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 : Other animal
Related people (5)

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
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) - In Progress
- Transcriptomics of Anopheles – Plasmodium vivax interactions towards identification of malaria transmission blocking targets(Catherine BOURGOUIN - Functional Genetics of Infectious Diseases) - In Progress
- Mapping of Enhancers from transcriptome data(Christian MUCHARDT - Epigenetic Regulation) - In Progress

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
Blaise LI
I obtained a PhD in phylogeny in 2008 at the Muséum National d’Histoire Naturelle in Paris, then worked as a post-doc in Torino (Italy, 2009 – 2011) and Faro (Portugal, 2011 – 2013) where I worked on methodological aspects of phylogeny. In 2013, I have been hired as research engineer in bioinformatics at the Institut de Génétique Humaine in Montpellier where I wrote tools to analyse high-throughput sequencing data, especially small RNA-seq. This is also the kind of job I do now at Institut Pasteur, since 2016. I enjoy programming in Python, I’m interested in evolutionary biology, and I find teaching the UNIX command-line and other practical computer skills a rewarding activity. I’m also particularly involved in a course introducing PhD students (and sometimes other staff at Institut Pasteur) to R programming and basic descriptive statistics. The course support is available on-line and can hopefully be studied autonomously: https://hub-courses.pages.pasteur.fr/R_pasteur_phd/First_steps_RStudio.html One of my main activities is the development of automated data analysis workflows using Snakemake. My published work is available here: http://www.normalesup.org/~bli/useful.html
KeywordsGenomicsNon coding RNATranscriptomicsSofware development and engineeringGeneticsWorkflow and pipeline development
Organisms
Insect or arthropodOther animalDrosophila melanogaster (Fruit fly)C. elegans
Projects (6)
- Bioinformatic analysis of paired alpha and beta T cell receptor sequences obtained at the single cell level by illumina sequencing(Lisa CHAKRABARTI - Virus and Immunity) - In Progress
- Training project for bacterial ChIP-seq Analysis on Streptococcus agalactiae(Maria vittoria MAZZUOLI - Biology of Gram-Positive Pathogens) - Closed
- Understanding the pathways of small RNA production during Meiotic Silencing by Unpaired DNA (MSUD) in the fungus Neurospora crassa(Eugene GLADYSHEV - Other) - 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 (11)
- SHERLOCK4HAT - WP1.1(Brice ROTUREAU - Group: Trypanosome transmission) - In Progress
- 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
Related projects (56)
search for transcrition factors upregulating Tgfb1 expression in FHL2-/- cells
Transcriptome of Human sperm
gRNA library design
Molecular analysis of muscle stem cells
Analyse de données de microarray
sequence conservation in the vicinity of Gli3 binding sites in the mouse genome
Mise a disposition d'un(e) bioinformaticien(ne) du hub pour les analyses bioinformatiques du transcriptome et de l epigenome
ANALYSIS OF TRANSCRIPTIONAL MODULATIONS RELATED TO CELL DEATH PROCESSES IN MURINE BONE-MARROW DERIVED MACROPHAGES AND DENDRITIC CELLS INFECTED BY LEISHMANIA AMAZONENSIS
individual-nucleotide resolution Cross-Linking and ImmunoPrecipitation (iCLIP) of Argonaute proteins in C. elegans
HSC3D
Zebrafish microbiota
Rift valley fever NSm protein functional study
Identification of genes involved in the attenuation of virulence of rough M. abscessus Tn5 mutants in zebrafish
RNA analysis underlying phenotype of mouse model for autism
Utilize mouse models to study infection by HIV-1
Comparative analysis of gene expression pattern between samples of tumor and normal mice tissue
Gene ontology analysis of RNAseq data from uninfected and Leishmania-infected mouse macrophages
Comparative analysis of transcriptomic and proteomic data to study RNA and protein expression regulation during RVFV infection in mice.
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
Infection of Ixodes ricinus by Borrelia burgdorferi sensu lato by in peri-urban forests of France
Transcriptional profile of Nod2+ neurons upon MDP signaling
Comparing V-J gene usage for specific antibody generation
the role of host defense in female genital tract infection by Chlamydia trachomatis
Analysis of IFITM RNA levels in vraious cell types and tissues
Characterization of the role of Argonaute proteins in regulating germline gene expression at the transcriptional and the post-transcriptional levels.
Identification of Ago2-bound nuclear transcripts and genomic loci in adult zebrafish neural stem cells
Physical Contact between human and non human primates in Southeastern Cameroon
Identification of the mouse and/or rat orthologues of the human gene ANOS1, responsible for the X-chromosome-linked form of Kallmann syndrome
Characterization of Yolk Sac Derived Progenitors in the Fetal Liver
Heterogeneity of tissue resident stromal cells
Analysis of neuronal population dynamics in rodents during virtual navigation
Cellular plasticity during mammary gland development
Genome-wide interactions between HP1g and RNA.
Tissue-resident stromal cell heterogeneity
Genetic and statistical analysis of data produced with the Collaborative Cross at the Institut Pasteur
- Pascal CAMPAGNE
- Vincent GUILLEMOT
- Rachel TORCHET + 1 operator
Build a software to decipher Gephyrin alternative transcripts obtained with long read sequencing
Characterization of Yolk Sac Derived Progenitors in the Fetal Liver
Early transcriptional signature of T-cell memory after dengue vaccination
Heterogeneity of the skeletal muscle microenvironment
The anti-IgE antibody Omalizumab induces adverse reactions through engagement of Fc gamma receptors
Defining the differential contributions of CD4+ and CD8+ anti-CD19 CAR T cells to tumor outcome, immune recruitment and toxicity
Identification of mouse skin macrophage subpopulations
Secretome Analysis of OIS IL6KO SASP
Deciphering the transcriptome profil during rabies infection in brain in mouse and in human
Functinal analysis of proteome and phopshoproteome changes in murin intestine – mechanism of Streptococcus gallolyticus-induced carcinogenesis
Analysis of microbiota in Anopheles mosquitoes
Collaboration between CETEA, C2RA and Hub for optimization of experimental designs (3R)
- Anne BITON
- Pascal CAMPAGNE
- Vincent GUILLEMOT + 3 operators