The Epigenomic Landscape of Prokaryotes

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

BREX is a novel phage resistance system widespread in microbial genomes

(2014) T. Goldfarb et al.   EMBO JOURNAL

ModM DNA methyltransferase methylome analysis reveals a potential role for Moraxella catarrhalis phasevarions in otitis media

(2014) Luke V. Blakeway et al.   FASEB JOURNAL

The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach

(2014) Diego Gonzalez 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

Type II restriction endonucleases—a historical perspective and more

(2014) Alfred Pingoud et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Ana Sousa Manso et al.   Nature Communications

RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

(2013) Michael J Cipriano et al.   BMC GENOMICS

Entering the era of bacterial epigenomics with single molecule real time DNA sequencing

(2013) Brigid M Davis et al.   CURRENT OPINION IN MICROBIOLOGY

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

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

Characterization of Undermethylated Sites in Vibrio cholerae

(2013) A. B. Dalia et al.   JOURNAL OF BACTERIOLOGY

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

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

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

Type I restriction enzymes and their relatives

(2013) W. A. M. Loenen et al.   NUCLEIC ACIDS RESEARCH

The complex methylome of the human gastric pathogen Helicobacter pylori

(2013) Juliane Krebes et al.   NUCLEIC ACIDS RESEARCH

Type III restriction-modification enzymes: a historical perspective

(2013) Desirazu N. Rao et al.   NUCLEIC ACIDS RESEARCH

The other face of restriction: modification-dependent enzymes

(2013) Wil A. M. Loenen et al.   NUCLEIC ACIDS RESEARCH

Highlights of the DNA cutters: a short history of the restriction enzymes

(2013) Wil A. M. Loenen et al.   NUCLEIC ACIDS RESEARCH

Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA

(2013) A. H. Laszlo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands

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

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

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Going beyond five bases in DNA sequencing

(2012) Jonas Korlach et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

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

CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI

(2012) M. Wojciechowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Christina Kahramanoglou et al.   Nature Communications

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

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

IMG ER: a system for microbial genome annotation expert review and curation

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

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

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

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