Evolutionary Genomics of Salmonella enterica Subspecies

T3DB: an integrated database for bacterial type III secretion system

(2012) Yejun Wang et al.   BMC BIOINFORMATICS

Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages

(2012) R. K. Colwell et al.   Journal of Plant Ecology

A Genomic Island in Salmonella enterica ssp. salamae Provides New Insights on the Genealogy of the Locus of Enterocyte Effacement

(2012) P. Scott Chandry et al.   PLoS One

High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles

(2011) Yejun Wang et al.   BIOINFORMATICS

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

Analysis of the ArcA regulon in anaerobically grown Salmonella enterica sv. Typhimurium

(2011) Matthew R Evans et al.   BMC MICROBIOLOGY

PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species

(2011) Joseph J. Gillespie et al.   INFECTION AND IMMUNITY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

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

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

Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps

(2011) Christian Perez-Llamas et al.   PLoS One

COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia

(2011) Kristof Engelen et al.   PLoS One

Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota

(2011) P. Thiennimitr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recombination and Population Structure in Salmonella enterica

(2011) Xavier Didelot et al.   PLoS Genetics

Salmonella bongori Provides Insights into the Evolution of the Salmonellae

(2011) Maria Fookes et al.   PLoS Pathogens

RDP3: a flexible and fast computer program for analyzing recombination

(2010) D. P. Martin et al.   BIOINFORMATICS

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

The AI-2-dependent regulator LsrR has a limited regulon in Salmonella Typhimurium

(2010) Inge M Thijs et al.   CELL RESEARCH

Gut inflammation provides a respiratory electron acceptor for Salmonella

(2010) Sebastian E. Winter et al.   NATURE

Effective--a database of predicted secreted bacterial proteins

(2010) M.-A. Jehl et al.   NUCLEIC ACIDS RESEARCH

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes

(2009) Yeşim Soyer et al.   BMC EVOLUTIONARY BIOLOGY

Comparative genomic analysis uncovers 3 novel loci encoding type six secretion systems differentially distributed in Salmonella serotypes

(2009) Carlos J Blondel et al.   BMC GENOMICS

Lipocalin-2 Resistance Confers an Advantage to Salmonella enterica Serotype Typhimurium for Growth and Survival in the Inflamed Intestine

(2009) Manuela Raffatellu et al.   Cell Host & Microbe

Accurate Prediction of Secreted Substrates and Identification of a Conserved Putative Secretion Signal for Type III Secretion Systems

(2009) Ram Samudrala et al.   PLoS Pathogens

The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment

(2008) Wagied Davids et al.   BMC EVOLUTIONARY BIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Dealing with incongruence in phylogenomic analyses

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

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY