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Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

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(2013) Maha R Farhat et al.   NATURE GENETICS

Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas

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

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A systematic review of gyrase mutations associated with fluoroquinolone-resistant Mycobacterium tuberculosis and a proposed gyrase numbering system

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

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Fitness-compensatory mutations in rifampicin-resistant RNA polymerase

(2012) Gerrit Brandis et al.   MOLECULAR MICROBIOLOGY

Mycobacterium tuberculosis Population in Northwestern Russia: An Update from Russian-EU/Latvian Border Region

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High Resolution Discrimination of Clinical Mycobacterium tuberculosis Complex Strains Based on Single Nucleotide Polymorphisms

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(2012) Zarir F Udwadia   THORAX

Mutations ingidBConfer Low-Level Streptomycin Resistance in Mycobacterium tuberculosis

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Strain diversity, epistasis and the evolution of drug resistance in Mycobacterium tuberculosis

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Streptomycin Resistance and Lineage-Specific Polymorphisms in Mycobacterium tuberculosisgidBGene

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

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

(2011) Iñaki Comas et al.   NATURE GENETICS

Survival of Civilian and Prisoner Drug-Sensitive, Multi- and Extensive Drug- Resistant Tuberculosis Cohorts Prospectively Followed in Russia

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Survival of drug resistant tuberculosis patients in Lithuania: retrospective national cohort study

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Bacterial epidemiology and biology - lessons from genome sequencing

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

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Evolution of MRSA During Hospital Transmission and Intercontinental Spread

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Mycobacterium tuberculosis Eis Regulates Autophagy, Inflammation, and Cell Death through Redox-dependent Signaling

(2010) Dong-Min Shin et al.   PLoS Pathogens

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

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The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Activation of the eis gene in a W-Beijing strain of Mycobacterium tuberculosis correlates with increased SigA levels and enhanced intracellular growth

(2009) S. Wu et al.   MICROBIOLOGY-SGM

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

Mutational neighbourhood and mutation supply rate constrain adaptation in Pseudomonas aeruginosa

(2009) A. R. Hall et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach

(2009) Jing Tang et al.   PLoS Computational Biology

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

(2008) Jukka Corander et al.   BMC BIOINFORMATICS

GenoType MTBDR assays for the diagnosis of multidrug-resistant tuberculosis: a meta-analysis

(2008) D. I. Ling et al.   EUROPEAN RESPIRATORY JOURNAL

PGEToolbox: A Matlab Toolbox for Population Genetics and Evolution

(2008) J. J. Cai   JOURNAL OF HEREDITY