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

Inferring patient to patient transmission of Mycobacterium tuberculosisfrom whole genome sequencing data

(2013) Josephine M Bryant et al.   BMC INFECTIOUS DISEASES

Genetic characterization of compensatory evolution in strains carrying rpoB Ser531Leu, the rifampicin resistance mutation most frequently found in clinical isolates

(2013) G. Brandis et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Use of Whole Genome Sequencing to Determine the Microevolution of Mycobacterium tuberculosis during an Outbreak

(2013) Midori Kato-Maeda et al.   PLoS One

Putative Compensatory Mutations in the rpoC Gene of Rifampin-Resistant Mycobacterium tuberculosis Are Associated with Ongoing Transmission

(2012) M. de Vos et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences

(2012) Francesc Coll et al.   BIOINFORMATICS

Surveillance of anti-tuberculosis drug resistance in the world: an updated analysis, 2007–2010

(2012) Matteo Zignol et al.   BULLETIN OF THE WORLD HEALTH ORGANIZATION

SITVITWEB – A publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology

(2012) Christophe Demay et al.   INFECTION GENETICS AND EVOLUTION

Drug-Resistant Tuberculosis—Current Dilemmas, Unanswered Questions, Challenges, and Priority Needs

(2012) Alimuddin Zumla et al.   JOURNAL OF INFECTIOUS DISEASES

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Dynamic and complex Mycobacterium tuberculosis microevolution unrevealed by standard genotyping

(2012) Laura Pérez-Lago et al.   TUBERCULOSIS

Mutations ingidBConfer Low-Level Streptomycin Resistance in Mycobacterium tuberculosis

(2011) Sharon Y. Wong et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes

(2011) Iñaki Comas et al.   NATURE GENETICS

CREST maps somatic structural variation in cancer genomes with base-pair resolution

(2011) Jianmin Wang et al.   NATURE METHODS

Drug-Resistant Genotypes and Multi-Clonality in Plasmodium falciparum Analysed by Direct Genome Sequencing from Peripheral Blood of Malaria Patients

(2011) Timothy Robinson et al.   PLoS One

Effectiveness of the Standard WHO Recommended Retreatment Regimen (Category II) for Tuberculosis in Kampala, Uganda: A Prospective Cohort Study

(2011) Edward C. Jones-López et al.   PLOS MEDICINE

Identification of katG Mutations Associated with High-Level Isoniazid Resistance in Mycobacterium tuberculosis

(2010) H. Ando et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Molecular Detection of Mixed Infections ofMycobacterium tuberculosisStrains in Sputum Samples from Patients in Karonga District, Malawi

(2010) Kim Mallard et al.   JOURNAL OF CLINICAL MICROBIOLOGY

High-Resolution Typing by Integration of Genome Sequencing Data in a Large Tuberculosis Cluster

(2010) A. C. Schurch et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Multidrug-resistant and extensively drug-resistant tuberculosis: a threat to global control of tuberculosis

(2010) Neel R Gandhi et al.   LANCET

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Genomic Diversity among Drug Sensitive and Multidrug Resistant Isolates of Mycobacterium tuberculosis with Identical DNA Fingerprints

(2009) Stefan Niemann et al.   PLoS One

Rate and Amplification of Drug Resistance among Previously‐Treated Patients with Tuberculosis in Kampala, Uganda

(2008) Beth Temple et al.   CLINICAL INFECTIOUS DISEASES

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY