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

Epidemic arboviral diseases: priorities for research and public health

(2017) Annelies Wilder-Smith et al.   LANCET INFECTIOUS DISEASES

South-east Asian Zika virus strain linked to cluster of cases in Singapore, August 2016

(2016) Sebastian Maurer-Stroh et al.   Eurosurveillance

Zika, dengue, and chikungunya co-infection in a pregnant woman from Colombia

(2016) Wilmer E. Villamil-Gómez et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Evidence-based risk assessment and communication: a new global dengue-risk map for travellers and clinicians#

(2016) Emily S. Jentes et al.   JOURNAL OF TRAVEL MEDICINE

Zika Virus Associated with Microcephaly

(2016) Jernej Mlakar et al.   NEW ENGLAND JOURNAL OF MEDICINE

Insights into the molecular evolution of Dengue virus type 4 in Puerto Rico over two decades of emergence

(2016) Estelle Martin et al.   VIRUS RESEARCH

Laboratory-Enhanced Dengue Sentinel Surveillance in Colombo District, Sri Lanka: 2012-2014

(2016) Hasitha Tissera et al.   PLoS Neglected Tropical Diseases

Detection of Low Frequency Multi-Drug Resistance and Novel Putative Maribavir Resistance in Immunocompromised Pediatric Patients with Cytomegalovirus

(2016) Charlotte J. Houldcroft et al.   Frontiers in Microbiology

Application of targeted enrichment to next-generation sequencing of retroviruses integrated into the host human genome

(2016) Paola Miyazato et al.   Scientific Reports

Chikungunya: Evolutionary history and recent epidemic spread

(2015) Scott C. Weaver et al.   ANTIVIRAL RESEARCH

Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing

(2015) Silvie Van den Hoecke et al.   BMC GENOMICS

Enhanced virome sequencing using targeted sequence capture

(2015) Todd N. Wylie et al.   GENOME RESEARCH

Dengue

(2015) Maria G Guzman et al.   LANCET

Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness

(2015) G. Manokaran et al.   SCIENCE

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis

(2015) Thomas Briese et al.   mBio

Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing

(2015) Lasse Vinner et al.   Scientific Reports

Application of a target enrichment-based next-generation sequencing protocol for identification and sequence-based prediction of pneumococcal serotypes

(2014) Veranja Liyanapathirana et al.   BMC MICROBIOLOGY

Hemagglutinin 222D/G Polymorphism Facilitates Fast Intra-Host Evolution of Pandemic (H1N1) 2009 Influenza A Viruses

(2014) Nora Seidel et al.   PLoS One

Evolution of dengue in Sri Lanka—changes in the virus, vector, and climate

(2013) P.D.N.N. Sirisena et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

The global distribution and burden of dengue

(2013) Samir Bhatt et al.   NATURE

Quantitative real-time PCR detection of Zika virus and evaluation with field-caught Mosquitoes

(2013) Oumar Faye et al.   Virology Journal

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Dengue

(2012) Cameron P. Simmons et al.   NEW ENGLAND JOURNAL OF MEDICINE

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

Skip the Alignment: Degenerate, Multiplex Primer and Probe Design Using K-mer Matching Instead of Alignments

(2012) David A. Hysom et al.   PLoS One

Genomic Polymorphism of the Pandemic A (H1N1) Influenza Viruses Correlates with Viral Replication, Virulence, and Pathogenicity In Vitro and In Vivo

(2011) Lili Xu et al.   PLoS One

Specific Capture and Whole-Genome Sequencing of Viruses from Clinical Samples

(2011) Daniel P. Depledge et al.   PLoS One

Chikungunya virus: evolution and genetic determinants of emergence

(2011) Konstantin A Tsetsarkin et al.   Current Opinion in Virology

The Early Clinical Features of Dengue in Adults: Challenges for Early Clinical Diagnosis

(2011) Jenny G. H. Low et al.   PLoS Neglected Tropical Diseases

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Natural attenuation of dengue virus type-2 after a series of island outbreaks: A retrospective phylogenetic study of events in the South Pacific three decades ago

(2010) Argon Steel et al.   VIROLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH