A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data (Q31027575)

13 August 2017

A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data (English)

1 reference

13 August 2017

0 references

Amanda J Lea

1

1 reference

13 August 2017

Jenny Tung

series ordinal

2

1 reference

13 August 2017

Xiang Zhou

series ordinal

3

1 reference

13 August 2017

24 November 2015

1 reference

13 August 2017

1 reference

13 August 2017

11

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13 August 2017

11

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13 August 2017

e1005650

1 reference

Creative Commons Attribution 4.0 International

13 August 2017

start time

24 November 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

limma

object named as

limma

2 references

22 June 2022

https://europepmc.org/article/PMC/4657956

based on heuristic

inferred from PubMed Central ID database lookup

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

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21 June 2018

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DNA methylation signatures link prenatal famine exposure to growth and metabolism

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21 June 2018

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Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

21 June 2018

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Characterization of genome-methylome interactions in 22 nuclear pedigrees

21 June 2018

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

21 June 2018

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Contribution of genetic variation to transgenerational inheritance of DNA methylation

21 June 2018

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Trimmomatic: a flexible trimmer for Illumina sequence data

21 June 2018

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Genome-wide DNA methylation analysis of human pancreatic islets from type 2 diabetic and non-diabetic donors identifies candidate genes that influence insulin secretion

21 June 2018

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Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue

21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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Dynamics of DNA methylation in recent human and great ape evolution

21 June 2018

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21 June 2018

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Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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A six months exercise intervention influences the genome-wide DNA methylation pattern in human adipose tissue

21 June 2018

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DNA methylation of the BDNF gene and its relevance to psychiatric disorders

21 June 2018

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DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

21 June 2018

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21 June 2018

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Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis

21 June 2018

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In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes

21 June 2018

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Patterns of methylation heritability in a genome-wide analysis of four brain regions.

21 June 2018

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An integrated map of genetic variation from 1,092 human genomes

21 June 2018

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Factors underlying variable DNA methylation in a human community cohort

21 June 2018

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Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

21 June 2018

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

21 June 2018

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

21 June 2018

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An integrated encyclopedia of DNA elements in the human genome

21 June 2018

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Mapping cis- and trans-regulatory effects across multiple tissues in twins

21 June 2018

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The aging epigenome: DNA methylation from the cradle to the grave

21 June 2018

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DNA methylation: a promising landscape for immune system-related diseases.

21 June 2018

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Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence

21 June 2018

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Genome-wide efficient mixed-model analysis for association studies

21 June 2018

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

21 June 2018

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Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population

21 June 2018

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Social environment is associated with gene regulatory variation in the rhesus macaque immune system

21 June 2018

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Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel

21 June 2018

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Epigenetics and the environment: emerging patterns and implications

21 June 2018

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Genomic distribution and inter-sample variation of non-CpG methylation across human cell types

21 June 2018

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Identification of type 1 diabetes-associated DNA methylation variable positions that precede disease diagnosis.

21 June 2018

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A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

21 June 2018

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Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.

21 June 2018

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Increased methylation variation in epigenetic domains across cancer types

21 June 2018

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Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

21 June 2018

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

21 June 2018

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Allele-specific gene expression in a wild nonhuman primate population

21 June 2018

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Season of conception in rural gambia affects DNA methylation at putative human metastable epialleles

21 June 2018

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Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals

21 June 2018

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

21 June 2018

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Differential expression analysis for sequence count data

21 June 2018

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Resilience to social stress coincides with functional DNA methylation of the Crf gene in adult mice.

21 June 2018

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New approaches to population stratification in genome-wide association studies

21 June 2018

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A longitudinal study of epigenetic variation in twins

21 June 2018

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Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.

21 June 2018

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Understanding mechanisms underlying human gene expression variation with RNA sequencing

21 June 2018

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Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains

21 June 2018

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Variance component model to account for sample structure in genome-wide association studies

21 June 2018

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A high-resolution association mapping panel for the dissection of complex traits in mice

21 June 2018

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Bayesian inference for generalized linear mixed models

21 June 2018

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

21 June 2018

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Dynamic DNA methylation programs persistent adverse effects of early-life stress

21 June 2018

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Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context

21 June 2018

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BSMAP: whole genome bisulfite sequence MAPping program

21 June 2018

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Evolution of a malaria resistance gene in wild primates

21 June 2018

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The 1001 genomes project for Arabidopsis thaliana

21 June 2018

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Epigenetic mechanisms that underpin metabolic and cardiovascular diseases

21 June 2018

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

21 June 2018

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Generalized linear mixed models: a practical guide for ecology and evolution

21 June 2018

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

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4657956

Persistent epigenetic differences associated with prenatal exposure to famine in humans

21 June 2018

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Genes mirror geography within Europe

21 June 2018

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Efficient control of population structure in model organism association mapping

21 June 2018

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Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

21 June 2018

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Moderated statistical tests for assessing differences in tag abundance

21 June 2018

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Principal components analysis corrects for stratification in genome-wide association studies

21 June 2018

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A unified mixed-model method for association mapping that accounts for multiple levels of relatedness

21 June 2018

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Epigenetic programming by maternal behavior

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4657956

The International HapMap Project

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4657956

True paternal care in a multi-male primate society

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4657956

A human genome diversity cell line panel

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4657956

Estimation of pairwise relatedness with molecular markers.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4657956

Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4657956

Demethylation-induced developmental pleiotropy in Arabidopsis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4657956

Behavior predicts genes structure in a wild primate group

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4657956

Role for DNA methylation in genomic imprinting

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4657956

Characterization of an Arabidopsis thaliana DNA hypomethylation mutant

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4657956

FaST linear mixed models for genome-wide association studies

21 June 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1005650

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1005650

DNA methylation changes elicited by social stimuli in the brains of worker honey bees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1005650

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1005650

COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1005650

Epigenetic and genetic influences on DNA methylation variation in maize populations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1005650

Efficient computation with a linear mixed model on large-scale data sets with applications to genetic studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1005650

Patterns of population epigenomic diversity.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4657956

Maternal epigenetics and methyl supplements affect agouti gene expression in Avy/a mice

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4657956

Gene expression profiles of Arabidopsis Cvi seeds during dormancy cycling indicate a common underlying dormancy control mechanism

25 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26599596

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Reactivation of an inactive human X chromosome: evidence for X inactivation by DNA methylation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26599596

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PGEN.1005650

1 reference

13 August 2017

1 reference

13 August 2017

PubMed publication ID

26599596

1 reference