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@rasigadelab

PHE3ID Public Health, Epidemiology & Evolutionary Ecology of Infectious Diseases

We research ecology and evolution of pathogens, especially multidrug-resistant bacteria
README.md

PHE3ID is a research team of the Centre International de Recherche en Infectiologie of Lyon, FR. We focus on understanding and combating antimicrobial resistance using information methods.

Active coding members

  • Jean-Philippe Rasigade, MD-PhD. Team head.
  • Mélanie Colomb-Cotinat, PharmD. Lead epidemiologist.
  • Natacha Lenuzza, PhD. Applied mathematicien, research engineer.
  • Aurélie Fischer, Msc. Bioinformatician.
  • Malik Talbi, Msc. Bioinformatician, data manager.

Active projects

ResisTrack uses multi-scale ecosystem modelling to understand the emergence and diffusion of antimicrobial resistance in hospitals. ResisTrack makes heavy use of the msevol ecosystem simulator.

EpiTrack uses evolutionary-informed algorithms to scan hospital-wide microbiology diagnoses and detect epidemic clusters in real-time.

COMEDIA-Lyon is a One Health initiative to gather and analyze fine-grained data relevant to antimicrobial resistance at the local scale of the Lyon Metropolitan Area, France.

Involvement in other projects

ResTolTB investigates the roles and dynamics of genetically encoded drug tolerance in drug resistance emergence in Mycobacterium tuberculosis

Alumni coding members

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  1. thd thd Public

    Time-scaled haplotypic density (THD) implementation for R. Estimates epidemic success from pathogen genetic data.

    R 2 1

  2. msevol msevol Public

    Multi-scale evolution of antibiotic resistance

    C++

  3. Rshadow Rshadow Public

    Optimizer for R

Repositories

Showing 10 of 15 repositories
  • arg-clustering Public

    A differential equation model of the clustering of antimicrobial resistance genes (ARGs) on an idealized bacterial chromosome

    rasigadelab/arg-clustering’s past year of commit activity
    R 0 AGPL-3.0 0 0 0 Updated Dec 18, 2024
  • Rshadow Public

    Optimizer for R

    rasigadelab/Rshadow’s past year of commit activity
    0 0 0 0 Updated Dec 13, 2024
  • msevol Public

    Multi-scale evolution of antibiotic resistance

    rasigadelab/msevol’s past year of commit activity
    C++ 0 AGPL-3.0 0 0 0 Updated Nov 22, 2024
  • mathwiki Public

    A semi-random collection of possibly useful facts

    rasigadelab/mathwiki’s past year of commit activity
    0 0 0 0 Updated Nov 7, 2024
  • .github Public
    rasigadelab/.github’s past year of commit activity
    0 0 0 0 Updated Nov 1, 2024
  • bashpipes Public

    Common PHE3ID bash commands for bacterial molecular epidemiology

    rasigadelab/bashpipes’s past year of commit activity
    Nextflow 0 AGPL-3.0 0 0 0 Updated Sep 9, 2024
  • fpoiscpm Public

    Detect change of fuzzy event rate

    rasigadelab/fpoiscpm’s past year of commit activity
    R 0 AGPL-3.0 0 0 0 Updated Mar 28, 2024
  • taxonresolve Public

    Description

    rasigadelab/taxonresolve’s past year of commit activity
    Python 0 AGPL-3.0 1 0 1 Updated Dec 13, 2022
  • xdrtb_thd Public

    Accompanying code for Merker at al 2022.

    rasigadelab/xdrtb_thd’s past year of commit activity
    R 0 AGPL-3.0 0 0 0 Updated Jul 13, 2022
  • macotra-metabarcoding Public
    rasigadelab/macotra-metabarcoding’s past year of commit activity
    R 0 MIT 0 0 0 Updated May 5, 2022
View all repositories

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