Methylome Diversification through Changes in DNA Methyltransferase Sequence Specificity

Proteome variability amongHelicobacter pyloriisolates clustered according to genomic methylation

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

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

Comparing the genomes of Helicobacter pylori clinical strain UM032 and Mice-adapted derivatives

(2013) Yalda Khosravi et al.   Gut Pathogens

Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution

(2013) Maria Lluch-Senar et al.   PLoS Genetics

Functional Plasticity in the Type IV Secretion System of Helicobacter pylori

(2013) Roberto M. Barrozo et al.   PLoS Pathogens

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

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

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

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Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

(2012) Gang Fang et al.   NATURE BIOTECHNOLOGY

The methylomes of six bacteria

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Movement of DNA sequence recognition domains between non-orthologous proteins

(2012) Yoshikazu Furuta et al.   NUCLEIC ACIDS RESEARCH

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

(2012) Christina Kahramanoglou et al.   Nature Communications

MEME-ChIP: motif analysis of large DNA datasets

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

(2011) Mikihiko Kawai et al.   BMC MICROBIOLOGY

Transcriptional regulation by DNA methylation

(2011) Anna R. Poetsch et al.   CANCER TREATMENT REVIEWS

Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing

(2011) Tyson A. Clark et al.   NUCLEIC ACIDS RESEARCH

Domain Movement within a Gene: A Novel Evolutionary Mechanism for Protein Diversification

(2011) Yoshikazu Furuta et al.   PLoS One

Phasevarion Mediated Epigenetic Gene Regulation in Helicobacter pylori

(2011) Yogitha N. Srikhanta et al.   PLoS One

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

Characterization of an N6 adenine methyltransferase from Helicobacter pylori strain 26695 which methylates adjacent adenines on the same strand

(2010) Ritesh Kumar et al.   FEBS Journal

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Direct detection of DNA methylation during single-molecule, real-time sequencing

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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

Genome comparison and context analysis reveals putative mobile forms of restriction–modification systems and related rearrangements

(2010) Yoshikazu Furuta et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Geographic distribution of methyltransferases of Helicobacter pylori: evidence of human host population isolation and migration

(2009) Filipa F Vale et al.   BMC MICROBIOLOGY

‘Nothing is permanent but change’†- antigenic variation in persistent bacterial pathogens

(2009) Guy H. Palmer et al.   CELLULAR MICROBIOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Many paths to one goal? The proteins that recognize methylated DNA in eukaryotes

(2009) Nobuhiro Sasai et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity

(2009) Richard D. Morgan et al.   NUCLEIC ACIDS RESEARCH

The MmeI family: type II restriction–modification enzymes that employ single-strand modification for host protection

(2009) Richard D. Morgan et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

Helicobacter Pylori's Plasticity Zones Are Novel Transposable Elements

(2009) Dangeruta Kersulyte et al.   PLoS One

Clocks and switches: bacterial gene regulation by DNA adenine methylation

(2008) David A Low et al.   CURRENT OPINION IN MICROBIOLOGY

Maintenance Forced by a Restriction-Modification System Can Be Modulated by a Region in Its Modification Enzyme Not Essential for Methyltransferase Activity

(2008) S. Ohno et al.   JOURNAL OF BACTERIOLOGY

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

Quick identification of Type I restriction enzyme isoschizomers using newly developed pTypeI and reference plasmids

(2008) J. Ryu et al.   NUCLEIC ACIDS RESEARCH

The Helicobacter pylori HpyAXII restriction–modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components

(2008) Olivier Humbert et al.   NUCLEIC ACIDS RESEARCH