Julien Gagneur

According to our database, Julien Gagneur authored at least 16 papers between 2003 and 2025.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2025

Flashzoi: an enhanced Borzoi for accelerated genomic analysis.

Johannes Hingerl, Alexander Karollus, Julien Gagneur

Bioinform., 2025

2023

Modeling fragment counts improves single-cell ATAC-seq analysis.

Laura D. Martens, David S. Fischer, Vicente A. Yépez, Fabian J. Theis, Julien Gagneur

Dataset, September, 2023

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., February, 2023

2021

Predicting mean ribosome load for 5'UTR of any length using deep learning.

Alexander Karollus, Ziga Avsec, Julien Gagneur

PLoS Comput. Biol., 2021

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

Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks.

Ziga Avsec, Mohammadamin Barekatain, Jun Cheng, Julien Gagneur

Bioinform., 2018

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

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

Proceedings of the 50 Jahre Universitäts-Informatik in München, 2017

2012

Trading Running Time for Memory in Phylogenetic Likelihood Computations.

Fernando Izquierdo-Carrasco, Julien Gagneur, Alexandros Stamatakis

Proceedings of the BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve, Portugal, 1, 2012

2011

Selective Phenotyping, Entropy Reduction and the Mastermind Game.

Julien Gagneur, Markus C. Elze, Achim Tresch

BMC Bioinform., 2011

Model-based gene set analysis for Bioconductor.

Sebastian Bauer, Peter N. Robinson, Julien Gagneur

Bioinform., 2011

2008

4D<i>Xpress</i>: 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, Thorsten Henrich

Nucleic Acids Res., 2008

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, Alvis Brazma, Eileen E. M. Furlong, Joachim Wittbrodt, Thorsten Henrich

Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

2004

Computation of elementary modes: a unifying framework and the new binary approach.

Julien Gagneur, Steffen Klamt

BMC Bioinform., 2004

2003

Hierarchical Analysis of Dependency in Metabolic Networks.

Julien Gagneur, David B. Jackson, Georg Casari

Bioinform., 2003