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 : Human
Related people (10)

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 (23)
Etienne KORNOBIS
After a PhD in Biology in 2011 on population genetics and phylogeography on amazing little amphipods (Crangonyx, Crymostygius) at the University of Reykjavik (Iceland), I pursued my interest in Bioinformatics and Evolutionary Biology in various post-docs in Spain (MNCN Madrid, UB Barcelona). During this time, I investigated transcriptomic landscapes for various non-model species (groups Conus, Junco and Caecilians) using de novo assemblies and participated in the development of TRUFA, a web platform for de novo RNA-seq analysis. In July 2016, I integrated the Revive Consortium and the Epigenetic Regulation unit at Pasteur Institute, where my main focus were transcriptomic and epigenetic analyses on various thematics using short and long reads technologies, with a special interest in alternative splicing events detection. I joined the Bioinformatics and Biostatistics Hub in January 2018. My latest interests are long reads technologies, alternative splicing and achieving reproducibility in Bioinformatics using workflow managers, container technologies and literate programming.
KeywordsData managementData VisualizationSequence analysisTranscriptomicsWeb developmentGenome analysisProgram developmentExploratory data analysisSofware development and engineeringGeneticsEvolutionRead mappingWorkflow and pipeline developmentPopulation geneticsMotifs and patterns detectionGrid and cloud computing
Organisms
HumanInsect or arthropodOther animalAnopheles gambiae (African malaria mosquito)Mouse
Projects (3)
- Build a software to decipher Gephyrin alternative transcripts obtained with long read sequencing(allemand ERIC - Epigenetic Regulation) - Closed
- Transcriptomics of Anopheles – Plasmodium vivax interactions towards identification of malaria transmission blocking targets(Catherine BOURGOUIN - Functional Genetics of Infectious Diseases) - Closed
- Mapping of Enhancers from transcriptome data(Christian MUCHARDT - Epigenetic Regulation) - 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 (24)
- Exploring pathogenic mechanisms of chronic inflammatory disease: unresolved issues in IL-23/IL-17 biology(YAHIA HANANE - Immunoregulation) - Pending
- Identification of factors influencing the activity of bacteriophage within the gut of mammals(Devon CONTI - Other) - In Progress
- HKA: systemic analysis of two-component signalling(Arnaud FIRON - Biology of Gram-Positive Pathogens) - In Progress

Christophe MALABAT
After a PhD in biochemistry of the rapeseed proteins, during which I developed my first automated scripts for handling data processing and analysis, I join Danone research facility center for developing multivariate models for the prediction of milk protein composition using infrared spectrometry.
As I was already developing my own informatics tools, I decided to join the course of informatic for biology of the Institut Pasteur in 2007. At the end of the course I was recruited by the Institute and integrate the unit of “génétique des interactions macromoléculaires” of Alain Jacquier.
Within this group, I learn to handle sequencing data and I developed processing and analysis tools using python and R.
I also create a genome browser and database system for storing, retrieving and visualizing microarray data.
After 8 years within the Alain Jacquier’s lab, I join the Hub of bioinformatics and biostatistics as co-head of the team.
ClusteringData managementSequence analysisTranscriptomicsWeb developmentDatabaseGenome analysisProgram developmentScientific computingExploratory data analysisData and text miningIllumina HiSeqRead mappingLIMSIllumina MiSeqHigh Throughput ScreeningMultidimensional data analysisWorkflow and pipeline developmentRibosome profilingMotifs and patterns detection
Organisms
Projects (10)
- SHERLOCK4HAT - WP1.1(Brice ROTUREAU - Group: Trypanosome transmission) - Closed
- Remettre les servers Genolist comme LegioList, TuberclListe, Colibri etc en service(Carmen BUCHRIESER - Biology Of Intracellular Bacteria) - Closed
- Identification of eukaryotic 5'UTRs(Arnaud ECHARD - Membrane Traffic and Cell Division) - Closed

Violaine SAINT-ANDRÉ
After graduating from Paris VI University with a PhD in Genetics on the “Role of histone protein post-translational modifications in splicing regulation” that I performed in the Epigenetic Regulation unit at the Institut Pasteur, I carried out two post-doctoral experiences. I first worked for three years as a postdoctoral associate of the Whitehead Institute for Biomedical Research/MIT in Cambridge (USA). My main project consisted in the integration of genomic and epigenomic data in order to predict the transcription factors that are potentially at the core of the regulation of the cell-type specific gene expression programs. I then joined the Institut Curie where I deepened my experience in multi-omics data analyses and integration to identify non-coding RNAs involved in cancer progression. I have recently joined the HUB-C3BI of the Institut Pasteur where I am performing high-throughput data integration to better understand biological complexity and contribute to precision medicine development.
KeywordsATAC-seqChIP-seqEpigenomicsNon coding RNAPathway AnalysisRNA-seqSingle CellSystems BiologyTool DevelopmentTranscriptomicsData integrationGraph theory and analysisCell biology and developmental biology
Organisms
Human
Projects (1)

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
Amaury VAYSSE
Amaury
KeywordsOrganisms
Human
Projects (6)
- Understanding the mode of action of epigenetic inhibitors active against Plasmodium falciparum(Irina DOBRESCU - Biology of Host-parasite Interactions) - Pending
- A cost-effective molecular Tool for Strengthening Antimalarial drug Resistance surveillance in Africa (TSARA)(Didier MENARD - Group : Malaria Genetic and Resistance) - In Progress
- Search for genetic determinants of aminoglycoside tolerance(Zeynep BAHAROGLU - Bacterial Genome Plasticity) - In Progress
Vincent LAVILLE
NA
KeywordsBiostatistics
Organisms
Human
Projects (0)

Maguelonne ROUX
to complete
KeywordsComparative Genomics
Organisms
Human
Projects (0)
Nicolas TRAUT
Neuroanatomie Appliquée et Théorique
KeywordsOrganisms
Human
Projects (0)
Related projects (131)
Mapping the cell surface signature of the developing mouse heart
Characterisation of skeletal muscle stem cell properties in distinct physiological states
Transcriptome of Human sperm
Analyse de données de miRNA
Role of SUMO, a new epigenetic mark, in stress response
Mise a disposition d'un(e) bioinformaticien(ne) du hub pour les analyses bioinformatiques du transcriptome et de l epigenome
Transcriptome du fibroblaste cutané humain: une approche pré-expérimentale
Analyses protéine-protéine interactions
Analyses fonctionnel des protéines humains de type ubiquitin.
A long-term mission for an assigned CIH-embedded bioinformatician to provide bioinformatic support to the CIH community
Antibody sequencing by MS: Automation of analysis
Transciptomic analysis of dendritic cell response during Lassa virus infection
Factors determining HIV seeding in CD4+ T cell subpopulations
secretome analysis of human intestinal cells during shigella invasion
Label-free quantitative proteomics of Human Macrophages infected by M. tuberculosis
Methylome analysis of a human progeroid disease for the detection of progeroid-specific alterations and their link with regular ageing
Molecular analysis of muscle stem cells
Dissecting the peptidoglycan trafficking machinery using gene trap mutagenesis in near-haploid human cells
Deciphering the composition dynamics of infant gut microbiome
Regulation of Sirtuin 2-dependent histone deacetylation during bacterial infection
Measles virus protein C interplay with cellular apoptotic pathways; applications for cancer treatment
Impact of hepatic inflammation on microbiota
Transcriptional regulation of innate lymphoid cell plasticity versus differentiation
Mapping the genomic architecture of human neuroanatomical diversity
RNA analysis underlying phenotype of mouse model for autism
Gene Ontology and sequence analysis of proteomics data on mycolactone effects on dendritic cells.
Cytokinesis study
Activation of plasmacytoïd dendritic cells by arenaviruses : transcriptomic analysis
Analysis of DNA methylation in the presence and absence of antibiotics in wt and mutant V. cholerae.
In silico analyses of a novel LincRNA potentially involved in type I IFN response
JASS: an online tool for the joint analysis of GWAS summary statistics
- Vincent GUILLEMOT
- Hanna JULIENNE
- Pierre LECHAT + 1 operator
Single cell analysis of HIV-specific CD4+ T cell differentiation
Comparative analysis of gene expression in different human cell clones
Quantitative temporal analysis of cellular proteins regulated by HBV in primary human hepatocytes
Genetic profile of patients with dyslexia
ModeMood: Modeling Mood Disorders
Metabolic characterization of ILCs under homeostatic or stress conditions
Heritability of the melatonin synthesis pathway in Autism Spectrum Disorders
Genotype to phenotype analysis of immune responses in chronic inflammatory diseases
Analysis of IFITM RNA levels in vraious cell types and tissues
DNA encapsulation of human resources for research projects on immune system and inflammatory diseases
Physical Contact between human and non human primates in Southeastern Cameroon
Insight into the Immune System: A bioresource and data-sharing platform to study chronic inflammatory diseases (IsIShare)
Analysis of methylation for HIV patients with co-infections
Identification of the mouse and/or rat orthologues of the human gene ANOS1, responsible for the X-chromosome-linked form of Kallmann syndrome
MOODel: Modeling Mood Disorders
Exploring immunological mechanisms of human graft-verus-host disease after hematopoietic stem cell transplantation
Dynamic and integrative multidimensional OMICs analysis of the cellular senescence fate
The Flemmingsome: the proteome of intact cytokinetic midbodies
Identification of immune response signatures that correlate with therapeutic responses to TNF inhibitors using machine-learning algorithms
functional enrichment of RNA processing factors associated with proteins of influenza viruses
Identification of eukaryotic 5'UTRs
High content screening of mitochondrial morphology defects in mitochondrial genetic diseases
Toxin induced dephosphorylation of H3S10
Role of the Topoisomerase 1 and Guanine quadruplexes as transcriptional regulators
Asymptomatic pathogen carriage in stunted and non-stunted children living in Antananarivo, Madagascar
Functional interactomics of SKAP2
Determination of host response elicited by different Salmonella lifestyles
Identification d’une mémoire épigénomique à Streptococcus pneumoniae
- Claudia CHICA
- Rachel LEGENDRE
- Adrien PAIN + 1 operator
Gene expression and its regulation during and after inpatient detoxification of cocaine: a link to relapse?
Analyse transcriptionnelle du cellules cancéreuse intestinal vs normales après co-culture avec la bactérie associée au cancer Streptococcus gallolyticus
Build a software to decipher Gephyrin alternative transcripts obtained with long read sequencing
Optimisation of freeze and conservation method of peripherical blood mononucleated cells
The anti-IgE antibody Omalizumab induces adverse reactions through engagement of Fc gamma receptors
Quality controls for human plasmas and serums stored in biobanks
Antiviral activities of anti-HIV-1 antibodies
Mechanisms of HIV-1-infected cells susceptibility to Fc effector functions
Multiparametric immunophenotyping of whole blood in IFN-treated multiple sclerosis patients
Proteome remodeling induces by the Cytotoxic Necrotizing Factors 1
ICARE
Assessing the role of gut microbiota in spondyloarthritis patients and impact of anti-TNF treament on its composition
Bioinformatic analysis of paired alpha and beta T cell receptor sequences obtained at the single cell level by illumina sequencing
Role of Tunneling nanotubes in Glioblastoma
Impact of APC gene mutations on anti-tumoral immune responses
Shigella targeting of human colonic Lamina Propria Mononuclear Cells
Deciphering the transcriptome profil during rabies infection in brain in mouse and in human
Flemmingsome: A Midbody Remnant Proteome Database
Modulation of cellular pathways involved in neuropathology of rabies infection
Mitochondrial polarization identifies functionally mature human NK cells
Parvimonas micra's impact on primary human colonic cells DNA methylation
Small RNA signature on RIG-I like receptors
French GWAS Covid webpage
Correlative analysis between lipid droplets number and volume in hepatocytes infected by hepatitis C virus variants
Effect of metabolic disturbance on the host transcriptional profile during Chlamydia infection
Setup of bioinformatic pipelines for paleo(meta)genomics
Induction of highly efficient HIV-specific CD8+ T cell responses
Phages - bacteria interactions network of the healthy human gut
Single-cell characterization of autoreactive IgG-secreting cells in Immune thrombocytopenia
Regulation of IL-23 Receptor expression
Defining the effects of TNF-blockers and IL-17A-inhibitors on immune responses in spondyloarthritis patients, analysis of protein and gene expression signatures
Transcriptional profiling of the innate immune response of human fibroblasts of the LabEx Milieu interieur collection: interindividual variability and response to infection
Page web modélisation covid-19 pasteur
JASS 2 : Integrating functional annotation to a multi-trait GWAS web application
PacBio sequencing of DM1 cells treated with a TALEN
Imprinting by immune cross regulation modulate airway allergic inflammation
Human ORFeome LIMS and website
Understanding IL-23 role in chronic inflammatory diseases in innate and adaptative immune cells
Tests serologics anti-CNF1
Etude de l’évolution des Troubles Olfactifs chez les patients ayant une perte de l’odorat persistante des suites de la COVID-19
Modification and reliance of Chlamydia trachomatis on host cell metabolism
Characterization of a broad spectrum chemical inhibitor targeting the endocytic pathway to prevent bacterial intoxications.
Regulation of IL23R expression
Clinical and biological characterisation of auto-antibodies to the nicotinic receptors in major psychiatric disorder patient
An online database of RNA-small molecules complexes for rational drug design
Effect of Chlamydia trachomatis infection on histone methylation and consequences
PacBio sequencing analysis of DM1 cells
Measles virus type 1 infection disturbs the mitochondrial network leading to type I interferon production through the RNA polymerase III/RIG-I pathway
Modelization of the timing of abscission
Exploring pathogenic mechanisms of chronic inflammatory disease: unresolved issues in IL-23/IL-17 biology
User experience design for Oncodash
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
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