Direct Amplification, Sequencing and Profiling of Chlamydia trachomatis Strains in Single and Mixed Infection Clinical Samples

Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

(2013) H. M. B. Seth-Smith et al.   GENOME RESEARCH

Culture-independent sequence analysis of Chlamydia trachomatis in urogenital specimens identifies regions of recombination and in-patient sequence mutations

(2013) T. E. Putman et al.   MICROBIOLOGY-SGM

Targeted genome enrichment for efficient purification of endosymbiont DNA from host DNA

(2013) Sandrine Geniez et al.   SYMBIOSIS

Short read sequence typing (SRST): multi-locus sequence types from short reads

(2012) Michael Inouye et al.   BMC GENOMICS

Population Genomics of Chlamydia trachomatis: Insights on Drift, Selection, Recombination, and Population Structure

(2012) Sandeep J. Joseph et al.   MOLECULAR BIOLOGY AND EVOLUTION

Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding

(2012) SAMUEL D. J. BROWN et al.   Molecular Ecology Resources

A framework for human microbiome research

(2012)   NATURE

Genome-wide recombination in Chlamydia trachomatis

(2012) Sandeep J Joseph et al.   NATURE GENETICS

Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

(2012) Simon R Harris et al.   NATURE GENETICS

Virulence determinants in the obligate intracellular pathogen Chlamydia trachomatis revealed by forward genetic approaches

(2012) B. D. Nguyen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Interplay of recombination and selection in the genomes of Chlamydia trachomatis

(2011) Sandeep J Joseph et al.   Biology Direct

Genital chlamydial infection: association between clinical features, organism genotype and load

(2011) H. Jalal et al.   JOURNAL OF MEDICAL MICROBIOLOGY

A draft genome of Yersinia pestis from victims of the Black Death

(2011) Kirsten I. Bos et al.   NATURE

Hypervirulent Chlamydia trachomatis Clinical Strain Is a Recombinant between Lymphogranuloma Venereum (L2) and D Lineages

(2011) N. Somboonna et al.   mBio

Development of a Transformation System for Chlamydia trachomatis: Restoration of Glycogen Biosynthesis by Acquisition of a Plasmid Shuttle Vector

(2011) Yibing Wang et al.   PLoS Pathogens

Hybrid selection for sequencing pathogen genomes from clinical samples

(2011) Alexandre Melnikov et al.   GENOME BIOLOGY

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

Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases

(2009) Paul S. Keim et al.   NATURE REVIEWS MICROBIOLOGY

High-Throughput Quantitative Polymerase Chain Reaction in Picoliter Droplets

(2008) Margaret Macris Kiss et al.   ANALYTICAL CHEMISTRY

Eliminating Blinding Trachoma

(2008) Joseph A. Cook   NEW ENGLAND JOURNAL OF MEDICINE

Multiple Chlamydiaceae Species in Trachoma: Implications for Disease Pathogenesis and Control

(2007) Deborah Dean et al.   PLOS MEDICINE