Julien Gagneur

Joined

July 2019

Names

Julien Gagneur

Emails

****@tum.de (Confirmed)

Personal Links

Career & Education History

Principal Researcher

Computational Health Center, Helmholtz Zentrum München (helmholtz-munich.de)

2020 – 2025

Principal Researcher

School of CIT, Technical University of Munich (tum.de)

2020 – 2025

Advisors, Relations & Conflicts

PhD Advisee

Jun Cheng

2014 – 2018

PhD Advisor

Georg Casari

2000 – 2004

Expertise

Quantitative genetics

Computational Biology

2020 – 2025

Publications

Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing
Daniela Klaproth-Andrade, Johannes Hingerl, Yanik Bruns, Nicholas H. Smith, Jakob Träuble, Mathias Wilhelm, Julien Gagneur
- OpenReview Archive Direct Upload
- Readers: Everyone
Towards Open-Search De Novo Peptide Sequencing via Mass-Based Zero-Shot Learning
Christian Nix, Daniela Klaproth-Andrade, Yanik Bruns, Mathias Wilhelm, Julien Gagneur
- Submitted to NeurIPS 2025
- Readers: Everyone
The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data
Dennis Hecker, Fatemeh Behjati-Ardakani, Alexander Karollus, Julien Gagneur, Marcel H. Schulz
- Bioinform. 2023
- Readers: Everyone
Predicting mean ribosome load for 5'UTR of any length using deep learning
Alexander Karollus, Ziga Avsec, Julien Gagneur
- PLoS Comput. Biol. 2021
- Readers: Everyone
GenoGAM 2.0: scalable and efficient implementation of genome-wide generalized additive models for gigabase-scale genomes
Georg Stricker, Mathilde Galinier, Julien Gagneur
- BMC Bioinform. 2018
- Readers: Everyone
Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks
Ziga Avsec, Mohammadamin Barekatain, Jun Cheng, Julien Gagneur
- 2018 (modified: 15 May 2025)
- Bioinform. 2018
- Readers: Everyone
GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis
Georg Stricker, Alexander Engelhardt, Daniel Schulz, Matthias Schmid, Achim Tresch, Julien Gagneur
- Bioinform. 2017
- Readers: Everyone
Bioinformatics Advances Biology and Medicine by Turning Big Data Troves into Knowledge
Julien Gagneur, Caroline C. Friedel, Volker Heun, Ralf Zimmer, Burkhard Rost
- 50 Jahre Universitäts-Informatik in München 2017
- Readers: Everyone
Bioinformatics advances biology and medicine by turning big data troves into knowledge
Julien Gagneur, Caroline C. Friedel, Volker Heun, Ralf Zimmer, Burkhard Rost
- Inform. Spektrum 2017
- Readers: Everyone
Trading Running Time for Memory in Phylogenetic Likelihood Computations
Fernando Izquierdo-Carrasco, Julien Gagneur, Alexandros Stamatakis
- BIOINFORMATICS 2012
- Readers: Everyone

View all 16 publications

Co-Authors

View all 47 co-authors