Scaling single-cell genomics from phenomenology to mechanism

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

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Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.

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Spatial reconstruction of single-cell gene expression data

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Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

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

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

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Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

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An anatomically comprehensive atlas of the adult human brain transcriptome

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THE MAJOR TRANSITIONS OF EVOLUTION

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Spatially resolved, highly multiplexed RNA profiling in single cells

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A mesoscale connectome of the mouse brain

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Tumour evolution inferred by single-cell sequencing

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

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Single-cell chromatin accessibility reveals principles of regulatory variation

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The Growth of Biological Thought: Diversity, Evolution, and Inheritance

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

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Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

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Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

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Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types

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Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

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Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

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

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Diffusion pseudotime robustly reconstructs lineage branching

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Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

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Transcriptional landscape of the prenatal human brain

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

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Single-cell messenger RNA sequencing reveals rare intestinal cell types

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CEL-seq: single-cell RNA-seq by multiplexed linear amplification

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Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

Tirosh, I., Venteicher, A. S., Hebert, C. M., Escalante, L. E., Patel, A. P., Yizhak, K., Fisher, J. M., Rodman, C., Mount, C., Filbin, M. G., et al. (2016) · Nature · doi:10.1038/nature20123 · Cited by 1,216 · see citing works

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

Shalek, A. K., Satija, R., Adiconis, X., Gertner, R. S., Gaublomme, J. T., Raychowdhury, R., Schwartz, S., Yosef, N., Malboeuf, C., Lu, D., et al. (2013) · Nature · doi:10.1038/nature12172 · Cited by 1,190 · see citing works

Quantitative single-cell RNA-seq with unique molecular identifiers

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Microglia development follows a stepwise program to regulate brain homeostasis

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Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

Shekhar, K., Lapan, S. W., Whitney, I. E., Tran, N. M., Macosko, E. Z., Kowalczyk, M., Adiconis, X., Levin, J. Z., Nemesh, J., Goldman, M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.07.054 · Cited by 1,176 · see citing works

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

Zong, C., Lu, S., Chapman, A. R., & Xie, X. S. (2012) · Science · doi:10.1126/science.1229164 · Cited by 1,154 · see citing works

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

Corces, M. R., Buenrostro, J. D., Wu, B., Greenside, P. G., Chan, S. M., Koenig, J. L., Snyder, M. P., Pritchard, J. K., Kundaje, A., Greenleaf, W. J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3646 · Cited by 1,151 · see citing works

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

Buettner, F., Natarajan, K. N., Casale, F. P., Proserpio, V., Scialdone, A., Theis, F. J., Teichmann, S. A., Marioni, J. C., & Stegle, O. (2015) · Nature Biotechnology · doi:10.1038/nbt.3102 · Cited by 1,136 · see citing works

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

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CEL-seq2: sensitive highly-multiplexed single-cell RNA-Seq

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Multiplexed ion beam imaging of human breast tumors

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Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

Paul, F., Arkin, Y., Giladi, A., Jaitin, D. A., Kenigsberg, E., Keren-Shaul, H., Winter, D., Lara-Astiaso, D., Gury, M., Weiner, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.013 · Cited by 1,082 · see citing works

BioNumbers—the database of key numbers in molecular and cell biology

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Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

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Organization of the mitotic chromosome

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Highly Multiplexed Subcellular RNA Sequencing in Situ

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Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

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In situ sequencing for RNA analysis in preserved tissue and cells

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Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

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Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

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The Types of Retinal Ganglion Cells: Current Status and Implications for Neuronal Classification

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Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

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Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

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Whole-organism lineage tracing by combinatorial and cumulative genome editing

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Clonal evolution of glioblastoma under therapy

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G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

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Toward understanding and exploiting tumor heterogeneity

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Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

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Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

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Diffusion maps for high-dimensional single-cell analysis of differentiation data

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<i>destiny</i> : diffusion maps for large-scale single-cell data in R

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Tissue biology perspective on macrophages

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Revealing the vectors of cellular identity with single-cell genomics

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Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

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Single-cell genomics unveils critical regulators of Th17 cell pathogenicity

Gaublomme, J. T., Yosef, N., Lee, Y., Gertner, R. S., Yang, L. V., Wu, C., Pandolfi, P. P., Mak, T., Satija, R., Shalek, A. K., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.009 · Cited by 575 · see citing works

Wishbone identifies bifurcating developmental trajectories from single-cell data

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Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm

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Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

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Punctuated copy number evolution and clonal stasis in triple-negative breast cancer

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Integrated genome and transcriptome sequencing of the same cell

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Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

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Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

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T cell fate and clonality inference from single-cell transcriptomes

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Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics

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High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

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Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia

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Decoding the regulatory network of early blood development from single-cell gene expression measurements

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A comprehensive transcriptional map of primate brain development

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Deconstructing transcriptional heterogeneity in pluripotent stem cells

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Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

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