Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

Cryptic ecology among host generalistCampylobacter jejuniin domestic animals

(2014) Samuel K. Sheppard et al.   MOLECULAR ECOLOGY

Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not

(2014) Jessica Hedge et al.   mBio

Whole-Genome Sequencing Shows That Patient-to-Patient Transmission Rarely Accounts for Acquisition of Staphylococcus aureus in an Intensive Care Unit

(2013) J. R. Price et al.   CLINICAL INFECTIOUS DISEASES

Real-Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole-Genome Multilocus Sequence Typing

(2013) A. J. Cody et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Marked host specificity and lack of phylogeographic population structure ofCampylobacter jejuniin wild birds

(2013) Petra Griekspoor et al.   MOLECULAR ECOLOGY

Diverse Sources of C. difficile Infection Identified on Whole-Genome Sequencing

(2013) David W. Eyre et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

(2013) S. K. Sheppard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Progressive genome-wide introgression in agriculturalCampylobacter coli

(2012) Samuel K. Sheppard et al.   MOLECULAR ECOLOGY

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Closely related Campylobacter jejuni strains from different sources reveal a generalist rather than a specialist lifestyle

(2011) Eugenia Gripp et al.   BMC GENOMICS

Niche segregation and genetic structure of Campylobacter jejuni populations from wild and agricultural host species

(2011) SAMUEL K. SHEPPARD et al.   MOLECULAR ECOLOGY

Evolutionary Dynamics of Complete Campylobacter Pan-Genomes and the Bacterial Species Concept

(2010) Tristan Lefébure et al.   Genome Biology and Evolution

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Phylodynamics and Human-Mediated Dispersal of a Zoonotic Virus

(2010) Chiraz Talbi et al.   PLoS Pathogens

CampylobacterGenotyping to Determine the Source of Human Infection

(2009) Samuel K. Sheppard et al.   CLINICAL INFECTIOUS DISEASES

Assigning the source of human campylobacteriosis in New Zealand: A comparative genetic and epidemiological approach

(2009) Petra Mullner et al.   INFECTION GENETICS AND EVOLUTION

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Rapid Evolution and the Importance of Recombination to the Gastroenteric Pathogen Campylobacter jejuni

(2008) D. J. Wilson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast, accurate and simulation-free stochastic mapping

(2008) V. N Minin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Tracing the Source of Campylobacteriosis

(2008) Daniel J. Wilson et al.   PLoS Genetics