Next-generation technologies and data analytical approaches for epigenomics (Q30712646)

26 June 2017

title

Next-generation technologies and data analytical approaches for epigenomics (English)

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26 June 2017

Olivier Thas

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Tim De Meyer

object named as

Tim De Meyer

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author name string

Klaas Mensaert

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26 June 2017

Simon Denil

2

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26 June 2017

Geert Trooskens

3

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26 June 2017

Wim Van Criekinge

4

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26 June 2017

publication date

10 December 2013

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Environmental and Molecular Mutagenesis

26 June 2017

published in

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26 June 2017

volume

55

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26 June 2017

issue

3

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26 June 2017

page(s)

155-170

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methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

26 June 2017

cites work

1 reference

Differential expression analysis for sequence count data

21 January 2018

1 reference

Epigenetics and environmental chemicals

21 January 2018

1 reference

Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer.

21 January 2018

1 reference

NucleoFinder: a statistical approach for the detection of nucleosome positions.

21 January 2018

1 reference

Summarizing and correcting the GC content bias in high-throughput sequencing

21 January 2018

1 reference

An operational definition of epigenetics

21 January 2018

1 reference

High density DNA methylation array with single CpG site resolution

21 January 2018

1 reference

Quantitative comparison of genome-wide DNA methylation mapping technologies.

21 January 2018

1 reference

Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution

21 January 2018

1 reference

Epigenetic control of plant stress response

21 January 2018

1 reference

F-Seq: a feature density estimator for high-throughput sequence tags

21 January 2018

1 reference

Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax

21 January 2018

1 reference

Whole-genome DNA methylation profiling using MethylCap-seq.

21 January 2018

1 reference

Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage

21 January 2018

1 reference

BS Seeker: precise mapping for bisulfite sequencing

21 January 2018

1 reference

Sequence overlap between autosomal and sex-linked probes on the Illumina HumanMethylation27 microarray.

21 January 2018

1 reference

Quantitative DNA methylation analysis identifies a single CpG dinucleotide important for ZAP-70 expression and predictive of prognosis in chronic lymphocytic leukemia

21 January 2018

1 reference

RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.

21 January 2018

1 reference

Bisulfite sequencing of DNA.

21 January 2018

1 reference

Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing

21 January 2018

1 reference

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

21 January 2018

1 reference

RNA-SeQC: RNA-seq metrics for quality control and process optimization

21 January 2018

1 reference

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

21 January 2018

1 reference

High sequence specificity of micrococcal nuclease

21 January 2018

1 reference

Landscape of transcription in human cells

21 January 2018

1 reference

STAR: ultrafast universal RNA-seq aligner

21 January 2018

1 reference

Environmental epigenomics in human health and disease

21 January 2018

1 reference

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

21 January 2018

1 reference

Impact of experience-dependent and -independent factors on gene expression in songbird brain

21 January 2018

1 reference

lumi: a pipeline for processing Illumina microarray

21 January 2018

1 reference

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis

21 January 2018

1 reference

DNA hypomethylation in cancer cells

21 January 2018

1 reference

An integrated encyclopedia of DNA elements in the human genome

21 January 2018

1 reference

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

21 January 2018

1 reference

A DNA methylation fingerprint of 1628 human samples

21 January 2018

1 reference

nucleR: a package for non-parametric nucleosome positioning.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Controls of nucleosome positioning in the human genome.

21 January 2018

1 reference

CpG methylation has differential effects on the binding of YY1 and ETS proteins to the bi-directional promoter of the Surf-1 and Surf-2 genes

21 January 2018

1 reference

Differential analysis for high density tiling microarray data

21 January 2018

1 reference

Epigenetics and gene expression

21 January 2018

1 reference

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

21 January 2018

1 reference

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

21 January 2018

1 reference

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data

21 January 2018

1 reference

Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands

21 January 2018

1 reference

Methylation-specific digital karyotyping

21 January 2018

1 reference

Comprehensive methylome analysis of ovarian tumors reveals hedgehog signaling pathway regulators as prognostic DNA methylation biomarkers

21 January 2018

1 reference

Transcript mapping with high-density oligonucleotide tiling arrays

21 January 2018

1 reference

ChIPseqR: analysis of ChIP-seq experiments

21 January 2018

1 reference

Radiation-induced bystander effects in vivo are epigenetically regulated in a tissue-specific manner

21 January 2018

1 reference

Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome.

21 January 2018

1 reference

An integrated software system for analyzing ChIP-chip and ChIP-seq data

21 January 2018

1 reference

Nucleosome positioning and gene regulation: advances through genomics

21 January 2018

1 reference

Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine

21 January 2018

1 reference

Genomic mapping of 5-hydroxymethylcytosine in the human brain

21 January 2018

1 reference

Environmental epigenomics and disease susceptibility

21 January 2018

1 reference

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

21 January 2018

1 reference

Non-coding RNAs as regulators of gene expression and epigenetics.

21 January 2018

1 reference

A high-throughput DNA methylation analysis of a single cell

21 January 2018

1 reference

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

21 January 2018

1 reference

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

21 January 2018

1 reference

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.

21 January 2018

1 reference

Nutritional control of reproductive status in honeybees via DNA methylation

21 January 2018

1 reference

High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology

21 January 2018

1 reference

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

21 January 2018

1 reference

The fate is not always written in the genes: epigenomics in epidemiologic studies

21 January 2018

1 reference

Fast gapped-read alignment with Bowtie 2

21 January 2018

1 reference

A beta-mixture model for dimensionality reduction, sample classification and analysis

21 January 2018

1 reference

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

21 January 2018

1 reference

MethPrimer: designing primers for methylation PCRs

21 January 2018

1 reference

Whole genome DNA methylation analysis based on high throughput sequencing technology

21 January 2018

1 reference

SOAP2: an improved ultrafast tool for short read alignment

21 January 2018

1 reference

Human DNA methylomes at base resolution show widespread epigenomic differences

21 January 2018

1 reference

NONCODE: an integrated knowledge database of non-coding RNAs

21 January 2018

1 reference

A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data

21 January 2018

1 reference

DNA methylation polymorphisms precede any histological sign of atherosclerosis in mice lacking apolipoprotein E.

21 January 2018

1 reference

SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips

21 January 2018

1 reference

A myriad of miRNA variants in control and Huntington's disease brain regions detected by massively parallel sequencing

21 January 2018

1 reference

Conserved role of intragenic DNA methylation in regulating alternative promoters

21 January 2018

1 reference

Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis

21 January 2018

1 reference

MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system.

21 January 2018

1 reference

High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA.

21 January 2018

1 reference

A novel and universal method for microRNA RT-qPCR data normalization

21 January 2018

1 reference

Applications of DNA tiling arrays for whole-genome analysis

21 January 2018

1 reference

Microfluidic-based multiplex qRT-PCR identifies diagnostic and prognostic microRNA signatures in the sera of prostate cancer patients

21 January 2018

1 reference

omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data

21 January 2018

1 reference

Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA.

21 January 2018

1 reference

Measuring the methylome in clinical samples: improved processing of the Infinium Human Methylation450 BeadChip Array.

21 January 2018

1 reference

ChIP-seq: advantages and challenges of a maturing technology

21 January 2018

1 reference

Computation for ChIP-seq and RNA-seq studies

21 January 2018

1 reference

5-hydroxymethylcytosine and its potential roles in development and cancer.

21 January 2018

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Epigenetic modifications and human disease

21 January 2018

1 reference

Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array

21 January 2018

1 reference

MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells

21 January 2018

1 reference

Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer

21 January 2018

1 reference

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

21 January 2018

1 reference

Moderated statistical tests for assessing differences in tag abundance

21 January 2018

1 reference

Copy-number-aware differential analysis of quantitative DNA sequencing data

21 January 2018

1 reference

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

21 January 2018

1 reference

A scaling normalization method for differential expression analysis of RNA-seq data

21 January 2018

1 reference

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping

21 January 2018

1 reference

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

21 January 2018

1 reference

SHRiMP: accurate mapping of short color-space reads

21 January 2018

1 reference

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

21 January 2018

1 reference

A window into third-generation sequencing

21 January 2018

1 reference

Dynamic regulation of nucleosome positioning in the human genome

21 January 2018

1 reference

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

21 January 2018

1 reference

Scoring and analysis of methylation-sensitive amplification polymorphisms for epigenetic population studies

21 January 2018

1 reference

Microarray-based DNA methylation profiling: technology and applications

21 January 2018

1 reference

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome

21 January 2018

1 reference

Single-cell sequencing-based technologies will revolutionize whole-organism science

21 January 2018

1 reference

Detection and quantification of methylation in DNA using solid-state nanopores

21 January 2018

1 reference

MicroRNA expression is down-regulated and reorganized in prefrontal cortex of depressed suicide subjects

21 January 2018

1 reference

Repitools: an R package for the analysis of enrichment-based epigenomic data

21 January 2018

1 reference

The language of covalent histone modifications

21 January 2018

1 reference

Histone acetylation and transcriptional regulatory mechanisms

21 January 2018

1 reference

Determinants of nucleosome positioning

21 January 2018

1 reference

Signals and combinatorial functions of histone modifications

21 January 2018

1 reference

Gene body methylation is conserved between plant orthologs and is of evolutionary consequence

21 January 2018

1 reference

Epigenetic reprogramming and imprinting in origins of disease

21 January 2018

1 reference

Complete pipeline for Infinium(®) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation.

21 January 2018

1 reference

How to map billions of short reads onto genomes

21 January 2018

1 reference

Significance analysis of microarrays applied to the ionizing radiation response

21 January 2018

1 reference

Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2).

21 January 2018

1 reference

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

21 January 2018

1 reference

Determinants of nucleosome organization in primary human cells

21 January 2018

1 reference

cDNA normalization by hydroxyapatite chromatography to enrich transcriptome diversity in RNA-seq applications

21 January 2018

1 reference

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

21 January 2018

1 reference

IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data

21 January 2018

1 reference

SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures.

21 January 2018

1 reference

Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA.

21 January 2018

1 reference

Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells

21 January 2018

1 reference

Environmental exposure measurement in cancer epidemiology

21 January 2018

1 reference

Standardization of real-time PCR gene expression data from independent biological replicates

21 January 2018

1 reference

Epigenomics: mapping the methylome

21 January 2018

1 reference

PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data

21 January 2018

1 reference

RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing

21 January 2018

1 reference

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data

21 January 2018

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Mapping the genome landscape using tiling array technology

21 January 2018

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Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells

21 January 2018

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Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.

21 January 2018

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Model-based analysis of ChIP-Seq (MACS)

21 January 2018

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Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq

21 January 2018

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Charting a dynamic DNA methylation landscape of the human genome

21 January 2018

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Erratum: Corrigendum: Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

21 January 2018

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Uncovering the role of 5-hydroxymethylcytosine in the epigenome

21 January 2018

1 reference

7 January 2021

Fast wavelet based functional models for transcriptome analysis with tiling arrays

1 reference

7 January 2021

Chromatin immunoprecipitation assay

1 reference

7 January 2021

Evaluation of the Infinium Methylation 450K technology

1 reference

7 January 2021

Epigenetics and the environment: emerging patterns and implications

1 reference

7 January 2021

Genome-wide profiling of promoter methylation in human

1 reference

7 January 2021

Moderate folate depletion increases plasma homocysteine and decreases lymphocyte DNA methylation in postmenopausal women

1 reference

7 January 2021

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

1 reference

7 January 2021

Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique

1 reference

7 January 2021

Identifiers

DOI

10.1002/EM.21841

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26 June 2017

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