Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria

Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis

(2022) Lisa Nonaka et al.   PLoS One

Novel transferable resistance-nodulation-division pump gene cluster tmexCD2-toprJ2 that confers tigecycline resistance in Raoultella ornithinolytica

(2021) Cheng-Zhen Wang et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria

(2021) Jessika Consuegra et al.   Nature Communications

Characterization of TMexCD3-TOprJ3, an RND-type efflux system conferring resistance to tigecycline in Proteus mirabilis, and its associated Integrative Conjugative Element

(2021) Qian Wang et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

TaxonKit: A practical and efficient NCBI taxonomy toolkit

(2021) Wei Shen et al.   Journal of Genetics and Genomics

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Identification of Tn553, a novel Tn554-related transposon that carries a complete blaZ-blaR1-blaI β-lactamase operon in Staphylococcus aureus

(2021) Henrike Krüger et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids

(2021) Romain Durand et al.   PLoS Genetics

Characterization of IncHI1B Plasmids Encoding Efflux Pump TmexCD2-ToprJ2 in Carbapenem-Resistant Klebsiella variicola, Klebsiella quasipneumoniae, and Klebsiella michiganensis Strains

(2021) Yujiao Wang et al.   Frontiers in Microbiology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Emergence of a Plasmid-Encoded Resistance-Nodulation-Division Efflux Pump Conferring Resistance to Multiple Drugs, Including Tigecycline, in Klebsiella pneumoniae

(2020) Luchao Lv et al.   mBio

DNA–protein cross-link repair: what do we know now?

(2020) Huimin Zhang et al.   Cell and Bioscience

Toxin-Antitoxin Gene Pairs Found in Tn3 Family Transposons Appear To Be an Integral Part of the Transposition Module

(2020) Gipsi Lima-Mendez et al.   mBio

Tn6674, a Novel Enterococcal optrA-Carrying Multiresistance Transposon of the Tn554 Family

(2019) Dexi Li et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates

(2019) Michael Feldgarden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Molecular mechanisms of topoisomerase 2 DNA–protein crosslink resolution

(2019) Amanda A. Riccio et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

OUP accepted manuscript

(2018)   BIOINFORMATICS

Interplay of a non-conjugative integrative element and a conjugative plasmid in the spread of antibiotic resistance via suicidal plasmid transfer from an aquaculture Vibrio isolate

(2018) Lisa Nonaka et al.   PLoS One

The global distribution and spread of the mobilized colistin resistance gene mcr-1

(2018) Ruobing Wang et al.   Nature Communications

Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle

(2018) Xiaoying Li et al.   BMC GENOMICS

Evolution of Sphingomonad Gene Clusters Related to Pesticide Catabolism Revealed by Genome Sequence and Mobilomics of Sphingobium herbicidovorans MH

(2017) Tue Kjærgaard Nielsen et al.   Genome Biology and Evolution

Integrative and conjugative elements and their hosts: composition, distribution and organization

(2017) Jean Cury et al.   NUCLEIC ACIDS RESEARCH

Unlocking Tn3-family transposase activity in vitro unveils an asymetric pathway for transposome assembly

(2017) Emilien Nicolas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems

(2017) et al.   Genes

Four genes essential for recombination define GInts, a new type of mobile genomic island widespread in bacteria

(2017) Leire Bardaji et al.   Scientific Reports

Pangenome Evolution in the Marine BacteriumAlteromonas

(2016) Mario López-Pérez et al.   Genome Biology and Evolution

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

Integrative and Conjugative Elements (ICEs): What They Do and How They Work

(2015) Christopher M. Johnson et al.   Annual Review of Genetics

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

JPred4: a protein secondary structure prediction server

(2015) Alexey Drozdetskiy et al.   NUCLEIC ACIDS RESEARCH

Insertion Sequence IS 26 Reorganizes Plasmids in Clinically Isolated Multidrug-Resistant Bacteria by Replicative Transposition

(2015) Susu He et al.   mBio

Is Leclercia adecarboxylata a New and Unfamiliar Marine Pathogen?

(2014) Y. Keren et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Movement of IS26-Associated Antibiotic Resistance Genes Occurs via a Translocatable Unit That Includes a Single IS26 and Preferentially Inserts Adjacent to Another IS26

(2014) C. J. Harmer et al.   mBio

The Master Activator of IncA/C Conjugative Plasmids Stimulates Genomic Islands and Multidrug Resistance Dissemination

(2014) Nicolas Carraro et al.   PLoS Genetics

Various pAQU plasmids possibly contribute to disseminate tetracycline resistance gene tet(M) among marine bacterial community

(2014) Lisa Nonaka et al.   Frontiers in Microbiology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeny and organization of recombinase in trio (RIT) elements

(2013) N. Ricker et al.   PLASMID

Novel Conjugative Transferable Multiple Drug Resistance Plasmid pAQU1 from Photobacterium damselae subsp. damselae Isolated from Marine Aquaculture Environment

(2012) Lisa Nonaka et al.   MICROBES AND ENVIRONMENTS

Genome Engineering in Vibrio cholerae: A Feasible Approach to Address Biological Issues

(2012) Marie-Eve Val et al.   PLoS Genetics

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Differences of genetic diversity and antibiotics susceptibility of Pseudomonas aeruginosa isolated from hospital, river and coastal seawater

(2010) Lisa Nonaka et al.   Environmental Microbiology Reports

New mobile genetic elements in Cupriavidus metallidurans CH34, their possible roles and occurrence in other bacteria

(2009) Rob Van Houdt et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

GenomeMatcher: A graphical user interface for DNA sequence comparison

(2008) Yoshiyuki Ohtsubo et al.   BMC BIOINFORMATICS

A conserved anti-repressor controls horizontal gene transfer by proteolysis

(2008) Baundauna Bose et al.   MOLECULAR MICROBIOLOGY

Revised nomenclature for transposable genetic elements

(2008) Adam P. Roberts et al.   PLASMID