Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona

Prevalence of Salmonella in Vegetables from Mexico

(2016) CAROLINA QUIROZ-SANTIAGO et al.   JOURNAL OF FOOD PROTECTION

High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach

(2012) Marc W Allard et al.   BMC GENOMICS

Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection

(2012) J. A. Neuman et al.   BRIEFINGS IN BIOINFORMATICS

Salmonella Prevalence and Antimicrobial Susceptibility from the National Animal Health Monitoring System Swine 2000 and 2006 Studies

(2012) C. A. HALEY et al.   JOURNAL OF FOOD PROTECTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

Emergence and global spread of epidemic healthcare-associated Clostridium difficile

(2012) Miao He 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

Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

(2012) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

CRISPR Typing and Subtyping for Improved Laboratory Surveillance of Salmonella Infections

(2012) Laëtitia Fabre et al.   PLoS One

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

Persisting Viral Sequences Shape Microbial CRISPR-based Immunity

(2012) Ariel D. Weinberger et al.   PLoS Computational Biology

Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

(2012) Mark Achtman et al.   PLoS Pathogens

A Whole-Genome Single Nucleotide Polymorphism-Based Approach To Trace and Identify Outbreaks Linked to a Common Salmonella enterica subsp. enterica Serovar Montevideo Pulsed-Field Gel Electrophoresis Type

(2011) Henk C. den Bakker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica

(2011) Henk C den Bakker et al.   BMC GENOMICS

Global Monitoring of Salmonella Serovar Distribution from the World Health Organization Global Foodborne Infections Network Country Data Bank: Results of Quality Assured Laboratories from 2001 to 2007

(2011) Rene S. Hendriksen et al.   Foodborne Pathogens and Disease

Comparative Genomics of 28 Salmonella enterica Isolates: Evidence for CRISPR-Mediated Adaptive Sublineage Evolution

(2011) W. F. Fricke et al.   JOURNAL OF BACTERIOLOGY

The Salmonella enterica Pan-genome

(2011) Annika Jacobsen et al.   MICROBIAL ECOLOGY

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

(2011) Ankur Mutreja et al.   NATURE

VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors

(2011) L. Chen et al.   NUCLEIC ACIDS RESEARCH

Rapid Pneumococcal Evolution in Response to Clinical Interventions

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

The Impact of Recombination on dN/dS within Recently Emerged Bacterial Clones

(2011) Santiago Castillo-Ramírez et al.   PLoS Pathogens

Salmonella enterica serovar Agona European outbreak associated with a food company

(2010) N. NICOLAY et al.   EPIDEMIOLOGY AND INFECTION

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers et al.   GENOME RESEARCH

Evolution and Population Structure of Salmonella enterica Serovar Newport

(2010) V. Sangal et al.   JOURNAL OF BACTERIOLOGY

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

(2010) Giovanna Morelli et al.   NATURE GENETICS

Molecular analysis of Salmonella serotypes at different stages of commercial turkey processing

(2010) P. N. Anderson et al.   POULTRY SCIENCE

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Microevolution of Helicobacter pylori during Prolonged Infection of Single Hosts and within Families

(2010) Giovanna Morelli et al.   PLoS Genetics

Multilocus Sequence Typing of Outbreak-Associated Listeria monocytogenes Isolates to Identify Epidemic Clones

(2009) Henk C. den Bakker et al.   Foodborne Pathogens and Disease

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

(2009) J. Muller et al.   NUCLEIC ACIDS RESEARCH

A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis

(2009) S. R. Leopold et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Supplement 2003–2007 (No. 47) to the White-Kauffmann-Le Minor scheme

(2009) Martine Guibourdenche et al.   RESEARCH IN MICROBIOLOGY

The Defective Prophage Pool of Escherichia coli O157: Prophage–Prophage Interactions Potentiate Horizontal Transfer of Virulence Determinants

(2009) Md Asadulghani et al.   PLoS Pathogens

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

The Origins of Ecological Diversity in Prokaryotes

(2008) Frederick M. Cohan et al.   CURRENT BIOLOGY

Salmonella enterica Serovar Senftenberg Human Clinical Isolates Lacking SPI-1

(2008) Q. Hu et al.   JOURNAL OF CLINICAL MICROBIOLOGY

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS