Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi

Estimating the burden of scrub typhus: A systematic review

(2017) Ana Bonell et al.   PLoS Neglected Tropical Diseases

Endemic Scrub Typhus in South America

(2016) Thomas Weitzel et al.   NEW ENGLAND JOURNAL OF MEDICINE

Defying Muller’s Ratchet: Ancient Heritable Endobacteria Escape Extinction through Retention of Recombination and Genome Plasticity

(2016) Mizue Naito et al.   mBio

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Orientia tsutsugamushi, agent of scrub typhus, displays a single metapopulation with maintenance of ancestral haplotypes throughout continental South East Asia

(2015) Patimaporn Wongprompitak et al.   INFECTION GENETICS AND EVOLUTION

Improved Quantification, Propagation, Purification and Storage of the Obligate Intracellular Human Pathogen Orientia tsutsugamushi

(2015) Suparat Giengkam et al.   PLoS Neglected Tropical Diseases

The Diversity and Geographical Structure of Orientia tsutsugamushi Strains from Scrub Typhus Patients in Laos

(2015) Rattanaphone Phetsouvanh et al.   PLoS Neglected Tropical Diseases

Orientia, rickettsia, and leptospira pathogens as causes of CNS infections in Laos: a prospective study

(2015) Sabine Dittrich et al.   Lancet Global Health

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

Molecular Phylogenetic Analysis of Orientia tsutsugamushi Based on the groES and groEL Genes

(2013) Satoru Arai et al.   VECTOR-BORNE AND ZOONOTIC DISEASES

Diversity of the 47-kD HtrA Nucleic Acid and Translated Amino Acid Sequences from 17 Recent Human Isolates of Orientia

(2013) Ju Jiang et al.   VECTOR-BORNE AND ZOONOTIC DISEASES

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

(2012) Limin Fu et al.   BIOINFORMATICS

Orientia tsutsugamushi in Human Scrub Typhus Eschars Shows Tropism for Dendritic Cells and Monocytes Rather than Endothelium

(2012) Daniel H. Paris et al.   PLoS Neglected Tropical Diseases

A Rickettsia Genome Overrun by Mobile Genetic Elements Provides Insight into the Acquisition of Genes Characteristic of an Obligate Intracellular Lifestyle

(2011) J. J. Gillespie et al.   JOURNAL OF BACTERIOLOGY

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Phylogenetic Analysis of 56-kDa Type-Specific Antigen Gene of Orientia tsutsugamushi Isolates in Taiwan

(2010) Hsiu-Ying Lu et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Rickettsial evolution in the light of comparative genomics

(2010) Vicky Merhej et al.   BIOLOGICAL REVIEWS

Genome Comparison and Phylogenetic Analysis of Orientia tsutsugamushi Strains

(2010) K. Nakayama et al.   DNA RESEARCH

Diversity of Orientia tsutsugamushi clinical isolates in Cambodia reveals active selection and recombination process

(2010) Veasna Duong et al.   INFECTION GENETICS AND EVOLUTION

Isolation of a NovelOrientiaSpecies (O. chutosp. nov.) from a Patient Infected in Dubai

(2010) Leonard Izzard et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Rising from the Ashes: DNA Repair in Deinococcus radiodurans

(2010) Michael M. Cox et al.   PLoS Genetics

High Rates of Homologous Recombination in the Mite Endosymbiont and Opportunistic Human Pathogen Orientia tsutsugamushi

(2010) Piengchan Sonthayanon et al.   PLoS Neglected Tropical Diseases

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

A highly sensitive quantitative real-time PCR assay based on the groEL gene of contemporary Thai strains of Orientia tsutsugamushi

(2009) D.H. Paris et al.   CLINICAL MICROBIOLOGY AND INFECTION

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

First Report of an Orientia tsutsugamushi Type TA716–Related Scrub Typhus Infection in Thailand

(2009) Rose McGready et al.   VECTOR-BORNE AND ZOONOTIC DISEASES

The Whole-genome Sequencing of the Obligate Intracellular Bacterium Orientia tsutsugamushi Revealed Massive Gene Amplification During Reductive Genome Evolution

(2008) K. Nakayama et al.   DNA RESEARCH

Genetic typing of the 56-kDa type-specific antigen gene of contemporaryOrientia tsutsugamushiisolates causing human scrub typhus at two sites in north-eastern and western Thailand

(2008) Stuart D. Blacksell et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Genome Sequence of the Fish Pathogen Renibacterium salmoninarum Suggests Reductive Evolution away from an Environmental Arthrobacter Ancestor

(2008) G. D. Wiens et al.   JOURNAL OF BACTERIOLOGY