A5047919662- Gene expression and cancer classification
- Plant Molecular Biology Research
- Molecular Biology Techniques and Applications
- Bayesian Methods and Mixture Models
- Plant Disease Resistance and Genetics
- Plant nutrient uptake and metabolism
- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Plant Reproductive Biology
- Bioinformatics and Genomic Networks
- Photosynthetic Processes and Mechanisms
- Bioenergy crop production and management
- Genetic and phenotypic traits in livestock
- Legume Nitrogen Fixing Symbiosis
- Animal Genetics and Reproduction
- Chromosomal and Genetic Variations
- Plant Stress Responses and Tolerance
- Plant-Microbe Interactions and Immunity
- Plant Pathogens and Fungal Diseases
- Statistical Methods and Inference
- Advanced Clustering Algorithms Research
- Forest ecology and management
- Polysaccharides and Plant Cell Walls
- Developmental Biology and Gene Regulation
- Collagen: Extraction and Characterization
Université Paris-Saclay
2016-2025
Centre National de la Recherche Scientifique
2014-2025
Institut des Sciences des Plantes de Paris Saclay
2015-2025
Université Paris Cité
2016-2025
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
1997-2025
AgroParisTech
2012-2025
Département Mathématiques et Informatique Appliquées
2012-2024
Mathématiques et Informatique Appliquées
2012-2024
Université Claude Bernard Lyon 1
2009-2023
Université Paris-Sud
2007-2020
Abstract The complete sequence of the Arabidopsis thaliana genome revealed thousands previously unsuspected genes, many which cannot be ascribed even putative functions. One largest and most enigmatic gene families discovered in this way is characterized by tandem arrays pentatricopeptide repeats (PPRs). We describe a detailed bioinformatic analysis 441 members PPR family plus genomic genetic data on expression (microarray data), localization (green fluorescent protein red fusions), general...
TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1 (TFL2/LHP1) is the only Arabidopsis protein with overall sequence similarity to (HP1) family of metazoans and S. pombe. TFL2/LHP1 represses transcription numerous genes, including flowering-time genes FLOWERING LOCUS T (FT) C (FLC), as well floral organ identity AGAMOUS (AG) APETALA 3 (AP3). These are also regulated by proteins Polycomb repressive complex 2 (PRC2), it has been proposed that represents a potential stabilizing factor PRC2...
The conserved Target of Rapamycin (TOR) kinase forms high molecular mass complexes and is a major regulator cellular adaptations to environmental cues. Lethal with Sec Thirteen 8/G protein β subunit-like (LST8/GβL) member the TOR complexes, two putative LST8 genes are present in Arabidopsis thaliana, which only one (LST8-1) significantly expressed. LST8-1 able complement yeast lst8 mutations interacts kinase. Mutations gene resulted reduced vegetative growth apical dominance abnormal...
Summary During a compatible interaction, root‐knot nematodes ( Meloidogyne spp.) induce the redifferentiation of root cells into multinucleate nematode feeding (giant cells). Hyperplasia and hypertrophy surrounding leads to formation gall. We investigated plant response by carrying out global analysis gene expression during gall in Arabidopsis, using giant cell‐enriched tissues. Among 22 089 genes monitored with complete Arabidopsis transcriptome microarray gene‐specific tag, we identified...
Summary This article is concerned with variable selection for cluster analysis. The problem regarded as a model in the model‐based analysis context. A generalizing of Raftery and Dean (2006, Journal American Statistical Association 101 , 168–178) proposed to specify role each variable. does not need any prior assumptions about linear link between selected discarded variables. Models are compared Bayesian information criterion. Variable obtained through an algorithm embedding two backward...
Abstract Background Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such drought tolerance. Here we assess genotype-dependent component drought-induced transcriptome response in two poplar genotypes differing Drought-induced responses were analysed leaves and root apices compared with available data from other Populus species. Results Using multi-species designed microarray, genomic DNA-based selection probesets provided...
CATdb is a free resource available at http://urgv.evry.inra.fr/CATdb that provides public access to large collection of transcriptome data for Arabidopsis thaliana produced by single Complete Transcriptome Micro Array (CATMA) platform. CATMA probes consist gene-specific sequence tags (GSTs) 150-500 bp. The v2 version contains 24 576 GST representing most the predicted A. genes, and 615 tiling chloroplastic mitochondrial genomes. Data in are entirely processed with same standardized protocol,...
Abstract Background Mitogen-activated protein kinases (MAPKs) are key regulators of immune responses in animals and plants. In Arabidopsis , perception microbe-associated molecular patterns (MAMPs) activates the MAPKs MPK3, MPK4 MPK6. Increasing information depicts events activated by MAMPs plants, but specific cooperative contributions these signalling largely unclear. Results this work, we analyse behaviour MPK3 MPK6 mutants early late triggered MAMP flg22 from bacterial flagellin. A...
The identification of biomarker signatures in omics molecular profiling is usually performed to predict outcomes a precision medicine context, such as patient disease susceptibility, diagnosis, prognosis, and treatment response. To identify these signatures, we have developed discovery tool, called BioDiscML. From collection samples their associated characteristics, i.e., the biomarkers (e.g., gene expression, protein levels, clinico-pathological data), BioDiscML exploits various feature...
Abstract Phenotypic plasticity can contribute to crop adaptation challenging environments. Plasticity indices are potentially useful identify the genetic basis of phenotypic plasticity. Numerous methods exist measure However, their ability capture QTL with environmental effects remains elusive. Here, we analyzed a published multi-trial maize phenotyping dataset that examined water stress response leaf area, shoot biomass and use efficiency, calculating for these traits using seven different...
We have assembled approximately 20 000 Arabidopsis thaliana promoter regions, compatible with functional studies that require cloning and microarray applications. The fragments can be captured as modular entry clones (MultiSite Gateway format) via site-specific recombinational cloning, transferred into vectors of choice to investigate transcriptional networks. also amplified by PCR printed on glass arrays. In combination immunoprecipitation protein-DNA complexes (ChIP-chip), these arrays...
Although the contribution of cytonuclear interactions to plant fitness variation is relatively well documented at interspecific level, prevalence intraspecific level remains poorly investigated. In this study, we set up a field experiment explore range effects that have on fitness-related traits in Arabidopsis thaliana To do so, created unique series 56 cytolines resulting from cytoplasmic substitutions among eight natural accessions reflecting within-species genetic diversity. An assessment...
Abstract Background Soluble sugars, which play a central role in plant structure and metabolism, are also involved the responses to number of stresses, act as metabolite signalling molecules that activate specific or hormone-crosstalk transduction pathways. The different roles exogenous sucrose tolerance Arabidopsis thaliana plantlets herbicide atrazine oxidative stress were studied by transcriptomic approach using CATMA arrays. Results Parallel situations xenobiotic sucrose-induced presence...
Background Large-scale gene expression profiling of peripheral blood mononuclear cells from Rheumatoid Arthritis (RA) patients could provide a molecular description that reflects the contribution diverse cellular responses associated with this disease. The aim our study was to identify profiles for RA patients, using Illumina technology, gain insights into mechanisms. Methodology/Principal Findings Human-6v2 Expression BeadChips were used complete genome-wide transcript (PBMCs) 18 and 15...
Identifying the connections between molecular and physiological processes underlying diversity of drought stress responses in plants is key for basic applied science. Drought response involves a large number pathways subsequent processes. Therefore, it constitutes an archetypical systems biology model. We first inferred gene-phenotype network exploiting differences eight sunflower (Helianthus annuus) genotypes to two scenarios. Large transcriptomic data were obtained with Affymetrix...
Characterizing the transcriptome of eukaryotic organisms is essential for studying gene regulation and its impact on phenotype. The realization that anti-sense (AS) noncoding RNA transcription pervasive in many genomes has emphasized our limited understanding post-transcriptional regulation. Numerous mechanisms including convergent transcription, anti-correlated expression sense AS transcripts, RNAi remain ill-defined. Here, we have combined microarray analysis high-throughput sequencing...
Fusarium Head Blight (FHB) caused primarily by graminearum (Fg) is one of the major diseases small-grain cereals including bread wheat. This disease both reduces yields and causes quality losses due to production deoxynivalenol (DON), type B trichothecene mycotoxin. DON has been described as a virulence factor enabling efficient colonization spikes fungus in wheat, but its precise role during infection process still elusive. Brachypodium distachyon (Bd) model cereal species which shown be...
Abstract Background RNAseq is nowadays the method of choice for transcriptome analysis. In last decades, a high number statistical methods, and associated bioinformatics tools, analysis were developed. More recently, studies realised neutral comparison using benchmark datasets, shedding light on most appropriate approaches data Results DiCoExpress script-based tool implemented in R that includes methods chosen based their performance comparisons studies. uses pre-existing packages including...
Despite the essential role of specialized metabolites (SMs) in interaction plants with environment, studying ability crop seeds to produce these protective compounds has been neglected. Furthermore, a myriad SMs, providing an interesting model investigate their diversity and plasticity. Camelina sativa gained lot interest past few years as rustic oilseed crop. A characterization seed SM landscapes six camelina genotypes grown field harvested during five growing seasons undertaken this work....
In cDNA microarray experiments all samples are labeled with either Cy3 or Cy5. Systematic and gene-specific dye bias effects have been observed in dual-color experiments. contrast to systematic which can be corrected by a normalization method, the is not completely suppressed may alter conclusions about differentially expressed genes.The taken into account using an analysis of variance model. We propose index, named label measure bias. It requires at least two self-self hybridization...
Cultivated for centuries, the varieties of rose have been selected based on a number flower traits. Understanding genetic and molecular basis that contributes to these traits will impact future improvements this economically important ornamental plant. In study, we used scanning electron microscopy sections meristems flowers establish precise morphological calendar from early development stages senescing flowers. Global gene expression was investigated floral meristem initiation up...
Abstract Background Recent literature on the differential role of genes within networks distinguishes core from peripheral genes. If previous works have shown contrasting features between them, whether such categorization matters for phenotype prediction remains to be studied. Results We measured 17 phenotypic traits 241 cloned genotypes a Populus nigra collection, covering growth, phenology, chemical and physical properties. also sequenced RNA each genotype built co-expression define found...