Salmonella enterica Phylogeny Based on Whole-Genome Sequencing Reveals Two New Clades and Novel Patterns of Horizontally Acquired Genetic Elements

A genomic overview of the population structure of Salmonella

(2018) Nabil-Fareed Alikhan et al.   PLoS Genetics

The Salmonella Effector SteD Mediates MARCH8-Dependent Ubiquitination of MHC II Molecules and Inhibits T Cell Activation

(2016) Ethel Bayer-Santos et al.   Cell Host & Microbe

Long-term live-cell imaging reveals new roles for Salmonella effector proteins SseG and SteA

(2016) Sarah E. McQuate et al.   CELLULAR MICROBIOLOGY

Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database

(2016) Marc W. Allard et al.   JOURNAL OF CLINICAL MICROBIOLOGY

New insights about excisable pathogenicity islands in Salmonella and their contribution to virulence

(2016) Pamela A. Nieto et al.   MICROBES AND INFECTION

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Global MLST of Salmonella Typhi Revisited in Post-genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types

(2016) Kien-Pong Yap et al.   Frontiers in Microbiology

Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data

(2015) Shaokang Zhang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Diversity of Plasmids Encoding Virulence and Resistance Functions in Salmonella enterica subsp. enterica Serovar Typhimurium Monophasic Variant 4,[5],12:i:- Strains Circulating in Europe

(2014) Patricia García et al.   PLoS One

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp. enterica Inferred from Genome-Wide Reference-Free SNP Characters

(2013) Ruth E. Timme et al.   Genome Biology and Evolution

When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes

(2013) Shea N. Gardner et al.   PLoS One

Evolutionary Genomics of Salmonella enterica Subspecies

(2013) P. T. Desai et al.   mBio

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

(2012) Mark Achtman et al.   PLoS Pathogens

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

Evolution and Population Structure of Salmonella enterica Serovar Newport

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Delivery of a Salmonella Typhi Exotoxin from a Host Intracellular Compartment

(2008) Stefania Spanò et al.   Cell Host & Microbe

Molecular Phylogeny of the Salmonellae: Relationships among Salmonella Species and Subspecies Determined from Four Housekeeping Genes and Evidence of Lateral Gene Transfer Events

(2008) J. R. McQuiston et al.   JOURNAL OF BACTERIOLOGY

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

(2008) Kathryn E Holt et al.   NATURE GENETICS