Collaborations

Academic or Industrial collaboration that wants to utilise the MI data and/or samples has to submit a project to the MI data and sample committee. The projects approved by this committee are detailed below


Title – Validity of a new analysis method on published flow cytometry data
Person in charge – Wolfgang Losert
Affiliation – University of Maryland

Title – Role of HLA ClassII in the humoral response
Person in charge – John Altin
Affiliation – Altin Laboratory, TGEN

Title – Analysis of cellular signaling pathways and genetic networks in chronic inflammatory diseases patient samples
Person in charge – Lars Rogge
Affiliation – Institut Pasteur

Title – Characterising the relationship between polygenic risk for autoimmunity and immune responses
Person in charge – Zia Khan (Genentech)
Affiliation – Genentech Inc.

Title – Understanding the effects of CMV infection
Person in charge – Amir Horowitz
Affiliation – Horowitz Laboratory /Icahn School of Medicine at Mount Sinai

Title – Immune function in patient undergoing immune modulating interventions
Person in charge – Susanne Dam Poulson
Affiliation – Department of Infectious Disease, University of Copenhagen

Title – Inter-individual variability of the oxylipin response
Persons in charge – Cecile Gladine and Andre Mazur
Affiliation – UMR 1019 INRA/Université Clermont Auvergne

Title - Using VirScan to study heterogeneity in pathogen-induced immune responses Persons in charge – Petter BRODIN and Lluis QUINTANA-MURCI
Affiliation – Karolinska Institutet and Institut Pasteur

Title – Determining the frequency of CD3+CD8+CD16+ T cells in the healthy population Person in charge – Nicolas Degauque
Affiliation – Centre Hospitalier, Universitaire de Nantes

Title – Epigenomic variation in immune cells associated with aging
Person in charge – Duygu Ucar
Affiliation – Jackson Laboratory for Genomic Medicine

Title – Causes of natural variation in the immune system – a mendelian Randomisation Persons in charge – George Davey-Smith and Ruth Mitchell
Affiliation – Medical Research Council Integrative Epidemiology Unit (MRC IEU), University of Bristol

Title – Variability in induced immune responses to TLR stimulation
Person in charge – Allyson Byrd and Matthew ALBERT
Affiliation – Genentech Inc.

Title - Characterisation of the innate immune system of Exposed Seronegative women from the Irish anti-D cohort to understand mechanisms of natural resistance to viral infection.
Person in charge – Cliona O'FARELLY
Affiliation – Trinity College Dublin

Title – Late-Spike haplotype dosage association with immune cell type abundances or marker abundances
Person in charge – Soumya Raychaudhuri and Maria Gutierrez-Arcelus
Affiliation – Broad Insitute of Harvard and MIT.

Title – Comparison of the Polygenic score between individuals with Bipolardisorder and the healthy population
Person in charge – Stephane Jamain
Affiliation – INSERM U955

Title – Comparison of Milieu Intérieur immune response data with samples from patients with primary immunodeficiencies
Person in charge – Petter Brodin
Affiliation – Karolinska Institutet

Title – Identification of the dietary patterns to explain gut microbiome configurations Person in charge – Julien Tap
Affiliation – Danone Research

Title - Evaluating the level of Candida colonization
Person in charge - Christophe D’Enfert and Marie-Elisabeth Bougnoux
Affiliation – Institut Pasteur

Title – Soluble immune inhibitory factors as drivers of immune (dys)function in health and disease
Person in charge – Sisse Rye Ostrowski
Affiliation – Department of Clinical Immunology, University of Copenhagen

Title – Defining how the microbiome at a functional level influences a healthy immune response
Person in charge – Darragh Duffy, Deepti Nagarkar, Allyson Byrd, Magnus Fontes.Affiliation – Institut Pasteur, Genentech, Institut Roche
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Title – Effects of detailed immune cell phenotypes on common immune-mediated diseases, using an Mendelian randomisation (MR) approach.
Personin charge – Petar Scepanovic and Elias Allara
Affiliation – University of Cambridge

Title – Prospective study of Gut microbiome-Immunome relations in the context of the man-microbes symbiosis as a key feature in health and disease.
Personin charge – Sébastien Fromentin
Affiliation – MetaGenoPolis lab INRA

Title – Investigating immune profile datasets from the MIC to better understand environmental and genetic sources of immune variation.
Personin charge – Joseph C. Devlin
Affiliation – New York University

Title – Role of inborn errors of immunity in response to SAR-CoV2 infection
Person in charge – Jean-Laurent Casanova
Affiliation – INSERM

Title – Metabolomic analysis og the gut microbiota to better understand how it impacts a healthy human response (continuity of the previous Genentech collaboration, see above)
Person in charge – Allyson Byrd
Affiliation – Genentech

Title – Impact of CMV status on lymphocyte subpopulations in cancer patients and healthy donors.
Person in charge – Ana Lalanne
Affiliation – Institut Curie

Title – Study of genomic structural variation in the MIC, and its impact on immune phenotype variability and its heritability.
Person in charge – Rayan Chikhi and Riccardo Vicedomini
Affiliation – Institut Pasteur

Title – Genome-Wide Association Study (GWAS) to identify genetic variants associated with susceptibility and severity to COVID19 in the French population
Person in charge – Hanna Julienne, Léo Hanches and Hugues Aschard
Affiliation – Institut Pasteur

Title – Identify the transcriptomics signature of latent CMV infection
Person in charge – Atul Butte, Hu Zicheng
Affiliation – University of California San Francisco

Title – Understanding variable immunity to respiratory infections with an aim to improve vaccination strategies
Person in charge – Darragh Duffy, Jim Di Santo, & Daniel Larocque
Affiliation – Institut Pasteur, Sanofi Pasteur

Title – Identifying representative individuals as faecal donor candidates to create an adult rat model transplanted with human fecal samples by using microbiota information of the MIC.
Person in charge – Mathieu Almeida, Nicolas Pons
Affiliation – INRAE

Title – Integrating genetic and microbiome risk profiles for disease prediction using multivariate analysis
Person in charge – Petar Scepanovic
Affiliation – Roche Basel, Switzerland

Title – Establishing a baseline gut microbiota index of healthy volunteers.
Person in charge – Rafi Ahmad
Affiliation – Inland Norway University

Title – MICMAT
Person in charge – Christophe Boetto, Hugues Aschard
Affiliation – Institut Pasteur

Title – Exploring Pathogenic Mechanisms of Chronic Inflammatory Diseases: unresolved issues in IL-23/IL-17 biology
Person in charge – Ikram Mezgiche, Elisabetta Bianchi, Lars Rogge
Affiliation – Institut Pasteur

Title – Pilot study for the evaluation of innate responses from phagocytes differentiated from iPSCs generated by MIC.
Person in charge – Pierre Guermonprez
Affiliation – Université de Paris

Title – Influence of sex hormones on anti-bacterial immunity
Person in charge – Molly Ingersoll
Affiliation – Institut Pasteur/Cochin Institut

Title – Human genetic susceptibility to invasive listeriosis
Person in charge – Marc Lecuit
Affiliation – Institut Pasteur

Title – Assessing the influence of confounding factors and sequencing technology on
microbiome composition

Person in charge – Jacob Wirbel, Georg Zeller
Affiliation – EMBL-Heidelberg

Title – Genetic determinants of COVID-19 disease
Person in charge – Hugues ASCHARD - COVID GWAS
Affiliation – Institut Pasteur

Title – An ethnically diverse genomic reference resource for the human heavy and light chain immunoglobulin loci
Person in charge – Melissa Smith, Ronald Gregg
Affiliation – University of Louisville School of Medicine

Title – Immunological landscape representation by unsupervised machine learning for mapping of immune dysfunction
Person in charge – Adrian Zucco, Cameron MacPherson
Affiliation – Rigshospitalet, Copenhagen

Title – “Toxic” microbiome and progression of chronic kidney disease. A prospective study
Person in charge – Florence Thirion
Affiliation – INRAE, MetaGenoPolis

Title The role of the microbiota -triggered antigen stimulation in development and progression of chronic lymphocytic leukemia
Person in charge – Michal Kielbs, Krzysztof Giannopoulos
Affiliation – Medical University of Lublin Chodzki

Title – Role of the microbiota in the defense against multridrug resistant Enterobacteriaceae
Person in charge – Carles Ubeda
Affiliation – Microbiota, infection, and inflammation – FISABIO

Title – Understanding functional relevance of inter-individual variations in microbiota composition
Person in charge – Benoit Chassaing
Affiliation – INSERM U1016, Université de Paris, Institut Cochin

Title – Identification of genetic variants associated with thrombotic thrombocytopenic purpura
Person in charge – Thierry Hieu, Anavaj Sakuntabhai
Affiliation – Institut Pasteur

Title – Development of novel genotype-phenotype association framework for mechanistic microbiome study
Person in charge – Menghan Liu
Affiliation – Columbia University

Title – A low-dimensional consensus map relating variability in autoimmune disease to variability in healthy individuals
Person in charge – Behnam Yousefi, Benno Schwikowski
Affiliation – Institut Pasteur

Title – Understanding at a functional level what determines observed variance in immune responses to TLR stimulation in a healthy human population.
Person in charge – Magnus Fontes
Affiliation – Institut Roche/Genentech

Title – Serological assessment of antibody responses to routine vaccines and respiratory virus infection.
Person in charge – Michael White
Affiliation – Institut Pasteur

Title – Understanding the role of microbial and lifestyle factors as regulators of haematopoiesis in healthy individuals
Person in charge – Jason Cosgrove
Affiliation – Institut Curie

Title – Large-scale exploration of the microbiome/immunome dialogue in autoimmune diseases
Person in charge – Oscar Gitton-Quent
Affiliation – MetaGenoPolis – INRAE

Title – A cis-regulatory element drives the expression of ERAP2 through autoimmune disease risk SNPs
Person in charge – Jonas Kuiper
Affiliation – Kuiper Lab, University Medical Center Utrecht

Title – Using Machine Learning to Discern the Cellular Mechanism(s) Underpinning the Influence of KIR-HLA genotype on T-cell Dynamics
Person in charge – Becca Asquith
Affiliation – Department of Infectious Disease, Imperial College London

Title – iTARGET
Person in charge – Victoria Meslier and Mathieu Almeida
Affiliation – MetaGenoPolis, INRAE

Title – Functional Interactions and Global Diversity in Gut Microbiomes: Advancing Microbial Community Type Identification with Deep Learning Approaches
Person in charge – Vanessa Dumeaux
Affiliation – Dumeaux Laboratory, Western University

Title – Gene editing of the SNP rs2204985 associated with thymopoiesis level in healthy humans
Person in charge – Antoine TOUBERT
Affiliation – INSERM U1160, Institut de Recherche Saint-Louis, Université de Paris.

Title – Development of an explainable AI-based platform predicting biological and clinical features based on DNA methylation
Person in charge – Vincent Bouget
Affiliation – Scienta Lab
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Title – Parameters governing the human thymic function during aging
Person in charge – Antoine TOUBERT
Affiliation – Institut de Recherche Saint-Louis, Université de Paris

Title – Vieillissement, Infections et Épigénétique – Investigating how Viral Infections Shape Epigenetic Ageing and Health
Person in charge – Matt McElheron and Nollaig Bourke
Affiliation – Trinity College Dublin, Ireland

Title - Characterisation of the crosstalk between Archaea and Negativicutes with the intestinal mucosa in the context of health and inflammation
Person in charge – Camille Martin-Gallausiaux and Simonetta Gribaldo
Affiliation – Institut Pasteur

Title - Development of network analysis tools for deciphering the interactions and organization of microbial guilds
Person in charge - Magali Berland
Affiliation - MetaGenoPolis, INRAE

Title - Immunity, Inflammation, and Coagulation in COVID-19: a cohort study of Fiocruz workers
Person in charge - Itauá Leston Araujo and Adriana Bonomo
Affiliation - Laboratory on Thymus Research - Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro-Brazil

Title - MICMAT --> request to expand dataset. raw data for the Shotgun data for fecal microbiota (see above MICMAT 1st request for collaboration).
Person in charge - Raphael MALAK and Hugues Aschard
Affiliation - Institut Pasteur

Title - Impact of rs2204985 on peripheral blood mononuclear cells composition
Person in charge - Vivien Beziat
Affiliation - INSERM - Institut Imagine

Title - Fine tuning of the Genetic association with human thymic function
Person in charge - Emmanuel Clave and Antoine Toubert
Affiliation - Institut de Recherche Saint-Louis

Title - Age associated immune cell signatures in a diverse healthy American
Person in charge - Hanane Touil and Philip De Jager
Affiliation - Columbia University – De Jager Lab

Title - Rhu immunolife
Person in charge - Giacomo Vitali and Mathieu Almeida
Affiliation - MetaGenoPolis - INRAe

Title - Cellular and molecular correlates of hematopoietic aging and cancer risk
Person in charge - Matthew Park and Nader Yatim
Affiliation - Icahn School of Medicine at Mount Sinai

How to collaborate with us

Researchers can obtain access to the Milieu Intérieur data, biological samples and methodology by submitting a research proposal to:

Current collaborations