Whole-genome bisulfite sequencing with improved accuracy and cost

Data quality of whole genome bisulfite sequencing on Illumina platforms

(2018) Amanda Raine et al.   PLoS One

Associating cellular epigenetic models with human phenotypes

(2017) Tuuli Lappalainen et al.   NATURE REVIEWS GENETICS

A pooling-based approach to mapping genetic variants associated with DNA methylation

(2015) Irene M. Kaplow et al.   GENOME RESEARCH

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

(2015) Qing Li et al.   NUCLEIC ACIDS RESEARCH

Genome-wide assays that identify and quantify modified cytosines in human disease studies

(2015) Netha Ulahannan et al.   Epigenetics & Chromatin

Improved tagmentation-based whole-genome bisulfite sequencing for input DNA from less than 100 mammalian cells

(2015) Hanlin Lu et al.   Epigenomics

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

(2014) Martin J. Aryee et al.   BIOINFORMATICS

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation

(2014) M. Ronnerblad et al.   BLOOD

Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers

(2014) Bo Zhang et al.   BMC GENOMICS

Kidney Cancer Is Characterized by Aberrant Methylation of Tissue-Specific Enhancers That Are Prognostic for Overall Survival

(2014) C. Y. Hu et al.   CLINICAL CANCER RESEARCH

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer

(2014) Phillippa C. Taberlay et al.   GENOME RESEARCH

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

(2014) Zhihao Ding et al.   PLoS Genetics

Widespread DNA hypomethylation at gene enhancer regions in placentas associated with early-onset pre-eclampsia

(2013) J. D. Blair et al.   MOLECULAR HUMAN REPRODUCTION

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

Comparative annotation of functional regions in the human genome using epigenomic data

(2013) Kyoung-Jae Won et al.   NUCLEIC ACIDS RESEARCH

Transcription Factor Occupancy Can Mediate Active Turnover of DNA Methylation at Regulatory Regions

(2013) Angelika Feldmann et al.   PLoS Genetics

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

(2013) Dvir Aran et al.   GENOME BIOLOGY

Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development

(2013) Yi-An Ko et al.   GENOME BIOLOGY

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing

(2012) Andrew Adey et al.   GENOME RESEARCH

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

(2012) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

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

(2012) M. J. Booth et al.   SCIENCE

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

(2012) Jovana Maksimovic et al.   GENOME BIOLOGY

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

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

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

(2011) Felix Krueger et al.   BIOINFORMATICS

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

Directional DNA Methylation Changes and Complex Intermediate States Accompany Lineage Specificity in the Adult Hematopoietic Compartment

(2011) Emily Hodges et al.   MOLECULAR CELL

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Optimized design and data analysis of tag-based cytosine methylation assays

(2010) Masako Suzuki et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) C. Schmidl et al.   GENOME RESEARCH

High-throughput bisulfite sequencing in mammalian genomes

(2009) Zachary D. Smith et al.   METHODS

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

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

(2009) Martin Kircher et al.   GENOME BIOLOGY

Survival in Nuclear Waste, Extreme Resistance, and Potential Applications Gleaned from the Genome Sequence of Kineococcus radiotolerans SRS30216

(2008) Christopher E. Bagwell et al.   PLoS One