(Q38256379)

1 September 2017

1 reference

title

Statistical methods for detecting differentially methylated loci and regions (English)

1 reference

1 September 2017

0 references

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25278959%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Abdullah Kahraman

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25278959%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Helen Lindsay

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25278959%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Lukas M Weber

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25278959%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

author name string

Charity W Law

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25278959%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Malgorzata Nowicka

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25278959%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Xiaobei Zhou

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25278959%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

publication date

16 September 2014

1 reference

1 September 2017

Frontiers in Genetics

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25278959%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

volume

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25278959%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

page(s)

324

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25278959%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

4 June 2020

minfi

object named as

minfi

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

limma

object named as

limma

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

svaseq: removing batch effects and other unwanted noise from sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Normalization of RNA-seq data using factor analysis of control genes or samples

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

MethylSig: a whole genome DNA methylation analysis pipeline.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

DMAP: differential methylation analysis package for RRBS and WGBS data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

MOABS: model based analysis of bisulfite sequencing data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Accounting for cellular heterogeneity is critical in epigenome-wide association studies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

BLUEPRINT: mapping human blood cell epigenomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

A-clustering: a novel method for the detection of co-regulated methylation regions, and regions associated with exposure

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Charting a dynamic DNA methylation landscape of the human genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

An optimized algorithm for detecting and annotating regional differential methylation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

A data-driven approach to preprocessing Illumina 450K methylation array data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Perspectives of international human epigenome consortium

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Dynamic DNA methylation across diverse human cell lines and tissues

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Analysing and interpreting DNA methylation data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

DNA methylation arrays as surrogate measures of cell mixture distribution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Genomic landscape of human allele-specific DNA methylation.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

DNA methylation signatures for breast cancer classification and prognosis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Removing technical variability in RNA-seq data using conditional quantile normalization

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Mechanisms for the inheritance of chromatin states

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Protocol matters: which methylome are you actually studying?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

The NIH Roadmap Epigenomics Mapping Consortium

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Tackling the epigenome: challenges and opportunities for collaboration

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Generalizing moving averages for tiling arrays using combined p-value statistics.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

International network of cancer genome projects

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Principles and challenges of genomewide DNA methylation analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Human DNA methylomes at base resolution show widespread epigenomic differences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

An operational definition of epigenetics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Capturing heterogeneity in gene expression studies by surrogate variable analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Epigenetic programming by maternal behavior

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

DNA methylation patterns and epigenetic memory

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Whole-genome haplotyping using long reads and statistical methods

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

Genome-wide DNA methylation events in TMPRSS2-ERG fusion-negative prostate cancers implicate an EZH2-dependent mechanism with miR-26a hypermethylation.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4165320

DNA methylation: Bisulphite modification and analysis

31 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25278959

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Cancer genomics: from discovery science to personalized medicine

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25278959

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.3389/FGENE.2014.00324

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25278959%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25278959%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

PubMed publication ID

25278959

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25278959%20AND%20SRC:MED&resulttype=core&format=json