E. Bonnet

发表

Module Network Inference from a Cancer Gene Expression Data Set Identifies MicroRNA Regulated Modules

Y. van de Peer, E. Bonnet, M. Tatari, 2010, PloS one.

ROMA: Representation and Quantification of Module Activity from Target Expression Data

E. Barillot, E. Bonnet, L. Calzone, 2016, Front. Genet..

Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps

E. Barillot, E. Bonnet, L. Calzone, 2015, Oncogenesis.

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

Corinne Da Silva, Susana M. Coelho, J. Poulain, 2010, Nature.

zt: A Sofware Tool for Simple and Partial Mantel Tests

Yves Van de Peer, Eric Bonnet, Y. Peer, 2002 .

The genome of Tetranychus urticae reveals herbivorous pest adaptations

Stefan R. Henz, Richard M. Clark, Stephen D. Hudson, 2011, Nature.

Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes.

P. Rouzé, Y. van de Peer, E. Bonnet, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Generic eukaryotic core promoter prediction using structural features of DNA.

Yvan Saeys, Eric Bonnet, Thomas Abeel, 2008, Genome research.

Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples

C. Jubin, E. Bonnet, L. Mesrob, 2018, PloS one.

The small RNA world of plants.

P. Rouzé, Y. van de Peer, E. Bonnet, 2006, The New phytologist.

A Tandem Affinity Purification-based Technology Platform to Study the Cell Cycle Interactome in Arabidopsis thaliana*S

Eric Bonnet, Kris Laukens, Thomas De Vijlder, 2007, Molecular & Cellular Proteomics.

DEVEA: an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data

E. Bonnet, J. Deleuze, F. Pérez-Sanz, 2022, F1000Research.

[Biological network modelling and precision medicine in oncology].

E. Barillot, E. Bonnet, L. Calzone, 2014, Bulletin du Cancer.

Using convolutional neural networks for the classification of breast cancer images

E. Bonnet, 2021, 2108.13661.

Towards system level modeling of functional modules and regulatory pathways using genome-scale data

Y. Peer, E. Bonnet, A. Joshi, 2010 .

Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data

Yves Van de Peer, Tom Michoel, Eric Bonnet, 2010, Bioinform..

Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences

Yves Van de Peer, Pierre Rouzé, Eric Bonnet, 2004, Bioinform..

TAPIR, a web server for the prediction of plant microRNA targets, including target mimics

Yves Van de Peer, Ying He, Eric Bonnet, 2010, Bioinform..

Whole-Genome Bisulfite Sequencing for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution.

E. Bonnet, J. Deleuze, J. Tost, 2018, Methods in molecular biology.

Systematic analysis of TruSeq, SMARTer and SMARTer Ultra-Low RNA-seq kits for standard, low and ultra-low quantity samples

Robert Olaso, Cyril Dalmasso, Christophe Ambroise, 2019, Scientific Reports.

Conceptual and computational framework for logical modelling of biological networks deregulated in diseases

Andrei Zinovyev, Emmanuel Barillot, Arnau Montagud, 2019, Briefings Bioinform..

NaviCell Web Service for network-based data visualization

Inna Kuperstein, Emmanuel Barillot, Eric Bonnet, 2015, Nucleic Acids Res..

Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages

Andrei Zinovyev, Emmanuel Barillot, Eric Bonnet, 2016, The R Journal.

The Ectocarpus genome and brown algal genomics: the Ectocarpus Genome Consortium

Corinne Da Silva, Gildas Le Corguillé, Susana M. Coelho, 2012 .

Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development.

Anagha Joshi, Tom Michoel, Eric Bonnet, 2009, Molecular bioSystems.

Comprehensive analysis of RNA-seq kits for standard, low and ultra-low quantity samples

E. Bonnet, C. Ambroise, J. Deleuze, 2019, bioRxiv.

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Chris J. Myers, Carole Goble, Dagmar Waltemath, 2011, Standards in Genomic Sciences.

Scalable hardware accelerator for comparing DNA and protein sequences

Yvan Saeys, Yves Van de Peer, Dirk Stroobandt, 2006, InfoScale '06.

Reactive astrocytes promote proteostasis in Huntington’s disease through the JAK2-STAT3 pathway

M. Guillermier, F. Petit, G. Bonvento, 2021, bioRxiv.

RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis

Piotr Gawron, Anna Niarakis, Marek Ostaszewski, 2020, Database J. Biol. Databases Curation.

The JAK2-STAT3 pathway controls a beneficial proteostasis response of reactive astrocytes in Huntington’s disease

M. Guillermier, F. Petit, G. Bonvento, 2021 .

Methylated ccfDNA from plasma biomarkers of Alzheimer's disease using targeted bisulfite sequencing.

E. Bonnet, J. Deleuze, S. Brohard, 2022, Epigenomics.

Integrative Multi-omics Module Network Inference with Lemon-Tree

Tom Michoel, Eric Bonnet, Laurence Calzone, 2014, PLoS Comput. Biol..

Single cell transcriptome sequencing of stimulated and frozen human peripheral blood mononuclear cells

E. Bonnet, J. Deleuze, C. Derbois, 2023, Scientific data.

DEVEA: an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data.

E. Bonnet, J. Deleuze, F. Pérez-Sanz, 2022, F1000Research.

Learning Differential Module Networks Across Multiple Experimental Conditions.

Tom Michoel, Eric Bonnet, Pau Erola, 2017, Methods in molecular biology.

Validating module network learning algorithms using simulated data

Kathleen Marchal, Yvan Saeys, Koenraad Van Leemput, 2007, BMC Bioinformatics.

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats

Emmanuel Barillot, Eric Bonnet, Laurence Calzone, 2013, BMC Systems Biology.

Practical use of BiNoM: a biological network manager software.

Andrei Zinovyev, Emmanuel Barillot, Laurence Calzone, 2013, Methods in molecular biology.

Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Frank T. Bergmann, Lucian P. Smith, E. Bonnet, 2018, Standards in genomic sciences.

Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell R packages

Andrei Zinovyev, Emmanuel Barillot, Eric Bonnet, 2016, bioRxiv.

Validating module network learning algorithms using simulated data

Y. Saeys, Steven Maere, M. Kuiper, 2007, BMC Bioinformatics.

Validating module network learning algorithms using simulated data

Y. Saeys, Steven Maere, Y. Peer, 2007, BMC Bioinformatics.

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Frank T. Bergmann, Lucian P. Smith, E. Bonnet, 2011, Standards in Genomic Sciences.

OCSANA: optimal combinations of interventions from network analysis

E. Barillot, E. Bonnet, A. Zinovyev, 2013, Bioinform..