Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580

Genome variation and molecular epidemiology of Salmonella Typhimurium pathovariants

(2018) Priscilla Branchu et al.   INFECTION AND IMMUNITY

Role of a single noncoding nucleotide in the evolution of an epidemic African clade ofSalmonella

(2018) Disa L. Hammarlöf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Salmonella within Hosts

(2018) Jennifer R. Tanner et al.   TRENDS IN MICROBIOLOGY

Regulation of Flagellum Biosynthesis in Response to Cell Envelope Stress in Salmonella enterica Serovar Typhimurium

(2018) Imke Spöring et al.   mBio

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

(2018) Nicole E. Wheeler et al.   PLoS Genetics

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

Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa

(2017) Philip M. Ashton et al.   Genome Medicine

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

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

Three-dimensional organotypic co-culture model of intestinal epithelial cells and macrophages to study Salmonella enterica colonization patterns

(2017) Jennifer Barrila et al.   NPJ Microgravity

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries

(2016) Lars Barquist et al.   BIOINFORMATICS

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

(2016) Larissa A. Singletary et al.   mBio

Poor biofilm-forming ability and long-term survival of invasiveSalmonellaTyphimurium ST313

(2016) Girish Ramachandran et al.   Pathogens and Disease

Disseminated infections with antibiotic-resistant non-typhoidalSalmonellastrains: contributions of host and pathogen factors

(2016) Kristen L. Lokken et al.   Pathogens and Disease

Quantitative bacterial transcriptomics with RNA-seq

(2015) James P Creecy et al.   CURRENT OPINION IN MICROBIOLOGY

A BTP1 prophage gene present in invasive non-typhoidalSalmonelladetermines composition and length of the O-antigen of the lipopolysaccharide

(2015) Erica Kintz et al.   MOLECULAR MICROBIOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

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

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

Characterization of the Invasive, Multidrug Resistant Non-typhoidal Salmonella Strain D23580 in a Murine Model of Infection

(2015) Jiseon Yang 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

RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium

(2015) Shabarinath Srikumar et al.   PLoS Pathogens

Fast and efficient three-step target-specific curing of a virulence plasmid in Salmonella enterica

(2015) Marcos H de Moraes et al.   AMB Express

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

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

(2014) David Coil et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

The Role of the st313-td Gene in Virulence of Salmonella Typhimurium ST313

(2014) Ana Herrero-Fresno et al.   PLoS One

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

Unprecedented High-Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing

(2014) T. Conway et al.   mBio

Structure-based mechanism for Na+/melibiose symport by MelB

(2014) Abdul S. Ethayathulla et al.   Nature Communications

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Structural analysis of O-polysaccharide chains extracted from different Salmonella Typhimurium strains

(2013) Francesca Micoli et al.   CARBOHYDRATE RESEARCH

An Infection-Relevant Transcriptomic Compendium for Salmonella enterica Serovar Typhimurium

(2013) Carsten Kröger et al.   Cell Host & Microbe

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium

(2013) Lars Barquist et al.   NUCLEIC ACIDS RESEARCH

A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection

(2013) Brooke L. Deatherage Kaiser et al.   PLoS One

A model based criterion for gene expression calls using RNA-seq data

(2013) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

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

High-throughput comparison of gene fitness among related bacteria

(2012) Rocio Canals et al.   BMC GENOMICS

Visualizing next-generation sequencing data with JBrowse

(2012) O. Westesson et al.   BRIEFINGS IN BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Invasive African nontyphoidal Salmonella requires high levels of complement for cell-free antibody-dependent killing

(2012) Yun Shan Goh et al.   JOURNAL OF IMMUNOLOGICAL METHODS

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

(2012) Nicholas A Feasey et al.   LANCET

YdiV: a dual function protein that targets FlhDC for ClpXP-dependent degradation by promoting release of DNA-bound FlhDC complex

(2012) Akiko Takaya et al.   MOLECULAR MICROBIOLOGY

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

(2012) Chinyere K Okoro et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identification of a common immune signature in murine and human systemic Salmonellosis

(2012) S.-J. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

(2012) C. Kroger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Dalliance: interactive genome viewing on the web

(2011) T. A. Down et al.   BIOINFORMATICS

Engineering multiple genomic deletions in Gram-negative bacteria: analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440

(2011) Esteban Martínez-García et al.   ENVIRONMENTAL MICROBIOLOGY

Salmonella enterica Serovar Typhimurium Colonizing the Lumen of the Chicken Intestine Grows Slowly and Upregulates a Unique Set of Virulence and Metabolism Genes

(2011) P. C. Harvey et al.   INFECTION AND IMMUNITY

EAL Domain Protein YdiV Acts as an Anti-FlhD4C2 Factor Responsible for Nutritional Control of the Flagellar Regulon in Salmonella enterica Serovar Typhimurium

(2011) T. Wada et al.   JOURNAL OF BACTERIOLOGY

Genome Sequences of Salmonella enterica Serovar Typhimurium, Choleraesuis, Dublin, and Gallinarum Strains of Well- Defined Virulence in Food-Producing Animals

(2011) E. J. Richardson et al.   JOURNAL OF BACTERIOLOGY

Probing Cellular Processes with Oligo-Mediated Recombination and Using the Knowledge Gained to Optimize Recombineering

(2011) James A. Sawitzke et al.   JOURNAL OF MOLECULAR BIOLOGY

Activation of cryptic aminoglycoside resistance in Salmonella enterica

(2011) Sanna Koskiniemi et al.   MOLECULAR MICROBIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

(2010) Chad Laing et al.   BMC BIOINFORMATICS

Reproducible Science

(2010) A. Casadevall et al.   INFECTION AND IMMUNITY

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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