The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs

Genetic Determinants of Drug Resistance inMycobacterium tuberculosisand Their Diagnostic Value

(2016) Maha R. Farhat et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

dfrA thyADouble Deletion inpara-Aminosalicylic Acid-Resistant Mycobacterium tuberculosis Beijing Strains

(2016) Danesh Moradigaravand et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

(2016) Jody E. Phelan et al.   BMC GENOMICS

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

(2016) Jody Phelan et al.   BMC Medicine

Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a TBNET/RESIST-TB consensus statement

(2016) J. Domínguez et al.   INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE

Twenty Years of Global Surveillance of Antituberculosis-Drug Resistance

(2016) Matteo Zignol et al.   NEW ENGLAND JOURNAL OF MEDICINE

Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis

(2016) Andrea D. Tyler et al.   PLoS One

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis

(2015) Ernest D Benavente et al.   BMC BIOINFORMATICS

Clinical Application of Whole-Genome Sequencing To Inform Treatment for Multidrug-Resistant Tuberculosis Cases

(2015) Adam A. Witney et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples

(2015) Amanda C. Brown et al.   JOURNAL OF CLINICAL MICROBIOLOGY

High Frequency of Resistance, Lack of Clinical Benefit, and Poor Outcomes in Capreomycin Treated South African Patients with Extensively Drug-Resistant Tuberculosis

(2015) Elize Pietersen et al.   PLoS One

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

(2015) Phelim Bradley et al.   Nature Communications

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

(2015) Francesc Coll et al.   Genome Medicine

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

Revisiting susceptibility testing in MDR-TB by a standardized quantitative phenotypic assessment in a European multicentre study

(2014) E. Cambau et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

PolyTB: A genomic variation map for Mycobacterium tuberculosis

(2014) Francesc Coll et al.   TUBERCULOSIS

A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains

(2014) Mark D. Preston et al.   Nature Communications

Global control of tuberculosis: from extensively drug-resistant to untreatable tuberculosis

(2014) Keertan Dheda et al.   Lancet Respiratory Medicine

Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance

(2013) Hongtai Zhang et al.   NATURE GENETICS

Variant Callers for Next-Generation Sequencing Data: A Comparison Study

(2013) Xiangtao Liu et al.   PLoS One

Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing

(2013) Taane G. Clark et al.   PLoS One

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

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

(2010) A. McKenna et al.   GENOME RESEARCH

Quantitative Drug Susceptibility Testing of Mycobacterium tuberculosis by Use of MGIT 960 and EpiCenter Instrumentation

(2009) B. Springer et al.   JOURNAL OF CLINICAL MICROBIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION