Genomic and epidemiological monitoring of yellow fever virus transmission potential

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 structural features of the yellow fever virus from the 2016–2017 Brazilian outbreak

(2018) Mariela Martínez Gómez et al.   JOURNAL OF GENERAL VIROLOGY

The seasonal influence of climate and environment on yellow fever transmission across Africa

(2018) Arran Hamlet et al.   PLoS Neglected Tropical Diseases

MERS-CoV spillover at the camel-human interface

(2018) Gytis Dudas et al.   eLife

Existing and potential infection risk zones of yellow fever worldwide: a modelling analysis

(2018) Freya M Shearer et al.   Lancet Global Health

Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015–16: a modelling study

(2017) Moritz U G Kraemer et al.   LANCET INFECTIOUS DISEASES

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

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

Genome analysis of yellow fever virus of the ongoing outbreak in Brazil reveals polymorphisms

(2017) Myrna C Bonaldo et al.   MEMORIAS DO INSTITUTO OSWALDO CRUZ

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

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

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

(2017) N. R. Faria et al.   NATURE

Virus genomes reveal factors that spread and sustained the Ebola epidemic

(2017) Gytis Dudas et al.   NATURE

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

Yellow Fever — Once Again on the Radar Screen in the Americas

(2017) Catharine I. Paules et al.   NEW ENGLAND JOURNAL OF MEDICINE

Tracking the return of Aedes aegypti to Brazil, the major vector of the dengue, chikungunya and Zika viruses

(2017) Panayiota Kotsakiozi et al.   PLoS Neglected Tropical Diseases

High resolution global gridded data for use in population studies

(2017) Christopher T. Lloyd et al.   Scientific Data

Impending extinction crisis of the world’s primates: Why primates matter

(2017) Alejandro Estrada et al.   Science Advances

Potential risk of re-emergence of urban transmission of Yellow Fever virus in Brazil facilitated by competent Aedes populations

(2017) Dinair Couto-Lima et al.   Scientific Reports

Genomic and epidemiological characterisation of a dengue virus outbreak among blood donors in Brazil

(2017) Nuno R. Faria et al.   Scientific Reports

SERAPHIM: studying environmental rasters and phylogenetically informed movements

(2016) Simon Dellicour et al.   BIOINFORMATICS

Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data

(2016) Simon Dellicour et al.   BMC BIOINFORMATICS

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

(2016) Edward C. Holmes et al.   NATURE

Spread and establishment of Aedes albopictus in southern Switzerland between 2003 and 2014: an analysis of oviposition data and weather conditions

(2016) Eleonora Flacio et al.   Parasites & Vectors

Zika virus in the Americas: Early epidemiological and genetic findings

(2016) N. R. Faria et al.   SCIENCE

Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates

(2016) Mandev S. Gill et al.   SYSTEMATIC BIOLOGY

Interim Guidance for Interpretation of Zika Virus Antibody Test Results

(2016) Ingrid B. Rabe et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty

(2015) Guy Baele et al.   SYSTEMATIC BIOLOGY

The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus

(2015) Moritz UG Kraemer et al.   eLife

High-resolution gridded population datasets for Latin America and the Caribbean in 2010, 2015, and 2020

(2015) Alessandro Sorichetta et al.   Scientific Data

Effects of Local Habitat Variation on the Behavioral Ecology of Two Sympatric Groups of Brown Howler Monkey (Alouatta clamitans)

(2015) Linda Jung et al.   PLoS One

Efficient Bayesian inference under the structured coalescent

(2014) Timothy G. Vaughan et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

An effective approach for gap-filling continental scale remotely sensed time-series

(2014) Daniel J. Weiss et al.   ISPRS JOURNAL OF PHOTOGRAMMETRY AND REMOTE SENSING

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Yellow Fever in Africa: Estimating the Burden of Disease and Impact of Mass Vaccination from Outbreak and Serological Data

(2014) Tini Garske et al.   PLOS MEDICINE

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

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

Chikungunya Fever: A Clinical and Virological Investigation of Outpatients on Reunion Island, South-West Indian Ocean

(2013) Simon-Djamel Thiberville et al.   PLoS Neglected Tropical Diseases

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

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

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

Genomic and Phylogenetic Characterization of Brazilian Yellow Fever Virus Strains

(2012) M. R. T. Nunes et al.   JOURNAL OF VIROLOGY

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

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

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

Dynamic behavior of sylvatic yellow fever in Brazil (1954-2008)

(2011) Fernando Portela Câmara et al.   Revista da Sociedade Brasileira de Medicina Tropical

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

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

Bayesian random local clocks, or one rate to rule them all

(2010) Alexei J Drummond et al.   BMC BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

Yellow Fever Virus Exhibits Slower Evolutionary Dynamics than Dengue Virus

(2009) A. A. Sall et al.   JOURNAL OF VIROLOGY

Febre amarela: estudo de um surto

(2009) Mirtes Ribeiro et al.   Revista da Sociedade Brasileira de Medicina Tropical