Within Host Evolution Selects for a Dominant Genotype of Mycobacterium tuberculosis while T Cells Increase Pathogen Genetic Diversity

Molecular epidemiology of Mycobacterium africanum in Ghana

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Co-evolution ofMycobacterium tuberculosisandHomo sapiens

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Essential Role of the ESX-5 Secretion System in Outer Membrane Permeability of Pathogenic Mycobacteria

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Mycobacterium africanum Is Associated with Patient Ethnicity in Ghana

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Group Selection and Contribution of Minority Variants during Virus Adaptation Determines Virus Fitness and Phenotype

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Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

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Selection bias at the heterosexual HIV-1 transmission bottleneck

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Consequences of genomic diversity in Mycobacterium tuberculosis

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Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

(2013) Iñaki Comas et al.   NATURE GENETICS

Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

(2013) Tami D Lieberman et al.   NATURE GENETICS

Genome dynamics during experimental evolution

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BCG immunotherapy for bladder cancer—the effects of substrain differences

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HIV Infection Disrupts the Sympatric Host–Pathogen Relationship in Human Tuberculosis

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The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations

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Dynamic Population Changes in Mycobacterium tuberculosis During Acquisition and Fixation of Drug Resistance in Patients

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

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Tuberculosis Pathogenesis and Immunity

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Deep resequencing of serial sputum isolates of Mycobacterium tuberculosis during therapeutic failure due to poor compliance reveals stepwise mutation of key resistance genes on an otherwise stable genetic background

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Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

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

Sequence-specific error profile of Illumina sequencers

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Variation among Genome Sequences of H37Rv Strains of Mycobacterium tuberculosis from Multiple Laboratories

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ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

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Epidemiological and clinical consequences of within-host evolution

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Bottlenecks and the Maintenance of Minor Genotypes during the Life Cycle of Trypanosoma brucei

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The Sequence Alignment/Map format and SAMtools

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Fast and accurate short read alignment with Burrows-Wheeler transform

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Differences between tuberculosis cases infected withMycobacterium africanum, West African type 2, relative to Euro-AmericanMycobacterium tuberculosis: an update

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High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography

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