Joint profiling of DNA methylation and chromatin architecture in single cells

Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution

(2019) Yibin Liu et al.   NATURE BIOTECHNOLOGY

TheHoxDcluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes

(2017) Eddie Rodríguez-Carballo et al.   GENES & DEVELOPMENT

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA

(2017) Shicheng Guo et al.   NATURE GENETICS

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

The DNA methyltransferase family: a versatile toolkit for epigenetic regulation

(2017) Frank Lyko   NATURE REVIEWS GENETICS

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

(2017) Chongyuan Luo et al.   SCIENCE

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

Genome-wide mapping and analysis of chromosome architecture

(2016) Anthony D. Schmitt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

Single-cell epigenomics: techniques and emerging applications

(2015) Omer Schwartzman et al.   NATURE REVIEWS GENETICS

cocor: A Comprehensive Solution for the Statistical Comparison of Correlations

(2015) Birk Diedenhofen et al.   PLoS One

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

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

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu et al.   GENOME BIOLOGY

Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain

(2011) Junjie U. Guo et al.   CELL

Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome

(2010) R. Shoemaker et al.   GENOME RESEARCH

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE