Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes

DNA methylation in bacteria: from the methyl group to the methylome

(2015) María A Sánchez-Romero et al.   CURRENT OPINION IN MICROBIOLOGY

Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N6-adenine DNA methyltransferases of Neisseria meningitidis

(2015) Kate L. Seib et al.   NUCLEIC ACIDS RESEARCH

Phasevarions Mediate Epigenetic Regulation of Antimicrobial Susceptibility in Neisseria meningitidis

(2014) Freda E.-C. Jen et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

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

Type II restriction endonucleases—a historical perspective and more

(2014) Alfred Pingoud et al.   NUCLEIC ACIDS RESEARCH

Diversification of bacterial genome content through distinct mechanisms over different timescales

(2014) Nicholas J. Croucher et al.   Nature Communications

A random six-phase switch regulates pneumococcal virulence via global epigenetic changes

(2014) Ana Sousa Manso et al.   Nature Communications

Comprehensive Mapping of the Escherichia coli Flagellar Regulatory Network

(2014) Devon M. Fitzgerald et al.   PLoS Genetics

Methylome Diversification through Changes in DNA Methyltransferase Sequence Specificity

(2014) Yoshikazu Furuta et al.   PLoS Genetics

Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation

(2013) Tyson A Clark et al.   BMC BIOLOGY

Exploring the Roles of DNA Methylation in the Metal-Reducing Bacterium Shewanella oneidensis MR-1

(2013) M. L. Bendall et al.   JOURNAL OF BACTERIOLOGY

Programmed Heterogeneity: Epigenetic Mechanisms in Bacteria

(2013) Josep Casadesús et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle

(2013) J. B. Kozdon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic

(2013) Zhixing Feng et al.   PLoS Computational Biology

Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding

(2013) Kevin S. Myers et al.   PLoS Genetics

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

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

DNA Methylation Impacts Gene Expression and Ensures Hypoxic Survival of Mycobacterium tuberculosis

(2013) Scarlet S. Shell et al.   PLoS Pathogens

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

(2012) E. E. Schadt et al.   GENOME RESEARCH

Natural Transformation of an Engineered Helicobacter pylori Strain Deficient in Type II Restriction Endonucleases

(2012) X.-S. Zhang et al.   JOURNAL OF BACTERIOLOGY

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

(2012) Gang Fang et al.   NATURE BIOTECHNOLOGY

Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase

(2012) Elizabeth A Manrao et al.   NATURE BIOTECHNOLOGY

The methylomes of six bacteria

(2012) Iain A. Murray et al.   NUCLEIC ACIDS RESEARCH

Context-dependent conservation of DNA methyltransferases in bacteria

(2012) Aswin Sai Narain Seshasayee 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

Phase variation: how to create and coordinate population diversity

(2011) Marjan W van der Woude   CURRENT OPINION IN MICROBIOLOGY

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

Phasevarion Mediated Epigenetic Gene Regulation in Helicobacter pylori

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

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

(2010) Heng Li et al.   BIOINFORMATICS

Phase and antigenic variation in mycoplasmas

(2010) Christine Citti et al.   Future Microbiology

Phase variation controls expression of Salmonella lipopolysaccharide modification genes by a DNA methylation-dependent mechanism

(2010) S. E. Broadbent et al.   MOLECULAR MICROBIOLOGY

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

(2010) Benjamin A Flusberg et al.   NATURE METHODS

The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes

(2010) Yogitha N. Srikhanta et al.   NATURE REVIEWS MICROBIOLOGY

The Origin of the Haitian Cholera Outbreak Strain

(2010) Chen-Shan Chin et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Molecular Chaperones in Pathogen Virulence: Emerging New Targets for Therapy

(2008) Len Neckers et al.   Cell Host & Microbe

Clocks and switches: bacterial gene regulation by DNA adenine methylation

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

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE