Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics

Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses

(2019) Daniel Wüthrich et al.   JOURNAL OF VIROLOGICAL METHODS

Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study

(2019) Adrian Egli et al.   BMJ Open

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Estimating the annual attack rate of seasonal influenza among unvaccinated individuals: A systematic review and meta-analysis

(2018) Mitchell P. Somes et al.   VACCINE

Stochastic processes constrain the within and between host evolution of influenza virus

(2018) John T McCrone et al.   eLife

Mortality, morbidity, and hospitalisations due to influenza lower respiratory tract infections, 2017: an analysis for the Global Burden of Disease Study 2017

(2018) Christopher E Troeger et al.   Lancet Respiratory Medicine

The Structured Coalescent and Its Approximations

(2017) Nicola F. Müller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data

(2016) Denise Kühnert et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of Ebola virus: Insights from the 2013–2016 epidemic

(2016) Edward C. Holmes et al.   NATURE

Global environmental drivers of influenza

(2016) Ethan R. Deyle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Global circulation patterns of seasonal influenza viruses vary with antigenic drift

(2015) Trevor Bedford et al.   NATURE

Efficient Bayesian inference under the structured coalescent

(2014) Timothy G. Vaughan et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Estimates of the reproduction number for seasonal, pandemic, and zoonotic influenza: a systematic review of the literature

(2014) Matthew Biggerstaff et al.   BMC INFECTIOUS DISEASES

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2

(2014) Philippe Lemey et al.   PLoS Pathogens

Age Distribution of Influenza Like Illness Cases during Post-Pandemic A(H3N2): Comparison with the Twelve Previous Seasons, in France

(2013) Clément Turbelin et al.   PLoS One

Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci

(2012) M. S. Gill et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

Prevalence of Seropositivity to Pandemic Influenza A/H1N1 Virus in the United States following the 2009 Pandemic

(2012) Carrie Reed et al.   PLoS One

Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)

(2012) T. Stadler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Geographical Mixing of 2009 Human H1N1 Influenza A Virus in a Single University Community

(2011) E. C. Holmes et al.   JOURNAL OF VIROLOGY

Estimating the Basic Reproductive Number from Viral Sequence Data

(2011) Tanja Stadler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans

(2011) J. Bahl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Migration Dynamics Underlie Evolution and Persistence of Human Influenza A (H3N2)

(2010) Trevor Bedford et al.   PLoS Pathogens

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Estimating the impact of school closure on influenza transmission from Sentinel data

(2008) Simon Cauchemez et al.   NATURE

The Global Circulation of Seasonal Influenza A (H3N2) Viruses

(2008) C. A. Russell et al.   SCIENCE