Joint profiling of histone modifications and transcriptome in single cells from mouse brain

Systematic identification of silencers in human cells

(2020) Baoxu Pang et al.   NATURE GENETICS

Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development

(2020) Chew Yee Ngan et al.   NATURE GENETICS

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification

(2019) Wai Lim Ku et al.   NATURE METHODS

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Profiling of Pluripotency Factors in Single Cells and Early Embryos

(2019) Sarah J. Hainer et al.   CELL

Transcription factors and 3D genome conformation in cell-fate decisions

(2019) Ralph Stadhouders et al.   NATURE

Transcriptional Dysregulation Study Reveals a Core Network Involving the Progression of Alzheimer's Disease

(2019) Guofeng Meng et al.   Frontiers in Aging Neuroscience

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer

(2019) Kevin Grosselin et al.   NATURE GENETICS

Profiling chromatin states using single-cell itChIP-seq

(2019) Shanshan Ai et al.   NATURE CELL BIOLOGY

CoBATCH for High-Throughput Single-Cell Epigenomic Profiling

(2019) Qianhao Wang et al.   MOLECULAR CELL

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome

(2019) Chenxu Zhu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq)

(2019) Benjamin Carter et al.   Nature Communications

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

(2018) Sebastian Preissl et al.   NATURE NEUROSCIENCE

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

A chromatin integration labelling method enables epigenomic profiling with lower input

(2018) Akihito Harada et al.   NATURE CELL BIOLOGY

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

(2017) Xiaoji Wu et al.   GENES & DEVELOPMENT

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Generation of pure GABAergic neurons by transcription factor programming

(2017) Nan Yang et al.   NATURE METHODS

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Chongyuan Luo et al.   SCIENCE

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

(2016) Dylan Mooijman et al.   NATURE BIOTECHNOLOGY

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Transcription factors Sox5 and Sox6 exert direct and indirect influences on oligodendroglial migration in spinal cord and forebrain

(2015) Tina Baroti et al.   GLIA

Fli-1 controls transcription from the MCP-1 gene promoter, which may provide a novel mechanism for chemokine and cytokine activation

(2015) Mara L. Lennard Richard et al.   MOLECULAR IMMUNOLOGY

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

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

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

Transcription factor Sox11 is essential for both embryonic and adult neurogenesis

(2013) Yong Wang et al.   DEVELOPMENTAL DYNAMICS

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

An Epigenetic Signature for Monoallelic Olfactory Receptor Expression

(2011) Angeliki Magklara et al.   CELL

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

(2011) Jason Ernst et al.   NATURE

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

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

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

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS