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

af Gagneur, Julien, Klamt, Steffen
Udgivet 2004

Measures of RNA metabolism rates: Toward a definition at the level of single bonds

af Wachutka, Leonhard, Gagneur, Julien
Udgivet i Transcription (2016)

GenoGAM 2.0: scalable and efficient implementation of genome-wide generalized additive models for gigabase-scale genomes

af Stricker, Georg, Galinier, Mathilde, Gagneur, Julien
Udgivet i BMC Bioinformatics (2018)

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

af Karollus, Alexander, Avsec, Žiga, Gagneur, Julien
Udgivet i PLoS Comput Biol (2021)

Identification of mitochondrial disease genes through integrative analysis of multiple datasets

af Aiyar, Raeka S., Gagneur, Julien, Steinmetz, Lars M.
Udgivet 2008

GOing Bayesian: model-based gene set analysis of genome-scale data

af Bauer, Sebastian, Gagneur, Julien, Robinson, Peter N.
Udgivet 2010

Model-based gene set analysis for Bioconductor

af Bauer, Sebastian, Robinson, Peter N., Gagneur, Julien
Udgivet 2011

Selective Phenotyping, Entropy Reduction, and the Mastermind game

af Gagneur, Julien, Elze, Markus C, Tresch, Achim
Udgivet 2011

Modular decomposition of protein-protein interaction networks

af Gagneur, Julien, Krause, Roland, Bouwmeester, Tewis, Casari, Georg
Udgivet 2004

Caenorhabditis elegans CES-1 Snail Represses pig-1 MELK Expression To Control Asymmetric Cell Division

af Wei, Hai, Yan, Bo, Gagneur, Julien, Conradt, Barbara
Udgivet i Genetics (2017)

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

af Avsec, Žiga, Barekatain, Mohammadamin, Cheng, Jun, Gagneur, Julien
Udgivet i Bioinformatics (2018)

Global donor and acceptor splicing site kinetics in human cells

af Wachutka, Leonhard, Caizzi, Livia, Gagneur, Julien, Cramer, Patrick
Udgivet i eLife (2019)

MTSplice predicts effects of genetic variants on tissue-specific splicing

af Cheng, Jun, Çelik, Muhammed Hasan, Kundaje, Anshul, Gagneur, Julien
Udgivet i Genome Biol (2021)

Publisher Correction: MTSplice predicts effects of genetic variants on tissue-specific splicing

af Cheng, Jun, Çelik, Muhammed Hasan, Kundaje, Anshul, Gagneur, Julien
Udgivet i Genome Biol (2021)

Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle

af Zacher, Benedikt, Lidschreiber, Michael, Cramer, Patrick, Gagneur, Julien, Tresch, Achim
Udgivet i Mol Syst Biol (2014)

Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast

af Cheng, Jun, Maier, Kerstin C., Avsec, Žiga, Rus, Petra, Gagneur, Julien
Udgivet i RNA (2017)

Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model

af Glas, Julia, Dümcke, Sebastian, Zacher, Benedikt, Poron, Don, Gagneur, Julien, Tresch, Achim
Udgivet i Nucleic Acids Res (2016)

Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN

af Zacher, Benedikt, Michel, Margaux, Schwalb, Björn, Cramer, Patrick, Tresch, Achim, Gagneur, Julien
Udgivet i PLoS One (2017)

CAGI5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice

af Cheng, Jun, Çelik, Muhammed Hasan, Nguyen, Yen Duong, Avsec, Žiga, Gagneur, Julien
Udgivet i Hum Mutat (2019)

Genome-wide allele- and strand-specific expression profiling

af Gagneur, Julien, Sinha, Himanshu, Perocchi, Fabiana, Bourgon, Richard, Huber, Wolfgang, Steinmetz, Lars M
Udgivet 2009