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Origins and dynamics of oral dysbiosis associated with environmental enteric dysfunction. Preventive intervention in Central African infants. Objectives and research hypothesis Considering that the presence of oropharyngeal pathobionts in the duodenum and the gut […]

The project at a glance: An unexpected finding was the discovery that muscle stem cells in different anatomical locations are programmed with distinct upstream regulators prior to acquiring myogenic identity. This intriguing observation is […]

We develop a complete workflow to perform automated sequential smFISH experiments on a microscope. This includes building plans for hardware, opens-source control software, and robust experimental protocols for regular and amplified FISH. Lastly, we […]

Sorry, this entry is only available in FR.

  Congenital heart surgery is a challenging surgical disciplines due to the broad spectrum of conditions and high variability of patient anatomies. Extensive understanding of the complex spatial relationship between anatomical structures is mandatory […]

The popCell project aims to characterize the variation in immune response to SARS-CoV-2 of peripheral blood mononuclear cells (PBMCs) from > 200 adult, healthy volunteers of West European, Central African and East Asian origin, […]

The DECIDER project aims to develop diagnostic tools and treatments for high-grade serous ovarian cancer with the help of AI methods. The aim is to identify earlier those patients who do not respond well […]

This project aims at understanding the dynamical behaviour of drosophila larva. The larva is a ~10000 neurons that exhibit complex behaviour dynamics in response to external stimuli and to possible internal states. This project is […]

Gram-negative bacteria are delimited by an envelope composed of two membranes (the outer and the inner-membranes) separated by the periplasmic space. This envelope includes macromolecular machines that ensure and regulate exchanges between the bacterium […]

Our team identified the first mutations in the SHANK3 gene, showing it’s role in autism and Phelan-McDermid Syndrome (PMS). Thanks to a donation from the French Association of Phelan-McDermid Syndrome, we will continue the […]

Artemisinins, combined with another antimalarial, are the core component of Artemisinin-based Combination Therapies (ACTs): the front-line antimalarial drugs. Today the fight against malaria faces to the emergence of resistance of the parasite Plasmodium falciparum […]

The ERA PerMed PARIS project combines preclinical research with advanced bioinformatics and medical ethics research to evolve the state of the art in the personalised treatment of chemoresistant high-grade serous ovarian cancer.

Human transcriptome profiles typically contain gene expression values for many thousands of genes, thus representing points in a high-dimensional feature space. A principal technical challenge in understanding the pathways involved in the disease and […]

This project aims to characterize the mircrociruit structure of small animals’ brains and link this to how the brain processes information and encodes behavior.  The project relies on simultaneous access to recent synapse-resolution wiring […]

Summary COVID-19 represents a massive health threat for humans and has already caused huge economic problems all over the world. Profound knowledge of SARS-CoV-2 interaction with the host and the host immune response are […]

Exponentially increasing costs of pharmaceutical development – a phenomenon known as Eroom’s law – is a call for innovation. Here, we propose to integrate scattered genetic information on drug targets to guide their selection. […]

Sorry, this entry is only available in FR.

Sorry, this entry is only available in FR.

Sorry, this entry is only available in FR.

Linked-reads are a valuable technologies laying in between short reads and long reads. LR technologies allow the simulation of long reads using barcoded short reads. But the chemistry of such technologies have a limitation […]

To perform assignment of 16S sequences to bacterial genera and statistical analysis of variations of bacterial populations collected from mice feces

Cassandre is a project of personal database system, integrating a “user-friendly” interface to manage and explore multiple sets of large-scale experimental results in biology. Large-scale experiments that generate quantitative data, such as changes in […]

AEGIS is a Marie Skłodowska -Curie Innovative Training Network (ITN) for early stage researchers (ESR) funded by the European Commission under the H2020 Programme the EU framework programme for research and innovation. The principal […]

The Mathematical Modelling of Infectious Diseases Unit works closely with public health agencies in France and abroad to provide modelling support during epidemics so that our assessments can contribute to evidence-based decision making and […]

In 2019 we published several results on ancestral reconstruction, notably in Molecular Biology and Evolution, Systematic Biology and Bioinformatics. The reconstruction of ancestral scenarios is widely used to study the evolution of characters along […]

Bacterial genomes are mainly composed of two types of replicons: chromosomes and plasmids. Plasmids are accessory mobile genetic elements acquired by horizontal transfer between strains or species. Their domestication by new hosts is of […]

Towards the design of new nitrogen fixing symbionts Elucidate how the capacity to establish a nitrogen fixing symbiosis with legumes has been acquired by new bacterial taxons via a lab-evolution experiment should allow developping […]

Design of Antiviral drugs for Bronchiolitis Virus using a novel therapeutic target.

Luc Blassel’s PhD project (funded by PRAIRIE – supervision O. Gascuel) is to apply machine learning techniques to the analysis of sequence data. Traditional sequence alignment and analysis methods might not be able to […]

Protein structure determination is crucial for understanding protein function, as it paves the way to the discovery of new drugs and of new approaches to control pathological biological processes. The recent advances in structural […]

Zoonotic viruses are viruses that have an animal reservoir but may also infect humans. The 2009 A(H1N1)pdm09 influenza pandemic, the SARS epidemic in 2003, the recent emergence of a novel coronavirus in the Middle […]

Autism spectrum disorders (ASD) are a heterogeneous group of pervasive neurodevelopmental disorders affecting approximately 1% of the population. The diagnosis of ASD is based on impairments in reciprocal social communication and stereotyped behaviors. Behind […]

Bacteria display several mechanisms to adapt to their host-environment and successfully colonise it. One important mechanism of adaptation concerns the regulation of gene expression in response to external signals such as the presence of […]

New therapeutic strategies are needed to combat the pandemics and the spread of multidrug resistant form of tuberculosis. This collaborative project between our group and Institut Pasteur of Korea aims to decipher the molecular […]

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another. Life science uses many different formats. They may be old, or with complex syntax and converting […]

The Institut Pasteur has voluminous activities of microbial strain characterisation, in the context of epidemiological surveillance, biological resource centres collections management, and research. These activities involve National Reference Centers, WHO-collaborative centers, biological resources centers […]

Bioweb is a web portal to search and access the bioinformatics resources available at the Institut Pasteur. It provides an overview of the resources available in the central infrastructure, as well as features to identify […]

About Bip:Bip The project Bip:Bip promotes an integrated use of known and modelled three-dimensional structures of proteins as an aid in complete genome annotation. The architectural organization of biological macromolecules is essential for the […]

Our group is exploring the human brain using Magnetic Resonance Imaging (MRI) and electroencephalogram (EEG). These approaches are combined with our genetic data in order to better understand the genetic and phenotypic diversity of […]

Centre for the Analysis of Complex Systems in Complex Environments About CACSICE Cells function through transient interactions of macromolecular complexes. Understanding fully the dynamic processes of life at the molecular level requies understanding the […]

Concerted effort to address rational drug design against Chagas disease Through a multidisciplinary approach that combine medicinal chemistry, structural bioinformatics, molecular docking and immunobiology of the infectious process, we identified two new inhibitors of […]

CNF1 is a toxin that catalyzes the permanent activation of host RhoA, Rac1 and Cdc42 small GTPases by selective deamidation of a glutamine residue into a glutamic acid. This 1 dalton post-translational modification can […]

In the HERCULES EU project, we are studying samples from high-grade serous ovarian cancer tumours. The samples are analysed using mass cytometry, DNA, RNA and ChIP (chromatin immunoprecipitation) sequencing; and computational tools to find […]

During the last decades, structural biology allowed to incredibly improve the information on the biological objects, from single biomolecules to molecular assemblies, and to get a better description  of the physics underlying the interactions […]

This is the webpage for the Data Integration Group. The goal of this group is to inform, teach, learn about Data Integration at the Hub of Bioinformatics and Biostatistics. For now, registration is  limited […]

To perform the assembly of a bacterial genome from Illumina sequencing in order to submit it to the MicroScope/MaGe platform of Genoscope.

Deep learning methods use artificial neural networks to learn complex mappings between raw numeric input data and higher order semantic outputs. These computational techniques are at the heart of recent advances in artificial intelligence, with breakthrough […]

  Nipah virus (NiV) is a bat-borne paramyxovirus found throughout South and South East Asia. With a case fatality ratio of >70% and no available treatment or vaccines, NiV has been identified by the […]

Hydrogen Deuterium eXchange followed by Mass Spectrometry (HDX-MS) is a recognized biophysical tool in structural biology capable of probing protein/ligand interactions, conformational changes, and protein folding and dynamics. The use of improved HDX-MS workflows […]

A Unique Software Platform for Complex Image Analysis Using Virtual Reality         DIVA (Data Integration and Visualization in Augmented and Virtual Environments)  is a software platform jointly developed by the Decision and Bayesian […]

The evolutionary roles of repeats Stress is often faced in nature, whether from lack of nutrients, arrival of competitors or predators, or the presence of toxic substances. The survival of stressed organisms can be […]

The cornerstone of the ELIXIR Tools platform is the bio.tools ELIXIR Tools and Data Services Registry, a discovery portal for a wide range of key bioinformatics resources, which is developed through ELIXIR-EXCELERATE Work Package […]

Ce projet vise à comprendre les interactions fonctionnelles et mécaniques entre chromosomes, périphérie nucléaire et cytosquelette, ainsi que leur influence sur la stabilité génomique, à travers des approches in vivo et in vitro chez […]

A Bayesian Framework for Cellular Structural Biology Objective : “The functioning of a single cell or organism is governed by the laws of chemistry and physics. The bridge from biology to chemistry and physics […]

Human Evolutionary Immunogenomics: population genetic variation in immune responses Recent genome-wide association studies have successfully identified rare and common variants that correlate with complex traits. However, they have provided us with little insight into […]

Prokaryotes evolve rapidly new functionalities by horizontal gene transfer delivered by mobile genetic elements (MGE). MGE increase relatedness between individuals and thereby might also promote the establishment of microbial social networks. Many studies have […]

The folding of eukaryotic and prokaryotic chromosomes consists of an assortment of intertwined structural features. The resulting complex networks of contacts is highly dynamic and interacts functionally with, or regulates metabolic processes ranging from […]

Cette page est destinée aux participants de la cohorte SUIVITHEQUE inclus dans l’étude MicMat afin d’y retrouver : la notice d’information sur la protection des données à caractère personnel est accessible ici les résultats […]

Around 1% of children are diagnosed with autism spectrum disorders (ASD), yet there are currently no drugs designed specifically to treat their main symptoms. Working to change this is the IMI-funded EU-AIMS project. The […]

Inferences concerning the action of selection provide a powerful tool for predicting regions of the genome associated with disease. As infectious diseases exert strong selection pressures, the identification of immunity-related genes targeted by selection […]

Project context and summary : The phylogenetic position and status of “giant viruses”, formerly called NucleoCytoplasmic Large DNA viruses (NCLDV) or putative order Megavirales, are controversial. Many preliminary phylogenetic analyses have been published, but […]

Type IV pili and pseudopili: structure, dynamics, assembly and molecular function Type IV pili and pseudopili assembled by type 2 secretion systems (T2SS) are thin dynamic fibers that perform diverse functions, from  adherence, motility, […]

By integrating cutting-edge knowledge and technology in the fields of genomics, population genetics, immunology and bioinformatics, our aim is to establish a thorough understanding of how variable the human immune response is in the […]

High-throughput sequencing has revolutionized our abilities to track and characterize novel bacterial strains as they emerge and disseminate globally. Genome-based epidemiological typing systems provide ultimate resolution for strain discrimination. Genome sequences may also be […]

The pathogenesis of HIV infection, and in particular the development of immunodeficiency, remains incompletely understood. During HIV infection both innate and adaptive immune responses are raised, but they appear to be insufficient or too […]

Listeriolysin S is a bacteriocin specifically produced in the intestine of orally infected mice and necessary for Listeria monocytogenes survival in this organ. In order to investigate whether this toxin might influence the composition […]

Neurolisteriosis is a common and frequently fatal complication of Listeria monocytogenes infection in human and ruminants. It has a high impact on human and animal health, but only little is known about its pathogenesis. […]

The most important cultural innovation witnessed by modern humans has probably been the transition from a hunter-gatherer nomadic mode of subsistence to an agricultural sedentary lifestyle. This transition occurred in many parts of the […]

Dengue causes significant morbidity and mortality worldwide, with millions of symptomatic cases occurring throughout the central band of the world each year. Large increases in cases are often associated with a shift in predominant […]

This project is a part of the international Infect-Era program, AMOEBAC: Entamoeba histolytica-bacterium interaction and the role of this interaction in intestinal pathogenesis (http://www.infect-era.eu/2nd-call-2014) The aim of this investigation is to understand the induced […]

In the JOBIM 2021 conference, we are launching a pilot project on gender speaking differences in academia. Through this evidence-based and mixed-method study, we intend to answer the following question: how to create the conditions for gender-equal expression in scientific conferences? Objective […]

The LISTERIAGEN project aims to identify host genetic factors associated with susceptibility to listeriosis.

This project aims at understanding the synaptic environment at the single receptor scale. Now that large amounts of dynamical single molecule data are available and that single molecule science is slowly transitioning into a big […]

[Version française]… Cocaine addiction (CocAdd) is a major public health issue affecting 3% of the worlwide population, without validated pharmacotherapy. Nicotinic acetylcholine receptors (nAChRs)have been repeatedly associated in Human and rodent response to cocaine. […]

In order to characterize the mechanisms leading to autism spectrum disorders, we are studying several mouse models. These models are mutated in a gene of interest that has been associated with ASD in genetic […]

Neonatal acquisition of ESBL-PE in the community of a Low-Income Country  Severe bacterial infections are a leading cause of neonatal deaths, with low income countries (LICs) bearing the highest burden. In LICs, neonatal bacterial […]

Primary Sjögren’s syndrome is an autoimmune disease affecting exocrine glands resulting in dryness of the eyes and the mouth with multiple systemic complications in different organs. In 30% to 50% of the patients, systemic […]

New Generation Phylogeny.fr: Refactoring Phylogeny.fr for innovative phylogenetic services Phylogeny.fr is one of the main server available today able to run phylogenetic analysis pipelines. In the context of scientific workflows, none of the workflow […]

The one-dimensional sequence of the genome is carried by long polymers (chromosomes), which fold in the three dimensional volume of the nucleus. How this folding occurs and what it implies for genome function remains […]

Networks provide an efficient formalism to study many complex real-world systems. They provide a natural modeling framework of structural and functional brain networks, protein interaction networks, social interactions, information and epidemic spreading, and infrastructural […]

When individuals get infected by a pathogens, they will develop antibodies against that pathogen that will continue to circulate in their blood. By using assays that can detect these antibodies, we can develop an […]

The Paris Autism Research International Sib-pair (PARIS) Study has been launched as a collaborative project by Prof. M. Leboyer (Paris) and Prof. C. Gillberg (Göteborg) in the 2000s. Its main goal is to join […]

PHINDaccess is a twinning initiative aimed to serve as a lever for Omics research performance of the Institut Pasteur de Tunis (IPT), aspiring to raise its positioning as an excellence center in the field […]

Phylogeography is a field of study concerned with the principles and processes governing the geographic distributions of genealogical lineages, especially those within or among closely related species. [Avise et al. Ann Rev Ecol Syst […]

Fluorescence microscopy is a defining technology in cellular biology but the diffraction of light limits the resolution of standard microscopes to ~200 nm, thus preventing detailed analyses of molecular structures. We are actively interested […]

Protein-Protein Interactions (PPIs) are involved in most biological process and diseases. With a recently estimated number of 370,000 PPIs in humans, they constitute a large ‘reservoir’ for therapeutic development compared to ‘conventional’ drug targets. […]

Pathogenic protozoans of the trypanosomatid group still remain a major world health problem. Cycling between insect vectors and mammalian hosts, Trypanosoma cruzi is the causative agent of Chagas disease, while over 20 Leishmania species […]

This PTR aims to gain novel insight into the nature, the expression, and the regulation of Leishmania virulence factors through the investigation of genetics, transcriptomics, and proteomics differences between (i) virulent and avirulent L. […]

We published in Nature in 2018 a renewed version of the phylogenetic bootstrap, which was proposed by Joseph Felsenstein more than 30 years ago. This method, based on resampling and replications, is used extensively […]

Cliquer ici pour aller à l’enquête Confinement, mesures barrières, limitation des rassemblements etc. Les mesures de prévention actuellement mises en place sont inédites. Elles ont fondamentalement modifié les contacts que nous avons au quotidien. […]

The project SoNeTAA (Social Neuroscience for Therapeutic Approaches in Autism) combines human-human and human-machine interactions with electroencephalography (EEG) recording to approach social cognition from a situated and reciprocal standpoint. The project especially focuses on […]

To design effective ways to mitigate the spread of a pathogen in a population, it is important to first have a good understanding of the transmission characteristics of the pathogen as well as the […]

Protein secretion in bacteria is highly specific. Substrates secreted via the Type II secretion nanomachines are fully folded prior to secretion and are specifically recognized in their native state. In some cases, they even […]

In the context of the Swiss consortium InfectX (www.infectx.ch), we have previously performed siRNA, microRNA and drug screens  to investigate signaling pathways modulating invasion of host cells by the bacterial pathogen Listeria monocytogenes. In […]

New TARGETs for osteoporosis: from mesenchymal stem cells to the regulation of osteogenesis and BONE mass.

We received a grant by Campus France (PHC Carlos J Finlay, 2019-20210) to collaborate with the team of Dr Vivian Kourí Cardellá from Instituto de Medicina Tropical Pedro Kourí (Habana) on the dynamics of […]

The wide range of phenotypic variation in human populations may reflect distinctive processes of selection/adaptation to variable environmental conditions (e.g. climate, pathogens, nutritional resources). The advent of genome-wide datasets allows testing different hypotheses concerning […]

Replication-associated gene dosage effects Maximal growth rates are central to microbial life-history strategies because there is a trade-off between fast growth in copiotrophs and scavenging potential in slow-growing oligotrophs. When E. coli’s generation time […]

We develop phylodynamics models and methods to study viral epidemics, in particular HIV. This new, trendy domain is in between usual mathematical epidemiology, typically based on compartment models, and phylogenetics. The models used in […]

Sleep difficulties are a major concern for families with ASD, but are often considered as an epiphenomenon, and therefore do not catch the attention of the medical and scientific community. In 2008, we reported […]

Entamoeba histolytica is a protozoan parasite and an amitochondriate pathogenic amoeba, which may cause dysentery and liver abscess in humans (i.e. amoebiasis). Differential pathogenicity is observed among E. histolytica strains: strain HM1:IMSS is virulent […]

In order to understand the spread of infectious diseases, we are often interested in the transmission relationship between pairs of cases. The use of pathogen sequences has revolutionized our ability to characterize the relationship […]

The goal of this project is to set sequence analysis tools to evaluate the frequency of mutations within a pool of bacteriophage genomes sequenced by NGS.

The Innovative Training Network ViBrANT (Viral and Bacterial Adhesin Network Training) brings together world-leading European scientists to train 15 graduate students (early stage researchers) in interdisciplinary research into viral and bacterial adhesins. ViBrANT is […]

The Viral Host Range database (VHRdb) represents a unique resource for the community to rapidly find, document analyze and disseminate data related to the range of hosts that a virus can infect. Over the […]

Virus discovery and epidemic tracing from high throughput metagenomic sequencing VIROGENESIS is a research project under the EC H2020 framework (2015-2018), that will develop bioinformatics software applications to fully exploit the potential of high-throughput Next-Generation-Sequencing […]