Effects of Host, Sample, and in vitro Culture on Genomic Diversity of Pathogenic Mycobacteria

Genome analysis identifies a spontaneous nonsense mutation in ppsD leading to attenuation of virulence in laboratory-manipulated Mycobacterium tuberculosis

(2019) Shyamasree De Majumdar et al.   BMC GENOMICS

Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia

(2019) Mary B O'Neill et al.   MOLECULAR ECOLOGY

Targeted DNA enrichment and whole genome sequencing of Neisseria meningitidis directly from clinical specimens

(2018) Stephen A. Clark et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Epidemiological and genomic determinants of tuberculosis outbreaks in First Nations communities in Canada

(2018) Alexander Doroshenko et al.   BMC Medicine

Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions

(2018) James Stimson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Digitally Barcoding Mycobacterium tuberculosis Reveals In Vivo Infection Dynamics in the Macaque Model of Tuberculosis

(2017) Constance J. Martin et al.   mBio

Transcriptome analysis of mycobacteria in sputum samples of pulmonary tuberculosis patients

(2017) Sumedha Sharma et al.   PLoS One

Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy

(2016) Isobella Honeyborne et al.   BMC Medicine

Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis

(2016) Tami D Lieberman et al.   NATURE MEDICINE

Sputum is a surrogate for bronchoalveolar lavage for monitoring Mycobacterium tuberculosis transcriptional profiles in TB patients

(2016) Benjamin J. Garcia et al.   TUBERCULOSIS

The Landscape of Realized Homologous Recombination in Pathogenic Bacteria

(2015) Koji Yahara et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Within patient microevolution of Mycobacterium tuberculosis correlates with heterogeneous responses to treatment

(2015) Qingyun Liu et al.   Scientific Reports

Diversity of Mycobacterium tuberculosis across Evolutionary Scales

(2015) Mary B. O’Neill et al.   PLoS Pathogens

Ancient Whole Genome Enrichment Using Baits Built from Modern DNA

(2014) Jacob M. Enk et al.   MOLECULAR BIOLOGY AND EVOLUTION

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

(2014) Francesc Coll et al.   Nature Communications

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

(2013) Maha R Farhat et al.   NATURE GENETICS

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

Population Structure of Mixed Mycobacterium tuberculosis Infection Is Strain Genotype and Culture Medium Dependent

(2013) Madeleine Hanekom et al.   PLoS One

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

(2013) Caitlin S. Pepperell et al.   PLoS Pathogens

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

High-Resolution Phenotypic Profiling Defines Genes Essential for Mycobacterial Growth and Cholesterol Catabolism

(2011) Jennifer E. Griffin et al.   PLoS Pathogens

Effect of serial subculturing on the genetic composition and cytotoxic activity of Mycobacterium tuberculosis

(2010) C. A. Molina-Torres et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Is Mycobacterium tuberculosis stressed out? A critical assessment of the genetic evidence

(2010) Christina L. Stallings et al.   MICROBES AND INFECTION

The clonal composition of Mycobacterium tuberculosis in clinical specimens could be modified by culture

(2010) Ana Martín et al.   TUBERCULOSIS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Cytological and Transcript Analyses Reveal Fat and Lazy Persister-Like Bacilli in Tuberculous Sputum

(2008) Natalie J Garton et al.   PLOS MEDICINE