A5080851047- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Bacterial Genetics and Biotechnology
- Bioinformatics and Genomic Networks
- Biofuel production and bioconversion
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Biomedical Text Mining and Ontologies
- Viral Infectious Diseases and Gene Expression in Insects
- Semantic Web and Ontologies
- Process Optimization and Integration
- Protein purification and stability
- Gene expression and cancer classification
- Bacteriophages and microbial interactions
- Cell Image Analysis Techniques
- Enzyme Catalysis and Immobilization
- Probiotics and Fermented Foods
- Fungal and yeast genetics research
- Amino Acid Enzymes and Metabolism
- Genomics and Phylogenetic Studies
- Algal biology and biofuel production
- Fermentation and Sensory Analysis
- Rough Sets and Fuzzy Logic
- Mass Spectrometry Techniques and Applications
- Simulation Techniques and Applications
Mathématiques et Informatique Appliquées du Génome à l'Environnement
2015-2024
Université Paris-Saclay
2016-2023
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2022-2023
Microbiologie de l’alimentation au service de la santé
2013
Institut National de la Recherche Agronomique
2012
Laboratoire Ampère
2009-2011
École Centrale de Lyon
2009-2010
Sciences pour L’Œnologie
2008
Outside In Acquisition and analysis of large data sets promises to move us toward a greater understanding the mechanisms by which biological systems are dynamically regulated respond external cues. Now, two papers explore responses bacterium changing nutritional conditions (see Perspective Chalancon et al. ). Nicolas (p. 1103 ) measured transcriptional regulation for more than 100 different conditions. Greater amounts antisense RNA were generated expected appeared be produced alternative...
Adaptation of cells to environmental changes requires dynamic interactions between metabolic and regulatory networks, but studies typically address only one or a few layers regulation. For nutritional shifts two preferred carbon sources Bacillus subtilis, we combined statistical model-based data analyses transcript, protein, metabolite abundances promoter activities. malate was rapid primarily controlled posttranscriptionally compared with the slow, mainly transcriptionally adaptation...
Few genome-scale models of organisms focus on the regulatory networks and none them integrates all known levels regulation. In particular, regulations involving metabolite pools are often neglected. However, link metabolic to genetic network through regulations, including those effectors transcription factors or riboswitches. Consequently, they play pivotal roles in global organization networks.We report manually curated reconstruction central metabolism Bacillus subtilis (transcriptional,...
In the growing field of systems biology, knowledge protein concentrations is highly required to truly understand metabolic and adaptational networks within cells. Therefore we established a workflow relying on long chromatographic separation mass spectrometric analysis by data independent, parallel fragmentation all precursor ions at same time (LC/MSE). By prevention discrimination co-eluting low high abundant peptides average sequence coverage 40% could be achieved, resulting in...
Abstract Background Redox homeostasis is essential to sustain metabolism and growth. We recently reported that yeast cells meet a gradual increase in imposed NADPH demand by progressively increasing flux through the pentose phosphate (PP) acetate pathways exchanging NADH for cytosol, via transhydrogenase-like cycle. Here, we studied mechanisms underlying this metabolic response, combination of gene expression profiling analyses extracellular intracellular metabolites 13 C-flux analysis....
Abstract Complex regulatory programs control cell adaptation to environmental changes by setting condition‐specific proteomes. In balanced growth, bacterial protein abundances depend on the dilution rate, transcript and transcript‐specific translation efficiencies. We revisited current theory claiming invariance of efficiency. By integrating genome‐wide transcriptome datasets from a library synthetic gfp ‐reporter fusions, we demonstrated that efficiencies in Bacillus subtilis decreased up...
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging reproduce reuse simulations, in part, because the numerous formats methods for simulating various subsystems scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find use simulation tools, we developed BioSimulators (https://biosimulators.org), central registry of capabilities...
3-hydroxypropanoic acid (3-HP) is an important biomass-derivable platform chemical that can be converted into a number of industrially relevant compounds. There have been several attempts to produce 3-HP from renewable sources in cell factories, focusing mainly on Escherichia coli, Klebsiella pneumoniae and Saccharomyces cerevisiae. Despite the significant progress made this field, commercially exploitable large-scale production microbial strains has still not achieved. In study we...
We introduce a manually constructed and curated regulatory network model that describes the current state of knowledge transcriptional regulation Bacillus subtilis. The corresponds to an updated enlarged version central metabolism originally proposed in 2008. extended original whole genome by integration information from DBTBS, compendium data includes promoters, transcription factors (TFs), binding sites, motifs, regulated operons. Additionally, we consolidated our with all on included...
Resource allocation based models were shown to capture the main bacterial cell design principles in steady-state, thus managing resource between processes, and fine growth rate. This paper introduces basis of extension dynamical conditions. The framework is applied a bioreactor operating batch mode for optimizing production added-value compounds by bacteria. optimal predicted strategy analyzed discussed light strategies obtained with other types models. should offer new opportunities...
Efficient resource allocation can contribute to an organism's fitness and improve evolutionary success. Resource Balance Analysis (RBA) is a computational framework that models growth-optimal proteome configurations in various environments. RBA software enables the construction of on genome scale calculation medium-specific, cell states including metabolic fluxes abundance macromolecular machines. However, existing lacks simple programming interface for non-expert users, easy use...
Abstract Summary: Live Cell Array (LCA) technology allows the acquisition of high-resolution time-course profiles bacterial gene expression by systematic assessment fluorescence in living cells carrying either transcriptional or translational fluorescent protein fusion. However, direct estimation promoter activities time-dependent derivation datasets generates high levels noise. Here, we present BasyLiCA, a user-friendly open-source interface and database dedicated to automatic storage...
High-throughput technologies produce huge amounts of heterogeneous biological data at all cellular levels. Structuring these together with knowledge is a critical issue in biology and requires integrative tools methods such as bio-ontologies to extract share valuable information. In parallel, the development recent whole-cell models using systemic cell description opened alternatives for integration. Integrating within bio-ontology would help progress integration modeling synergistically. We...
The rational bacterial strain design is a major challenge in synthetic biology. This paper deals with the optimization of for specific processes taking place bioreactor. Such problems are namely maximizing growth and production product interest. First, model combining internal behavior cells bioreactor environment developed assuming mass balance biological constraints. assumes that proteins can be controlled. problem then solved constant variables returns an optimal strategy strains.
In this paper, we investigate the cell design of bacteria during exponential growth. To purpose, propose to formulate problem as a non differentiable convex optimization equivalent Linear Programming feasibility problem. Its resolution predicts for specific medium not only distribution metabolic fluxes and maximal growth rate, but also concentrations ribosomes proteins involved in network thus composition different rates. Moreover, our model recovers known modular structure regulation...