Single-cell RNA-Seq reports the mRNA abundances of every gene in the genome in many individual cells in a single experiment. In collaboration with Jay Shendure’s lab and scientists at Illumina, we recently developed sci-RNA-seq, which uses combinatorial cellular indexing, captures transcriptomes for tens of thousands of cells in a single experiment for a fraction of the cost of alternative methods. The technique scales sublinearly in time and cost, enabling the profiling of all the cells in whole animals.


Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters

A single-cell time-lapse of mouse prenatal development from gastrula to birth

Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy

Single cell, whole embryo phenotyping of pleiotropic disorders of mammalian development

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

Multipotent progenitors and hematopoietic stem cells arise independently from hemogenic endothelium in the mouse embryo

Embryo-scale, single-cell spatial transcriptomics

High‐throughput, microscope‐based sorting to dissect cellular heterogeneity

IL-2 enhances ex vivo–expanded regulatory T-cell persistence after adoptive transfer

Sci-fate characterizes the dynamics of gene expression in single cells

The promise of single-cell genomics in plants

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

Connect-seq to superimpose molecular on anatomical neural circuit maps

Single-cell transcriptomic comparison of human fetal retina, hPSC-derived retinal organoids, and long-term retinal cultures

Massively multiplex chemical transcriptomics at single cell resolution

Supervised classification enables rapid annotation of cell atlases

A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition

Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development

Dynamics of gene expression in single root cells of Arabidopsis thaliana

The accessible chromatin landscape of the murine hippocampus at single-cell resolution

The single-cell transcriptional landscape of mammalian organogenesis

A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets

A genome-wide framework for mapping gene regulation via cellular genetic screens

Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome

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

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

On the design of CRISPR-based single-cell molecular screens

Extreme heterogeneity of influenza virus infection in single cells

Reversed graph embedding resolves complex single-cell trajectories

Comprehensive single-cell transcriptional profiling of a multicellular organism

Single-cell mRNA quantification and differential analysis with Census

Single-cell transcriptome sequencing recent advances and remaining challenges

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis

Defining cell types and states with single-cell genomics