Hierarchical Analysis of Dependency in Metabolic Networks. - Julien Gagneur; David B. Jackson; Georg Casari (Bioinform., 2003)

Computation of elementary modes: a unifying framework and the new binary approach. - Julien Gagneur; Steffen Klamt (BMC Bioinform., 2004)

Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress. - Yannick Haudry; Chuang Kee Ong; Laurence Ettwiller; Hugo Bérubé; Ivica Letunic; Misha Kapushesky; Paul-Daniel Weeber; Xi Wang; Julien Gagneur; Charles Girardot; Detlev Arendt; Peer Bork; et al. (APBC, 2008)

4DXpress: a database for cross-species expression pattern comparisons. - Yannick Haudry; Hugo Bérubé; Ivica Letunic; Paul-Daniel Weeber; Julien Gagneur; Charles Girardot; Misha Kapushesky; Detlev Arendt; Peer Bork; Alvis Brazma; Eileen E. M. Furlong; Joachim Wittbrodt; et al. (Nucleic Acids Res., 2008)

Model-based gene set analysis for Bioconductor. - Sebastian Bauer 002; Peter N. Robinson; Julien Gagneur (Bioinform., 2011)

Selective Phenotyping, Entropy Reduction and the Mastermind Game. - Julien Gagneur; Markus C. Elze; Achim Tresch (BMC Bioinform., 2011)

Trading Running Time for Memory in Phylogenetic Likelihood Computations. - Fernando Izquierdo-Carrasco; Julien Gagneur; Alexandros Stamatakis (BIOINFORMATICS, 2012)

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)

GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis. - Georg Stricker; Alexander Engelhardt; Daniel Schulz; Matthias Schmid; Achim Tresch; Julien Gagneur (Bioinform., 2017)

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)

Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks. - Ziga Avsec; Mohammadamin Barekatain; Jun Cheng 007; Julien Gagneur (Bioinform., 2018)

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)

Predicting mean ribosome load for 5'UTR of any length using deep learning. - Alexander Karollus; Ziga Avsec; Julien Gagneur (PLoS Comput. Biol., 2021)

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)

Modeling fragment counts improves single-cell ATAC-seq analysis. - Laura D. Martens; David S. Fischer; Vicente A. Yépez; Fabian J. Theis; Julien Gagneur (Zenodo, 2023)