Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids

Full-Length Nucleotide Sequences ofmcr-1-Harboring Plasmids Isolated from Extended-Spectrum-β-Lactamase-Producing Escherichia coli Isolates of Different Origins

(2016) Katrin Zurfluh et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

mcr-1.2, a NewmcrVariant Carried on a Transferable Plasmid from a Colistin-Resistant KPC Carbapenemase-Producing Klebsiella pneumoniae Strain of Sequence Type 512

(2016) Vincenzo Di Pilato et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Complete Nucleotide Sequence of an IncI2 Plasmid CoharboringblaCTX-M-55andmcr-1

(2016) Jian Sun et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Escherichia coli Harboringmcr-1andblaCTX-Mon a Novel IncF Plasmid: First Report ofmcr-1in the United States

(2016) Patrick McGann et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Colistin resistance inSalmonellaandEscherichia coliisolates from a pig farm in Great Britain

(2016) Muna F. Anjum et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Complete sequence of an IncFII plasmid harbouring the colistin resistance genemcr-1isolated from Belgian pig farms

(2016) B. B. Xavier et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Co-occurrence ofmcr-1and ESBL on a single plasmid inSalmonella enterica

(2016) Yong-Qiang Yang et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Colistin resistance gene mcr-1 harboured on a multidrug resistant plasmid

(2016) Surbhi Malhotra-Kumar et al.   LANCET INFECTIOUS DISEASES

Emergence of the mcr-1 colistin resistance gene in carbapenem-resistant Enterobacteriaceae

(2016) Hong Du et al.   LANCET INFECTIOUS DISEASES

Dissemination of the mcr-1 colistin resistance gene

(2016) Chanping Zhi et al.   LANCET INFECTIOUS DISEASES

Investigation of a plasmid genome database for colistin-resistance gene mcr-1

(2016) Satowa Suzuki et al.   LANCET INFECTIOUS DISEASES

Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study

(2016) Yi-Yun Liu et al.   LANCET INFECTIOUS DISEASES

Assessing structural variation in a personal genome—towards a human reference diploid genome

(2015) Adam C English et al.   BMC GENOMICS

Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data

(2015) Katrine G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

IncI shufflons: Assembly issues in the next-generation sequencing era

(2015) Michael S.M. Brouwer et al.   PLASMID

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

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

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

(2014) David Coil et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Functional genomics to identify the factors contributing to successful persistence and global spread of an antibiotic resistance plasmid

(2014) Jennifer L Cottell et al.   BMC MICROBIOLOGY

Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

(2014) K. G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Sequences of Two Related Multiple Antibiotic Resistance Virulence Plasmids Sharing a Unique IS26-Related Molecular Signature Isolated from Different Escherichia coli Pathotypes from Different Hosts

(2013) Carola Venturini et al.   PLoS One

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genomic approaches to studying the human microbiota

(2012) George M. Weinstock   NATURE

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities

(2011) Hikaru Suenaga   ENVIRONMENTAL MICROBIOLOGY

Therapeutic options for infections withEnterobacteriaceaeproducing carbapenem-hydrolyzing enzymes

(2011) Matthew E Falagas et al.   Future Microbiology

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

(2010) Thomas D. Otto et al.   BIOINFORMATICS

Interactive microbial genome visualization with GView

(2010) Aaron Petkau et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Next generation sequencing of microbial transcriptomes: challenges and opportunities

(2009) Arnoud H.M. van Vliet   FEMS MICROBIOLOGY LETTERS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

(2008) Tim Carver et al.   BIOINFORMATICS

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY