Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro

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

(2021) Chenxu Zhu et al.   NATURE METHODS

Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression

(2021) Steven J. Wu et al.   NATURE BIOTECHNOLOGY

Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues

(2021) Marek Bartosovic et al.   NATURE BIOTECHNOLOGY

Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions

(2021) Haiqing Xiong et al.   NATURE METHODS

Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization

(2021) Ana Rita Pombo Antunes et al.   NATURE NEUROSCIENCE

Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

(2021) Elliott Swanson et al.   eLife

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

(2021) Eleni P. Mimitou et al.   NATURE BIOTECHNOLOGY

The RNA Atlas expands the catalog of human non-coding RNAs

(2021) Lucia Lorenzi et al.   NATURE BIOTECHNOLOGY

Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment and disease

(2021) Aparna Nathan et al.   NATURE IMMUNOLOGY

Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro

(2021) Ian A. Mellis et al.   Cell Systems

Simultaneous profiling of multiple chromatin proteins in the same cells

(2021) Sneha Gopalan et al.   MOLECULAR CELL

Differential abundance testing on single-cell data using k-nearest neighbor graphs

(2021) Emma Dann et al.   NATURE BIOTECHNOLOGY

Single-cell chromatin state analysis with Signac

(2021) Tim Stuart et al.   NATURE METHODS

Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity

(2020) Woo Jun Shim et al.   Cell Systems

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

(2019) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

CoBATCH for High-Throughput Single-Cell Epigenomic Profiling

(2019) Qianhao Wang et al.   MOLECULAR CELL

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

(2019) Benjamin Carter et al.   Nature Communications

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

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

(2017) Alicia N Schep et al.   NATURE METHODS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Transcription Factor T-bet Orchestrates Lineage Development and Function in the Immune System

(2017) Axel Kallies et al.   TRENDS IN IMMUNOLOGY

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

(2015) Evan Z. Macosko et al.   CELL

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

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

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

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Signals and Combinatorial Functions of Histone Modifications

(2011) Tamaki Suganuma et al.   Annual Review of Biochemistry

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

Supervised principal component analysis: Visualization, classification and regression on subspaces and submanifolds

(2010) Elnaz Barshan et al.   PATTERN RECOGNITION

Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation

(2009) Kairong Cui et al.   Cell Stem Cell

Global Mapping of H3K4me3 and H3K27me3 Reveals Specificity and Plasticity in Lineage Fate Determination of Differentiating CD4+ T Cells

(2009) Gang Wei et al.   IMMUNITY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS