Publications

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Selection of relevant publications from iMEAN members

Mathematical modelling

Intercellular cooperation in a fungal plant pathogen facilitates host colonization

Rémi Peyraud, Malick Mbengue, Adelin Barbacci, and Sylvain Raffaele
Proc Natl Acad Sci U S. 2019

# Spatiotemporal Plant Infection Modeling # Genome-Scale Network Modeling # Omics

Control of primary metabolism by a virulence regulatory network promotes robustness in a plant pathogen

Rémi Peyraud, Ludovic Cottret, Lucas Marmiesse, and Stéphane Genin
Nat Commun. 2018

# Genome-Scale Network Modeling # Plant Environment modeling # Omics # Evolution

A Resource Allocation Trade-Off between Virulence and Proliferation Drives Metabolic Versatility in the Plant Pathogen Ralstonia solanacearum

Rémi Peyraud, Ludovic Cottret, Lucas Marmiesse, Jérôme Gouzy, and Stéphane Genin
PLoS Pathog. 2016

# Genome-Scale Network Modeling # Omics # Flux Balance Analysis

A Resource Allocation Trade-Off between Virulence and Proliferation Drives Metabolic Versatility in the Plant Pathogen Ralstonia solanacearum

Rémi Peyraud, Ludovic Cottret, Lucas Marmiesse, Jérôme Gouzy, and Stéphane Genin
PLoS Pathog. 2016

# Genome-Scale Network Modeling # Omics # Flux Balance Analysis

Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1

Rémi Peyraud, Kathrin Schneider, Patrick Kiefer, Stéphane Massou, Julia A Vorholt, and Jean-Charles Portais
BMC Syst Biol. 2011

# Genome-Scale Network Modeling # Omics # Fluxomics

Bioinformatics tools

FlexFlux: combining metabolic flux and regulatory network analyses

Lucas Marmiesse, Rémi Peyraud, and Ludovic Cottret
BMC Syst Biol. 2015

# Genome-Scale Network Modeling # Software

Review

Advances on plant–pathogen interactions from molecular toward systems biology perspectives

Rémi Peyraud, Ullrich Dubiella, Adelin Barbacci, Stéphane Genin, Sylvain Raffaele and Dominique Roby
Plant J. 2017

# Plant microbes interaction modeling # Genome-Scale Network Modeling # Omics

Synthetic biology

Engineering Methylobacterium extorquensfor de novo synthesis of the sesquiterpenoid α-humulene from methanol

Frank Sonntag, Cora Kroner, Patrice Lubuta, Rémi Peyraud, Angelika Horst Markus Buchhaupt and Jens Schrader
Metab Eng. 2015

# Synthetic biology # Genome-Scale Network Modeling

Omics

Demonstration of the ethylmalonyl-CoA pathway by using 13C metabolomics.

Rémi Peyraud, Patrick Kiefer, Philipp Christen, Stephane Massou, Jean-Charles Portais, Julia A. Vorholt
Proc Natl Acad Sci U S A. 2009

# Omics # Fluxomics # Metabolic pathway modeling

Enhanced in planta Fitness through Adaptive Mutations in EfpR, a Dual Regulator of Virulence and Metabolic Functions in the Plant Pathogen Ralstonia solanacearum.

Anthony Perrier, Rémi Peyraud, David Rengel, Xavier Barlet, Emmanuel Lucasson, Jérôme Gouzy, Nemo Peeters, Stéphane Genin, Alice Guidot
PLoS Pathog. 2016

# Omics # Evolution

Genomics

Codon optimization underpins generalist parasitismn in fungi.

Thomas Badet, Remi Peyraud, Malick Mbengue, Olivier Navaud, Mark Derbyshire, Richard P Oliver, Adelin Barbacci, Sylvain Raffaele
Elife. 2017

# Genomics # Evolution # Cell Machinery Modeling

Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.

Vuilleumier S, Chistoserdova L, Lee MC, Bringel F, Lajus A, Zhou Y, Gourion B, Barbe V, Chang J, Cruveiller S, Dossat C, Gillett W, Gruffaz C, Haugen E, Hourcade E, Levy R, Mangenot S, Muller E, Nadalig T, Pagni M, Penny C, Peyraud R, Robinson DG, Roche D, Rouy Z, Saenampechek C, Salvignol G, Vallenet D, Wu Z, Marx CJ, Vorholt JA, Olson MV, Kaul R, Weissenbach J, Médigue C, Lidstrom ME.
PLoS One. 2009

# Genomics # Genome annotation

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