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    57 repositories

    • Plaque_early_sporulation

      Public
      This repository has the code and data for the plaque project
      Jupyter Notebook
      •1•0•0•0•Updated May 22, 2024May 22, 2024

    • LatentPeriodVariability

      Public
      Code for: Accounting for Cellular-Level Variation in Lysis: Implications for Virus-Host Dynamics
      MATLAB
      •4•0•0•0•Updated Apr 29, 2024Apr 29, 2024

    • VIMIMO-Virus-Microbe-modeller

      Public
      Create, test and deploy Bayesian virus-microbe infection models for community experiments and population time series
      Jupyter Notebook
      •2•0•0•0•Updated Nov 2, 2023Nov 2, 2023

    • localcovid19now

      Public
      processing and mapping COVID-19 case data at subnational scales
      R
      •
      MIT License
      •6•0•0•0•Updated Jan 23, 2023Jan 23, 2023

    • DilutionMethod-ViralLysisEstimation

      Public
      Code for: The effect of strain level diversity on robust inference of virus-induced mortality
      PostScript
      •
      MIT License
      •1•0•0•0•Updated Oct 31, 2022Oct 31, 2022

    • Bet_hedging_dormancy

      Public
      MATLAB
      •
      MIT License
      •1•0•0•0•Updated Jun 2, 2022Jun 2, 2022

    • vaccine_allocation

      Public
      MATLAB
      •0•0•0•0•Updated Mar 18, 2022Mar 18, 2022

    • ArbitriumLysisLysogeny

      Public
      Optimizing the lysis-lysogeny decision based on arbitrium concentration
      MATLAB
      •0•1•0•0•Updated Jul 9, 2021Jul 9, 2021

    • Networks_Immune_Shielding

      Public
      MATLAB
      •3•0•0•0•Updated Jun 30, 2021Jun 30, 2021

    • COVID_Control_2020

      Public
      MATLAB
      •0•0•0•0•Updated Apr 1, 2021Apr 1, 2021

    • Demory_Temperature-driven_virus_dynamics

      Public
      This code reproduces the figures in "A thermal trade-off between viral production and degradation drives phytoplankton-virus population dynamics"
      MATLAB
      •
      MIT License
      •2•1•0•0•Updated Aug 18, 2020Aug 18, 2020

    • MAGEmodel_covid19_GA

      Public
      Metapopulation AGe-structured Epidemiological (MAGE) model for COVID-19 in Georgia
      Jupyter Notebook
      •
      MIT License
      •5•5•0•0•Updated Jun 15, 2020Jun 15, 2020

    • WeitzGroup.github.io

      Public
      This is the front end of the Weitz Group github user page
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 3, 2020Jun 3, 2020

    • flat_reporting

      Public
      Lags in the reporting of cases can cause misleading interpretation
      R
      •
      MIT License
      •0•0•0•0•Updated May 15, 2020May 15, 2020

    • community_scale_metabolism_NPSG

      Public
      All associated code, figures, and data products for "Community-scale Synchronization and Temporal Partitioning of Gene Expression, Metabolism and Lipid Biosynthesis in Oligotrophic Ocean Surface Waters"
      R
      •1•0•0•0•Updated May 8, 2020May 8, 2020

    • covid_shield_immunity

      Public
      Modeling the Role of ‘Shield Immunity’ in Reducing COVID-19 Epidemic Spread
      Jupyter Notebook
      •
      Other
      •7•7•0•0•Updated May 5, 2020May 5, 2020

    • analyzing_microbiome_timeseries

      Public
      Jupyter Notebook
      •
      MIT License
      •12•15•0•0•Updated Mar 16, 2020Mar 16, 2020

    • coronavirus_asymptomatic

      Public
      Linking asymptomatic case characteristics with the epidemic potential of coronavirus-like outbreaks
      MATLAB
      •4•0•0•0•Updated Mar 4, 2020Mar 4, 2020

    • Guanlin_Phage_therapy_control

      Public
      MATLAB
      •1•0•0•0•Updated Mar 2, 2020Mar 2, 2020

    • Guanlin_when_be_temperate

      Public
      MATLAB
      •
      MIT License
      •1•0•0•0•Updated Feb 11, 2020Feb 11, 2020

    • phage_antibiotic

      Public
      MATLAB
      •
      MIT License
      •3•0•0•0•Updated Jan 6, 2020Jan 6, 2020

    • CLas_prophages

      Public
      TeX
      •
      MIT License
      •1•0•0•0•Updated Sep 11, 2019Sep 11, 2019

    • Genomic-fluidity-scripts

      Public
      A collection of Perl scripts to calculate gene-level similarity among annotated genomes as used in Kislyuk et al. BMC Genomics 12: 32 (2011). The scripts can be executed from the command line and the only dependencies are BioPerl and NCBI BLAST. Separately, we include a MATLAB script to calculate fluidity and its variance directly from matrices …
      Perl
      •
      GNU General Public License v3.0
      •2•2•1•1•Updated Sep 9, 2019Sep 9, 2019

    • Demory_light_driven_infection

      Public
      MATLAB
      •
      MIT License
      •3•0•0•0•Updated Jul 11, 2019Jul 11, 2019

    • nutrient_explicit_phage_bacteria_games

      Public
      MATLAB
      •
      MIT License
      •1•1•0•0•Updated Jun 14, 2019Jun 14, 2019

    • game_theory_Euler

      Public
      MATLAB
      •2•0•0•0•Updated May 14, 2019May 14, 2019

    • Immunocommensal_TiM

      Public
      This repository contains the MATLAB scripts used to generate the figures in the paper "Not by (Good) Microbes Alone: Towards Immunocommensal Therapies" by Chung Yin Leung and Joshua S. Weitz (Trends in Microbiology, in press, available online https://doi.org/10.1016/j.tim.2018.12.006).
      MATLAB
      •
      MIT License
      •2•0•0•0•Updated Feb 12, 2019Feb 12, 2019

    • immune-phage-synergy

      Public
      MATLAB scripts for simulating a model of phage therapy with bacteria, phage and immune cell populations.
      MATLAB
      •
      MIT License
      •2•2•0•0•Updated Feb 12, 2019Feb 12, 2019

    • Immunophage-synergy-in-vivo

      Public
      MATLAB scripts for simulating an in vivo model of phage therapy in acute pneumonia by Pseudomonas aeruginosa.
      MATLAB
      •
      MIT License
      •2•0•0•0•Updated Feb 12, 2019Feb 12, 2019

    • Leung_conflict_attach_2016

      Public
      Scripts for generating bipartite networks using a conflicting attachment model. The networks generated can be visualized and analyzed for modularity and nestedness.
      MATLAB
      •
      MIT License
      •4•2•0•0•Updated Feb 12, 2019Feb 12, 2019