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

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Single-cell biology: beyond the sum of its parts

(2020) Alexander F. Schier   NATURE METHODS

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

Inference and effects of barcode multiplets in droplet-based single-cell assays

(2020) Caleb A. Lareau et al.   Nature Communications

CiteFuse enables multi-modal analysis of CITE-seq data

(2020) Hani Jieun Kim et al.   BIOINFORMATICS

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

(2020) Joseph M. Replogle et al.   NATURE BIOTECHNOLOGY

Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer

(2020) Yonatan Katzenelenbogen et al.   CELL

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

(2020) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

Purifying Selection against Pathogenic Mitochondrial DNA in Human T Cells

(2020) Melissa A. Walker et al.   NEW ENGLAND JOURNAL OF MEDICINE

Disease Stage-Specific Pathogenicity of CD138 (Syndecan 1)-Expressing T Cells in Systemic Lupus Erythematosus

(2020) Lunhua Liu et al.   Frontiers in Immunology

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics

(2020) Anna S. Nam et al.   NATURE REVIEWS GENETICS

Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells

(2019) Jan. P. Gerlach et al.   Scientific Reports

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

CRISPResso2 provides accurate and rapid genome editing sequence analysis

(2019) Kendell Clement et al.   NATURE BIOTECHNOLOGY

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

(2019) Leif S. Ludwig et al.   CELL

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

(2019) Molly Gasperini et al.   CELL

The barcode, UMI, set format and BUStools

(2019) Páll Melsted et al.   BIOINFORMATICS

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

(2019) Eleni P. Mimitou et al.   NATURE METHODS

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Multiplexed single-cell RNA-seq via transient barcoding for simultaneous expression profiling of various drug perturbations

(2019) Dongju Shin et al.   Science Advances

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

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

(2019) Christopher S. McGinnis et al.   NATURE METHODS

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

(2019) Jellert T. Gaublomme et al.   Nature Communications

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

Landscape of stimulation-responsive chromatin across diverse human immune cells

(2019) Diego Calderon et al.   NATURE GENETICS

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

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

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

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins

(2019) Jase Gehring et al.   NATURE BIOTECHNOLOGY

Immune monitoring using mass cytometry and related high-dimensional imaging approaches

(2019) Felix J. Hartmann et al.   Nature Reviews Rheumatology

Massively multiplex chemical transcriptomics at single-cell resolution

(2019) Sanjay R. Srivatsan et al.   SCIENCE

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

(2018) Rachel E. Gate et al.   NATURE GENETICS

Bias, robustness and scalability in single-cell differential expression analysis

(2018) Charlotte Soneson et al.   NATURE METHODS

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

(2018) Junyue Cao et al.   SCIENCE

Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens

(2018) Aleksandra Wroblewska et al.   CELL

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

(2018) Adam J. Rubin et al.   CELL

Integrative Proteomics and Phosphoproteomics Profiling Reveals Dynamic Signaling Networks and Bioenergetics Pathways Underlying T Cell Activation

(2017) Haiyan Tan et al.   IMMUNITY

Discovery of stimulation-responsive immune enhancers with CRISPR activation

(2017) Dimitre R. Simeonov et al.   NATURE

Somatic mutations reveal asymmetric cellular dynamics in the early human embryo

(2017) Young Seok Ju et al.   NATURE

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Human haematopoietic stem cell lineage commitment is a continuous process

(2017) Lars Velten et al.   NATURE CELL BIOLOGY

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

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

(2017) Julia Joung et al.   Nature Protocols

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

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

(2016) Atray Dixit et al.   CELL

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

(2016) Gozde Korkmaz et al.   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

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

(2015) Evan Z. Macosko et al.   CELL

Longitudinal Changes in CD4+ T-Cell Memory Responses Induced by BCG Vaccination of Newborns

(2013) Andreia P. Soares, Cheong K. C. Kwong Chung, Terry Choice, E. Jane Hughes, Gail Jacobs, Esme Janse van Rensburg, Gloria Khomba, Marwou de Kock, Lesedi Lerumo, Lebohang Makhethe, Mbulelo H. Maneli, Bernadette Pienaar, Erica Smit, Nontobeko G. Tena-Coki, Leandre van Wyk, W. Henry Boom et al.   JOURNAL OF INFECTIOUS DISEASES

Generation and Activation of Multiple Dimeric Transcription Factors within the NF- B Signaling System

(2008) S. Basak et al.   MOLECULAR AND CELLULAR BIOLOGY

CTLA-4 trafficking and surface expression

(2008) Elke Valk et al.   TRENDS IN IMMUNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY