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

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

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

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

(2018) Jason D. Buenrostro et al.   CELL

Highly scalable generation of DNA methylation profiles in single cells

(2018) Ryan M Mulqueen et al.   NATURE BIOTECHNOLOGY

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

(2018) Sebastian Preissl et al.   NATURE NEUROSCIENCE

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders 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

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

(2018) Lindsey W. Plasschaert et al.   NATURE

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

(2018) Darren A. Cusanovich et al.   NATURE

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

(2018) Junyue Cao et al.   SCIENCE

Cyclosporine H Overcomes Innate Immune Restrictions to Improve Lentiviral Transduction and Gene Editing In Human Hematopoietic Stem Cells

(2018) Carolina Petrillo et al.   Cell Stem Cell

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Activity-Regulated Transcription: Bridging the Gap between Neural Activity and Behavior

(2018) Ee-Lynn Yap et al.   NEURON

A rapid and robust method for single cell chromatin accessibility profiling

(2018) Xi Chen et al.   Nature Communications

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

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

Sequencing thousands of single-cell genomes with combinatorial indexing

(2017) Sarah A Vitak et al.   NATURE METHODS

Single-cell epigenomics: Recording the past and predicting the future

(2017) Gavin Kelsey et al.   SCIENCE

Dysregulation of regulatory CD56 bright NK cells/T cells interactions in multiple sclerosis

(2016) Alice Laroni et al.   JOURNAL OF AUTOIMMUNITY

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner 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

Somatostatin-expressing neurons in cortical networks

(2016) Joanna Urban-Ciecko et al.   NATURE REVIEWS NEUROSCIENCE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

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

(2015) Wenfei Jin et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje 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

Serotonin, neural markers, and memory

(2015) Alfredo Meneses   Frontiers in Pharmacology

Proinflammatory Signaling Regulates Hematopoietic Stem Cell Emergence

(2014) Raquel Espín-Palazón et al.   CELL

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

(2014) Sasan Amini et al.   NATURE GENETICS

Lhx1 maintains synchrony among circadian oscillator neurons of the SCN

(2014) Megumi Hatori et al.   eLife

A High-Resolution Enhancer Atlas of the Developing Telencephalon

(2013) Axel Visel et al.   CELL

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

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

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

(2012) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Epigenome-wide association studies for common human diseases

(2011) Vardhman K. Rakyan et al.   NATURE REVIEWS GENETICS

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Nurr1 Is Required for Maintenance of Maturing and Adult Midbrain Dopamine Neurons

(2009) B. Kadkhodaei et al.   JOURNAL OF NEUROSCIENCE

IFNα activates dormant haematopoietic stem cells in vivo

(2009) Marieke A. G. Essers et al.   NATURE

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

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

(2008) Alan P. Boyle et al.   CELL