Julien Gagneur

发表

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

Georg Stricker, Mathilde Galinier, Julien Gagneur, 2018, BMC Bioinformatics.

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

Georg Stricker, Mathilde Galinier, Julien Gagneur, 2018 .

Genome-wide generalized additive models

Achim Tresch, Matthias Schmid, Daniel Schulz, 2016 .

Selective Phenotyping, Entropy Reduction, and the Mastermind game

Achim Tresch, Julien Gagneur, Markus C. Elze, 2011, BMC Bioinformatics.

Trading Running Time for Memory in Phylogenetic Likelihood Computations

Alexandros Stamatakis, Julien Gagneur, Fernando Izquierdo-Carrasco, 2012, BIOINFORMATICS.

Base-resolution models of transcription factor binding reveal soft motif syntax

Avanti Shrikumar, Anshul Kundaje, Julien Gagneur, 2019, Nature Genetics.

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

Steffen Klamt, Julien Gagneur, J. Gagneur, 2004, BMC Bioinformatics.

Bioinformatics advances biology and medicine by turning big data troves into knowledge

Volker Heun, Burkhard Rost, Caroline C. Friedel, 2017, Informatik-Spektrum.

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

Jun Cheng, Julien Gagneur, Mohammadamin Barekatain, 2017, bioRxiv.

Combining brain imaging and genetic data using fast and efficient multivariate correlation analysis

Peter F. Stadler, Julien Gagneur, Claudia Grellmann, 2017 .

The genomic STate ANnotation package

Achim Tresch, Julien Gagneur, Benedikt Zacher, 2016 .

GenoGAM: Genome-wide generalized additive models for ChIP-seq analysis

Achim Tresch, Matthias Schmid, Daniel Schulz, 2016, bioRxiv.

Model-based gene set analysis for Bioconductor

Sebastian Bauer, Peter N. Robinson, Julien Gagneur, 2011, Bioinform..

Hierarchical Analysis of Dependency in Metabolic Networks

Julien Gagneur, Georg Casari, David B. Jackson, 2003, Bioinform..

GenoGAM: Genome-wide generalized additive models for ChIP-seq analysis

Achim Tresch, Matthias Schmid, Georg Stricker, 2017 .

4DXpress: a database for cross-species expression pattern comparisons

Thorsten Henrich, Joachim Wittbrodt, Peer Bork, 2007, Nucleic Acids Res..

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

Julien Gagneur, Žiga Avsec, Alexander Karollus, 2020, bioRxiv.

Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress

Xi Wang, Thorsten Henrich, Joachim Wittbrodt, 2008, APBC.

A physical and functional map of the human TNF-α/NF-κB signal transduction pathway

Giulio Superti-Furga, Bernhard Kuster, Julien Gagneur, 2004, Nature Cell Biology.

Dynamic regulation by polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila.

Julien Gagneur, Charles Girardot, Eileen E M Furlong, 2008, Developmental cell.

Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in Infancy

Thomas Meitinger, Julien Gagneur, Holger Prokisch, 2015, American journal of human genetics.

An Evaluation of High-Throughput Approaches to QTL Mapping in Saccharomyces cerevisiae

David J. Galas, Nikita A. Sakhanenko, Simon Anders, 2013, Genetics.

Modular decomposition of protein-protein interaction networks

Julien Gagneur, Georg Casari, Roland Krause, 2004, Genome Biology.

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

Achim Tresch, Julien Gagneur, Benedikt Zacher, 2014, Molecular systems biology.

STrand-specific ANnotation of genomic data

Achim Tresch, Julien Gagneur, J. Gagneur, 2014 .

Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis

Daniel Schulz, Julien Gagneur, Patrick Cramer, 2013, Cell.

Temporal Expression Profiling Identifies Pathways Mediating Effect of Causal Variant on Phenotype

Himanshu Sinha, Julien Gagneur, Saumya Gupta, 2015, PLoS genetics.

Genetic diagnosis of Mendelian disorders via RNA sequencing

Thomas Meitinger, Gabi Kastenmüller, Jerzy Adamski, 2017, Nature Communications.

Antisense expression increases gene expression variability and locus interdependency

Wolfgang Huber, Lars M Steinmetz, Julien Gagneur, 2011, Molecular systems biology.

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

Achim Tresch, Julien Gagneur, Don Poron, 2015, Nucleic acids research.

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

Alexander Sczyrba, Andreas Keller, Christian Drosten, 2020, Cell.

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

Julien Gagneur, J. Gagneur, Leonhard Wachutka, 2016, Transcription.

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

Mathias Wilhelm, Thomas A. Hopf, Mathias Uhlen, 2018, bioRxiv.

Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

Julien Gagneur, Patrick Cramer, Mariana Boroni, 2015, bioRxiv.

Genotype-Environment Interactions Reveal Causal Pathways That Mediate Genetic Effects on Phenotype

Julien Gagneur, Dana Pe'er, Oliver Stegle, 2013, PLoS genetics.

Meiotic Interactors of a Mitotic Gene TAO3 Revealed by Functional Analysis of its Rare Variant

Himanshu Sinha, Lars M Steinmetz, Julien Gagneur, 2016, G3: Genes, Genomes, Genetics.

Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle

Peer Bork, Lars M Steinmetz, Lars J Jensen, 2006, PLoS genetics.