(Q35813616)

10 August 2017

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

1 reference

10 August 2017

2

Xue-Song Zhang

1 reference

10 August 2017

4

Robert Sebra

1 reference

10 August 2017

11

Martin J Blaser

1 reference

10 August 2017

10

Andrew Chess

1 reference

10 August 2017

6

Gintaras Deikus

1 reference

10 August 2017

12

Eric E Schadt

1 reference

10 August 2017

9

Matthew K Waldor

1 reference

10 August 2017

John Beaulaurier

1

1 reference

10 August 2017

Shijia Zhu

3

1 reference

10 August 2017

Chaggai Rosenbluh

5

1 reference

10 August 2017

Nan Shen

7

1 reference

10 August 2017

Diana Munera

8

1 reference

10 August 2017

Gang Fang

13

1 reference

10 August 2017

language of work or name

English

0 references

publication date

15 June 2015

1 reference

10 August 2017

Nature Communications

1 reference

10 August 2017

6

1 reference

10 August 2017

7438

1 reference

Creative Commons Attribution 4.0 International

10 August 2017

start time

15 June 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N(6)-adenine DNA methyltransferases of Neisseria meningitidis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Diversification of bacterial genome content through distinct mechanisms over different timescales.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Comprehensive mapping of the Escherichia coli flagellar regulatory network

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Type II restriction endonucleases--a historical perspective and more

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Phasevarions mediate epigenetic regulation of antimicrobial susceptibility in Neisseria meningitidis.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Methylome diversification through changes in DNA methyltransferase sequence specificity.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

The complex methylome of the human gastric pathogen Helicobacter pylori

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Programmed heterogeneity: epigenetic mechanisms in bacteria

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive evolution

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

The methylomes of six bacteria

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Context-dependent conservation of DNA methyltransferases in bacteria

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Natural transformation of an engineered Helicobacter pylori strain deficient in type II restriction endonucleases

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Phasevarion mediated epigenetic gene regulation in Helicobacter pylori

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Phase variation: how to create and coordinate population diversity.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

The origin of the Haitian cholera outbreak strain

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Phase and antigenic variation in mycoplasmas.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

The primary transcriptome of the major human pathogen Helicobacter pylori

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

The Sequence Alignment/Map format and SAMtools

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Molecular chaperones in pathogen virulence: emerging new targets for therapy.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Real-time DNA sequencing from single polymerase molecules

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Role of futC slipped strand mispairing in Helicobacter pylori Lewisy phase variation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Bacterial populations as perfect gases: genomic integrity and diversification tensions in Helicobacter pylori

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Epigenetic gene regulation in the bacterial world

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Antimutator role of the DNA glycosylase mutY gene in Helicobacter pylori

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

N6-methyl-adenine: an epigenetic signal for DNA-protein interactions

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Extensive DNA Inversions in the B. fragilis Genome Control Variable Gene Expression

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

A novel method for accurate operon predictions in all sequenced prokaryotes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Transcriptional phase variation of a type III restriction-modification system in Helicobacter pylori

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Dam- and OxyR-dependent phase variation of agn43: essential elements and evidence for a new role of DNA methylation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

The CcrM DNA methyltransferase of Agrobacterium tumefaciens is essential, and its activity is cell cycle regulated

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Switching of flagellar motility in Helicobacter pylori by reversible length variation of a short homopolymeric sequence repeat in fliP, a gene encoding a basal body protein

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Epigenetic phase variation of the pap operon in Escherichia coli.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Selfish behavior of restriction-modification systems

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Structure and function of DNA methyltransferases.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

The Escherichia coli chromosome contains specific, unmethylated dam and dcm sites

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

A whole genome approach to in vivo DNA-protein interactions in E. coli

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Clocks and switches: bacterial gene regulation by DNA adenine methylation.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

A multistep epigenetic switch enables the stable inheritance of DNA methylation states.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

The diversity within an expanded and redefined repertoire of phase-variable genes in Helicobacter pylori

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4490391

Post-segregational killing by restriction modification gene complexes: observations of individual cell deaths

24 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26074426

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Clinical and pathological importance of heterogeneity in vacA, the vacuolating cytotoxin gene of Helicobacter pylori

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26074426

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NCOMMS8438

1 reference

10 August 2017

0 references

1 reference

10 August 2017

PubMed publication ID

26074426

1 reference