Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018

Haemagogus leucocelaenus and Haemagogus janthinomys are the primary vectors in the major yellow fever outbreak in Brazil, 2016–2018

(2019) Filipe Vieira Santos de Abreu et al.   Emerging Microbes & Infections

Evidence for multiple sylvatic transmission cycles during the 2016–2017 yellow fever virus outbreak, Brazil

(2018) A. Moreira-Soto et al.   CLINICAL MICROBIOLOGY AND INFECTION

Genomic and epidemiological monitoring of yellow fever virus transmission potential

(2018) N. R. Faria et al.   SCIENCE

ATLANTIC-PRIMATES: a dataset of communities and occurrences of primates in the Atlantic Forests of South America

(2018) Laurence Culot et al.   ECOLOGY

Global yellow fever vaccination coverage from 1970 to 2016: an adjusted retrospective analysis

(2017) Freya M Shearer et al.   LANCET INFECTIOUS DISEASES

Using Viral Gene Sequences to Compare and Explain the Heterogeneous Spatial Dynamics of Virus Epidemics

(2017) Simon Dellicour et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

(2017) Joshua Quick et al.   Nature Protocols

SERAPHIM: studying environmental rasters and phylogenetically informed movements

(2016) Simon Dellicour et al.   BIOINFORMATICS

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Yellow fever

(2015) Thomas P. Monath et al.   JOURNAL OF CLINICAL VIROLOGY

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

Advanced Yellow Fever Virus Genome Detection in Point-of-Care Facilities and Reference Laboratories

(2012) C. Domingo et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

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

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unifying the spatial epidemiology and molecular evolution of emerging epidemics

(2012) O. G. Pybus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon

(2011) Nuno R. Faria et al.   INFECTION GENETICS AND EVOLUTION

Isolation of yellow fever virus (YFV) from naturally infectied Haemagogus (Conopostegus) leucocelaenus (diptera, cukicudae) in São Paulo State, Brazil, 2009

(2011) Renato Pereira de Souza et al.   REVISTA DO INSTITUTO DE MEDICINA TROPICAL DE SAO PAULO

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

(2011) Daniel L. Ayres et al.   SYSTEMATIC BIOLOGY

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

(2010) P. Lemey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Yellow fever in Brazil: thoughts and hypotheses on the emergence in previously free areas

(2010) Pedro Fernando da Costa Vasconcelos   REVISTA DE SAUDE PUBLICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS