Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements (Q35319065)

7 August 2017

title

Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements (English)

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7 August 2017

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3

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7 August 2017

Barbara E. Engelhardt

object named as

Barbara E Engelhardt

series ordinal

5

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Jordana T. Bell

object named as

Jordana T Bell

series ordinal

4

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Tim D. Spector

series ordinal

2

object named as

Tim D Spector

1 reference

7 August 2017

Weiwei Zhang

1

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7 August 2017

publication date

24 January 2015

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7 August 2017

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7 August 2017

volume

16

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7 August 2017

page(s)

14

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Creative Commons Attribution 2.0 Generic

7 August 2017

copyright license

start time

24 January 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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DNase I sensitivity QTLs are a major determinant of human expression variation

12 July 2018

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Dissecting the regulatory architecture of gene expression QTLs

12 July 2018

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Cohort Profile: TwinsUK and healthy ageing twin study

12 July 2018

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Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment

12 July 2018

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A DNA methylation fingerprint of 1628 human samples

12 July 2018

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Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

12 July 2018

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CpG islands and the regulation of transcription

12 July 2018

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A genome-wide comparison of the functional properties of rare and common genetic variants in humans

12 July 2018

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Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

12 July 2018

1 reference

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DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Identifying a high fraction of the human genome to be under selective constraint using GERP++.

12 July 2018

1 reference

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A map of human genome variation from population-scale sequencing

12 July 2018

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Epigenetic drivers of genetic alterations

12 July 2018

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Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

12 July 2018

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Conserved role of intragenic DNA methylation in regulating alternative promoters

12 July 2018

1 reference

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Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain

12 July 2018

1 reference

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

12 July 2018

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Genetic heterogeneity in human disease

12 July 2018

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RUNX3 is multifunctional in carcinogenesis of multiple solid tumors

12 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Genetic control of individual differences in gene-specific methylation in human brain.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

General transcription factor binding at CpG islands in normal cells correlates with resistance to de novo DNA methylation in cancer cells

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Dynamic changes in the human methylome during differentiation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Principles and challenges of genomewide DNA methylation analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

VEZF1 elements mediate protection from DNA methylation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

An epigenetic signature in peripheral blood predicts active ovarian cancer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

DNA methylation: an introduction to the biology and the disease-associated changes of a promising biomarker.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Human DNA methylomes at base resolution show widespread epigenomic differences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

A flexible and accurate genotype imputation method for the next generation of genome-wide association studies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Profile analysis and prediction of tissue-specific CpG island methylation classes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Histone methylation marks play important roles in predicting the methylation status of CpG islands

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Genome-scale DNA methylation maps of pluripotent and differentiated cells

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Loss of heterozygosity and microsatellite instability on chromosome arm 10q in neuroblastoma.

12 July 2018

1 reference

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Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Epigenetics in development

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

DNA methylation profiling of human chromosomes 6, 20 and 22

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Computational prediction of methylation status in human genomic sequences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

RUNX3 is frequently inactivated by dual mechanisms of protein mislocalization and promoter hypermethylation in breast cancer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Myc-binding-site recognition in the human genome is determined by chromatin context

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

A map of recent positive selection in the human genome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Epigenetic inactivation of the RUNX3 gene in lung cancer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

A haplotype map of the human genome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

RUNX3 inactivation by point mutations and aberrant DNA methylation in bladder tumors.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

ROCR: visualizing classifier performance in R

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Prediction of methylated CpGs in DNA sequences using a support vector machine

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

DNA methylation 40 years later: Its role in human health and disease

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

The ENCODE (ENCyclopedia Of DNA Elements) Project

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Transcriptional regulation by zinc-finger proteins Sp1 and MAZ involves interactions with the same cis-elements.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

The human genome browser at UCSC

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Causal relationship between the loss of RUNX3 expression and gastric cancer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Independent repression of a GC-rich housekeeping gene by Sp1 and MAZ involves the same cis-elements

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Epigenetics: regulation through repression

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Sp1 elements protect a CpG island from de novo methylation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

DNase I hypersensitive sites in Drosophila chromatin occur at the 5' ends of regions of transcription.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Biplots in biomedical research.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

CpG islands as gene markers in the human genome.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Epigenome-wide association studies without the need for cell-type composition

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Prediction of methylation CpGs and their methylation degrees in human DNA sequences.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Identification of genetic elements that autonomously determine DNA methylation states.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

High density DNA methylation array with single CpG site resolution

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Epigenetic mechanisms that regulate cell identity.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Predicting DNA methylation susceptibility using CpG flanking sequences

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Predicting methylation status of CpG islands in the human brain.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is associated with G to A mutations in K-ras in colorectal tumorigenesis

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4389802

Distant conserved sequences flanking endothelial-specific promoters contain tissue-specific DNase-hypersensitive sites and over-represented motifs

24 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25616342

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

DNA methylation and cancer

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25616342

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13059-015-0581-9

1 reference

Dimensions Publication ID

7 August 2017

1 reference

0 references

1 reference

7 August 2017

1 reference