Genome-Wide Diversity and Phylogeography of Mycobacterium avium subsp. paratuberculosis in Canadian Dairy Cattle

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

(2015) Christina Ahlstrom et al.   BMC GENOMICS

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

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

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations

(2012) Roman Biek et al.   PLoS Pathogens

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

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

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

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

Divergent cytokine responses of macrophages to Mycobacterium avium subsp. paratuberculosis strains of Types II and III in a standardized in vitro model

(2011) Erika Borrmann et al.   VETERINARY MICROBIOLOGY

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

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

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

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

(2009) Marcel A. Behr   INFLAMMATORY BOWEL DISEASES

Insertion and Deletion Events That Define the PathogenMycobacterium aviumsubsp.paratuberculosis

(2008) David C. Alexander et al.   JOURNAL OF BACTERIOLOGY

Estimates for local and movement-based transmission of bovine tuberculosis in British cattle

(2008) D. M Green et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparing Network Analysis Measures to Determine Potential Epidemic Size of Highly Contagious Exotic Diseases in Fragmented Monthly Networks of Dairy Cattle Movements in Ontario, Canada

(2008) C. Dubé et al.   Transboundary and Emerging Diseases

Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty

(2007) Joe Parker et al.   INFECTION GENETICS AND EVOLUTION