Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies

The Tohoku Medical Megabank Project: Design and Mission

(2016) Shinichi Kuriyama et al.   JOURNAL OF EPIDEMIOLOGY

Epigenomic profiling reveals an association between persistence of DNA methylation and metabolic memory in the DCCT/EDIC type 1 diabetes cohort

(2016) Zhuo Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

(2016) Sebastian Moran et al.   Epigenomics

Association of DNA Methylation Differences With Schizophrenia in an Epigenome-Wide Association Study

(2016) Carolina Montano et al.   JAMA Psychiatry

Adjustment of Cell-Type Composition Minimizes Systematic Bias in Blood DNA Methylation Profiles Derived by DNA Collection Protocols

(2016) Yuh Shiwa et al.   PLoS One

Intraindividual dynamics of transcriptome and genome-wide stability of DNA methylation

(2016) Ryohei Furukawa et al.   Scientific Reports

DNA Methylation of Lipid-Related Genes Affects Blood Lipid LevelsCLINICAL PERSPECTIVE

(2015) Liliane Pfeiffer et al.   Circulation-Cardiovascular Genetics

DNA Methylation of the Aryl Hydrocarbon Receptor Repressor Associations With Cigarette Smoking and Subclinical AtherosclerosisCLINICAL PERSPECTIVE

(2015) Lindsay M. Reynolds et al.   Circulation-Cardiovascular Genetics

Type 2 diabetes and leucocyte DNA methylation: an epigenome-wide association study in over 1,500 older adults

(2015) Ines Florath et al.   DIABETOLOGIA

Diversity Outbred: A New Generation of Mouse Model

(2015) Charles W. Schmidt   ENVIRONMENTAL HEALTH PERSPECTIVES

Epigenome-wide association study (EWAS) of BMI, BMI change and waist circumference in African American adults identifies multiple replicated loci

(2015) Ellen W. Demerath et al.   HUMAN MOLECULAR GENETICS

Epigenome-wide association study identifiesTXNIPgene associated with type 2 diabetes mellitus and sustained hyperglycemia

(2015) Carolina Soriano-Tárraga et al.   HUMAN MOLECULAR GENETICS

Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals

(2015) Yosuke Kawai et al.   JOURNAL OF HUMAN GENETICS

An epigenome-wide association study of total serum immunoglobulin E concentration

(2015) Liming Liang et al.   NATURE

Whole-genome fingerprint of the DNA methylome during human B cell differentiation

(2015) Marta Kulis et al.   NATURE GENETICS

Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation

(2015) Norihiro Kato et al.   NATURE GENETICS

Post-conversion targeted capture of modified cytosines in mammalian and plant genomes

(2015) Qing Li et al.   NUCLEIC ACIDS RESEARCH

Epigenome-wide study identifies novel methylation loci associated with body mass index and waist circumference

(2015) Stella Aslibekyan et al.   Obesity

DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip

(2015) Denise L Walker et al.   Epigenomics

Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants

(2015) Fiona Allum et al.   Nature Communications

Intermediate DNA methylation is a conserved signature of genome regulation

(2015) GiNell Elliott et al.   Nature Communications

Hypomethylation of smoking-related genes is associated with future lung cancer in four prospective cohorts

(2015) Francesca Fasanelli et al.   Nature Communications

Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals

(2015) Masao Nagasaki et al.   Nature Communications

Functional and Phenotypic Plasticity of CD4+T Cell Subsets

(2015) Tiffany Caza et al.   Biomed Research International

DNA Methylation of Lipid-Related Genes Affects Blood Lipid LevelsCLINICAL PERSPECTIVE

(2015) Liliane Pfeiffer et al.   Circulation-Cardiovascular Genetics

DNA Methylation of the Aryl Hydrocarbon Receptor Repressor Associations With Cigarette Smoking and Subclinical AtherosclerosisCLINICAL PERSPECTIVE

(2015) Lindsay M. Reynolds et al.   Circulation-Cardiovascular Genetics

Epigenome-wide association of DNA methylation markers in peripheral blood from Indian Asians and Europeans with incident type 2 diabetes: a nested case-control study

(2015) John C Chambers et al.   Lancet Diabetes & Endocrinology

An efficient quantitation method of next-generation sequencing libraries by using MiSeq sequencer

(2014) Fumiki Katsuoka et al.   ANALYTICAL BIOCHEMISTRY

Epigenome-Wide Association Study of Fasting Blood Lipids in the Genetics of Lipid-Lowering Drugs and Diet Network Study

(2014) Marguerite R. Irvin et al.   CIRCULATION

Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation

(2014) Loukia G Tsaprouni et al.   Epigenetics

The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation

(2014) Lei Zhao et al.   GENOME RESEARCH

DNA methylation and body-mass index: a genome-wide analysis

(2014) Katherine J Dick et al.   LANCET

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

(2014) Michael J Ziller et al.   NATURE METHODS

Reduction of Systematic Bias in Transcriptome Data from Human Peripheral Blood Mononuclear Cells for Transportation and Biobanking

(2014) Hideki Ohmomo et al.   PLoS One

New concepts in DNA methylation

(2014) Albert Jeltsch et al.   TRENDS IN BIOCHEMICAL SCIENCES

Global Analysis of DNA Methylation Variation in Adipose Tissue from Twins Reveals Links to Disease-Associated Variants in Distal Regulatory Elements

(2013) Elin Grundberg et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Helper T-cell identity and evolution of differential transcriptomes and epigenomes

(2013) Golnaz Vahedi et al.   IMMUNOLOGICAL REVIEWS

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

(2013) Yun Liu et al.   NATURE BIOTECHNOLOGY

Recommendations for the design and analysis of epigenome-wide association studies

(2013) Karin B Michels et al.   NATURE METHODS

Tagmentation-based whole-genome bisulfite sequencing

(2013) Qi Wang et al.   Nature Protocols

From promises to practical strategies in epigenetic epidemiology

(2013) Jonathan Mill et al.   NATURE REVIEWS GENETICS

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

(2013) William A. Pastor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Tobacco Smoking Leads to Extensive Genome-Wide Changes in DNA Methylation

(2013) Sonja Zeilinger et al.   PLoS One

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and Their Differentiated Derivatives

(2012) Kristopher L. Nazor et al.   Cell Stem Cell

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility

(2012) Lovisa E. Reinius et al.   PLoS One

High resolution profiling of human exon methylation by liquid hybridization capture-based bisulfite sequencing

(2011) Junwen Wang et al.   BMC GENOMICS

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

Epigenome-wide association studies for common human diseases

(2011) Vardhman K. Rakyan et al.   NATURE REVIEWS GENETICS

Evaluation of the Infinium Methylation 450K technology

(2011) Sarah Dedeurwaerder et al.   Epigenomics

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Maintaining Cell Identity through Global Control of Genomic Organization

(2010) Gioacchino Natoli   IMMUNITY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

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

(2009) Rafael A Irizarry et al.   NATURE GENETICS

Rethinking how DNA methylation patterns are maintained

(2009) Peter A. Jones et al.   NATURE REVIEWS GENETICS

Genome-wide DNA methylation profiling using Infinium®assay

(2009) Marina Bibikova et al.   Epigenomics

Monocyte-Mediated Defense Against Microbial Pathogens

(2008) Natalya V. Serbina et al.   Annual Review of Immunology

CD4 T cells: fates, functions, and faults

(2008) J. Zhu et al.   BLOOD

Personal genomes: The case of the missing heritability

(2008) Brendan Maher   NATURE