A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands

Detecting Horizontal Gene Transfer between Closely Related Taxa

(2015) Orit Adato et al.   PLoS Computational Biology

PanGP: A tool for quickly analyzing bacterial pan-genome profile

(2014) Yongbing Zhao et al.   BIOINFORMATICS

A comprehensive analysis of Helicobacter pylori plasticity zones reveals that they are integrating conjugative elements with intermediate integration specificity

(2014) Wolfgang Fischer et al.   BMC GENOMICS

Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes

(2014) Corey M. Hudson et al.   NUCLEIC ACIDS RESEARCH

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2014) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

Methylome Diversification through Changes in DNA Methyltransferase Sequence Specificity

(2014) Yoshikazu Furuta et al.   PLoS Genetics

Evolution of Pan-Genomes of Escherichia coli, Shigella spp., and Salmonella enterica

(2013) E. N. Gordienko et al.   JOURNAL OF BACTERIOLOGY

Chromosome Painting In Silico in a Bacterial Species Reveals Fine Population Structure

(2013) Koji Yahara et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-Wide Survey of Mutual Homologous Recombination in a Highly Sexual Bacterial Species

(2012) Koji Yahara et al.   Genome Biology and Evolution

Complete Genome Sequences of Two Helicobacter pylori Bacteriophages Isolated from Japanese Patients

(2012) J. Uchiyama et al.   JOURNAL OF VIROLOGY

Genome, Integration, and Transduction of a Novel Temperate Phage of Helicobacter pylori

(2012) Cheng-Hung Luo et al.   JOURNAL OF VIROLOGY

Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing

(2012) Vivek Anantharaman et al.   Molecular BioSystems

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

(2012) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world

(2012) Ikuo Uchiyama et al.   NUCLEIC ACIDS RESEARCH

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

Age of the Association between Helicobacter pylori and Man

(2012) Yoshan Moodley et al.   PLoS Pathogens

PGAP: pan-genomes analysis pipeline

(2011) Yongbing Zhao et al.   BIOINFORMATICS

Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes

(2011) Mikihiko Kawai et al.   BMC MICROBIOLOGY

The Salmonella enterica Pan-genome

(2011) Annika Jacobsen et al.   MICROBIAL ECOLOGY

Eukaryote-Like Serine/Threonine Kinases and Phosphatases in Bacteria

(2011) S. F. F. Pereira et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A reverse transcriptase-related protein mediates phage resistance and polymerizes untemplated DNA in vitro

(2011) Chen Wang et al.   NUCLEIC ACIDS RESEARCH

Birth and death of genes linked to chromosomal inversion

(2011) Y. Furuta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phosphoproteome analysis of the pathogenic bacterium Helicobacter pylori reveals over-representation of tyrosine phosphorylation and multiply phosphorylated proteins

(2011) Ruiguang Ge et al.   PROTEOMICS

Genome Sequencing Reveals a Phage in Helicobacter pylori

(2011) P. Lehours et al.   mBio

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

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer

(2010) Wolfgang Fischer et al.   NUCLEIC ACIDS RESEARCH

Standard operating procedure for computing pangenome trees

(2010) Lars Snipen et al.   Standards in Genomic Sciences

A Global Overview of the Genetic and Functional Diversity in the Helicobacter pylori cag Pathogenicity Island

(2010) Patrick Olbermann et al.   PLoS Genetics

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

(2010) Claudio Donati et al.   GENOME BIOLOGY

Multiple genome alignment for identifying the core structure among moderately related microbial genomes

(2009) Ikuo Uchiyama   BMC GENOMICS

Helicobacter pylori in Health and Disease

(2009) Timothy L. Cover et al.   GASTROENTEROLOGY

Helicobacter Pylori's Plasticity Zones Are Novel Transposable Elements

(2009) Dangeruta Kersulyte et al.   PLoS One

The Peopling of the Pacific from a Bacterial Perspective

(2009) Y. Moodley et al.   SCIENCE

GenomeMatcher: A graphical user interface for DNA sequence comparison

(2008) Yoshiyuki Ohtsubo et al.   BMC BIOINFORMATICS

Evaluation of genomic island predictors using a comparative genomics approach

(2008) Morgan GI Langille et al.   BMC BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

Systematic Survey for Novel Types of Prokaryotic Retroelements Based on Gene Neighborhood and Protein Architecture

(2008) K. K. Kojima et al.   MOLECULAR BIOLOGY AND EVOLUTION

A diversity of uncharacterized reverse transcriptases in bacteria

(2008) Dawn M. Simon et al.   NUCLEIC ACIDS RESEARCH