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

Missing Data and Influential Sites: Choice of Sites for Phylogenetic Analysis Can Be As Important As Taxon Sampling and Model Choice

(2013) Liat Shavit Grievink et al.   Genome Biology and Evolution

Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease

(2013) Honour C. McCann et al.   PLoS Pathogens

Genomes-based phylogeny of the genus Xanthomonas

(2012) Luis M Rodriguez-R et al.   BMC MICROBIOLOGY

Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

(2012) Chinyere K Okoro et al.   NATURE GENETICS

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

(2012) Kathryn E Holt et al.   NATURE GENETICS

Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

(2012) Simon R Harris et al.   NATURE GENETICS

Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis

(2012) Y. Cui et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus

(2012) P. R. McAdam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae

(2012) Brendan Epstein et al.   PLoS Genetics

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

(2011) C. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates

(2011) David A. Baltrus et al.   PLoS Pathogens

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

Impact of recombination on bacterial evolution

(2010) Xavier Didelot et al.   TRENDS IN MICROBIOLOGY

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli

(2009) Y. Ogura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae

(2009) J. Chun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics