Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

(2015) Matthias Merker et al.   NATURE GENETICS

Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal

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Evolution and transmission of drug-resistant tuberculosis in a Russian population

(2014) Nicola Casali et al.   NATURE GENETICS

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

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Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007–12, with whole pathogen genome sequences: an observational study

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Aminoglycoside Cross-Resistance in Mycobacterium tuberculosis Due to Mutations in the 5′ Untranslated Region ofwhiB7

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Binding Pocket Alterations in Dihydrofolate Synthase Confer Resistance topara-Aminosalicylic Acid in Clinical Isolates of Mycobacterium tuberculosis

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para-Aminosalicylic Acid Is a Prodrug Targeting Dihydrofolate Reductase inMycobacterium tuberculosis

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Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

(2013) Andreas Roetzer et al.   PLOS MEDICINE

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

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Microevolution of extensively drug-resistant tuberculosis in Russia

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The heterogeneous evolution of multidrug-resistant Mycobacterium tuberculosis

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Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

(2011) Christopher B Ford et al.   NATURE GENETICS

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

(2011) Iñaki Comas et al.   NATURE GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

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Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Overexpression of the chromosomally encoded aminoglycoside acetyltransferase eis confers kanamycin resistance in Mycobacterium tuberculosis

(2009) M. A. Zaunbrecher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA