians establish genetic diagnoses and improving diagnostic yield by around 10%.

Sequence-to-Function Model

Regulatory Genomics

Rare Diseases

Human Genetics

Since 2020

2012

2005

2004

2024 - ERC recipient - ERC Synergy project EPIC

Qi, Q. ; Tomaz da Silva, P. ; Vangalis, V. ; Dockx, S. ; Steensels, J. ; Voordeckers, K. ; Gagneur, J. ; Verstrepen, K.J.

Intron location and sequence modulate gene expression in Yarrowia lipolytica.

Morsy, H. ; Kim, H. ; Jang, G. ; Zaki, M.S. ; Severino, M. ; Abdelrazek, I.M. ; Hussien, H. ; Self, E. ; Albaradie, R.S. ; Bakur, K. ; Firoozfar, Z. ; Efthymiou, S. ; Noureldeen, M.M. ; Nabil, A. ; Alvi, J.R. ; Molavi, F. ; Alavi, S. ; Alibakhshi, R. ; Topcu, V. ; Mancilar, H. ; Uctepe, E. ; Yesilyurt, A. ; Aldhalaan, H. ; Showki Tous, E.S. ; Alhaddad, B. ; Elbendary, H.M. ; Scardamaglia, A. ; Murphy, D. ; Yépez, V.A. ; Gagneur, J. ; Omar, T.I. ; Abd Elmaksoud, M. ; Vandrovocova, J. ; Abdalla, E. ; Reilly, M.M. ; Sultan, T. ; Alkuraya, F.S. ; Gleeson, J.G. ; Um, J.W. ; Houlden, H. ; Ko, J. ; Maarofian, R.

MDGA2 homozygous loss-of-function variants cause developmental and epileptic encephalopathy.

Yépez, V.A. ; Demidov, G. ; Ellwanger, K. ; Laurie, S. ; Luknárová, R. ; Joseph Maran, M.I. ; Hentrich, T. ; Sagath, L. ; van der Sanden, B. ; Astuti, G. ; Neveling, K. ; Batlle-Masó, L. ; Beijer, D. ; Brechtmann, F. ; Caballero-Oteyza, A. ; Dabad, M. ; Denommé-Pichon, A.S. ; Doornbos, C. ; Eddafir, Z. ; Estévez-Arias, B. ; Kilicarslan, O.A. ; Kolen, I.H.M. ; Krass, L. ; Lohmann, K. ; Londhe, S. ; López-Martín, E. ; Maassen, K. ; Macken, W. ; Martínez-Delgado, B. ; Mei, D. ; Mertes, C. ; Minardi, R. ; Morsy, H. ; Mueller, J.S. ; Natera-de Benito, D. ; Nelson, I. ; Oud, M.M. ; Paramonov, I. ; Picó, D. ; Piscia, D. ; Polavarapu, K. ; Raineri, E. ; Savarese, M. ; Smal, N. ; Steehouwer, M. ; Steyaert, W. ; Swertz, M.A. ; Thomsen, M. ; Töpf, A. ; Van de Vondel, L. ; van der Vries, G. ; Vitobello, A. ; Wilke, C. ; Zurek, B. ; T' Hoen, P.B. ; Matalonga, L. ; Vissers, L.E.L.M. ; Gilissen, C. ; Schulze-Hentrich, J. ; Beltran, S. ; Esteve-Codina, A. ; Hoischen, A. ; Gagneur, J. ; Graessner, H.

Author Correction: The Solve-RD Solvathons as a pan-European interdisciplinary collaboration to diagnose patients with rare disease.

Klaproth-Andrade, D. ; Bruns, Y. ; Gabriel, W. ; Nix, C. ; Bergant, V. ; Pichlmair, A. ; Wilhelm, M. ; Gagneur, J.

Modanovo: A unified model for post-translational modification-aware de novo sequencing using experimental spectra from in vivo and synthetic peptides.

Klaproth-Andrade, D. ; Scheller, I.F. ; Tsitsiridis, G. ; Liokatis, S. ; Mertes, C. ; Smirnov, D. ; Prokisch, H. ; Yépez, V.A. ; Gagneur, J.

PROTRIDER: Protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder.

Hingerl, J.C. ; Karollus, A. ; Gagneur, J.

Flashzoi: An enhanced Borzoi for accelerated genomic analysis.

Hingerl, J.C. ; Martens, L.D. ; Karollus, A. ; Manz, T. ; Buenrostro, J.D. ; Theis, F.J. ; Gagneur, J.

scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.

Li, J. ; Chu, B.B. ; Scheller, I. ; Gagneur, J. ; Maathuis, M.H.

Root cause discovery via permutations and Cholesky decomposition.

The Solve-RD Solvathons as a pan-European interdisciplinary collaboration to diagnose patients with rare disease.