Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica

Multilocus sequence typing of Salmonella Typhimurium reveals the presence of the highly invasive ST313 in Brazil

(2017) Fernanda Almeida et al.   INFECTION GENETICS AND EVOLUTION

A Systematic Review of the Incidence, Risk Factors and Case Fatality Rates of Invasive Nontyphoidal Salmonella (iNTS) Disease in Africa (1966 to 2014)

(2017) Ifeanyi Valentine Uche et al.   PLoS Neglected Tropical Diseases

Virulence of invasive Salmonella Typhimurium ST313 in animal models of infection

(2017) Girish Ramachandran et al.   PLoS Neglected Tropical Diseases

Genomic Analysis of Salmonella enterica Serovar Typhimurium from Wild Passerines in England and Wales

(2016) Alison E. Mather et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings

(2016) Nicholas A Feasey et al.   NATURE GENETICS

Microbial genome-wide association studies: lessons from human GWAS

(2016) Robert A. Power et al.   NATURE REVIEWS GENETICS

'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution

(2016) Alan McNally et al.   NATURE REVIEWS MICROBIOLOGY

Loss of Multicellular Behavior in Epidemic African Nontyphoidal Salmonella enterica Serovar Typhimurium ST313 Strain D23580

(2016) Larissa A. Singletary et al.   mBio

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe

(2016) David M. Aanensen et al.   mBio

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

(2016) John A. Lees et al.   Nature Communications

Identifying lineage effects when controlling for population structure improves power in bacterial association studies

(2016) Sarah G. Earle et al.   Nature Microbiology

Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host

(2016) Elizabeth J. Klemm et al.   Nature Microbiology

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

The advent of genome-wide association studies for bacteria

(2015) Peter E Chen et al.   CURRENT OPINION IN MICROBIOLOGY

Twenty years of bacterial genome sequencing

(2015) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

A random forest approach to capture genetic effects in the presence of population structure

(2015) Johannes Stephan et al.   Nature Communications

Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa

(2015) Chinyere K. Okoro et al.   PLoS Neglected Tropical Diseases

Invasive Salmonella Typhimurium ST313 with Naturally Attenuated Flagellin Elicits Reduced Inflammation and Replicates within Macrophages

(2015) Girish Ramachandran et al.   PLoS Neglected Tropical Diseases

Non-typhoidal Salmonella Typhimurium ST313 isolates that cause bacteremia in humans stimulate less inflammasome activation than ST19 isolates associated with gastroenteritis

(2015) Sarah Carden et al.   Pathogens and Disease

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Dissecting Vancomycin-Intermediate Resistance in Staphylococcus aureus Using Genome-Wide Association

(2014) Md Tauqeer Alam et al.   Genome Biology and Evolution

Predicting the virulence of MRSA from its genome sequence

(2014) M. Laabei et al.   GENOME RESEARCH

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

(2014) Rasmus Lykke Marvig et al.   NATURE GENETICS

Detecting epistasis in human complex traits

(2014) Wen-Hua Wei et al.   NATURE REVIEWS GENETICS

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Parallel independent evolution of pathogenicity within the genus Yersinia

(2014) S. Reuter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patterns of genome evolution that have accompanied host adaptation inSalmonella

(2014) Gemma C. Langridge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Analysis of Salmonella Genomes Identifies a Metabolic Network for Escalating Growth in the Inflamed Gut

(2014) S.-P. Nuccio et al.   mBio

Postgenomic analysis of bacterial pathogens repertoire reveals genome reduction rather than virulence factors

(2013) V. Merhej et al.   Briefings in Functional Genomics

Explaining microbial phenotypes on a genomic scale: GWAS for microbes

(2013) B. E. Dutilh et al.   Briefings in Functional Genomics

The Type VI Secretion System Encoded in Salmonella Pathogenicity Island 19 Is Required for Salmonella enterica Serotype Gallinarum Survival within Infected Macrophages

(2013) Carlos J. Blondel et al.   INFECTION AND IMMUNITY

Genome dynamics during experimental evolution

(2013) Jeffrey E. Barrick et al.   NATURE REVIEWS GENETICS

Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted Salmonella enterica Serovar Typhimurium Pathovar

(2013) R. A. Kingsley et al.   mBio

Host Specificity of Bacterial Pathogens

(2013) A. Baumler et al.   Cold Spring Harbor Perspectives in Medicine

Invasive Non-Typhoidal Salmonella Typhimurium ST313 Are Not Host-Restricted and Have an Invasive Phenotype in Experimentally Infected Chickens

(2013) Bryony N. Parsons et al.   PLoS Neglected Tropical Diseases

PhenoLink - a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains

(2012) Jumamurat R Bayjanov et al.   BMC GENOMICS

Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle?

(2012) W. G. Touw et al.   BRIEFINGS IN BIOINFORMATICS

Type VI Secretion System-Associated Gene Clusters Contribute to Pathogenesis of Salmonella enterica Serovar Typhimurium

(2012) David T. Mulder et al.   INFECTION AND IMMUNITY

Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa

(2012) Nicholas A Feasey et al.   LANCET

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

(2012) Chinyere K Okoro et al.   NATURE GENETICS

The Perpetual Challenge of Infectious Diseases

(2012) Anthony S. Fauci et al.   NEW ENGLAND JOURNAL OF MEDICINE

Pulsed-Field Gel Electrophoresis Supports the Presence of Host-Adapted Salmonella enterica subsp. enterica Serovar Typhimurium Strains in the British Garden Bird Population

(2011) Becki Lawson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Classification with correlated features: unreliability of feature ranking and solutions

(2011) Laura Toloşi et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

YajL, Prokaryotic Homolog of Parkinsonism-associated Protein DJ-1, Functions as a Covalent Chaperone for Thiol Proteome

(2011) Hai-Tuong Le et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crystal structure of the FimD usher bound to its cognate FimC–FimH substrate

(2011) Gilles Phan et al.   NATURE

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

From the regulation of peptidoglycan synthesis to bacterial growth and morphology

(2011) Athanasios Typas et al.   NATURE REVIEWS MICROBIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Translational Defects in a Mutant Deficient in YajL, the Bacterial Homolog of the Parkinsonism-Associated Protein DJ-1

(2010) F. Kthiri et al.   JOURNAL OF BACTERIOLOGY

Gallstones play a significant role in Salmonella spp. gallbladder colonization and carriage

(2010) R. W. Crawford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

(2009) G. C. Langridge et al.   GENOME RESEARCH

Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype

(2009) R. A. Kingsley et al.   GENOME RESEARCH

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

(2008) N. R. Thomson et al.   GENOME RESEARCH

Mechanisms of pathogenesis and the evolution of parasite virulence

(2008) S. A. FRANK et al.   JOURNAL OF EVOLUTIONARY BIOLOGY