Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Measles virus and rinderpest virus divergence dated to the sixth century BCE

(2020) Ariane Düx et al.   SCIENCE

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

(2019) Daniel L Ayres et al.   SYSTEMATIC BIOLOGY

The 1918 influenza pandemic: 100 years of questions answered and unanswered

(2019) Jeffery K. Taubenberger et al.   Science Translational Medicine

HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

(2019) Sergei L Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA

(2017) Orr Ashenberg et al.   PLoS Pathogens

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

(2015) Martin D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios

(2014) Filip Bielejec et al.   BMC BIOINFORMATICS

RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

(2014) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

A synchronized global sweep of the internal genes of modern avian influenza virus

(2014) Michael Worobey et al.   NATURE

Second-Pandemic Strain of Vibrio cholerae from the Philadelphia Cholera Outbreak of 1849

(2014) Alison M. Devault et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genesis and pathogenesis of the 1918 pandemic H1N1 influenza A virus

(2014) M. Worobey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A simple and fast system for cloning influenza A virus gene segments into pHW2000- and pCAGGS-based vectors

(2013) Volker Czudai-Matwich et al.   ARCHIVES OF VIROLOGY

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

1918 Influenza Virus Hemagglutinin (HA) and the Viral RNA Polymerase Complex Enhance Viral Pathogenicity, but Only HA Induces Aberrant Host Responses in Mice

(2013) T. Watanabe et al.   JOURNAL OF VIROLOGY

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pandemic Influenza A Viruses Escape from Restriction by Human MxA through Adaptive Mutations in the Nucleoprotein

(2013) Benjamin Mänz et al.   PLoS Pathogens

High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic

(2012) Yong-Li Xiao et al.   JOURNAL OF PATHOLOGY

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

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

Autopsy series of 68 cases dying before and during the 1918 influenza pandemic peak

(2011) Z.-M. Sheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Isolation and molecular characterization of equine H3N8 influenza viruses from pigs in China

(2009) Jiagang Tu et al.   ARCHIVES OF VIROLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Quantitative biochemical rationale for differences in transmissibility of 1918 pandemic influenza A viruses

(2008) A. Srinivasan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA