Simultaneous quantification of protein–DNA contacts and transcriptomes in single cells

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo

(2018) Gabriel N Aughey et al.   eLife

The Implication of Early Chromatin Changes in X Chromosome Inactivation

(2018) Jan Jakub Żylicz et al.   CELL

Simultaneous mapping of active DNA demethylation and sister chromatid exchange in single cells

(2017) Xiaoji Wu et al.   GENES & DEVELOPMENT

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

(2017) Ilya M. Flyamer et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

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

(2016) Yu Hou et al.   CELL RESEARCH

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction

(2016) Dylan Mooijman et al.   NATURE BIOTECHNOLOGY

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

(2015) Jop Kind et al.   CELL

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

(2015) Wenfei Jin et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

(2015) Matthias Farlik et al.   Cell Reports

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

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Multiscale representation of genomic signals

(2014) Theo A Knijnenburg et al.   NATURE METHODS

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

(2013) Jop Kind et al.   CELL

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

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence

(2012) W. Meuleman et al.   GENOME RESEARCH

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

An auxin-based degron system for the rapid depletion of proteins in nonplant cells

(2009) Kohei Nishimura et al.   NATURE METHODS

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories

(2008) Michael J Boedigheimer et al.   BMC GENOMICS

X Inactivation Counting and Choice Is a Stochastic Process: Evidence for Involvement of an X-Linked Activator

(2008) Kim Monkhorst et al.   CELL

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression

(2008) Asako Sakaue-Sawano et al.   CELL

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL