Identifying Likely Transmission Pathways within a 10-Year Community Outbreak of Tuberculosis by High-Depth Whole Genome Sequencing

Temporal dynamics of Mycobacterium tuberculosis genotypes in New South Wales, Australia

(2014) Ulziijargal Gurjav et al.   BMC INFECTIOUS DISEASES

Enhanced tuberculosis outbreak investigation using whole genome sequencing and IGRA

(2014) P. W. Smit et al.   EUROPEAN RESPIRATORY JOURNAL

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

(2014) Frederic Bertels et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis

(2014) Tao Luo et al.   TUBERCULOSIS

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

Evolutionary robust SNPs reveal the misclassification of Mycobacterium tuberculosis Beijing family strains into sublineages

(2013) Noriko Nakanishi et al.   INFECTION GENETICS AND EVOLUTION

Epidemic Spread of Multidrug-Resistant Tuberculosis in Johannesburg, South Africa

(2013) B. J. Marais et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Whole Genome Sequencing Analysis of Intrapatient Microevolution in Mycobacterium tuberculosis: Potential Impact on the Inference of Tuberculosis Transmission

(2013) Laura Pérez-Lago et al.   JOURNAL OF INFECTIOUS DISEASES

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis

(2013) Christopher B Ford et al.   NATURE GENETICS

Sterilization of granulomas is common in active and latent tuberculosis despite within-host variability in bacterial killing

(2013) Philana Ling Lin et al.   NATURE MEDICINE

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

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

Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients

(2013) Matthias Merker et al.   PLoS One

Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study

(2013) Josephine M Bryant et al.   Lancet Respiratory Medicine

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

High-throughput microbial population genomics using the Cortex variation assembler

(2012) Zamin Iqbal et al.   BIOINFORMATICS

Mixed-Strain Mycobacterium tuberculosis Infections and the Implications for Tuberculosis Treatment and Control

(2012) T. Cohen et al.   CLINICAL MICROBIOLOGY REVIEWS

Rapid Whole-Genome Sequencing for Investigation of a Suspected Tuberculosis Outbreak

(2012) M. E. Torok et al.   JOURNAL OF CLINICAL MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

Insights from Genomics into Bacterial Pathogen Populations

(2012) Daniel J. Wilson   PLoS Pathogens

Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis

(2011) Josephine F. Reyes et al.   INFECTION GENETICS AND EVOLUTION

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

(2011) Nigel J. Saunders et al.   JOURNAL OF INFECTION

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak

(2011) Jennifer L. Gardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genomic Stability over 9 Years of an Isoniazid Resistant Mycobacterium tuberculosis Outbreak Strain in Sweden

(2011) Linus Sandegren et al.   PLoS One

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

TubercuList – 10 years after

(2010) Jocelyne M. Lew et al.   TUBERCULOSIS

r2cat: synteny plots and comparative assembly

(2009) P. Husemann et al.   BIOINFORMATICS