Julien Gagneur

17 papers B 1Journal 14Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Flashzoi: an enhanced Borzoi for accelerated genomic analysis.
Bioinform.
Johannes Hingerl, Alexander Karollus, Julien Gagneur
2025 J jnl
PROTRIDER: protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder.
Bioinform.
Daniela Klaproth-Andrade, Ines F. Scheller, Georgios Tsitsiridis, Stefan Loipfinger, Christian Mertes, Dmitrii Smirnov, Holger Prokisch, Vicente A. Yépez, Julien Gagneur
2025 J jnl
Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data.
Bioinform.
Sarah Ouologuem, Laura D. Martens, Anna C. Schaar, Maiia Shulman, Julien Gagneur, Fabian J. Theis
2023 J jnl
The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data.
Bioinform.
Dennis Hecker, Fatemeh Behjati-Ardakani, Alexander Karollus, Julien Gagneur, Marcel H. Schulz
2021 J jnl
Predicting mean ribosome load for 5'UTR of any length using deep learning.
PLoS Comput. Biol.
Alexander Karollus, Ziga Avsec, Julien Gagneur
2018 J jnl
GenoGAM 2.0: scalable and efficient implementation of genome-wide generalized additive models for gigabase-scale genomes.
BMC Bioinform.
Georg Stricker, Mathilde Galinier, Julien Gagneur
2018 J jnl
Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks.
Bioinform.
Ziga Avsec, Mohammadamin Barekatain, Jun Cheng, Julien Gagneur
2017 — ch.
Bioinformatics Advances Biology and Medicine by Turning Big Data Troves into Knowledge.
50 Jahre Universitäts-Informatik in München
Julien Gagneur, Caroline C. Friedel, Volker Heun, Ralf Zimmer, Burkhard Rost
2017 J jnl
Bioinformatics advances biology and medicine by turning big data troves into knowledge.
Inform. Spektrum
Julien Gagneur, Caroline C. Friedel, Volker Heun, Ralf Zimmer, Burkhard Rost
2017 J jnl
GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis.
Bioinform.
Georg Stricker, Alexander Engelhardt, Daniel Schulz, Matthias Schmid, Achim Tresch, Julien Gagneur
2012 — conf
Trading Running Time for Memory in Phylogenetic Likelihood Computations.
BIOINFORMATICS
Fernando Izquierdo-Carrasco, Julien Gagneur, Alexandros Stamatakis
2011 J jnl
Model-based gene set analysis for Bioconductor.
Bioinform.
Sebastian Bauer, Peter N. Robinson, Julien Gagneur
2011 J jnl
Selective Phenotyping, Entropy Reduction and the Mastermind Game.
BMC Bioinform.
Julien Gagneur, Markus C. Elze, Achim Tresch
2008 J jnl
4D
Nucleic Acids Res.
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
2008 B conf
Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress.
APBC
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
2004 J jnl
Computation of elementary modes: a unifying framework and the new binary approach.
BMC Bioinform.
Julien Gagneur, Steffen Klamt
2003 J jnl
Hierarchical Analysis of Dependency in Metabolic Networks.
Bioinform.
Julien Gagneur, David B. Jackson, Georg Casari