My research consists mainly in biological data analysis, modelling, and methodological developments. The themes I work on tend to be very diverse, and highly dependent of my collaborations. One central theme of my research is the interaction and co-evolution between hosts and pathogens, either bacteria or viruses. One problem that I focus on in particular is codon usage and nucleotide composition, their causes, and their functions in these interactions.

I have various projects, past (published or not) and present. If you are interested by any of them, as a student, a potential collaborator, or just to know if you could apply the methods to your own research, feel free to contact me.

For internship positions, you can have a look here (in French)

Running

Meloidogyne genome structure Using genome composition statistics to better understand Meloidogyne genome structure (collaboration with EGJ Danchin in ISA)
Wolbachia biodiversity Development of a statistical methodology to analyze biodiversity data of Wolbachia infections (collaboration with M. Cariou and S. Charlat in LBBE)
Pattern detection in graphs Biological applications of a new algorithm of pattern detection in graphs (collaboration with H. Soldano et G. Santini in ABI).
Methanococcales evolution Co-evolution of codon usage and amino acid content in Methanococcales (collaboration with M. Lecocq and C. Brochier-Armanet in LBBE).

Older works

Genome composition, codon usage bias and host-pathogen interactions

Codon usage evolution Development of a phylogenetic evolutionary model including codon usage bias as a selective force. Published
Recognition of pathogens by the innate immune system Meta-analysis of the links between viral genomic composition and innate immune system activation. Published
Blue tongue virus Comparative analysis of codon usage in the blue tongue virus and its hosts by large scale analysis of genomic data (collaboration with F. Arnaud and C. Terzian).
Lentiviruses genome synthesis Synthesis of artificial SIV and other lentiviruses to test as potential living vaccines Published.
Lentiviruses codon usage Analysis of HIV-1 and other lentiviruses codon usage and nucleotidic content, and comparison with those of their hosts Published
L. lactis gene expression Analysis and modelling of a full dataset of gene expression for L. lactis, where all variables from mRNA concentration to protein concentration have been measured, to model completely the translation phase (collaboration with M. Cocaign-Bousquet)
Codon usage and tRNA content in bacteriophages Cross-analysis of the relationship between codon usage and tRNA content in bacteriophages and their hosts Published
Codon usage and codon robustness Analysis of codon usage in the light of differential codon robustness to mutations (in collaboration with G. Cambray)
Clustering of bacterial genes according to their codon bias Development and application of an algorithm to cluster genes according to their codon bias, ans application to E. coli and B. subtilis Published

Biological networks

Inference of the signalling network in yeast Development of a message-passing algorithm to infer the signallosome using gene expression and protein interaction data, and application to the yeast pheromone pathway Published and Published
Combinatorial effects in the PDR regulatory network in yeast Application of a message-passing algorithm to infer the combinatorial regulations in the PDR subnetwork, in yeast Published
Steiner trees to cluster biological datasets Application of a new clustering algorithm based on Steiner trees to various biological datasets, and comparison with previous results Published
Salmonella pathogenicity genetic regulation Formal analysis of the genetic structure regulating the expression of SPI-1 operon in Salmonella enterica Published
QTL analysis driven by regulatory network data Analysis of QTL data in yeast where regulatory network data were used to pre-select genes of interests and increase the analyses statistical power (in collaboration with M. Vergassola)

Others

Virus Quantitation by optical microscopy Statistical analyses dedicated to the development of a new methodology of virus quantitation. Published
Transposon detection Development of scripts analyzing RepeatMasker files to find transposons Published; available Software!
FOXL2 targets Chip-ChIP data analysis to uncover the promoter(s) sequence(s) targeted by the transcription factor FOXL2 Published
DNA barcode design Development of an optimisation tool to generate DNA barcodes for highly multiplexed sequencing applications (collaboration with S. Charlat)
Omic analyses of dosage compensation An analysis combining the use of proteomic and RNA-seq data to show that dosage compensation of protein-complexes genes on the X chromosome do occur Published
CUT 5' origins Analysis of a new dataset of CUT sequences to develop a predictive model of CUT transcription (collaboration with A. Jacquier and M. Vergassola)
Multivariate electrochemical comparative data analysis Development of a methodology to compare multivariate datasets measured by univariate electrochemical techniques (collaboration with C. Giroud, F. Lemaître and C. Policar)
FOXL2 regulations Analysis of the biological properties and promoters of genes regulated by FOXL2 Published
Organization of crystal/bistable genes in yeast Looking for the genomic properties in the organization of genes so-called crystal or bistable, according to their chromatin state (in collaboration with L. Palmeira)
Infotaxis in a multi-source environment Generalization of the infotaxis approach when the searcher is surrounded by more than one source and has to find quickly one Published
Protein structure and the role of methionine against oxidation Search for protein structures that could use methionine as a defense against ROS (in collaboration with A. Danchin and M. Vergassola)
Multi-agent modelisation of hydrothermal ecosytems Development of a multi-agent model for the larval dispersal problem in hydrothermal ecosystems Published