scMethBank: a database for single-cell whole genome DNA methylation maps

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

(2021) Rongxin Fang et al.   Nature Communications

DeconPeaker, a Deconvolution Model to Identify Cell Types Based on Chromatin Accessibility in ATAC-Seq Data of Mixture Samples

(2020) Huamei Li et al.   Frontiers in Genetics

MethylResolver—a method for deconvoluting bulk DNA methylation profiles into known and unknown cell contents

(2020) Douglas Arneson et al.   Communications Biology

Using local alignment to enhance single-cell bisulfite sequencing data efficiency

(2019) Peng Wu et al.   BIOINFORMATICS

EWAS Data Hub: a resource of DNA methylation array data and metadata

(2019) Zhuang Xiong et al.   NUCLEIC ACIDS RESEARCH

BPRMeth: a flexible Bioconductor package for modelling methylation profiles

(2018) Chantriolnt-Andreas Kapourani et al.   BIOINFORMATICS

HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation

(2018) Qing Huan et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

EWAS Atlas: a curated knowledgebase of epigenome-wide association studies

(2018) Mengwei Li et al.   NUCLEIC ACIDS RESEARCH

Single-cell multiomics sequencing and analyses of human colorectal cancer

(2018) Shuhui Bian et al.   SCIENCE

Single-cell DNA methylome sequencing of human preimplantation embryos

(2017) Ping Zhu et al.   NATURE GENETICS

MethBank 3.0: a database of DNA methylomes across a variety of species

(2017) Rujiao Li et al.   NUCLEIC ACIDS RESEARCH

scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells

(2017) Yuan Cao et al.   Genes

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Single-cell epigenomics: techniques and emerging applications

(2015) Omer Schwartzman et al.   NATURE REVIEWS GENETICS

DNA methylation dynamics of the human preimplantation embryo

(2014) Zachary D. Smith et al.   NATURE

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

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

(2014) Sébastien A Smallwood et al.   NATURE METHODS

An optimized algorithm for detecting and annotating regional differential methylation

(2013) Sheng Li et al.   BMC BIOINFORMATICS

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

(2013) H. Guo et al.   GENOME RESEARCH

DNA methylation dynamics during the mammalian life cycle

(2012) J. A. Hackett et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

QDMR: a quantitative method for identification of differentially methylated regions by entropy

(2011) Yan Zhang et al.   NUCLEIC ACIDS RESEARCH

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH