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Bedford Lab (@blab)

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nextflu

Real-time tracking of influenza evolution

sars-like-cov

This is a one-off Nextstrain build for SARS-like coronaviruses

blotter

bedford lab research

rt-from-frequency-dynamics

beta-cov

One-off nextstrain build for betacoronavirus

global-migration

Analysis of global migration patterns of seasonal influenza viruses

ncov-phylodynamics

Phylodynamic estimation of nCoV incidence and prevalence

zika-seq

Pipelines to do MinION sequencing of Zika virus

ncov-wa-d614g

sarscov2-adaptive-evolution

Jupyter Notebook

ncov-omicron

Nextstrain build targeted to Omicron

dengue-antigenic-dynamics

Dengue antigenic variation and evolutionary dynamics

Jupyter Notebook

seasonal-cov-adaptive-evolution

Nextstrain builds for seasonal coronavirus

Jupyter Notebook

mers-structure

MERS-CoV spillover at the camel-human interface

Jupyter Notebook

antigenic-clustering

Detailed antigenic dynamics of influenza virus revealed by Bayesian phylogenetic clustering

size-genetic-clusters

Code and data for "Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences"

siv-cst

Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission

Jupyter Notebook

h5n1-cambodia

Within-host diversity in H5N1-infected humans and poultry in Cambodia

Jupyter Notebook

spatial-tumor-phylodynamics

Associated analyses for "State-dependent evolutionary models reveal modes of solid tumor growth"

flu-forecasting

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

Jupyter Notebook

cartography

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2

veme-2022

Workshop for VEME 2022: Real-time tracking of pathogen evolution using Nextstrain

evofr

Tools for evolutionary forecasting

Jupyter Notebook

stability

Analysis of stabilizing and destabilizing mutations in influenza evolution

ncov-variant-rt

Analysis of state-by-variant Rt estimates

markov-intermediate

Calculation of state-distributions along Markov chain

Jupyter Notebook

adaptive-evolution

An atlas of continuous adaptive evolution in endemic human viruses

Jupyter Notebook

mumps-wa-phylodynamics

Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State

Jupyter Notebook

h3n2-reassortment

Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season

Jupyter Notebook

ncov-early-outbreak

Nextstrain build to examine early outbreak of SARS-CoV-2 in Wuhan

ncov-variants

Nextstrain builds for particular variants of interest

hcc-tumor-evol

Spatial and clonal dynamics of hepatocellular carcinoma

Jupyter Notebook

ncov-cryptic-transmission

Cryptic transmission of SARS-CoV-2 in Washington State

zika-usvi

Evolutionary analysis of USVI Zika epidemic

Jupyter Notebook

zika-colombia

Genetic analysis of the Zika epidemic in Colombia

Jupyter Notebook

genomic-horizon

Temporal horizons of genomic epidemiology

Jupyter Notebook

rsv_adaptive_evo

Jupyter Notebook

mumps-seq

Protocols for sequencing mumps viruses

ebola-narrative-ms

Jupyter Notebook

ebola-dates

Imputing sampling dates from sample IDs and sequences

unsampled

Estimating unsampled viral diversity

Jupyter Notebook

ncov-wa-phylodynamics

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

popcast

Long-term forecasts for pathogen populations

coveme-2021

Materials relating to nextstrain tutorial presented at coVEME workshop 2021

roka

Evolutionary and epidemiological analysis of Roka HIV outbreak

Jupyter Notebook

fitness-dynamics

Comparing fitness dynamics across SARS-CoV-2, influenza H3 and influenza H1

ncov-usa-mig

norovirus

Nextstrain analysis of Norovirus

ncov-wa-build

Augur build for Washington SARS-CoV-2 sequences.

pathogen-embed

Create reduced dimension embeddings for pathogen sequences

sars2-within-host-selection

Correlating within-host and between-host fitness in SARS-CoV-2

ncov-forecasting-fit

Assessing accuracy of fitness model forecasts

Jupyter Notebook

cholera

Jupyter Notebook

snakemake-stats

A timeline of your Snakemake run generated from the --stats output.

atlas-of-viral-adaptation