Temporal Genomic Phylogeny Reconstruction Indicates a Geospatial Transmission Path of Salmonella Cerro in the United States and a Clade-Specific Loss of Hydrogen Sulfide Production

Antimicrobial resistance patterns of bovine Salmonella enterica isolates submitted to the Wisconsin Veterinary Diagnostic Laboratory: 2006–2015

(2017) J.R. Valenzuela et al.   JOURNAL OF DAIRY SCIENCE

SalmonellaPrevalence and Antimicrobial Susceptibility Among Dairy Farm Environmental Samples Collected in Texas

(2016) Lorraine D. Rodriguez-Rivera et al.   Foodborne Pathogens and Disease

Genomic and Phenotypic Analyses Reveal the Emergence of an Atypical Salmonella enterica Serovar Senftenberg Variant in China

(2016) Moataz Abd El Ghany et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

The Salmonella Effector Protein SopA Modulates Innate Immune Responses by Targeting TRIM E3 Ligase Family Members

(2016) Jana Kamanova et al.   PLoS Pathogens

Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems?

(2016) Louise Roer et al.   mSystems

Molecular Characterization of Salmonella enterica Serovar Aberdeen Negative for H2S Production in China

(2016) Fuli Wu et al.   PLoS One

Serotypes and Antimicrobial Resistance in Salmonella enterica Recovered from Clinical Samples from Cattle and Swine in Minnesota, 2006 to 2015

(2016) Samuel Hong et al.   PLoS One

Salmonellae interactions with host processes

(2015) Doris L. LaRock et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial d-amino acid oxidases: Recent findings and future perspectives

(2015) Shouji Takahashi et al.   Bioengineered

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

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

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States

(2014) Lorraine D Rodriguez-Rivera et al.   BMC GENOMICS

Increasing prevalence of hydrogen sulfide negative Salmonella in retail meats

(2014) Dachuan Lin et al.   FOOD MICROBIOLOGY

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

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

Subtype analysis of Salmonella isolated from subclinically infected dairy cattle and dairy farm environments reveals the presence of both human- and bovine-associated subtypes

(2014) L.D. Rodriguez-Rivera et al.   VETERINARY MICROBIOLOGY

Salmonella Evades d-Amino Acid Oxidase To Promote Infection in Neutrophils

(2014) Brian R. Tuinema et al.   mBio

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

(2014) Michael Inouye et al.   Genome Medicine

Regional Distribution of Two Dairy-Associated Salmonella enterica Serotypes

(2013) Jo Ann S. Van Kessel et al.   Foodborne Pathogens and Disease

Food Microbe Tracker: A Web-Based Tool for Storage and Comparison of Food-Associated Microbes

(2013) PAJAU VANGAY et al.   JOURNAL OF FOOD PROTECTION

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR 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

Prevalence of Salmonella Cerro in Laboratory-Based Submissions of Cattle and Comparison with Human Infections in Pennsylvania, 2005–2010

(2012) Deepanker Tewari et al.   Foodborne Pathogens and Disease

Characterization of DalS, an ATP-binding Cassette Transporter for d-Alanine, and Its Role in Pathogenesis inSalmonella enterica

(2012) Suzanne E. Osborne et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genetic Analysis of Non-Hydrogen Sulfide-Producing Salmonella enterica Serovar Typhimurium and S. enterica Serovar Infantis Isolates in Japan

(2012) Chieko Sakano et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

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

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

(2012) Mark Achtman et al.   PLoS Pathogens

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

The Effect of Clinical Outbreaks of Salmonellosis on the Prevalence of Fecal Salmonella Shedding Among Dairy Cattle in New York

(2010) Kevin J. Cummings et al.   Foodborne Pathogens and Disease

Salmonella enterica Serotype Cerro Among Dairy Cattle in New York: An Emerging Pathogen?

(2010) Kevin J. Cummings et al.   Foodborne Pathogens and Disease

Gut inflammation provides a respiratory electron acceptor for Salmonella

(2010) Sebastian E. Winter et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Salmonellosis Outcomes Differ Substantially by Serotype

(2008) Timothy F. Jones et al.   JOURNAL OF INFECTIOUS DISEASES