Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level

Genetic Structure of Mycobacterium avium subsp. paratuberculosis Population in Cattle Herds in Quebec as Revealed by Using a Combination of Multilocus Genomic Analyses

(2014) J. S. Sohal et al.   JOURNAL OF CLINICAL MICROBIOLOGY

High herd-level prevalence of Mycobacterium avium subspecies paratuberculosis in Western Canadian dairy farms, based on environmental sampling

(2014) R. Wolf et al.   JOURNAL OF DAIRY SCIENCE

Variable-number tandem repeats genotyping used to aid and inform management strategies for a bovine Johne’s disease incursion in tropical and subtropical Australia

(2014) Jane Oakey et al.   JOURNAL OF VETERINARY DIAGNOSTIC INVESTIGATION

Improved Short-Sequence-Repeat Genotyping of Mycobacterium avium subsp. paratuberculosis by Using Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

(2013) Christina Ahlstrom et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Inferring patient to patient transmission of Mycobacterium tuberculosisfrom whole genome sequencing data

(2013) Josephine M Bryant et al.   BMC INFECTIOUS DISEASES

Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association

(2012) John P Bannantine et al.   BMC GENOMICS

Using Tablet for visual exploration of second-generation sequencing data

(2012) I. Milne et al.   BRIEFINGS IN BIOINFORMATICS

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Genome-Wide Analysis of the Emerging Infection with Mycobacterium avium Subspecies paratuberculosis in the Arabian Camels (Camelus dromedarius)

(2012) Pallab Ghosh et al.   PLoS One

A Model-Based Bayesian Estimation of the Rate of Evolution of VNTR Loci in Mycobacterium tuberculosis

(2012) R. Zachariah Aandahl et al.   PLoS Computational Biology

Suspicion of Mycobacterium avium subsp. paratuberculosis Transmission between Cattle and Wild-Living Red Deer (Cervus elaphus) by Multitarget Genotyping

(2011) Isabel Fritsch et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Exploring the Zoonotic Potential of Mycobacterium avium Subspecies paratuberculosis through Comparative Genomics

(2011) James W. Wynne et al.   PLoS One

ConDeTri - A Content Dependent Read Trimmer for Illumina Data

(2011) Linnéa Smeds et al.   PLoS One

Resequencing the Mycobacterium avium subsp. paratuberculosis K10 Genome: Improved Annotation and Revised Genome Sequence

(2010) J. W. Wynne et al.   JOURNAL OF BACTERIOLOGY

Mycobacterium bovis genotypes in Northern Ireland: herd-level surveillance (2003 to 2008)

(2010) R. A. Skuce et al.   VETERINARY RECORD

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Occurrence of Mycobacterium avium subspecies paratuberculosis across host species and European countries with evidence for transmission between wildlife and domestic ruminants

(2009) Karen Stevenson et al.   BMC MICROBIOLOGY

Phylogenetic understanding of clonal populations in an era of whole genome sequencing

(2009) Talima Pearson et al.   INFECTION GENETICS AND EVOLUTION

The path to Crohnʼs disease: Is mucosal pathology a secondary event?

(2009) Marcel A. Behr   INFLAMMATORY BOWEL DISEASES

Molecular Typing of Mycobacterium bovis Strains Isolated in Italy from 2000 to 2006 and Evaluation of Variable-Number Tandem Repeats for Geographically Optimized Genotyping

(2009) M. B. Boniotti et al.   JOURNAL OF CLINICAL MICROBIOLOGY

On the evolution of ‘Indian Bison type’ strains of Mycobacterium avium subspecies paratuberculosis

(2009) J.S. Sohal et al.   MICROBIOLOGICAL RESEARCH

Genotyping of Genetically Monomorphic Bacteria: DNA Sequencing in Mycobacterium tuberculosis Highlights the Limitations of Current Methodologies

(2009) Iñaki Comas et al.   PLoS One

Combined Multilocus Short-Sequence-Repeat and Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem-Repeat Typing of Mycobacterium avium subsp. paratuberculosis Isolates

(2008) V. C. Thibault et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Mathematical Modelling of Mycobacterium tuberculosis VNTR Loci Estimates a Very Slow Mutation Rate for the Repeats

(2008) Andrew Grant et al.   JOURNAL OF MOLECULAR EVOLUTION