cobeylab

antigen-phylogeography

epidemic-deconvolution

Example code for deconvolving epidemic time series

flu_strain_compare

Visualizing mutations and PNGS changes between two strains

FluAImprinting

Data and code for Arevalo et al., 2019

FluVE_repeatvac_public

gcdynamics

Model of germinal center B-cell affinity maturation.

HPV-model

Influenza-immune-dynamics

Code to accompany the manuscript "Age-specific differences in the dynamics of protective immunity to influenza"

pyembedding

Python implementation of nonlinear embedding methods

Rt_estimation

Code to test Rt estimates against synthetic data

cobeylab/pyembedding

Python implementation of nonlinear embedding methods

cobeylab/antigen-phylogeography

cobeylab/HPV-model

cobeylab/gcdynamics

Model of germinal center B-cell affinity maturation.

cobeylab/influenza_phylogeography_manuscript

cobeylab/causality_manuscript

cobeylab/pneumo-resistance

cobeylab/flu-vaccine-sieve

cobeylab/H3N2_glycosylation

cobeylab/antigen

Simulating virus evolution and epidemiology

cobeylab/bcell_id_pop_model

Repository for B-Cell population dynamical models of immunodominance

cobeylab/ccm-letter

cobeylab/flu_response_aging

Collaboration with Patrick's Wilson's group, led by Carole Henry: Aged individuals no longer efficiently adapt their B cell responses to influenza

cobeylab/isotype_phylogenetics

This repository contains analyses for a collaboration led by Patrick Wilson's lab on the phylogenetic relatedness of B cells with different isotypes.