Profiling DNA Methylation Based on Next-Generation Sequencing Approaches: New Insights and Clinical Applications

Assessment of Capture and Amplicon-Based Approaches for the Development of a Targeted Next-Generation Sequencing Pipeline to Personalize Lymphoma Management

(2018) Stacy S. Hung et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Nanopore sequencing meets epigenetics

(2017) Michael C Schatz   NATURE METHODS

DNA methylation markers for diagnosis and prognosis of common cancers

(2017) Xiaoke Hao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Multiomics: Multiple Measurements from Single Cells

(2017) Iain C. Macaulay et al.   TRENDS IN GENETICS

New Insights into 5hmC DNA Modification: Generation, Distribution and Function

(2017) Dong-Qiao Shi et al.   Frontiers in Genetics

The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity

(2016) Johannes Dapprich et al.   BMC GENOMICS

Statistical method evaluation for differentially methylated CpGs in base resolution next-generation DNA sequencing data

(2016) Yun Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Single-cell triple omics sequencing reveals genetic, epigenetic and transcriptomic heterogeneity in hepatocellular carcinomas

(2016) Yu Hou et al.   CELL RESEARCH

Mechanisms, timescales and principles of trans-generational epigenetic inheritance in animals

(2016) Adam Klosin et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Epigenetic profiling to classify cancer of unknown primary: a multicentre, retrospective analysis

(2016) Sebastian Moran et al.   LANCET ONCOLOGY

BRAF Mutation Testing in Cell-Free DNA from the Plasma of Patients with Advanced Cancers Using a Rapid, Automated Molecular Diagnostics System

(2016) Filip Janku et al.   MOLECULAR CANCER THERAPEUTICS

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

The impact of next-generation sequencing on the DNA methylation–based translational cancer research

(2016) Javier Soto et al.   Translational Research

Absence of genomic hypomethylation or regulation of cytosine-modifying enzymes with aging in male and female mice

(2016) Niran Hadad et al.   Epigenetics & Chromatin

Profiling genome-wide DNA methylation

(2016) Wai-Shin Yong et al.   Epigenetics & Chromatin

High-Throughput Sequencing Technologies

(2015) Jason A. Reuter et al.   MOLECULAR CELL

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Targeted deep DNA methylation analysis of circulating cell-free DNA in plasma using massively parallel semiconductor sequencing

(2015) Felipe Vaca-Paniagua et al.   Epigenomics

Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis

(2015) Zhifu Sun et al.   Epigenomics

Targeted DNA Methylation Analysis by Next-generation Sequencing

(2015) Dustin R. Masser et al.   Jove-Journal of Visualized Experiments

Methylation-capture and Next-Generation Sequencing of free circulating DNA from human plasma

(2014) Kristina Warton et al.   BMC GENOMICS

Methodological aspects of whole-genome bisulfite sequencing analysis

(2014) S. Adusumalli et al.   BRIEFINGS IN BIOINFORMATICS

Advancing Small-Molecule-Based Chemical Biology with Next-Generation Sequencing Technologies

(2014) Chandran Anandhakumar et al.   CHEMBIOCHEM

Noninvasive Diagnosis of Actionable Mutations by Deep Sequencing of Circulating Free DNA in Lung Cancer from Never-Smokers: A Proof-of-Concept Study from BioCAST/IFCT-1002

(2014) S. Couraud et al.   CLINICAL CANCER RESEARCH

Circulating Tumor DNA as a Liquid Biopsy for Cancer

(2014) E. Heitzer et al.   CLINICAL CHEMISTRY

Gene body methylation of the dimethylarginine dimethylamino-hydrolase 2 (Ddah2) gene is an epigenetic biomarker for neural stem cell differentiation

(2014) Liselotte Bäckdahl et al.   Epigenetics

Circulating tumor DNA and circulating tumor cells in metastatic triple negative breast cancer patients

(2014) Jordan Madic et al.   INTERNATIONAL JOURNAL OF CANCER

Next-generation sequencing technologies: breaking the sound barrier of human genetics

(2014) E. M. Bahassi et al.   MUTAGENESIS

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution

(2014) Michael J. Booth et al.   Nature Chemistry

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

What is next generation sequencing?

(2013) Sam Behjati et al.   Archives of Disease in Childhood-Education and Practice Edition

BSeQC: quality control of bisulfite sequencing experiments

(2013) Xueqiu Lin et al.   BIOINFORMATICS

Estimation of CpG coverage in whole methylome next-generation sequencing studies

(2013) Edwin JCG van den Oord et al.   BMC BIOINFORMATICS

MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment

(2013) Shuying Sun et al.   BMC BIOINFORMATICS

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

(2013) Weilong Guo et al.   BMC GENOMICS

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

(2013) Alika K Maunakea et al.   CELL RESEARCH

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

Focused, high accuracy 5-methylcytosine quantitation with base resolution by benchtop next-generation sequencing

(2013) Dustin R Masser et al.   Epigenetics & Chromatin

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

Single molecule sensing with solid-state nanopores: novel materials, methods, and applications

(2012) Benjamin N. Miles et al.   CHEMICAL SOCIETY REVIEWS

Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing

(2012) K. C. A. Chan et al.   CLINICAL CHEMISTRY

Mapping recently identified nucleotide variants in the genome and transcriptome

(2012) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine

(2012) Miao Yu et al.   Nature Protocols

DNA methylation profiling in the clinic: applications and challenges

(2012) Holger Heyn et al.   NATURE REVIEWS GENETICS

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

(2012) M. J. Booth et al.   SCIENCE

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Next generation sequencing based approaches to epigenomics

(2011) M. Hirst et al.   Briefings in Functional Genomics

Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias

(2011) Shalima S. Nair et al.   Epigenetics

A DNA methylation fingerprint of 1628 human samples

(2011) A. F. Fernandez et al.   GENOME RESEARCH

Systematic assessment of reduced representation bisulfite sequencing to human blood samples: A promising method for large-sample-scale epigenomic studies

(2011) Li Wang et al.   JOURNAL OF BIOTECHNOLOGY

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

(2011) Hongcang Gu et al.   Nature Protocols

Epigenome-wide association studies for common human diseases

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

High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology

(2011) Xun Lan et al.   PLoS One

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

BRCA1 CpG Island Hypermethylation Predicts Sensitivity to Poly(Adenosine Diphosphate)- Ribose Polymerase Inhibitors

(2010) Jurgen Veeck et al.   JOURNAL OF CLINICAL ONCOLOGY

Whole-genome DNA methylation profiling using MethylCap-seq

(2010) Arie B. Brinkman et al.   METHODS

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

The implications of heterogeneous DNA methylation for the accurate quantification of methylation

(2010) Thomas Mikeska et al.   Epigenomics

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

Targeting DNA Methylation

(2009) J.-P. J. Issa et al.   CLINICAL CANCER RESEARCH

Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity

(2009) C. Schmidl et al.   GENOME RESEARCH

Finding the fifth base: Genome-wide sequencing of cytosine methylation

(2009) R. Lister et al.   GENOME RESEARCH

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

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

(2009) David Serre et al.   NUCLEIC ACIDS RESEARCH

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

Circulating mutant DNA to assess tumor dynamics

(2008) Frank Diehl et al.   NATURE MEDICINE

Epigenetics in Cancer

(2008) Manel Esteller   NEW ENGLAND JOURNAL OF MEDICINE

Discovery of bisulfite-mediated cytosine conversion to uracil, the key reaction for DNA methylation analysis — A personal account

(2008) Hikoya HAYATSU   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE