Profiling Chromatin Accessibility at Single-cell Resolution

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Interrogation of human hematopoiesis at single-cell and single-variant resolution

(2019) Jacob C. Ulirsch et al.   NATURE GENETICS

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

(2019) Leif S. Ludwig et al.   CELL

The role of chromatin accessibility in cis-regulatory evolution

(2019) Pei-Chen Peng et al.   Genome Biology and Evolution

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

(2019) Carmen Bravo González-Blas et al.   NATURE METHODS

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

(2019) Luyi Tian et al.   NATURE METHODS

Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA

(2019) Jin Xu et al.   eLife

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

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

(2019) Kevin Grosselin et al.   NATURE GENETICS

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

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

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

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

Supervised classification enables rapid annotation of cell atlases

(2019) Hannah A. Pliner et al.   NATURE METHODS

Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps

(2019) Camden Jansen et al.   PLoS Computational Biology

BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization

(2018) Carl G. de Boer et al.   BMC BIOINFORMATICS

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Transcript-indexed ATAC-seq for precision immune profiling

(2018) Ansuman T. Satpathy et al.   NATURE MEDICINE

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

(2018) Sebastian Preissl et al.   NATURE NEUROSCIENCE

Towards a map of cis-regulatory sequences in the human genome

(2018) Meng Niu et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations

(2018) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell type transcriptome atlas for the planarianSchmidtea mediterranea

(2018) Christopher T. Fincher et al.   SCIENCE

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

(2018) Mireya Plass et al.   SCIENCE

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation

(2018) Jonathan Packer et al.   TRENDS IN GENETICS

Unsupervised clustering and epigenetic classification of single cells

(2018) Mahdi Zamanighomi et al.   Nature Communications

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

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

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche

(2018) Ysbrand M. Nusse et al.   NATURE

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

(2018) Junyue Cao et al.   SCIENCE

The Cancer Epigenome: Exploiting Its Vulnerabilities for Immunotherapy

(2018) Helen Loo Yau et al.   TRENDS IN CELL BIOLOGY

High-throughput chromatin accessibility profiling at single-cell resolution

(2018) Anja Mezger et al.   Nature Communications

A Cosine Similarity-Based Method to Infer Variability of Chromatin Accessibility at the Single-Cell Level

(2018) Stanley Cai et al.   Frontiers in Genetics

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

(2018) Adam J. Rubin et al.   CELL

Mesenchymal Precursor Cells in Adult Nerves Contribute to Mammalian Tissue Repair and Regeneration

(2018) Matthew J. Carr et al.   Cell Stem Cell

Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes

(2018) Timothy R. Hammond et al.   IMMUNITY

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Mechanoresponsive stem cells acquire neural crest fate in jaw regeneration

(2018) Ryan C. Ransom et al.   NATURE

Classifying cells with Scasat, a single-cell ATAC-seq analysis tool

(2018) Syed Murtuza Baker et al.   NUCLEIC ACIDS RESEARCH

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity

(2018) Xingqi Chen et al.   Nature Communications

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

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

(2017) Alicia N Schep et al.   NATURE METHODS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions

(2017) Xingwang Li et al.   Nature Protocols

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Genome-wide prediction of DNase I hypersensitivity using gene expression

(2017) Weiqiang Zhou et al.   Nature Communications

Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data

(2017) Chengchen Zhao et al.   PLoS One

Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9

(2017) Lindsey Montefiori et al.   Scientific Reports

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing

(2016) Xingqi Chen et al.   NATURE METHODS

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest

(2015) Sara L. Prescott et al.   CELL

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

(2015) Evan Z. Macosko 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

A microfluidic device for epigenomic profiling using 100 cells

(2015) Zhenning Cao et al.   NATURE METHODS

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

(2015) Christian Schmidl et al.   NATURE METHODS

Uncovering drug-responsive regulatory elements

(2015) Marcelo R Luizon et al.   PHARMACOGENOMICS

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

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

Identification of altered cis-regulatory elements in human disease

(2015) Anthony Mathelier et al.   TRENDS IN GENETICS

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

(2014) Suhas S.P. Rao et al.   CELL

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso 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

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

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

(2013) Takashi Nagano et al.   NATURE

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang 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

Chromatin modifiers and remodellers: regulators of cellular differentiation

(2013) Taiping Chen et al.   NATURE REVIEWS GENETICS

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

(2011) Naim U Rashid et al.   GENOME BIOLOGY

Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors

(2010) Mazhar Adli et al.   NATURE METHODS

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

(2008) Alan P. Boyle et al.   CELL