Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia

Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples

(2019) Uma Sangumathi Kamaraj et al.   PLoS Neglected Tropical Diseases

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Understanding dengue virus evolution to support epidemic surveillance and counter-measure development

(2018) S. Pollett et al.   INFECTION GENETICS AND EVOLUTION

Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples

(2018) Liana E. Kafetzopoulou et al.   Eurosurveillance

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

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

BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing

(2017) Chun Hang Au et al.   Scientific Reports

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

Genomic analysis and growth characteristic of dengue viruses from Makassar, Indonesia

(2015) R. Tedjo Sasmono et al.   INFECTION GENETICS AND EVOLUTION

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

(2015) Nicholas J Loman et al.   NATURE METHODS

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

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

Ultrafast Approximation for Phylogenetic Bootstrap

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

The global distribution and burden of dengue

(2013) Samir Bhatt et al.   NATURE

A method for full genome sequencing of all four serotypes of the dengue virus

(2010) Joseph G. Christenbury et al.   JOURNAL OF VIROLOGICAL METHODS

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

Periodic re-emergence of endemic strains with strong epidemic potential—A proposed explanation for the 2004 Indonesian dengue epidemic

(2007) Swee Hoe Ong et al.   INFECTION GENETICS AND EVOLUTION