Labex IBEID, Integrative Biology of Emerging Infectious Diseases.

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Research axes

In our integrative approach, we bring a new vision of the infectious disease biology, a continuum from the etiological agent study to the host immunity considering the environment and the vectors.

Our Research Axes

the Labex IBEID aims to cover all the research areas in a One Health approach, we defined five major axes to:


  • Explore the host diversity and complexity, to understand both in humans and animals the essential factors defending the host and maintaining the balance between tolerance and immune response
  • Explore the host-microbe interactions, to identify novel targets for vaccinology and therapeutics
  • Explore the microbial diversity and complexity, studying all the different kind of etiological agent (viruses, bacteria, parasites, fungi) to stay prepared for any new epidemiologic challenge
  • Explore the microbe-vector interactions, to identify new way to contain pathogen dissemination through development of on field diagnostics, microbial competition strategy or vector vaccinology
  • Explore the biology of vectors, to anticipate the next emergence

Transversally, Labex IBEID supports the development of a high-level technological environment constantly updated to ensure that all partners have access to the best equipment.

Our Scientific Program

Structuring Program

The Labex IBEID network of experts is at the frontline to identify the next scientific talents and anticipate future needed expertise in France. To structure the Emerging Infectious Diseases research field, we developed three key actions:

  • Junior groups (G5/U5) and research unit creation
  • Springboard 2 Independence (S2I) fellowship to support senior post-doc transition to permanent researcher
  • Collaborative projects fundings to synergize expertise and explore new research thematic


  • Research Units & Junior Groups

  • Springboard 2 Independence (S2I)

  • Grant intra labex (GIL)

Research Units & Junior Groups

This structuring action of Labex IBEID aims to identify and support young talents and senior experts to address the upcoming challenges of emerging infectious diseases.

  • Frédéric Barras

    Integrative and Molecular Microbiology

  • David Bikard

    Engineering CRISPR Systems to Study and Combat Pathogenic Bacteria (Perpetuated in Research Unit in 2019)

  • Simon Cauchemez

    Analysis and Modeling of Infectious Disease Epidemics to Support Evidence-Based Policy Making in France

  • Nolwenn Dheilly

    Discovery of Pathogens (Formerly Directed by Marc Eloit)

  • Guillaume Duménil

    Pathogenesis of Vascular Infections

  • Eugene Gladyshev

    Epigenetics and Molecular Genetics (Perpetuated in Research Unit in 2023)

  • Mathilde Gendrin

    Insect Vector Microbiota

  • Louis Lambrechts

    Virus-Insect Interactions (Perpetuated in Research Unit in 2017)

  • Giulia Manina

    Microbial Individuality and Infection

  • Damien Vitour

    Innate Immunity, Interatomic Interactions, and Interspecific Transmission of Viral Infections

  • Michael White

    Epidemiology and Analysis of Infectious Diseases

Frédéric Barras

Partenaire du Labex IBEID

Adaptation au stress et Métabolisme chez les entérobactéries (SAMe)

We study how a broad range of basic functional processes are modified, and potentially coordinated, to control cellular homeostasis. Our research primarily uses E. coli as a model, but the concepts will also be tested on pathogens such as Salmonella or Shigella. Focusing on two global cellular processes, Fe-S cluster biogenesis and lipid homeostasis, allows us to study the impact of stress on aerobic and anaerobic metabolism, cell envelope homeostasis and membrane, redox changes, nutrient limitation, metabolic stress and antibiotics.
Molecular, biochemical and genetic approaches, as well as cutting-edge technologies (-omics, imaging, single-cell analysis), aim to achieve an integrated and mechanistic vision of the bacterial cell. Multiplying and diversifying the ways of approaching a process is very rewarding, and we collaborate with biochemists, structuralists, chemists, biophysicists, bioinformaticians and phylogeneticists.

David Bikard

Partenaire du Labex IBEID

Biologie de Synthèse

The Synthetic Biology Group investigates genetic systems that emerge as a result of the arms race between bacteria and bacteriophages, and how these systems can be harnessed as novel biotechnological tools. Bacteriophages, the viruses of bacteria, impose a constant selective pressure on bacteria to evolve resistance mechanisms. The investigation of anti-phage systems has led to the discovery of fascinating molecular mechanisms. Some of these systems, such as restriction-methylation systems and CRISPR-Cas systems, have been harnessed into powerful molecular tools. Our laboratory works both on fundamental aspects of bacteria – phage interactions, and on the development of novel technologies to better study and control bacteria.

Simon Cauchemez

Partenaire du Labex IBEID

Modélisation Mathématique des Maladies Infectieuses

The main research objective of our unit is to develop state-of-the-art statistical and mathematical methods to address these challenges, with the aim to increase the understanding of how pathogens spread in populations, assess the impact of interventions, support policy making and optimize control strategies. Our approach is highly multidisciplinary, looking at infectious diseases through multiple perspectives (epidemiology, statistics, modelling, surveillance, public health, policy making, microbiology), multiple scales (intra-host, person-to-person transmission, spread at the local/national/international level) and multiple data streams (epidemiological, demographic, climatic, genomic, social media). We work closely with public health agencies in France and abroad to ensure our assessments can inform the public health response to epidemics.

Nolwenn Dheilly

Partenaire du Labex IBEID

Découverte de Pathogènes

Our main objective is to discover, characterize and demonstrate the role of new or unexpected infectious agents in clinical syndromes of unknown or poorly characterized etiology, including agents of zoonoses. Our three main missions are to identify factors that drive virus diversification and host jump, to identify zoonotic viruses and characterize the pathogenicity of viruses infecting humans. We thereby identify and characterize unknown viruses and also uncover unknown links between viruses in humans and animal reservoirs (wildlife, arthropod vectors and parasites). This ultimately leads to a better understanding of the epidemiological, clinical and pathophysiological features of diseases and, when possible, to novel diagnostic tests and targeted therapy.

Guillaume Duménil

Partenaire du Labex IBEID

Pathogenèse des infections vasculaires

We study the pathogenesis of Neisseria meningitidis (or meningococcus), a Gram-negative bacterium that recapitulates these different pathological effects. Outstanding questions in terms of understanding N. meningitidis pathogenesis include: how do bacteria cross the epithelium and reach the bloodstream? How do they survive in the blood? How do they damage vessels and reach the cerebrospinal fluid (i.e. cause septic shock and meningitis)? These questions open broader studies regarding tissue biology, bacterial adaptation to different environments and basic functions of the innate immune system. We address these questions at different scales.

Eugene Gladyshev

Partenaire du Labex IBEID

Epigénétique et Génétique Moléculaire

We are interested in discovering and characterizing new mechanisms that organize DNA in the nucleus. We are especially interested in understanding cytogenetic phenomena that apparently involve sequence-specific interactions between intact segments of chromosomal DNA. Such processes are remarkably ubiquitous, yet their molecular nature remains one of the most enigmatic unanswered questions in biology. Current & prospective projects in the lab include (i) discovering molecular factors that recognize repetitive DNA in Neurospora crassa, (ii) elucidating the mechanism of recruitment of DIM-5 to repetitive DNA in N. crassa, (iii) further understanding the DNA homology requirements for RIP and MSUD in N. crassa, (iv) using a range of imaging techniques to characterize the state of chromatin in the premeiotic nuclei of N. crassa, and (v) dissecting the role of heterochromatin during the invasive growth of the human pathogen Aspergillus fumigatus.

Mathilde Gendrin

G5 Groupe de recherche junior

Microbiote des Insectes Vecteurs

Our laboratory is based at the Institut Pasteur of Guyana. We are interested in the microbes naturally present in the mosquito’s organs (microbiota) and their influence on the mosquito. In particular, we study how the microbiota affects the mosquito’s ability to transmit diseases, particularly malaria.
We focus on the Anopheles darlingi mosquito, the main vector of malaria in the Americas region, which is still very poorly characterized despite its importance to public health.

Louis Lambrechts

Partenaire du Labex IBEID

Interactions Virus-Insectes

Our lab investigates the ecology, evolution and genetics of insect-virus interactions to advance our basic understanding of arthropod-borne virus (arbovirus) transmission by mosquitoes

Why is there variation in the ability of mosquitoes to transmit human pathogens and what causes this variation? Our research addresses these questions using the tools of genomics, quantitative genetics, and evolutionary ecology. Our primary study system is the transmission of dengue and Zika viruses by the mosquito Aedes aegypti. A major emphasis of the lab is to develop experimental approaches that account for the complexity of natural systems, where genetically diverse populations of mosquitoes interact with a wide variety of viruses, in a variable environment.

Giulia Manina

G5 Groupe de recherche junior

Individualité Microbienne et Infection

The group is primarily focused on tuberculosis, one of the deadliest human infections and a major a global health emergency . The causative agent, Mycobacterium tuberculosis, is an airborne slow growing microorganism (about 24 hours optimal generation time), which has established a robust association with its host over the course of coevolution. Our group is interested in investigating the molecular basis and the effects of cell-to-cell phenotypic heterogeneity. Is phenotypic heterogeneity crucial to modulate mycobacterial fitness and adaptation during infection? Is there any significant interplay among distinct subpopulations? What is the impact of the microenvironments towards mycobacterial diversification? To answer these and associated questions, we employ a multidisciplinary approach. We use on the one hand classical genetics and conventional microbiology and cell biology assays, and on the other hand single-cell techniques, including FACS and real-time epifluorescent microscopy in combination with custom-built microfluidic systems.

Damien Vitour

Partenaire du Labex IBEID

Laboratoire de Santé Animale - Virologie

This Joint Research Unit investigates zoonotic or epizootic virus of major human and veterinary public health importance. The scientific strategy includes fundamental questions regarding the biology of viral agents but also applied research on epidemiology, vaccinology and mechanisms of interactions between virus and host cell. As example, this unit evaluates original diagnostic tools for epidemiological surveillance and phylogenic studies of animal viruses. Special focuses are made on orbivirus, picornaviruses, neurovirology of zoonoses, enteric viruses, species barriers, adenovirus-derived vectors and Vaccines.

Michael White

G5 Groupe de recherche junior

Epidémiologie et Analyse des Maladies Infectieuses

Our inter-disciplinary team bring together diverse skill sets spanning mathematical modelling and statistics, molecular and serological assays, and the implementation of field-based epidemiological studies and clinical trials. We aim to use these tools to develop novel diagnostics for multiple infectious diseases ranging from malaria to SARS-CoV-2.

Grant intra labex (GIL)

Funding for Collaborative Projects from Labex IBEID to Create Synergies Between Different Expertises and Explore New Research Themes.

Louis Lambrechts – Mathilde Gendrin – Anavaj Sakuntabhai

Understanding the Effect of Plasma Lipoproteins on Dengue Virus Acquisition by Mosquitoes

Laurent Abel – Lluis Quintana-Murci

The Immunological and Genetic Basis of Severe Viral Diseases – The Case of Influenza and SARS-CoV-2 Viruses

Marija Backovic (Félix Rey) – Florence Buseyne (Antoine Gessain)

Envelope Protein Env of the Foamy Virus (FV) – Where the Virus Encounters Host Cells and the Immune System

Gérard Eberl – Ivo Gomperts Boneca

IMPRINT - Early Immunological Imprint of Susceptibility to Infection in Adults

Anna-Bella Failloux – Carla Saleh

ARCOTRA - Impact of ARbovirus CO-infections on Transmission by Aedes aegypti Mosquitoes

Thematic Program

The Labex IBEID supports selected projects of importance related to our scientific axes by funding doctoral and postdoctoral positions:

  • Calls for doctoral applications
  • Calls for postdoctoral applications
  • Funded postdoctoral projects

  • Funded PhD projects

Funded postdoctoral projects

Find all the postdoctoral fellows awarded through our thematic Post-Doc project calls.

Ladislav Simo Laboratory

Identification of ticks molecules that contribute to tick-borne pathogens transmission

Pavel Polyakov

Bayesian Monitoring of the Pandemic Risk of Emerging Infectious Diseases

Sonia Mondino

Legionella pneumophila nucleomodulins : characterization and identification of their targets in the host

Alessia Galgano

Pathogenesis of enterovirus 71, a human emerging encephalitogenic virus

Christelle Travaillé

Importance of trypanosome motility during the early infection in the mammalian host

Nuno Ribeiro-Palha

Study of Chikungunya virus replication and entry into mammalian cells

Bryan Mounce

Experimental evolution of arboviruses during natural transmission: identifying evolutionary trajectories and predicting emergence events

Nizar Fawal

Comparative genomic and phylogeographic analysis of two epidemic and multidrug resistant bacterial populations: Shigella dysenteriae type 1 (Shiga’s bacillus) and Salmonella Kentucky ST198

Simon Cauchemez Laboratory

Mieux comprendre les dynamiques de propagation des maladies infectieuses émergentes dans les populations, dans l’espace et dans le temps

Guillaume Duménil Laboratory

Mechanisms of vascular damage during sepsis

Jean-Marc Ghigo Laboratory

Redox signaling of biofilm differentiation and dispersal in bacterial biofilms

Bernard Lagane

Heterogeneity of CC Chemokine Receptor 5 (CCR5) conformations: Characterization in living cells, molecular mechanisms and consequences on HIV pathogenesis and inhibition

Louis Lambrechts Laboratory

Functional characterization of mosquito genes involved in dengue virus transmission identified by RNA-seq at the individual midgut level

Richard Lo-Man Laboratory

Study of the neonatal BREG lymphocytes – Group B streptococcus interaction in neonatal sepsis.

Anavaj Sakuntabhai Laboratory

Effect of host-parasite interaction on the outcome of malaria infection

Amadou Alpha Sall

Viral genomic surveillance and human genome sequencing for improvement of detection, management and treatments of patients to control of Ebola virus epidemic in West Africa

Alexandre Alcaïs

Paradoxical reaction in Buruli ulcer as a model for the study of human genetics of immune reconstitution inflammatory syndrome

Ali Amara Laboratory

Molecular and cellular basis of Dengue virus entry into host cells

Catherine Bourgouin Laboratory

Proteo-transcriptomics of Anopheles –Plasmodium vivax interactions towards identification of malaria transmission blocking targets

Muriel Coulpier

Modeling viral infections of the central nervous system using induced human pluripotent stem cell and development of antiviral therapies.

Bruno Dupuy Laboratory

Exploring biology of anaerobic biofilms formation by Clostridium difficile and their roles in pathogenesis and relapse of the C. difficile infection

Marc Eloit Laboratory

Identification of potential pathogens.within metaviromes of reservoir species : the case of Ixodes ricinus ticks in Europe

Philippe Glaser Laboratory

Understanding the rise of carbapenemase-producing Escherichia coli

Lluis Quitana-Murci Laboratory

Comparative genomics of innate immunity in humans and non-human primates

Pascale Vonaesch

Investigation of the possible transmission of a dysbiotic microbiota from mothers to their offspring in the context of chronic malnutrition and environmental enteropathy

Rogerio Amino Laboratory

The role and validation of novel protective antigens from malaria pre-erythrocytic stages

Jan Madacki

Discovery of factors and mechanisms involved in the emergence of Mycobacterium tuberculosis as causative agent of tuberculosis

Carmen Buchrieser Laboratory

Complexity of bacterial pneumonia: understanding the impact of the lung microbiome on the severity of infection and the transmission of antibiotic resistance

Pablo Guardado-Calvo Laboratory

Structural vaccinology in Bunyavirus

Mélanie Hamon Laboratory

Role and long-term impact of H3 deacetylation during infection with Listeria monocytogenes

Didier Mazel Laboratory

Study of the mechanism of replication coordination between the two chromosomes of Vibrio cholerae

Armelle Phalipon Laboratory

Deciphering Shigella cross¬talks with human colonic immune cells

Brice Rotureau Laboratory

Unraveling the initial differentiation of metacyclic African trypanosomes in the skin after natural transmission

Eva Krupa

Microbiological monitoring: new horizons for tick-borne diseases

Karinna Rubio-Pena

The role of the VEX protein complex in the insect to mammalianhost transition

Robert Smith

A new mechanism to maintain the outer envelope in diderm Firmicutes: implications for the Gram-negative/Gram-positive transition

Aleksandra Kovacevic

Optimizing Antibiotics and VAccines in populations to Prevent infections with Antibiotic Resistant bacteria (AVAPAR project)

Eugen Pfeifer

Phage-plasmids: a genetic bridge between two worlds with consequences for the spread of antibiotic resistance genes

Julian Buchrieser

ZIKV infection and pathogenesis during pregnancy: Impact of Interferon-induced transmembrane (IFITM) proteins

Richard Girard

Metabolic characterization of malaria parasite crystalloid and determination of its role as an essential nutrient reservoir

Estelle Talouarn

Genetic basis of life-threatening COVID-19 pneumonia

Jost Enninga Laboratory

Rapid and robust in cellulo cryo electron tomography at molecular resolution of discrete infection steps of human pathogens via novel cryo CLEM techniques

Louis Lambrechts Laboratory

Viral genetic determinants of Zika virus transmissibility by mosquitoes

Jakub Czarnecki

Conjugative Killer plasmids as an alternative to antibiotics – CoKiP

Nadia Naffakh Laboratory

In vivo characterisation of the macromolecular influenza polymerase – host RNA polymerase II cap-snatching complex

Phuong Y Mai

Identifying and targeting the basis for Helicobacter pylori morphology

Clarisse Leseigneur

Investigation how eukaryotic domain capture might work: the evolution of a bacterial effector

Léa Pinon

Neutrophil decision making: what determines the mechanisms of Neisseria meningiditis clearance in human blood vessels?

Sandrine Lacour

Survival of Crimean-Congo Hemorrhagic Fever virus in the environment: modeling tick infection with Hazara virus and characterizing tick antiviral immunity mechanisms

Marc Lecuit Laboratory

Investigating host susceptibility factors to maternal-fetal listeriosis

Jean Marc Tsagmo

MeTryDer – Metabolic adaptation of African trypanosomes in the dermis

Maylis Layan

Short- and long-term impacts of COVID-19 on AMR in healthcare settings

Funded PhD projects

Find all the doctoral candidates awarded through our thematic doctoral thesis project calls.

Simonetta Gribaldo Laboratory

The diderm Firmicute Veillonella parvula as a model to discover new players involved in the biogenesis of the bacterial outer membrane

Louis Lambrechts Laboratory

Characterisation of a novel proviral function of Vago genes during dengue virus infection in Aedes aegypti mosquitoes

Javier Pizarro-Cerda Laboratory

Study of the Contribution of the Type IVB Icm/Dot Secretion System in the Pathogenicity of Yersinia pseudotuberculosis Strains Responsible for Far Eastern Scarlet-Like Fever (FESLF)

Sylvain Baize Laboratory

Molecular bases of arenavirus dsRNA recognition by intracellular sensors

Jean-Marc Ghigo Laboratory

Study of Diversity-Generating Retroelements in Bacteroides

Philippe Glaser Laboratory

Plasmid-bacteria interaction and chromosomal integration of resistance genes in the emergence of carbapenemase producing E. coli

Christophe d’Enfert Laboratory

Biosynthesis and function of the cell wall β-1,6-glucans in Candida albicans

Laurent Abel Laboratory

Auto-antibodies neutralizing type I interferons and their role in severe viral infections

Anna-Bella Failloux Laboratory

Influence de la co-infection d’arbovirus sur la transmission virale chez le moustique Aedes aegypti

Rogerio Amino Laboratory & Nathan Ribot (Germany)

A novel type of Plasmodium parasite multiplication (Pasteur-Paris University international program)

Frédéric Barras Laboratory & Veronica Schiaffi (Italy)

Historical, Evolutionary and Functional analysis of Iron-Sulfur cluster biosynthesis in procaryotes (Pasteur-Paris University international program)

Laurent Abel Laboratory

Découverte et caractérisation fonctionnelle de nouveaux défauts génétiques responsables de la tuberculose

Ivo Gomperts-Boneca Laboratory

Dynamics of coccoid formation in Helicobacter pylori and its role in pathogenicity

Stephan Zientara Laboratory

How tick-borne flaviviruses hijack the cell: dangerous liaisons between viral RNAand cellular proteins in human hosts and Ixodes ricinus ticks

Thérèse Couderc Laboratory

Deciphering the role of FHL1 in chikungunya virus infection and disease

Clara Bekirian - Christophe D'Enfert Laboratory

Biosynthesis and function of the cell wall β-1,6-glucans in Candida albicans

Jean-Marc Ghigo Laboratory

New phage-based genetic delivery tools for in vivo functional study of Bacteroidetes in host-associated microbiomes

Marie Bourdon - Laboratory

Genetic and Functional Characterization of Host Factors Influencing Sensitivity to Zika Virus in Mice

Jacinta Bustamante

Genetic Dissection of Recurrent Pulmonary Infections with Non-Tuberculous Mycobacteria in Humans

Nadine Cerf-Bensussan

Molecular determinants of the interactions between Segmented Filamentous bacterium and the gut epithelium

Louis Lambrechts

Influence of an insect-specific flavivirus on dengue virus transmission by mosquitoes

Mélanie Legrand

Study of the Impact of the Microbiota on Genome Dynamics in the Pathogenic Yeast Candida albicans

Giulia Manina

Elucidate the RNA turnover in single mycobacterial cells as a source of noise and adaptation

Nienke Buddelmeijer

Dynamics of bacterial cell shape and its role in pathogenicity

Didier Mazel

Identification of the Host-Factors involved in Integron Integrase-Mediated Recombination

Najma Rachidi

Role of Leishmania casein kinase 1 isoform 2 in host-pathogen interactions

Brice Sperandio

Deciphering the fundamental antimicrobial peptide gene regulatory network to specifically manipulate the expression of antimicrobial effectors

Sven van Teeffelen

Genetic control and robustness of cell-wall synthesis

Florence Buseyne

Human Infection with Zoonotic Simian Foamy Viruses: Specific Adaptive Immune Response with Study of Antiviral Activity of Specific Antibodies and T Lymphocytes

Jean-Marc Ghigo

Formation and functions of anaerobic bacterial biofilms

Philippe Glaser

Characterization of the emergence of Group B streptococcus neonatal infections

Nina Grau

Mechanistic understanding of the early steps of Chikungunya virus entry into the host cell

Marine Petit

Role of viral piRNAs on RNAi-mediated antiviral response

Iryna Nikolayeva

Integrative network analysis of dengue genome-wide association studies

Sylvie van der Werf

Impact of the PB1 Polymerase of Influenza A Viruses on Intrinsic Genetic Diversity of Viral Populations, Pathogenesis, and Host Specificity

Emergency Actions

The Labex IBEID maintains an emergency funding program constantly open to develop rapid responses to any health challenge.

  • 2023 - West Nile & Usutu

  • 2022 - MonkeyPox

  • 2020 - SARS-CoV-2

  • 2020 - SARS-CoV-2

  • 2020 - SARS-CoV-2

  • 2020 - SARS-CoV-2

  • 2020 - SARS-CoV-2

  • 2020 - SARS-CoV-2

  • 2020 - SARS-CoV-2

  • 2018 - Lyme Disease

  • 2018 - Plague

  • 2015 - Dengue

  • 2018 - Bluetongue Virus

  • 2016 - Zika

2023 - West Nile & Usutu

Stephan Zientara - UMR Virology - ANSES
Exceptional Circulation Situation of West Nile and Usutu Arboviruses in Livestock in Nouvelle-Aquitaine.

2022 - MonkeyPox

Pablo Guardado-Calvo - G5 Structural Biology of Infectious Diseases - Institut Pasteur
Deciphering the Molecular Mechanisms of the Antiviral TPOXX against Monkeypox

2020 - SARS-CoV-2

Ali Amara - UMR Biology of Emerging Viruses - Institut de recherche Saint-Louis
Identification of Host Cell Proteins Associated with the Genome of SARS-CoV-2 Virus

2020 - SARS-CoV-2

Etienne simon-Lorière - G5 - Institut Pasteur
Short Amplicon-Based Sequencing Technique for Low-Input Samples of SARS-CoV-2

2020 - SARS-CoV-2

Sylvie Van der Werf - Institut Pasteur
CoV-2 Sensing - Towards Controlled Detection of SARS-CoV-2 by the Innate Immune System

2020 - SARS-CoV-2

Olivier Schwartz - Institut Pasteur
CoronaFusion - SARS-CoV2 fusion, replication and host response.

2020 - SARS-CoV-2

Sylvie Van der Werf - Institut Pasteur
Profiling of Intra-Viral and Virus-Host Interactions of SARS-CoV-2 Focused on Innate Immunity Signaling

2020 - SARS-CoV-2

Marco Vignuzzi - Institut Pasteur
SARS-DVG - Defective Viral Genomes as Antiviral Inhibitors of SARS-CoV-2

2020 - SARS-CoV-2

Marc Eloit - Institut Pasteur
SARS-CoV2-LIPS - Antibody Profiling in Convalescent Patients and Development of a Serological Test Applied to an Epidemiological Survey in Individuals Exposed to SARS-CoV-2

2018 - Lyme Disease

Jean-Claude Manuguerra - Institut Pasteur
Development of New Murine Models for Lyme Disease Using Collaborative Cross Mice

2018 - Plague

Javier Pizarro-Cerda - Institut Pasteur
Genomic Analysis of Yersinia pestis Strains Isolated During the Atypical Plague Epidemic of 2017 in Madagascar

2015 - Dengue

Harold Noel - Santé Publique France
Dynamics and Determinants of Local Transmission of Dengue Virus in Southern France

2018 - Bluetongue Virus

Damien Vitour - EnvA
Outbreak of Bluetongue Virus Serotype 4 in Corsica (France) in 2017

2016 - Zika

Arnaud Fontanet - Institut Pasteur
Surveillance of Zika-Related Microcephaly in Sub-Saharan Africa and Asia

Technology Program

Today, developing a science of excellence requires the best means to detect, quantify, and analyze various sets of samples or data. Labex IBEID supports the development of the best technological environment for all our partners.

  • Microscopy Platform - Stellaris 8

  • Mass Spectrometry Platform - Orbitrap Exploris 480

Microscopy Platform - Stellaris 8

The Stellaris 8 Falcon scanning confocal system (Leica Gmbh) is a state-of-the-art scanning confocal microscope. Coupled with innovative modules, the device provides access to a wealth of information about biological samples, including host-pathogen interactions and cellular environments, which were previously only accessible to experienced practitioners of this technique. The system benefits from advancements in the industry in extending both the light source and detectors into the infrared range. This not only allows light to penetrate deeper into the sample but also enables scientists to expand the possibilities of fluorescence labeling and multiplexing, thereby harnessing the latest developments in fluorescent probes.

This system is also equipped with more complex imaging modalities such as Fluorescence Lifetime Imaging Microscopy (FLIM) and Fluorescence Correlative Spectroscopy (FCS), which enable functional imaging. The capabilities offered by this system, as well as its ergonomic design, provide access to a modality that was previously reserved for experts. With this new tool, scientists can now better quantify host-pathogen interactions and gain a better understanding of the underlying mechanisms, thereby identifying appropriate treatments to counteract them.

This equipment is available thanks to the support of the Labex IBEID within the Photonics Bioimaging Platform (UTechS PBI) at the Pasteur Institute. Find all the information:

Mass Spectrometry Platform - Orbitrap Exploris 480

The Orbitrap Exploris 480 (Thermo Fisher Scientific, Bremen, Germany) comprises an atmospheric pressure ionization (API) ion source interfaced to a radiofrequency ion funnel via a high-capacity transfer tube (HCTT), a quadrupole mass filter, a C-trap, an ion-routing multipole (IRM), and an ultra-high-field Orbitrap mass analyzer. Ions are generated at atmospheric pressure (in this work, in a micro-electrospray ion source), pass through the HCTT to the ion funnel as described in Martins et al., then via a flat pole for selective mass injection as described in Scheltema et al., in a curved flat mast.

This equipment is available thanks to the support of the Labex IBEID within the Mass Spectrometry for Biology Platform (UTechS MSBio) at the Pasteur Institute. Find all the information:


  • 2023
  • 2022
  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013
  • 2012
  • 2011
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