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 : Virus
Related people (3)
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 (10)

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 (12)
- Centrosome and basal body function in human parasites(Philippe BASTIN - Trypanosome Cell Biology) - New
- 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) - Closed

Anna ZHUKOVA
A computer scientist by training, I am applying this knowledge to solve biological problems and am particularly interested in modelling of biological systems, knowledge inference, ontologies and data visualisation.
KeywordsAlgorithmicsData VisualizationMetabolomicsModelingPathway AnalysisPhylogeneticsSystems BiologyTool DevelopmentDatabaseProgram developmentScientific computingDatabases and ontologiesApplication of mathematics in sciencesSofware development and engineeringData and text miningEvolutionData integrationGraph theory and analysisWorkflow and pipeline developmentDiscrete and numerical optimization
Organisms
VirusHuman Immunodeficiency virus (HIV)
Projects (6)
- Modeling mitochondrial metabolism dormant Cryptococcus neoformans(Benjamin HOMMEL - Molecular Mycology) - Closed
- Measles virus protein C interplay with cellular apoptotic pathways; applications for cancer treatment(Alice MEIGNIÉ - Viral Genomics and Vaccination) - Closed
- Diffusion des mutations de résistance du VIH : modèles et méthodes d’estimation(Olivier GASCUEL - Evolutionary Bioinformatics) - Closed
Related projects (161)
Regulation of HIV replication by cellular DNA topology
An automatic pipeline to call SNPs from RNA-seq reads
Evolutionary relationships between giant viruses and eukaryotes
viral evolution around Ebola Treatment Centre in Macenta and according to disease outcomes
Détection de variants dans des données NGS (miSeq) de phage
Identification of new cellular parameters involved in HIV-1 integration selectivity
Single cell gene expression profiling of HIV-specific CD8+ T cells associated with HIV control
INNOV DIAG HPV
Updating the Topo IB gene tree
A reference panel of dengue vector genomes
Variant detection on NGS data
Analyses protéine-protéine interactions
Analyses fonctionnel des protéines humains de type ubiquitin.
L'analyses phylogénétique par séquence protéique, temporal et géographical
Un workflow pour l'analyses des polymorphismes des souches de grippe saisonnier.
Variant effects on influenza virus proteins
Meta-analysis of dengue transcriptomic data
Transciptomic analysis of dendritic cell response during Lassa virus infection
Factors determining HIV seeding in CD4+ T cell subpopulations
Host Range Database
Development of a bioinformatics workflow dedicated to the analysis of the viral metagenome: from NGS raw data to the identification of novel viruses
Environmental and human surveillance of polioviruses, VDPVs, and other enteroviruses in Madagascar during the switch from tOPV to bOPV
Rift valley fever NSm protein functional study
Diffusion des mutations de résistance du VIH : modèles et méthodes d’estimation
Identification of new or unexpected pathogens, including viruses, bacteria, fungi and parasites associated with acute or progressive diseases
IgBlast on Galaxy
Regulation of HIV-1 integration selectivity by chromatin
PhageTermini: a Fast and User-friendly Software to Determine Bacteriophage Packaging Mode and Termini
Determination of phage termini using NGS
Genomic analysis of bacterial evolution
Activation of plasmacytoïd dendritic cells by arenaviruses : transcriptomic analysis
Utilize mouse models to study infection by HIV-1
Characterization of the specific TCR repertoire preferentially expressed in spontaneously controlled HIV infection
Single cell analysis of HIV-specific CD4+ T cell differentiation
Comparative analysis of transcriptomic and proteomic data to study RNA and protein expression regulation during RVFV infection in mice.
Quantitative temporal analysis of cellular proteins regulated by HBV in primary human hepatocytes
Study of the early pathogenesis during Lassa fever in cynomolgus monkeys and its correlation with the outcome
- Thomas BIGOT
- Marie-Agnès DILLIES
- Rachel LEGENDRE + 2 operators
Graphical representation of co-expressed genes in various datasets
Recombination among enteroviruses
Lipid-binding domains in Vaccinia virus proteins
Transcriptomic analysis of blood cells from ebola infected patients
viral evolution around Ebola Treatment Center in Macenta
The resurgence of a neglected disease, Yellow fever: from jungle to urban environments
Analysis of IFITM RNA levels in vraious cell types and tissues
Phage infection dynamics in the gut of gnotobiotic mice
An Aedes albopictus-driven epidemiological prediction for arboviral diseases outbreak in Europe
functional enrichment of RNA processing factors associated with proteins of influenza viruses
Asymptomatic pathogen carriage in stunted and non-stunted children living in Antananarivo, Madagascar
LGP2 binds PACT to regulate RIG-I- and MDA5-mediated antiviral response
Role of RNA primary and secondary structure in non-homologous recombination
Chikungunya virus adaptation to a low temperature in a French population Ae. albopictus
Analysis of Internal Deletions in EV71
Targetting the function of a hypothetical protein
Implementation of the ViroScreen workflow in Galaxy
Deciphering the transcriptome profil during rabies infection in brain in mouse and in human
Modulation of cellular pathways involved in neuropathology of rabies infection
Identification of internal methylations of RABV mRNAs using RiboMeth sequencing approach
Determination of RABV RNAs signatures recognized by RLRs
Small RNA signature on RIG-I like receptors
Building a database with a pattern mining system designed for virus nucleic acid data
Analysis of the transcriptome during lyssavirus infection in torpid bat: an in vitro model. Act 1
Correlative analysis between lipid droplets number and volume in hepatocytes infected by hepatitis C virus variants
Modulation of Flu transmission in Niger , according to climate variations over the past ten years
Search for genetic determinants of aminoglycoside tolerance
Identification, structural and functional analyses of peptides from SARS-Cov2 binding with high affinity to MHC-E and impact on NK cell responses in SARS-Cov2 infection
Setup of bioinformatic pipelines for paleo(meta)genomics
Phages - bacteria interactions network of the healthy human gut
Changes in cellular pathways during SARS-CoV-2 infection upon drug treatment
HPV RNA-SEQ
Mosquito vector competence for different RVFV variants
Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms
Validation of interactions between SARS-CoV-2 proteins and cellular proteins
Page web modélisation covid-19 pasteur
Analysis of genes transcription profiles in E.coli after expression of the T4 phage protein Ndd
Rabomism - Understanding rabies virus tropism
Comparing viral replication of intergenotypic hepatitis C virus Core recombinants
RNA virus discovery
Analysis of the viral diversity of coronaviruses in field samples.
CORSER-4 Cohort Study: Assessment of the humoral immune response to COVID-19 vaccination in each subpopulation defined by type of vaccination regimen, at 1-3-6-12-24 months
Quick phage data mining
Viral metagenomic in Chinese bats and their associated ectoparasites.
Viral metagenomic in noctule bats from East Europe
Measles virus type 1 infection disturbs the mitochondrial network leading to type I interferon production through the RNA polymerase III/RIG-I pathway
Evaluation in cellulo of the impact of insecticide usage on arbovirus population
Genetic diversity of yellow fever virus populations in mosquitoes
Genetic diversity of arbovirus populations in Aedes aegypti mosquitoes from Colombia
Better characterization of long chimeric virus-human reads after target enrichment on integrated viral genomes.
FLAVIMMUNITY
Deciphering mutation signatures on hepatitis B virus genome
Detection of newly produced NIRVS in mosquito persistently infected cells
Red Cross health workers and the continuity of care in the COVID-19 pandemic: A mixed methods operational approach
Chikungunya virus adaptation to a low temperature in a French population Ae. albopictus
Building a database with a pattern mining system designed for virus nucleic acid data
Genetic diversity of arbovirus populations in Aedes aegypti mosquitoes from Colombia
An Aedes albopictus-driven epidemiological prediction for arboviral diseases outbreak in Europe
Evaluation in cellulo of the impact of insecticide usage on arbovirus population
Detection of newly produced NIRVS in mosquito persistently infected cells
An automatic pipeline to call SNPs from RNA-seq reads
A reference panel of dengue vector genomes
Meta-analysis of dengue transcriptomic data
An Aedes albopictus-driven epidemiological prediction for arboviral diseases outbreak in Europe
Detection of newly produced NIRVS in mosquito persistently infected cells
viral evolution around Ebola Treatment Centre in Macenta and according to disease outcomes
Transcriptomic analysis of blood cells from ebola infected patients
viral evolution around Ebola Treatment Center in Macenta
Environmental and human surveillance of polioviruses, VDPVs, and other enteroviruses in Madagascar during the switch from tOPV to bOPV
Recombination among enteroviruses
Role of RNA primary and secondary structure in non-homologous recombination
Analysis of Internal Deletions in EV71
Quantitative temporal analysis of cellular proteins regulated by HBV in primary human hepatocytes
Deciphering mutation signatures on hepatitis B virus genome
Correlative analysis between lipid droplets number and volume in hepatocytes infected by hepatitis C virus variants
Comparing viral replication of intergenotypic hepatitis C virus Core recombinants
Regulation of HIV replication by cellular DNA topology
Identification of new cellular parameters involved in HIV-1 integration selectivity
Single cell gene expression profiling of HIV-specific CD8+ T cells associated with HIV control
Factors determining HIV seeding in CD4+ T cell subpopulations
Diffusion des mutations de résistance du VIH : modèles et méthodes d’estimation
IgBlast on Galaxy
Regulation of HIV-1 integration selectivity by chromatin
Utilize mouse models to study infection by HIV-1
Characterization of the specific TCR repertoire preferentially expressed in spontaneously controlled HIV infection
Single cell analysis of HIV-specific CD4+ T cell differentiation
INNOV DIAG HPV
HPV RNA-SEQ
Analyses fonctionnel des protéines humains de type ubiquitin.
L'analyses phylogénétique par séquence protéique, temporal et géographical
Un workflow pour l'analyses des polymorphismes des souches de grippe saisonnier.
Variant effects on influenza virus proteins
functional enrichment of RNA processing factors associated with proteins of influenza viruses
Modulation of Flu transmission in Niger , according to climate variations over the past ten years
Transciptomic analysis of dendritic cell response during Lassa virus infection
Development of a bioinformatics workflow dedicated to the analysis of the viral metagenome: from NGS raw data to the identification of novel viruses
Study of the early pathogenesis during Lassa fever in cynomolgus monkeys and its correlation with the outcome
- Thomas BIGOT
- Marie-Agnès DILLIES
- Rachel LEGENDRE + 2 operators