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  • team
  • department
  • center
  • program_project
  • nrc
  • whocc
  • project
  • software
  • tool
  • patent
  • Administrative Staff
  • Assistant Professor
  • Associate Professor
  • Clinical Research Assistant
  • Clinician Researcher
  • Department Manager
  • Full Professor
  • Graduate Student
  • Honorary Professor
  • Lab assistant
  • Non-permanent Researcher
  • Permanent Researcher
  • Pharmacist
  • PhD Student
  • Physician
  • Post-doc
  • Prize
  • Project Manager
  • Research Associate
  • Research Engineer
  • Retired scientist
  • Technician
  • Undergraduate Student
  • Veterinary
  • Visiting Scientist
  • Deputy Director of Center
  • Deputy Director of Department
  • Deputy Director of National Reference Center
  • Deputy Head of Facility
  • Director of Center
  • Director of Department
  • Director of Institute
  • Director of National Reference Center
  • Group Leader
  • Head of Facility
  • Head of Operations
  • Head of Structure
  • Honorary President of the Departement
  • Labex Coordinator
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Scientific Fields
Diseases
Organisms
Applications
Technique

Courses

10:00
29
Oct 2018
Course

Bacterial strain nomenclatures applied to international epidemiological surveillance: A Theoretical and Hands-on Course

This two-day course will provide participants both theory and hands-on practical exercises on bacterial strain nomenclatures using the core genome MLST concept. Focus will be put on the BIGSdb software tool and database and […]
Biodiversity and Epidemiology of Bacterial Pathogens
Sylvain Brisse
2018-10-29 10:00:00 2018-10-30 17:00:00 Europe/Paris Bacterial strain nomenclatures applied to international epidemiological surveillance: A Theoretical and Hands-on Course This two-day course will provide participants both theory and hands-on practical exercises on bacterial strain nomenclatures using the core genome MLST concept. Focus will be put on the BIGSdb software tool and database and […] 25 Rue du Dr Roux, 75015 Paris, France

Transversal Projects

INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations

IINCEPTION Goal The Inception’s goal is to develop a core structure to mobilize data resources, numerical sciences, and fundamental experimental biology in a range of health issues (Official website here : https://www.inception-program.fr/en). Inception program […]

PIBnet – Pasteur International Bioresources network

The PIBnet program aims at harmonizing microbial strain biobanking and analytical methods deployed within the microbiological expertise laboratories in Paris and throughout the International Network of Institut Pasteur. It is a large collaborative program […]

LabEx IBEID – Integrative Biology of Emerging Infectious Diseases

Presentation The aim of the Integrative Biology of Emerging Infectious Diseases (IBEID) project, coordinated by Professors Philippe Sansonetti and Pascale Cossart, is to develop a structure to anticipate and tackle emerging infectious diseases (EIDs). […]

Projects

Project
Not started
6 Members

(FR) PERT-SEVERE II – Impact de l’expression bactérienne et de la réponse immunitaire dans la gravité de la coqueluche

Julie Toubiana (PI)

Sorry, this entry is only available in French.
Project
Ongoing
4 Members

PER-SEVERE: Defining the contribution of variable microbial factors and host immunity to pertussis severity

Carla Rodrigues (PI)

Whooping cough is a respiratory disease caused by a bacterium (Bordetella Pertussis) which can, in certain cases and in particular in infants, be severe or even fatal (this is called malignant whooping cough). The […]
Project
Ongoing
10 Members

HoloZcan – Deep Learning Powered Holographic Microscopy for Biothreat Detection on Field

Mariana Ferrari (PI)

The project is a Research and Innovation Action, its funding originates from the H2020-EU.3.7.5. – Increase Europe’s resilience to crises and disasters budget line, topic : SU-DRS04-2019-2020 – Chemical, biological, radiological and nuclear (CBRN) […]
Project
Ongoing
8 Members

The SARA project: Surveillance of Antibiotic Resistance in Africa, an integrative project of the Pasteur Network

Sylvain Brisse (PI)

Antibiotic resistance is one of the most serious threats to global health. The consequences for human health are particularly severe in low-resource countries, and in Africa in particular. The SARA project is funded by […]
Project
Ongoing
3 Members

Microbial Resource Research Infrastructure (MIRRI-ERIC)

Raquel Hurtado Ortiz (PI)

The Microbial Resource Research Infrastructure (MIRRI) is the pan-European distributed Research Infrastructure for the preservation, systematic investigation, provision and valorisation of microbial resources and biodiversity. It currently brings together 50+ microbial domain Biological Resource […]
Project
Ongoing
6 Members

IS_MIRRI21 – Implementation and Sustainability of Microbial Resource Research Infrastructure for the 21st century

Raquel Hurtado Ortiz (PI)

IS_MIRRI21 commenced in February 2020, which was officialised by the successful Kick-Off Meeting conducted on the 25th and 26th of March, 2020 under the coordination of University of Minho (UMINHO) from Portugal. This European […]
Project
Ongoing
8 Members

Oxford Nanopore sequencing for detection and surveillance of pathogens

Sylvain Brisse (PI)

This project intends to share expertise, developments, equipement and bioinformatics tools to apply Oxford Nanopore Technology sequencing to the detection, diagnostic and characterization of pathogens of public health importance. It corresponds to a collaboration […]
Project
Ongoing
3 Members

KlebNet: a One Health network bridging science and surveillance on antimicrobial resistant Klebsiella

Sylvain Brisse (PI)

Join us on Google groups! KlebNET e-mail distribution list on Google groups. Please ask for registration, by explaining your interest in Klebsiella research or surveillance and providing your institution, so that the moderators can […]
Project
Ongoing
8 Members

Bordetella and whooping cough: Population Biology and Vaccination

Sylvain Brisse (PI)

Our research on Bordetella ranges from the population biology and epidemiology of various Bordetella species, including Bordetella pertussis (the major agent of whooping cough), to studies of host-pathogen relationships and immunity. Current research lines […]
Project
Ongoing
6 Members

Diphtheria and Corynebacteria: genomics, evolution and epidemiology

Sylvain Brisse (PI)

Our research on Corynebacterium diphtheriae and related bacterial pathogenic species, including Corynebacterium ulcerans,  aims at defining the diversity, evolution and epidemiology of the agents of diphtheria and related infections. We study human and animal clinical […]
Project
Ongoing
7 Members

Population biology of the bacterial pathogen Klebsiella pneumoniae

Sylvain Brisse (PI)

Klebsiella pneumoniae is one of the most urgent threats to public health given its increasing resistance to antimicrobial agents including carbapenems, considered as last-resort antibiotics.  In this project we aim to understand the ecological, epidemiological and […]
Project
Ongoing
15 Members

Genomic taxonomy of bacterial strains: universal nomenclatures for epidemiology and population biology

Sylvain Brisse (PI)

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 […]
Project
Ongoing
3 Members

Bioinformatics of genome sequencing applied to epidemiological surveillance of infectious agents

Sylvain Brisse (PI)

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 […]

Software

Software
Ongoing
19 Members

BIGSdb-Pasteur

Sylvain Brisse (PI)

BIGSdb-Pasteur is the genomic-based strain taxonomy and nomenclature platform of Institut Pasteur, powered by the BIGSdb software developed at Oxford University. This web platform hosts collections of curated, open or private databases of bacterial […]
Software
Completed
3 Members

AlienTrimmer

Alexis Criscuolo (PI)

Contaminant oligonucleotide sequences such as primers and adapters can occur in both ends oƒ high-throughput sequencing (HTS) reads. AlienTrimmer was developed in order to detect and remove such contaminants. ßased on the decomposition oƒ […]

Publications

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