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 : Single Cell

Related people (3)

Violaine SAINT-ANDRÉ

Group : DETACHED - Detached : Labex milieu intérieur

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.


Keywords
ATAC-seqChIP-seqEpigenomicsNon coding RNAPathway AnalysisRNA-seqSingle CellSystems BiologyTool DevelopmentTranscriptomicsData integrationGraph theory and analysisCell biology and developmental biology
Organisms
Human
Projects (1)

Sébastien MELLA

Group : PLATEFORM - Detached : Cytometry and Biomarkers

Sébastien


Keywords

Organisms

Projects (0)

    Related projects (31)

    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.



    Project status : Closed

    A long-term mission for an assigned CIH-embedded bioinformatician to provide bioinformatic support to the CIH community

    The Center for Human Immunology (CIH) supports researchers involved in translational research projects by providing access to 16 different cutting edge technologies. Currently, the CIH hosts over 60 scientific projects coming from 8 departments of the Institut Pastuer and 5 external teams. In order to respond to the growing needs of these projects in the area of single cell analysis, the CIH has introduced a significant number of single-cell/single-molecule technologies over the past 2-3 years. These new technologies, such as the Personal Genome Machine (PGM) and Ion Proton sequencers, iSCAN microarray scanner, Nanostring technology for transcriptomics profiling and real-time PCR machine BioMark, give rise to large datasets with high dimensionality. Such trend, in terms of data complexity, is also true for flow cytometry technologies (currently reaching over 20 parameters per cell). The exploration of this data is generally beyond the scope of scientists involved in translational research projects. In order to maximize the research outcomes obtained from the analysis of these rich datasets, and to ensure that the full potential of our technologies can be served to the users of the CIH, we would require a proximity bioinformatics support. A CIH-embedded bioinformatician would: 1) design and implement standard analysis pipelines for each of the data-rich technologies of the CIH; 2) provide regular ‘bioinformatics clinics’ to allow scientists the possibility to customize standard pipelines to their specific needs; 3) run trainings on the ‘R software’ platform and other data analysis tools (such as Qlucore) of interest for the CIH users. The objective would be to empower the users to run exploratory analysis by themselves, and to teach good practices in terms of data management and data analysis.    



    Project status : In Progress

    Transcriptional regulation of innate lymphoid cell plasticity versus differentiation

    Over the last years, innate lymphoid cells (ILC) have been increasingly investigated. Despite the absence of antigen specific receptors, they belong to the lymphoid lineage and represent important sentinels for tissue homeostasis and inflammation. They contribute to numerous homeostatic and pathophysiological situations via specific cytokine production. ILC are currently divided into three groups based on the expression of specific transcription factors and secretion of cytokines. We focus this study on fetal ILC3 development. We have observed that contrary to lymphocytes, ILC can migrate toward lymphoid organs, tissues and mucosal sites as lymphoid precusors and terminate their developmental program in situ. In the fetal spleen, we observe different stages of ILC3 with precursors that are already RORgt+ but could still give rise to other ILC fate. Hence, these splenic ILC3 precursors were sorted and analyzed by microarrays. The identification of gene expression differences was used to design a single cell transcriptomic assay. The single cell transcriptomic assay is based on this specific selection of primers for transcription factors and cytokine receptors. We evaluate their differential expression in single cells at different stages of their plasticity. The aim is to decipher the progression from an ILC precursor stage to an another in one cell. We are also using the new polaris technology to detect and evaluate at different early timepoints the sequence of molecular events for changing ILC cell fate. In this case, we chose to use the sc RNAseq technology. The single cell transcriptomic will be analyzed and bioinformatic programs will be applied in order to organize the sequential molecular events and to build a hierarchical developmental model in case of ILC cell fate decisions.



    Project status : In Progress

    Single cell analysis of HIV-specific CD4+ T cell differentiation



    Project status : Closed

    Defining Shigella-targeting of human lamina propria mononuclear cells using CyTOF technology

    Invasion of human intestinal epithelial cells by Shigella flexneri is secondary to the delivery of bacterial effectors into the host cell cytoplasm via a type III secretion system (T3SS). By using a beta-lactamase reporter tool we observed that in contrast to the epithelium, human lymphocytes are mainly targeted by injection of T3SS effectors not resulting in subsequent cell invasion (Pinaud et al., 2017). Furthermore, we observed that the targeting process, in form of successful injection of effectors into the host cell, is dependent on glycan-glycan interactions between bacterial and host cell surfaces rendering the targeting process to be dependent on the activation state of the host cell (Belotserkovsky et al., 2018). CyTOF technology is a research tool used for phenotypic analysis of complex cell population allowing for the simultaneous labelling of up to 40 different surface and intracellular marker without issues of compensation as present in regular flow cytometry (van Unen et al., 2016). Using CyTOF technology and the beta-lactamase reporter tool, we will perform a detailed analysis of Shigella targeting in a complex cell population using human lamina propria mononuclear cells (LPMCs), isolated from human colon explants. Analysis will address the question if specific cellular subsets are preferentially targeted in the intestinal environment and if this differs from targeting of peripheral blood mononuclear cells (PBMCs) diverging in their immune phenotypes and cellular activation.



    Project status : Closed

    Characterization of Yolk Sac Derived Progenitors in the Fetal Liver

    Erythromyeloid progenitors (EMPs) originate from the yolk sac during early mouse development and migrate to the fetal liver via the circulation where they undergo massive expansion and differentiation into hematopoietic lineages. These events occur prior to the intraembryonic emergence of hematopoietic stem cells (HSCs). Unlike HSCs, EMPs cannot give rise to lymphoid lineages, nor can they provide long-term repopulation. As such, they are considered a transient fetal population, yet it is EMP-derived hematopoiesis that supports the growth and survival of the embryo prior to the establishment of long-term hematopoitic stem cells (HSCs). Hematopoietic cell differentiation occurs along a hierarchy of progenitors with either lymphoid or myeloid fates. Common myeloid progenitors (CMPs) give rise to further restricted granulocyte-monocyte progenitors (GMPs) and megakaryocyte-erythrocyte progenitors (MEPs). This hierarchy has been well documented in adult hematopoiesis, which occurs solely from HSCs. However, fetal hematopoiesis encompasses dual origins of myeloid lineages that can originate from either EMPs or HSCs. Using genetic pulse chase labeling, we are able to distinguish these two ontologies by positively labelling EMPs and their progeny. Currently, fetal liver progenitors have been characterised by direct comparison to markers and expression profiles that are established for adult hematopoiesis. Yet, fetal hematopoietic markers may not be regulated in the same manner as their adult counterparts. Furthermore, distinguishing EMP- versus HSC-derived progeny is technically challenging and has not been properly addressed with respect to fetal liver myelopoiesis. Therefore, using our genetic pulse chase labeling approach, we would like to rebuild the differentiation tree among myeloid fetal liver progenitors. We are using high parameter flow cytometry to re-evaluate progenitor sub-populations with an expanded repertoire of markers. Since heterogeneity among progenitors (in terms of gene expression and differentiation potential) can be misrepresented and difficult to characterize on the population level, we want to investigate this on the single cell level using MARS-Seq in combination with index sorting.



    Project status : In Progress

    Defining the differential contributions of CD4+ and CD8+ anti-CD19 CAR T cells to tumor outcome, immune recruitment and toxicity

    Gene-modified T cells expressing a chimeric antigen receptor (CAR) targeting the CD19 molecule have demonstrated promising clinical efficacy in the treatment of B cell malignancies. However, the frequent relapses and toxic adverse events such as cytokine release syndrome represent hurdles to the success of CAR T cell therapies. In most clinical settings, CAR T cells are generated from a mixture of autologous CD4+ and CD8+ T cells before being infused into patients. This inter-patient heterogeneity within the composition of CAR T cell products renders the large variety of response efficacy and toxicity difficult to interpret. Using a model of B cell aggressive lymphoma developing in the bone marrow, we investigate the differential contributions of CD4+ and CD8+ anti-CD19 CAR T cells to tumor outcome and changes in the tumor microenvironment. Our first in vivo imaging and flow cytometry results suggest that CD4+ CAR T cells have poor cytotoxic potential compared to CD8+ CAR T cell. On the other hand, CD4+ CAR T cells were largely responsible for the cytokine release syndrome and have a unique role in boosting the accumulation of NK cells at the tumor site. Using single cell RNAseq, we aim to identify the changes in the bone marrow tumor microenvironment induced by CD4+ and CD8+ CAR T cells, focusing on the recruitment of host specific immune cell populations and their activation status. Identifying specific contributions of the CD4+ and CD8+ CAR T cells to immune cell recruitment and tumor outcome would help designing optimal CAR T cell products, with important clinical implications.



    Project status : Awaiting Publication

    Shigella targeting of human colonic Lamina Propria Mononuclear Cells



    Project status : Declined

    Identifying new population(s) of NK cells involved in memory to bacterial infection



    Project status : In Progress

    Single-cell and spatial transcriptomics of cells of the hematopoietic and stromal lineages in the zebrafish embryo



    Project status : In Progress

    Role of the histone demethylase Kdm6b in ILC2 maturation and functional activation



    Project status : Pending

    OLFACTORY DYSFUNCTION, NEUROINFLAMMATION AND NEUROINVASION IN POST-ACUTE COVID-19 SYNDROME

    It is increasingly clear that SARS-CoV-2 infection does not only affect the airways, but also the central nervous system (CNS) by interfering with neurons, glial cells, and the immune response in the brain, sometimes leading to long-lasting neurological signs, including anosmia and anxio-depressive symptoms. These and other persistent symptoms constitute a new entity that is currently called Long-COVID or Post-Acute COVID-19 Syndrome (PACS), however, it still lacks definitive diagnostic criteria and a universally accepted definition, as well a fully comprehensive view of its causative mechanisms. Our working hypothesis is that SARS-CoV-2 and/or the related inflammatory response can trigger a central mechanism in the CNS leading to the persistence of symptoms. The persistence of virus (or viral components, in particular viral RNA) along with the persistence of inflammation in the CNS may be an underlying cause for the occurrence of persistent symptoms in long COVID patients. Consequently, our main objective is to understand the origin and the mechanisms responsible for the persistent neurological symptoms such as long-term anosmia/ageusia or anxio-depressive symptoms post- SARS-CoV-2 infection, and we will focus on how viral neuroinvasion, neuroinflammation and/or signal transmitted by the neural route (lung-brain or visceral-brain axis) account for long-term post COVID-19 CNS alterations. At the end, the LongNeuroCOVID project should lead to several impactful results. From the scientific point of view, this work will improve the understanding of the general mechanisms involved in the spatio-temporal dynamics of SARS-CoV-2 infection, from entry in the CNS to causing long-term inflammation and CNS alterations. Describing these fundamental mechanisms should be of broader interest to the scientific community, as these results may be applicable to other, less understood, neuroinvasive pathogens. For public health, the characterization, in a relevant animal model and in an in vitro model of human neural networks, of the neurotropism of SARS-CoV-2 and its direct or indirect impact on long-term symptoms will be instrumental to the development of future therapies aimed at these clinical presentations. Finally, at the neuropsychiatric level, this study should provide new and interesting findings regarding the occurrence of anxio-depressive signs following the infection by SARS-CoV-2 and their relation with anosmia and neuroinflammation.



    Project status : Pending

    Epigenetic regulation of NK cells



    Project status : Pending