Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Mobile real-time surveillance of Zika virus in Brazil

(2016) Nuno Rodrigues Faria et al.   Genome Medicine

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

De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies

(2016) Timokratis Karamitros et al.   PLoS One

A novel method for the multiplexed target enrichment of MinION next generation sequencing libraries using PCR-generated baits

(2015) Timokratis Karamitros et al.   NUCLEIC ACIDS RESEARCH

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

A Method Enabling High-Throughput Sequencing of Human Cytomegalovirus Complete Genomes from Clinical Isolates

(2014) Steven Sijmons et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Genomic and Functional Characteristics of Human Cytomegalovirus Revealed by Next-Generation Sequencing

(2014) Steven Sijmons et al.   Viruses-Basel

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Human Cytomegalovirus Subverts the Functions of Monocytes, Impairing Chemokine-Mediated Migration and Leukocyte Recruitment

(2013) Giada Frascaroli et al.   JOURNAL OF VIROLOGY

Characterization of human cytomegalovirus UL145 and UL136 genes in low-passage clinical isolates from infected Chinese infants

(2013) Bo Wang et al.   MEDICAL SCIENCE MONITOR

Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection

(2013) Nicholas Renzette et al.   PLoS Genetics

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Structural Variability of the Herpes Simplex Virus 1 GenomeIn VitroandIn Vivo

(2012) Charlotte Mahiet et al.   JOURNAL OF VIROLOGY

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

(2012) Pablo Cingolani et al.   Frontiers in Genetics

Human Cytomegalovirus UL144 Is Associated with Viremia and Infant Development Sequelae in Congenital Infection

(2010) A. Waters et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The impact of PCR-generated recombination on diversity estimation of mixed viral populations by deep sequencing

(2010) Irene Görzer et al.   JOURNAL OF VIROLOGICAL METHODS

Sequence Variability in Clinical and Laboratory Isolates of Herpes Simplex Virus 1 Reveals New Mutations

(2010) M. L. Szpara et al.   JOURNAL OF VIROLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Variability and recombination of clinical human cytomegalovirus strains from transplantation recipients

(2009) Muriel Faure-Della Corte et al.   JOURNAL OF CLINICAL VIROLOGY

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

DNAPlotter: circular and linear interactive genome visualization

(2008) T. Carver et al.   BIOINFORMATICS

Cloning and sequencing of a highly productive, endotheliotropic virus strain derived from human cytomegalovirus TB40/E

(2008) C. Sinzger et al.   JOURNAL OF GENERAL VIROLOGY

NF- B-Mediated Activation of the Chemokine CCL22 by the Product of the Human Cytomegalovirus Gene UL144 Escapes Regulation by Viral IE86

(2008) E. Poole et al.   JOURNAL OF VIROLOGY

Polymorphisms within human cytomegalovirus chemokine (UL146/UL147) and cytokine receptor genes (UL144) are not predictive of sequelae in congenitally infected children

(2008) Jinho Heo et al.   VIROLOGY