Expertise
Hub members Have many expertise, covering most of the fields in bioinformatics and biostatistics. You'll find below a non-exhaustive list of these expertise
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Searched keyword : Bacteria
Related people (5)
Thomas BIGOT
I joined the C3BI Hub in 2016 after a curriculum widely dedicated to Bioinformatics studies, and more precisely to Phylogeny and Evolution, topics of my PhD thesis. At Institut Pasteur, I am involved in projects dealing with sequences homology : alignments, hmm profiles, making homologous family databases, kmers signatures. I am also a developer (Python / C++) with a solid interest in optimization as well as in developing usable tools for final user such as automated pipeline for metagenomics sequence analysis. I’m currently embedded in Marc Eloit’s team (80% of my work time). My main task in this team is to develop strategies to identify, in their metagenomics samples, new pathogens, or new combination pathogen / symptoms. The rest of my time, I manage small projects and participate to the Hub life. I am currently experimenting with functional programming (for now, using Python) and its applicability to bioinformatics issues.
KeywordsAlgorithmicsScientific computingSofware development and engineeringParallel computingGraph theory and analysis
Organisms
BacteriaFungiVirus
Projects (9)
- DNMT and RNMT in Leishmania(Gerald SPAETH - Molecular Parasitology and Signaling) - In Progress
- Targetting the function of a hypothetical protein(Dariusz CZERNECKI - Structural Dynamics of Macromolecules) - Pending
- Defective interfering viral genomes of shrimps' viruses(Anastassia KOMAROVA - Viral Genomics and Vaccination) - Awaiting Publication

Pascal CAMPAGNE
Initially trained in evolutionary and environmental sciences, I studied population genetics and micro-evolutionary processes in a number of postdoctoral research projects. I recently joined the C3BI-Hub at the Institut Pasteur, where I work on various aspects involving Biostatistics and the analysis of genetic data.
KeywordsAssociation studiesGenomicsGenotypingBiostatisticsGeneticsEvolutionPopulation genetics
Organisms
BacteriaParasiteHumanInsect or arthropodOther animal
Projects (21)
- Analyse statistique de données de phénotypage à haut débit(Melanie LEGRAND - Fungal Biology and Pathogenicity) - Pending
- Identification of the genetic basis of bacteriophage-resistant isolates(Laurent DEBARBIEUX - Molecular Biology of Gene in Extremophiles) - Pending
- Collaboration between CETEA, C2RA and Hub for optimization of experimental designs (3R)(Myriam MATTEI - Center for Animal Resources and Research) - In Progress
Anđela DAVIDOVIĆ
I have a joint MSc degree in Mathematical Modelling from three European universities: University of L’Aquila (Italy), University of Nice-Sophia Antipolis (France) and Autonomous University of Barcelona (Spain). I also hold a PhD degree in Applied Mathematics and Scientific Computing from University of Bordeaux, France. I have done my PhD and one year of post-doc at INRIA Bordeaux Sud-Ouest, and partially at IHU-Liryc. During this time I studied how electrical signals propagate through the cardiac tissue under certain diseased conditions. My model of interest was the bidomain model, which is a system of partial differential equations that takes into account physiological properties of the cardiac cells and the spatial organization of the cardiac tissue. I worked on the mathematical multiscale analysis and numerical simulations of the problem to understand how structural changes of the tissue affect the propagation of the signal on the heart level. I collaborated with biologists and engineers of the IHU-Liryc to apply my model on a rat heart using high-resolution MRI data. For this I also worked on image analysis and image processing. I’ve joined the Institute Pasteur in February 2018 as a member of the HUB in Bioinformatics and Biostatistics. Currently I am working on stochastic mathematical modeling and inference for systems biology, gene expression, RNA transcription, etc.
KeywordsModelingScientific computingApplication of mathematics in sciencesGraphics and Image Processing
Organisms
BacteriaFungiInsect or arthropodEscherichia coliSaccharomyces cerevisiaeFly
Projects (2)

Julien GUGLIELMINI
After a PhD in Microbiology on bacterial toxin-antitoxin systems at the Free University of Brussels, I joined the Institut Pasteur for a 3 years postdoc in Eduardo Rocha’s lab. During this period, I performed comparative genomics and pylogenetic analysis on bacterial conjugation and type IV secretion systems. Then, I worked 2 years in Olivier Tenaillon’s team on the modelling and evolution of organismal complexity. I joined the HUB in 2015, and I am involved in phylogenetic and comparative genomics projects.
KeywordsGenomicsPhylogeneticsSequence analysisGenome analysisGeneticsEvolutionPopulation genetics
Organisms
ArchaeaBacteriaVirus
Projects (11)
- Evaluation of the mutation rate per site and dN/dS in the genomes of Yersinia enterocolitica(Cyril SAVIN - Yersinia) - Awaiting Publication
- Phylogenetic analysis of HHD-PDZ containing proteins(Nicolas WOLFF - Channel Receptors) - Awaiting Publication
- Phylogenetic analysis of insect-specific flaviviruses(Artem BAIDALIUK - Insect-Virus Interactions) - Closed

Rachel LEGENDRE
Rachel Legendre is a bioinformatics engineer. She completed her master degree in apprenticeship for two years at INRA in Jouy-en-Josas in the Genetic Animal department. She was involved in a project aiming at the detection and the expression analysis of micro-RNA involved in an equine disease. In 2012, she joined the Genomic, Structure and Translation Team at Paris-Sud (Paris XI) university. She worked principally on Ribosome Profiling data analysis, a new technique that allows to identify the position of the ribosome on the mRNA at the nucleotide level. Since november 2015, she worked at Institut Pasteur. During 4 years, she was detached to the Biomics Platform, where she was in charge of the bioinformatics analyses for transcriptomics and epigenomics projects. She was also involved in Long Reads (PacBio and Nanopore) developments with other bioinformaticians of Biomics. Since november 2019, she has joined the Hub of Bioinformatics and Biostatistics, et more precisely the Genome Organization Regulation and Expression group.
KeywordsAlgorithmicsChIP-seqEpigenomicsNon coding RNATranscriptomicsGenome analysisProgram developmentScientific computingSofware development and engineeringIllumina HiSeqRead mappingSequencingWorkflow and pipeline developmentChromatin accessibility assaysPac BioRibosome profiling
Organisms
BacteriaFungiParasiteHumanInsect or arthropodOther animal
Projects (18)
- The master regulator of virulence gene expression in Group B Streptococcus(Arnaud FIRON - Biology of Gram-Positive Pathogens) - Pending
- Transcriptional analysis of injured skeletal muscle(Eleonora ROSSI - Stroma, Inflammation and Tissue Repair) - Closed
- Small RNA signature on RIG-I like receptors(Anastasia KOMAROVA - Molecular Genetics of RNA Viruses) - In Progress
Related projects (137)
Image-based siRNA and drug screens of infection by the pathogen Listeria monocytogenes
Genomic approach for the identification of new targets of antimycobacterial drugs
MacSyFinder development: models data structure
HIghthroughput CRISPR-Cas9 screen in bacteria
Host microbiota modification by the pathogen Listeria monocytogenes
Whole-genome sequencing of microbial agents for disease surveillance, outbreak investigation, epidemiology and population biology
Transfert annotations
Genomic analyses of E. coli strains
Interactive web interfaces and Analysis Tools of Bacterial NGS data for Postgenomics Life Scientist
Analyses of SNP diversity of Legionella pneumophila strains
Methods to identify and characterize orthologs of genes encoding small proteins
Analyse de séquence 16S
Analysis of host epitranscriptional modifications upon colonisation with commensals and infection by bacterial pathogens
a web interface for MacSyFinder (a tool to detect macromolecular systems in genomes).
Identification of Transcription Start Sites and small RNAs in Leptospira interrogans by transcriptome analysis
A program to identify integrons, attC sites and gene cassettes
Assemblage de novo d'une souche d'E. coli
MicrocystOmics
- Christophe BÉCAVIN
- Rachel LEGENDRE
- Hugo VARET + 1 operator
MicrocystOmics
- Christophe BÉCAVIN
- Rachel LEGENDRE
- Hugo VARET + 1 operator
Regulation by phase variation and attenuation: looking for leader peptides containing repeats in the intergenic regions of streptococcal genomes
How ribosomal protein gene position impacts in the genome evolution during a long term evolution experiment.
Pasteur International Bioresources Network (PIBnet) bioinformatics: whole-genome sequencing of microbial agents for disease surveillance, outbreak investigation, epidemiology and population biology
Horizontal gene transfer in mycobacteria
Mise a disposition d'un(e) bioinformaticien(ne) du hub pour les analyses bioinformatiques du transcriptome et de l epigenome
Do faecal microbiome phages facilitate antibiotic resistance?
Deciphering the global response of human macrophages against M. tuberculosis
Genome On Rails
The Physiological Consequences of Altering Bacterial Cell Wall Synthesis
Comparative genomic and phylogenetic analysis of 14 Clostridium tetani strains
The contribution of ecological variation to the microbiome of Ae. aegypti
RNAseq analysis-gene ontology enrichment Clostridium tetani
SNP based analysis of French Bordetella pertussis isolates: comparison of isolates producing all the vaccine antigens to isolates producing only some of them.
Interactions and dynamics of fungal and bacterial microbiome in healthy people
Determination of SNPs in 6 genomes of Leptospira kirschneri serovar grippotyphosa
Listeriomics - Development of a web platform for visualization and analysis of Listeria omics data
Systems Biology of Cell Infection by the Bacterial Pathogen Listeria monocytogenes
Reconstruction of archaeal genomes from environmental metagenomic data
secretome analysis of human intestinal cells during shigella invasion
mechanism of toxin production by Klesiella pneumoniae
Comparative genomic and phylogenetic analysis of Clostridium baratii strains
Genomic analysis of small orfs of unknown function
Recherche de SNP chez une souche de leptospira biflexa d'interêt
Patho-evolution of mycobacterial strains
Comparative genomic and phylogenetic analysis of Clostridium botulinum strains
Label-free quantitative proteomics of Human Macrophages infected by M. tuberculosis
Comparative analysis of the virulence plasmids of Shigella Spp. and entero-invasive Escherichia coli
Host gene regulation in response to Listeria monocytogenes infection
Nanotherapeutics for multidrug-resistant tuberculosis
Identification of new or unexpected pathogens, including viruses, bacteria, fungi and parasites associated with acute or progressive diseases
Novel protein interaction in the assembly of photosynthetic prokaryotic complexes
Deciphering the composition dynamics of infant gut microbiome
Regulation of Sirtuin 2-dependent histone deacetylation during bacterial infection
Impact of hepatic inflammation on microbiota
Genomic differences of the same strains preserved in different culture collections
Genomic analysis of bacterial evolution
Detection of virulence Genes and genes of interest in Bacillus cereus
Analysis of DNA methylation in the presence and absence of antibiotics in wt and mutant V. cholerae.
Development of top-down proteomics for clinical microbiology
Add unit tests to IntegronFinder
A novel MacSyFinder module for detection of bacterial capsule systems on the future Galaxy platform.
Immune control of the gut microbiota and lifespan of A. stephensi.
Differentiation of Shigella species from Escherichia coli by MALDI-TOF mass spectrometry
Caractéristiques génomiques de souches d’Escherichia coli productrices de BLSE associées à un portage persistant après un voyage en zone tropicale
Role of PerR-regulated oxidative stress response in pathogen Leptospira virulence
Research of SNPs to explain the non virulent phenotype of a mutant of L. interrogans serovar Manilae L495 affecting the expression of a protein not involved in virulence
Automatic detection of antibiotic resistance genes
Extraction of sequence information from published genomes of commensal bacteria
MacSyDBCapsule
Characterization of an RNA binding protein of Listeria monocytogenes
Bioinformatic analysis of the adenylate cyclase CyaA toxin
Genomic analysis of catheter-related Escherichia coli infection
Infection of Ixodes ricinus by Borrelia burgdorferi sensu lato by in peri-urban forests of France
Relationships between ESBL-producing Escherichia coli from food and healthy mothers in Phnom Penh, Cambodia
Extended spectrum β-lactamase (ESBL) genes encode resistance to penicillins and cephalosporins and can be horizontally transferred among Enterobacteriaceae. More than 60% of healthy humans living in southeast Asia are faecal carriers of ESBL-producing Enterobacteriaceae (ESBL-PE), compared to <10% in Western Europe, suggesting diverse exposure routes. In Cambodia, meat and fish consumption is high and food safety is poorly enforced. Thus, we hypothesized that meat and fish could be a source of exposure to ESBL-PE. From Sept-Nov 2016, we conducted a meat sampling study in Phnom Penh in collaboration with the BIRDY program (http://www.birdyprogram.org/), an ongoing study of neonatal health in low-income countries. We evaluated ESBL-PE contamination among pork, fish, and chicken from two markets and collected survey data from BIRDY mothers. We performed whole genome sequencing on 87 ESBL-producing E. coli recovered from meat and fish and from 91 BIRDY mothers who provided faecal swabs less than one year prior. Now, we will conduct a two-step exploratory analysis of these WGS data:
- First, we will estimate the pairwise evolutionary distance between E. coli isolates, in order to infer a phylogenetic tree. We will use this tree to investigate such epidemiological questions as “Do E. coli sequences from women who reported eating poultry 3+ times/week cluster more closely with E. coli recovered from poultry samples, compared to women who reported never eating poultry?” This phylogenetic tree may be re-constructed using a finer resolution, as needed.
- Second, we will annotate all E. coli genomes in order to identify genomic islands related to antibiotic resistance. We will subsequently use logistic regression to model associations between BIRDY mothers’ reported dietary patterns (i.e. exposure) and the presence or absence of these genomic islands among the ESBL-E. coli they were colonized with (i.e., outcome).