Antibiotic Resistance, Core-Genome and Protein Expression in IncHI1 Plasmids inSalmonellaTyphimurium

Antimicrobial resistance in humans, livestock and the wider environment

(2015) M. Woolhouse et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Role for Tn6029 in the Evolution of the Complex Antibiotic Resistance Gene Loci in Genomic Island 3 in Enteroaggregative Hemorrhagic Escherichia coli O104:H4

(2015) Piklu Roy Chowdhury et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Complete sequences of IncHI1 plasmids carrying blaCTX-M-1 and qnrS1 in equine Escherichia coli provide new insights into plasmid evolution

(2014) Monika Dolejska et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Benchmarking of Methods for Genomic Taxonomy

(2014) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Complete sequence of multidrug resistance p9134 plasmid and its variants including natural recombinant with the virulence plasmid of Salmonella serovar Typhimurium

(2014) Tereza Kubasova et al.   PLASMID

Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae

(2014) S. Conlan et al.   Science Translational Medicine

Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

(2013) H. Hasman et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Evolution of IncHI1 plasmids: Two distinct lineages

(2013) Amy K. Cain et al.   PLASMID

Pan-Genome and Comparative Genome Analyses of Propionibacterium acnes Reveal Its Genomic Diversity in the Healthy and Diseased Human Skin Microbiome

(2013) S. Tomida et al.   mBio

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Complete sequencing of an IncHI1 plasmid encoding the carbapenemase NDM-1, the ArmA 16S RNA methylase and a resistance-nodulation-cell division/multidrug efflux pump

(2012) M. Dolejska et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhi P-stx-12

(2012) S. Y. Ong et al.   JOURNAL OF BACTERIOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Analysis of Antimicrobial Resistance Genes Detected in Multidrug-Resistant Salmonella enterica Serovar Typhimurium Isolated from Food Animals

(2011) LaShanda M. Glenn et al.   Microbial Drug Resistance

The genome sequence of the incompatibility group Iγ plasmid R621a: Evolution of IncI plasmids

(2011) Hiroyuki Takahashi et al.   PLASMID

Emergence of a Globally Dominant IncHI1 Plasmid Type Associated with Multiple Drug Resistant Typhoid

(2011) Kathryn E. Holt et al.   PLoS Neglected Tropical Diseases

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

Predicting Plasmid Promiscuity Based on Genomic Signature

(2010) H. Suzuki et al.   JOURNAL OF BACTERIOLOGY

Genome-wide analysis of the H-NS and Sfh regulatory networks in Salmonella Typhimurium identifies a plasmid-encoded transcription silencing mechanism

(2010) Shane C. Dillon et al.   MOLECULAR MICROBIOLOGY

Call of the wild: antibiotic resistance genes in natural environments

(2010) Heather K. Allen et al.   NATURE REVIEWS MICROBIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Resistance Plasmid Families in Enterobacteriaceae

(2009) A. Carattoli   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli

(2009) Y. Ogura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variation in Salmonella enterica Serovar Typhi IncHI1 Plasmids during the Global Spread of Resistant Typhoid Fever

(2008) M.-D. Phan et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Characterization of Salmonella enterica serovar Typhimurium conjugative plasmids transferring resistance to antibiotics and their interaction with the virulence plasmid

(2008) H. Hradecka et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY