MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects (Q34474031)

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English	MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects	scientific article

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scholarly article

1 reference

Europe PubMed Central

2 August 2017

MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects (English)

1 reference

Europe PubMed Central

2 August 2017

David T. Bonthron

6

object named as

David T Bonthron

0 references

2

object named as

Ian M Carr

0 references

Alexander Markham

5

object named as

Alexander F Markham

0 references

author name string

Carolina E Pardo

1

1 reference

Europe PubMed Central

2 August 2017

Christopher J Hoffman

3

1 reference

Europe PubMed Central

2 August 2017

Russell P Darst

4

1 reference

Europe PubMed Central

2 August 2017

Michael P Kladde

7

1 reference

Europe PubMed Central

2 August 2017

language of work or name

0 references

publication date

19 October 2010

1 reference

Europe PubMed Central

2 August 2017

Nucleic Acids Research

1 reference

Europe PubMed Central

2 August 2017

39

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Europe PubMed Central

2 August 2017

1

1 reference

Europe PubMed Central

2 August 2017

e5

1 reference

Europe PubMed Central

2 August 2017

copyright license

Creative Commons Attribution-NonCommercial 2.5 Generic

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

0 references

Bisulfite sequencing of DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Conservation and divergence of methylation patterning in plants and animals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Genome-wide evolutionary analysis of eukaryotic DNA methylation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Dynamic changes in the human methylome during differentiation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Human DNA methylomes at base resolution show widespread epigenomic differences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Coupling phosphate homeostasis to cell cycle-specific transcription: mitotic activation of Saccharomyces cerevisiae PHO5 by Mcm1 and Forkhead proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Single-molecule analysis of chromatin: changing the view of genomes one molecule at a time

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Bisulfite sequencing Data Presentation and Compilation (BDPC) web server--a useful tool for DNA methylation analysis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

DNA methylation in mouse embryonic stem cells and development.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Inheritance of an epigenetic mark: the CpG DNA methyltransferase 1 is required for de novo establishment of a complex pattern of non-CpG methylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

BiSearch: ePCR tool for native or bisulfite-treated genomic template.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Epigenetic inheritance in plants.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Sequence analysis and editing for bisulphite genomic sequencing projects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Cancer epigenomics: DNA methylomes and histone-modification maps

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

The epigenomics of cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Single-molecule and population probing of chromatin structure using DNA methyltransferases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

DNA methyltransferase probing of DNA-protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

The epigenetic progenitor origin of human cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

DNA methylation and human disease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Transposon silencing and imprint establishment in mammalian germ cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

EUKARYOTIC CYTOSINE METHYLTRANSFERASES

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

High-speed conversion of cytosine to uracil in bisulfite genomic sequencing analysis of DNA methylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Cloning of CviPII nicking and modification system from chlorella virus NYs-1 and application of Nt.CviPII in random DNA amplification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Nucleosomes facilitate their own invasion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Gene silencing in cancer in association with promoter hypermethylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

MethPrimer: designing primers for methylation PCRs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

DNA methylation patterns and epigenetic memory

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

DNA methylation, methyltransferases, and cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

A gene hypermethylation profile of human cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Microsoft Word macro for analysis of cytosine methylation by the bisulfite deamination reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Transcriptional activation of deoxyribonucleic acid polymerase alpha gene expression in MCF-7 cells by 17 beta-estradiol

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Methyl-specific DNA binding by McrBC, a modification-dependent restriction enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

MethTools--a toolbox to visualize and analyze DNA methylation data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

MLH1 promoter hypermethylation is associated with the microsatellite instability phenotype in sporadic endometrial carcinomas

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Cloning, characterization and expression of the gene coding for a cytosine-5-DNA methyltransferase recognizing GpC.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Biallelic inactivation of hMLH1 by epigenetic gene silencing, a novel mechanism causing human MSI cancers.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Gal4p-mediated chromatin remodeling depends on binding site position in nucleosomes but does not require DNA replication

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Crystal structure of the nucleosome core particle at 2.8 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Direct study of DNA-protein interactions in repressed and active chromatin in living cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

DNA methyltransferases and DNA site-specific endonucleases encoded by chlorella viruses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Mutation in the DNA mismatch repair gene homologue hMLH1 is associated with hereditary non-polyposis colon cancer.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Positioned nucleosomes inhibit Dam methylation in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

High sensitivity mapping of methylated cytosines

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Enzymes involved in the repair of damaged DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Procaryotic and eucaryotic traits of DNA methylation in spiroplasmas (mycoplasmas).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Nuclease hypersensitive regions with adjacent positioned nucleosomes mark the gene boundaries of the PHO5/PHO3 locus in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

The two positively acting regulatory proteins PHO2 and PHO4 physically interact with PHO5 upstream activation regions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Basic local alignment search tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Cloning, characterization, and expression in Escherichia coli of the gene coding for the CpG DNA methylase from Spiroplasma sp. strain MQ1(M.SssI).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Premeiotic instability of repeated sequences in Neurospora crassa

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Restriction and modification systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltransferase activity in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

A hit-and-run system for targeted genetic manipulations in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Reaction of bisulfite with the 5-hydroxymethyl group in pyrimidines and in phage DNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Characterization of Deoxycytidylate Methyltransferase in Xanthomonas oryzae Infected with Bacteriophage Xp12

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3017589

6 July 2018

Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ716

21 January 2018

Non-CpG cytosine methylation of p53 exon 5 in non-small cell lung carcinoma

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ716

21 January 2018

Chlorella viruses encode multiple DNA methyltransferases.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ716

21 January 2018

Mapping chromatin structure in vivo using DNA methyltransferases.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ716

21 January 2018

Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ716

21 January 2018

DNA methyltransferase probing of chromatin structure within populations and on single molecules

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ716

21 January 2018

Transcriptional activation of transforming growth factor alpha by estradiol: requirement for both a GC-rich site and an estrogen response element half-site.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ716

21 January 2018

MethylMapper: a method for high-throughput, multilocus bisulfite sequence analysis and reporting

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ716

21 January 2018

CpG PatternFinder: a Windows-based utility program for easy and rapid identification of the CpG methylation status of DNA.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ716

21 January 2018

CyMATE: a new tool for methylation analysis of plant genomic DNA after bisulphite sequencing.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ716

21 January 2018

Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation

1 reference

https://pubmed.ncbi.nlm.nih.gov/20959287

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites

1 reference

https://pubmed.ncbi.nlm.nih.gov/20959287

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Bisulfite sequencing protocol displays both 5-methylcytosine and N4-methylcytosine

1 reference

https://pubmed.ncbi.nlm.nih.gov/20959287

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

DNA methyltransferases as probes of chromatin structure in vivo

1 reference

https://pubmed.ncbi.nlm.nih.gov/20959287

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast

1 reference

https://pubmed.ncbi.nlm.nih.gov/20959287

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

N4,5-dimethylcytosine, a novel hypermodified base in DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/20959287

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKQ716

1 reference

Europe PubMed Central

2 August 2017

DBLP publication ID

journals/nar/PardoCHDMBK11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

Europe PubMed Central

2 August 2017

1 reference

Europe PubMed Central

2 August 2017

ResearchGate publication ID

0 references

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