Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

(2020) Victor M Corman et al.   Eurosurveillance

Estimation of the reproductive number of Novel Coronavirus (COVID-19) and the probable outbreak size on the Diamond Princess cruise ship: A data-driven analysis

(2020) Sheng Zhang et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

(2020) Jing Lu et al.   CELL

Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020

(2020) Kenji Mizumoto et al.   Eurosurveillance

Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series

(2020) Merle M Böhmer et al.   LANCET INFECTIOUS DISEASES

Command Suicidal Hallucination as Initial Presentation of Coronavirus Disease 2019 (COVID-19): A Case Report

(2020) Junaid Mirza et al.   PSYCHOSOMATICS

Introductions and early spread of SARS-CoV-2 in the New York City area

(2020) Ana S. Gonzalez-Reiche et al.   SCIENCE

Phylogenetic interpretation during outbreaks requires caution

(2020) Ch. Julián Villabona-Arenas et al.   Nature Microbiology

Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak

(2020) Tsuyoshi Sekizuka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution and epidemic spread of SARS-CoV-2 in Brazil

(2020) Darlan S. Candido et al.   SCIENCE

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

(2020) Xianding Deng et al.   SCIENCE

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

(2020) Andrew Rambaut et al.   Nature Microbiology

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

(2017) Nathan D. Grubaugh et al.   NATURE

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics

(2013) Anne Cori et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

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

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

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

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS