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
Searched keyword : Parasite
Related people (2)
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.
Association studiesGenomicsGenotypingBiostatisticsGeneticsEvolutionPopulation genetics
BacteriaParasiteHumanInsect or arthropodOther animal
- MLST versus Short Tandem repeats (Microsatellites) for Pneumocystis jirovecii genotyping(Maud GITS-MUSELLI - Molecular Mycology) - Pending
- Excess calorie intake early in life increases susceptibility to colitis in the adult(Ziad AL NABHANI - Microenvironment and Immunity) - In Progress
- Quality controls for human plasmas and serums stored in biobanks(HELENE LAUDE - Biological Resource Center of Institut Pasteur (CRBIP)) - Pending
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 joined the Bioinformatics and Biostatistics HUB at Pasteur Institute and she’s detached to the Biomics Pole in C2RT, where she is in charge of the bioinformatics analyses for transcriptomics and epigenomics projects. She’s also involved in Long Reads (PacBio and Nanopore) developments with other bioinformaticians of Biomics Pole.
AlgorithmicsChIP-seqEpigenomicsNon coding RNATranscriptomicsGenome analysisProgram developmentScientific computingSofware development and engineeringIllumina HiSeqRead mappingSequencingWorkflow and pipeline developmentChromatin accessibility assaysPac BioRibosome profiling
BacteriaFungiParasiteHumanInsect or arthropodOther animal
- Finding SNPs associated with Dengue infection in the mosquito Aedes aegypti(Merkling SARAH - Insect-Virus Interactions) - Pending
- Identification d’une mémoire épigénomique à Streptococcus pneumoniae(Christine CHEVALIER - Chromatin and Infection) - In Progress
- Genome-wide interactions between HP1g and RNA.(Christophe RACHEZ - Epigenetic Regulation) - In Progress
Related projects (22)
Across bacterial, archaeal and eukaryotic kingdoms, heat shock proteins (HSPs) are defined as a class of highly conserved chaperone proteins that are rapidly induced in response to temperature increase through dedicated heat shock transcription factors. While this transcriptional response governs cellular adaptation of fungal, plant and animal cells to thermic shock and other forms of stress, early-branching eukaryotes of the kinetoplastid order, including trypanosomatid parasites, lack classical mechanisms of transcriptional regulation and show largely constitutive expression of HSPs, thus raising important questions on the function of HSPs in the absence of stress and the regulation of their chaperone activity in response to environmental adversity. Understanding parasite-specific mechanisms of stress-response regulation is especially relevant for protozoan parasites of the genus Leishmania that are adapted for survival inside highly toxic phagolysosomes of host macrophages causing the various immuno-pathologies of leishmaniasis. To gain first insight into the role the heat shock repsonse for Leishmania differentiation and pathogenicity, we are studying the evolution and function of members of the HSP70 protein family combining bio-informatics and transgenics apporahces.
The aim of the project is to create a viewer that will help visualisation and correlation between genomic, transcriptomic, proteomic and metabolomic data generated by the comparison of amastigote and promastigote stages of the Leishmania donovani parasite.
Mise a disposition d'un(e) bioinformaticien(ne) du hub pour les analyses bioinformatiques du transcriptome et de l epigenome
La PF Transcriptome et Epigenome développe des projets de séquençage à haut débit (collaboration et service) avec des équipes du Campus. Ceux-ci couvrent l'ensemble des thématiques du campus ainsi qu'une large gamme d'organismes (des virus aux mammifères). La plate-forme exerce des activités de biologie humide (construction des librairies et séquençage) et de biologie sèche (analyse bioinformatiques et statistiques). La personne mise a disposition interagira étroitement avec les autres bioinformaticiens du pôle BioMics et du Hub. Ses activités concerneront notamment: - La participation à la conception et à la mise en place des projets avec les équipes demandeuses, la prise en charge des analyses et le reporting aux utilisateurs - La mise en place d'un workflow d'analyse bioinformatique des données de transcriptome /épigénome en étroite collaboration avec le C3BI, la DSI et les autres bioinformaticiens du pole. Ce workflow permettra le contrôle qualité des données, leur prétraitement, le mapping des séquences sur les génomes/transcriptomes de réference, et le comptage des reads pour les différents éléments de l'annotation - L'adaptation du workflow d'analyse aux questions biologiques et aux organismes étudiés dans le cadre des activités de la PF - L'activité de veille technologique et bibliographique (test et validation de nouveaux outils d'analyse, updates d'outils existants...) - La mise en place et le développement d'outils d'analyse adaptés aux futurs projets de la PF: single cell RNAseq, métatranscriptome, ChIPseq, analyse des isoformes de splicing.. Ceci se fera notamment via la réalisation d'analyses dédiées avec certains utilisateurs. Les outils mis en place et validés dans ce cadre seront ensuite utilisés pour l'ensemble des projets. - L'activité de communication et de formation (participation aux réunions du consortium France Génomique,formation permanente à l' Institut Pasteur… - la participation a d autres projets du Pole BioMics (selon disponibilité) Bernd Jagla, qui était le bioinformaticien de la plateforme a rejoint le Hub au 1er janvier 2016. Rachel Legendre est mise a disposition depuis le 2 novembre 2015 et remplace Bernd Jagla. Je souhaite que Rachel Legendre soit mise à disposition de la plateforme pour une durée d'au moins 2 ans.
The Sudanese L. donovani strain Ld1SA is the most important experimental reference strain in our field and has been used for various systems level analysis (DNAseq, RNAseq, proteomics). However, all these analyses are strongly compromised by the fact that the current L. donovani genome reference strain LdBPK is from Nepal and very different from the Sudanese isolate (only 60% of DNAseq reads can be mapped).
BioHub LeiSHield project This proposal summarizes the contribution of the BioHub to the LeiSHield action that may be carried out by a single BioHub Leishmania coordinator (Giovanni Bussotti). The coordinator will be implicated in the following actions: 1) Establish the link between LeiSHield members and the BioHub team for all questions regarding data analysis and interpretation. The coordinator will present to the BioHub the bio-informatics needs of the LeiSHield partners. Short (easy) tasks will be answered directly (following the BioHub open door strategy). For more involved tasks i twill be asked to deposit projects via the C3BI web site. 2) Coordinate the setup of an HTseq analysis pipeline, including quality control, read mapping, determination of CNV and SNPs, and data visualization using a combination of tools available at the BioHub, such as SyntView and Listeriomics. A link to Cedric Notredame will be established as scripts for Leishmania have been created there. 3) Oversee the submission of DNA from the different LeiSHield WPs to the IP HTseq facility, follow the progress, store the acquired data, and dispatch the datasets to the corresponding WP leaders. This will be coordinate with the Biomix infrastrcuture. 4) Apply the HTseq analysis pipeline (see point 1) on selected data sets for defined work packages, including WP4 (“Analysis of newly isolated anthroponotic L. donovani s.l. strains from Cyprus and correlation of genotypic profiles to tropism and drug resistance”), WP6 (“Population genetics of Brazilian L. infantum isolates from endemic areas presenting distinct transmission cycle”), WP7 (“Leishmania dovovani genome sequence diversity and disease tropism in the Sudan”), and WP9 (“Systems-wide analysis of Leishmania genomic and transcriptomic adaptation”). 5) Co-organize a course on HTseq data visualization (June 2016) with members of the BioHub team.
ANALYSIS OF TRANSCRIPTIONAL MODULATIONS RELATED TO CELL DEATH PROCESSES IN MURINE BONE-MARROW DERIVED MACROPHAGES AND DENDRITIC CELLS INFECTED BY LEISHMANIA AMAZONENSIS
Aim : In vitro infection of innate immune cells by L. amazonensis (L.am.) seems to be associated to an increase in resistance to cell death of infected cells. This project aims at deciphering the impact of in vitro L. amazonensis (L.am.) amastigotes infection on cell death processes including apoptosis, autophagy, pyroptosis and necroptosis in different host cells, i.e. Bone-marrow- derived macrophages (BMDMs) and dendritic cells (BMDCs) after one day of infection. Material : RNA samples were obtained from control and infected BMDMs (BALB/c mice) or BMDCs (BALB/c, C57BL/6 and DBA/2 mice) after their sorting by Fluorescence Activated- Cell sorting. For BALB/c BMDCs, amastigotes were also added to cells in presence of immune serum to trigger their opsonization. Samples were analysed a few years ago at the « Plateforme Transcriptome et Epigénome » with the Affymetrix technology. RNAs from BMDMs and BMDCs were analysed with the Affymetrix Mouse430_2 GeneChips and the Affymetrix Mouse Gene ST 1.0 arrays respectively.
ANALYSIS OF TRANSCRIPTIONNAL MODULATIONS INDUCED IN C57BL/6 BONE-MARROW DERIVED MACROPHAGES INFECTED BY LEISHMANIA AMAZONENSIS IN PRESENCE OR ABSENCE OF INFLAMMASOME-ACTIVATING CONDITIONS
Aim : When L. amazonensis (L.am.) amastigotes infect BMDMs, they induce multiple strategies to allow their survival and multiplication. This project aims at deciphering the transcriptional modulations induced after three days of in vitro infection of C57BL/6 BMDMs with L. amazonensis (L.am.) amastigotes, in unstimulated conditions, or conditions that induce NLRP3 inflammasome activation.
Mining the Plasmodium genome to identify novel blood stage antigens for use as malaria vaccine candidates
Malaria remains a major problem in many tropical countries with Plasmodium falciparum accounting for up to 1 million deaths, primarily in infants and children residing in endemic areas of sub-Saharan Africa. P. vivax, the other important species for human malaria is geographically more widespread and causes 80-100 million cases of malaria each year. All the pathology related to malaria is attributed to the blood stage of the parasite life cycle during which Plasmodium merozoites invade and multiply within host erythrocytes. We are interested in understanding the process of RBC invasion by malaria parasites at the molecular level with the goal of blocking their interaction with antibodies to inhibit invasion and kill the parasite. The first generation of recombinant blood stage malaria vaccine candidates based on antigens such as the merozoite surface protein (MSP1) and apical merozoite antigen-1 (AMA01) have been tested in field trials and failed to provide any efficacy against P. falciparum malaria. There is thus an urgent need to identify novel parasite antigens that play a role in invasion and can serve as vaccine candidates that elicit strong antibody responses that block blood stage parasite growth. In this project, we propose to mine the P. falciparum and P. vivax genome databases using bio-informatic tools to identify potential, novel blood stage invasion related parasite antigens that can serve as potential candidates for blood stage malara vaccines. Criteria such as expression profile, presence of conserved domains in orthologs from related plasmodium species, limited polymorphisms in field isolates, interaction with other invasion related proteins and localization to apical organelles or merozoite surface will be used to interrogate P. falciparum and P. vivax genome sequence data and identify potential invasion related antigens that will be selected for validation as vaccine candidates for malaria.
Chromosome amplification is commonly used by Leishmania during adaptation to environment. In this context it is challenging to look for genes relevant for parasite virulence/attenuation/drug resistance... To restrict this chromosomal amplification, a cosmid approach (CoSeq) has been chosen to select for genes that provide fitness gain to Leishmania donovani parasites in culture and in the animal. Therefore, a cosmid library has been generated with genomic DNA from the parasites which needs to be sequenced to control for genome coverage before transfection to the parasites. The transfected parasites will then be injected to animals or submitted to different culture conditions. Only those transfected with cosmids providing advantage under the studied conditions will be selected and will replicate. These cosmids will be extracted from the parasites and will be sequenced to reveal genes relevant for the parasite survival. The C3Bi would be implicated in the analyses of the sequencing data obtained from the PF1 (retrieve the data, mapping of the reads to Leishmania genome, estimation of the genome coverage, listing of genes selected for a given condition...).
Background: PLA2 is known to regulate vesicle secretion in diverse eukaryotic cells. We are interested in determining the putative role of PLA2 in secretion of apical vesicular organelles called micronemes and rhoptries in P. falciparum merozoites. PLA2 inhibitors such as 4-BPB are known to block growth of the related Apicomplexan parasite Toxoplasma gondii. There are 3 annotated PLA2 genes in the P. falciparum genome database (Pf3D70209100, PF3D71358000, PF3D70924000). We would like to analyze these putative PLA2 genes using bioinformatics to support our drug development studies.
Prediction of RNA-RNA interactions between a family of GC-rich ncRNAs and nascent transcripts of virulence genes in Plasmodium falciparum
In Plasmodium falciparum a virulence gene family with 60 var genes codes for the PfEMP1 surface proteins, which undergo antigenic variation. This epigenetically controlled mechanism promotes immune evasion of the parasite. As ncRNAs are emerging as relevant regulators of gene expression we are investigating a GC-rich ncRNA gene family consisting of 15 highly homologous members all positioned next to var gene clusters. We recently found that GC-rich ncRNA transcript associates with the distinct nuclear expression site in which a single var gene is transcribed. We hypothesize that GC-rich ncRNAs interact with the nascent mRNA of var virulence genes. We intend to predict potential RNA-RNA interaction with thermodynamic calculation provided by the RNAup software. In silico prediction of potential binding sites and strength of interaction will help to generate hypotheses and inform our further experimental design.
Identification of new or unexpected pathogens, including viruses, bacteria, fungi and parasites associated with acute or progressive diseases
Microbial discovery remains a challenging task for which there are a lot of unmet medical and public health needs. Deep sequencing has profoundly modified this field, which can be summarized in two questions : i) which pathogens or association of pathogens are associated with diseases of unknown etiology and ii) among microbes infecting animal (including arthropod) reservoirs, which ones are able to infect large vertebrates, including humans. We are currently addressing these two questions and our current request comes with the willingness for Institut Pasteur to increase its contribution and visibility of this thematic, in particular in relation with hospitals and the Institut Pasteur International network (IPIN). We expect to identify new microbes associated with human diseases, and this is expected to pave the way for basic research programs focusing on virulence mechanisms and host specificity, and will also lead to phylogenetic and epidemiological studies (frequency of host infection, mode of transmission etc...), as well as the development of improved diagnostic tests for human infections. Our objective is also to contribute to the efforts of Institut Pasteur in the field of infectious diseases, by building a pipeline, from sample to microbial identification, able to manage large cohorts of samples. This project is currently supported by the LABEX IBEID and the CITECH, and critically requires a bioIT support, justifying this application. Partners include different hospitals including Necker-Enfants malades University Hospital regarding patients with progressive disease, different IPIN laboratories, as well as INRA and CIRAD regarding animal/arthropod reservoirs.
We are interested in determining the differences in the transcriptome of select developmental stages of the malaria parasite, Plasmodium.
Gene ontology analysis of RNAseq data from uninfected and Leishmania-infected mouse macrophages. Scientific context During the course of cutaneous or visceral disease in humans or experimental animal models, the resolution of leishmanial infections or the control of parasite growth is dependent on appropriate innate and adaptive immune responses developed by the parasitized host. Leishmania largely evades and subverts these responses by its intracellular life style inside the mammalian host, where the parasites develop into amastigotes mainly within macrophages (BMDMs). We have focused our interest in the BMDM inflammasome and the way Leishmania amastigotes interfere or subvert BMDM inflammatory responses. Our recent data are in favor of an absence of stimulation, even a down-regulation of the inflammasome in BMDMs harboring replicating amastigotes at the gene and protein expression levels. To go further on this, we have performed RNAseq experiments on uninfected and infected BMDMs. This project was done at the “Transcriptome and Epigenome” platform and in close collaboration with the C3BI for normalization and statistical analysis procedures. Objective In the present proposal we will perform a deep analysis of the repartition of modulated genes between the different conditions using these RNAseq data. Using C3Bi expertise we will classify known functions of modulated genes into GO aspects i.e. molecular function, cellular component and biological process, visualize gene annotations and perform statistical analyses for the distribution of the annotated genes over the GO hierarchy for the different gene lists analyzed. Hopefully, these analyses will bring us a better understanding of the mechanisms underlying the subversion of BMDM functions in the innate and adaptive immune response to Leishmania infection which is a prerequisite to design novel anti-parasitic intervention strategies targeting the infected host cell rather than the parasite.
We are generating massive amounts of omics data for Leishmania donovani. Anna Zukhova enabled to use the BiNGO module of Cytoskape to perform and visualize our GO enrichment analyses. We would like to continue our collaboration and ask Anna's help to assess the current state of GO annotation of the Leishmania genome and if possible to complete it using domain searches or ortholog mapping from other genomes, including L. major, T. bruce or model organisms such as yeast. We expect that improvement of GO annotation will also us to better reveal enriched GO terms in our datasets and generate testable hypotheses.
Antimalarial drug resistance in Africa: A comprehensive molecular analysis of the emergence of artemisinin resistant parasites in Africa
We are involved, in collboration with the WHO, in the SaMARA which aims at detecting the emergence of antimalarial drug resistance in Africa. Samples (dried blood spots) are collected from the Nantio
Asymptomatic pathogen carriage in stunted and non-stunted children living in Antananarivo, Madagascar
This project is integrated in the analysis of the gut ecosystem of children implicated in the AFRIBIOTA project, a translational project performed within a consortium of researchers and medical doctor
Looking for DNMT (DNA methyltransferase) orthologs in Leishmania which could be potential targets of epigenetic inhibitors active against the parasite.