Ludovic Cottret
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View article: Insights into the metabolic specificities of pathogenic strains from the <i>Ralstonia solanacearum</i> species complex
Insights into the metabolic specificities of pathogenic strains from the <i>Ralstonia solanacearum</i> species complex Open
All the strains grouped under the species Ralstonia solanacearum represent a species complex responsible for many diseases on agricultural crops throughout the world. The strains have different lifestyles and host range. Here, we investiga…
View article: Insights into the metabolic specificities of pathogenic strains from the<i>Ralstonia solanacearum species complex</i>
Insights into the metabolic specificities of pathogenic strains from the<i>Ralstonia solanacearum species complex</i> Open
All the strains grouped under the species Ralstonia solanacearum represent a species complex which collectively constitute a devastating plant pathogen responsible of many diseases on agricultural crops throughout the world. The strains ha…
View article: Rhizocarpon geographicum Lichen Discloses a Highly Diversified Microbiota Carrying Antibiotic Resistance and Persistent Organic Pollutant Tolerance
Rhizocarpon geographicum Lichen Discloses a Highly Diversified Microbiota Carrying Antibiotic Resistance and Persistent Organic Pollutant Tolerance Open
As rock inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently…
View article: MERRIN: MEtabolic regulation rule INference from time series data
MERRIN: MEtabolic regulation rule INference from time series data Open
Motivation Many techniques have been developed to infer Boolean regulations from a prior knowledge network (PKN) and experimental data. Existing methods are able to reverse-engineer Boolean regulations for transcriptional and signaling net…
View article: <scp> <i>Rhizobium leguminosarum</i> </scp> symbiovar <scp> <i>viciae</i> </scp> strains are natural wheat endophytes that can stimulate root development
<span> <i>Rhizobium leguminosarum</i> </span> symbiovar <span> <i>viciae</i> </span> strains are natural wheat endophytes that can stimulate root development Open
Although rhizobia that establish a nitrogen‐fixing symbiosis with legumes are also known to promote growth in non‐legumes, studies on rhizobial associations with wheat roots are scarce. We searched for Rhizobium leguminosarum symbiovar vic…
View article: <i>Rhizocarpon geographicum</i>lichen discloses a highly diversified microbiota carrying antibiotic resistance and Persistent Organic Pollutants tolerance
<i>Rhizocarpon geographicum</i>lichen discloses a highly diversified microbiota carrying antibiotic resistance and Persistent Organic Pollutants tolerance Open
As rock-inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently…
View article: An integrated approach reveals how lipo‐chitooligosaccharides interact with the lysin motif receptor‐like kinase <scp>MtLYR3</scp>
An integrated approach reveals how lipo‐chitooligosaccharides interact with the lysin motif receptor‐like kinase <span>MtLYR3</span> Open
N‐ acetylglucosamine containing compounds acting as pathogenic or symbiotic signals are perceived by plant‐specific Lysin Motif Receptor‐Like Kinases (LysM‐RLKs). The molecular mechanisms of this perception are not fully understood, notabl…
View article: MtEFD and MtEFD2: Two transcription factors with distinct neofunctionalization in symbiotic nodule development
MtEFD and MtEFD2: Two transcription factors with distinct neofunctionalization in symbiotic nodule development Open
Rhizobium–legume nitrogen-fixing symbiosis involves the formation of a specific organ, the root nodule, which provides bacteria with the proper cellular environment for atmospheric nitrogen fixation. Coordinated differentiation of plant an…
View article: A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations
A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations Open
Predicting and understanding plant responses to perturbations require integrating the interactions between nutritional sources, genes, cell metabolism, and physiology in the same model. This can be achieved using metabolic modeling calibra…
View article: A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations
A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations Open
Predicting and understanding plant responses to perturbations requires integrating the interactions between nutritional sources, genes, cell metabolism and physiology in the same model. This can be achieved using metabolic modeling calibra…
View article: MERRIN: MEtabolic Regulation Rule INference from time series data (Docker image and notebooks)
MERRIN: MEtabolic Regulation Rule INference from time series data (Docker image and notebooks) Open
This record contains notebooks and Docker image for reproducing the results of the paper "MERRIN: MEtabolic Regulation Rule INference from time series data" published as part of the ECCB 2022 conference. Notebooks can be executed interacti…
View article: MERRIN: MEtabolic Regulation Rule INference from time series data (Docker image and notebooks)
MERRIN: MEtabolic Regulation Rule INference from time series data (Docker image and notebooks) Open
This record contains notebooks and Docker image for reproducing the results of the paper "MERRIN: MEtabolic Regulation Rule INference from time series data" published as part of the ECCB 2022 conference. Notebooks can be executed interacti…
View article: Investigation of the metabolic network of Xylella fastidiosa responsible of its fastidious growth
Investigation of the metabolic network of Xylella fastidiosa responsible of its fastidious growth Open
High proliferation rate and robustness are vital characteristics of bacterial pathogens that successfully colonize their hosts. The observation of drastically slow growth in some pathogens is thus paradoxical and remains unexplained. In th…
View article: Multi-organ genome-scale metabolic modeling of tomato plant
Multi-organ genome-scale metabolic modeling of tomato plant Open
International audience
View article: Supplementary material for "Learning Boolean controls in regulated metabolic networks: a case-study"
Supplementary material for "Learning Boolean controls in regulated metabolic networks: a case-study" Open
This record contains notebooks and Docker image for reproducing the learning of Boolean controls in regulated metabolic networks, and the case study presented in the CMSB 2021 conference proceeding article "Learning Boolean controls in reg…
View article: Supplementary material for "Learning Boolean controls in regulated metabolic networks: a case-study"
Supplementary material for "Learning Boolean controls in regulated metabolic networks: a case-study" Open
This record contains notebooks and Docker image for reproducing the learning of Boolean controls in regulated metabolic networks, and the case study presented in the CMSB 2021 conference proceeding article "" Visualize notebooks online: Ca…
View article: Supplementary material for "Learning Boolean controls in regulated metabolic networks: a case-study"
Supplementary material for "Learning Boolean controls in regulated metabolic networks: a case-study" Open
This record contains notebooks and Docker image for reproducing the learning of Boolean controls in regulated metabolic networks, and the case study presented in the CMSB 2021 conference proceeding article "Learning Boolean controls in reg…
View article: EffectorK, a comprehensive resource to mine for <i>Ralstonia, Xanthomonas,</i> and other published effector interactors in the <i>Arabidopsis</i> proteome
EffectorK, a comprehensive resource to mine for <i>Ralstonia, Xanthomonas,</i> and other published effector interactors in the <i>Arabidopsis</i> proteome Open
Pathogens deploy effector proteins that interact with host proteins to manipulate the host physiology to the pathogen's own benefit. However, effectors can also be recognized by host immune proteins, leading to the activation of defence re…
View article: <i>Rhizobium leguminosarum</i>symbiovar<i>viciae</i>strains are natural wheat endophytes and can stimulate root development and colonization by arbuscular mycorrhizal fungi
<i>Rhizobium leguminosarum</i>symbiovar<i>viciae</i>strains are natural wheat endophytes and can stimulate root development and colonization by arbuscular mycorrhizal fungi Open
Summary Although rhizobia establishing a nitrogen-fixing symbiosis with legumes are also known to promote growth in non-legumes, studies on rhizobia association with wheat roots are scarce. We searched for Rhizobium leguminosarum symbiovar…
View article: Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth
Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth Open
Xylella fastidiosa is one of the most important threats to plant health worldwide, causing disease in the Americas on a range of agricultural crops and trees, and recently associated with a critical epidemic affecting olive trees in Europe…
View article: EffectorK, a comprehensive resource to mine for pathogen effector targets in the Arabidopsis proteome
EffectorK, a comprehensive resource to mine for pathogen effector targets in the Arabidopsis proteome Open
Pathogens deploy effector proteins that interact with host proteins to manipulate the host physiology to the pathogen’s own benefit. However, effectors can also be recognized by host immune proteins leading to the activation of defense res…
View article: Genome-scale investigation of the metabolic determinants generating bacterial fastidious growth
Genome-scale investigation of the metabolic determinants generating bacterial fastidious growth Open
International audience
View article: An ancestral signalling pathway is conserved in plant lineages forming intracellular symbioses
An ancestral signalling pathway is conserved in plant lineages forming intracellular symbioses Open
Plants are the foundation of terrestrial ecosystems and their colonization of land was facilitated by mutualistic associations with arbuscular mycorrhizal fungi. Following that founding event, plant diversification has led to the emergence…
View article: Exploration of the growth-virulence trade-off in the plant pathogen Ralstonia solanacearum species complex
Exploration of the growth-virulence trade-off in the plant pathogen Ralstonia solanacearum species complex Open
R. solanacearum is one of the most devastating plant pathogens for agriculture due to its aggressiveness, its wide host spectrum, its vast geographical distribution and its long persistence in the soil. In many countries it infects many im…
View article: Sunflower resistance to multiple downy mildew pathotypes revealed by recognition of conserved effectors of the oomycete <i>Plasmopara halstedii</i>
Sunflower resistance to multiple downy mildew pathotypes revealed by recognition of conserved effectors of the oomycete <i>Plasmopara halstedii</i> Open
Summary Over the last 40 years, new sunflower downy mildew isolates ( Plasmopara halstedii ) have overcome major gene resistances in sunflower, requiring the identification of additional and possibly more durable broad‐spectrum resistances…
View article: LysM Receptor-Like Kinase and LysM Receptor-Like Protein Families: An Update on Phylogeny and Functional Characterization
LysM Receptor-Like Kinase and LysM Receptor-Like Protein Families: An Update on Phylogeny and Functional Characterization Open
Members of plant specific families of receptor-like kinases (RLKs) and receptor-like proteins (RLPs), containing 3 extracellular LysMs have been shown to directly bind and/or to be involved in perception of lipo-chitooligosaccharides (LCO)…