Single-Cell Transcriptomics Meets Lineage Tracing

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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Reversed graph embedding resolves complex single-cell trajectories

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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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RNA velocity of single cells

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mRNA-Seq whole-transcriptome analysis of a single cell

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Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells

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Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

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

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DNA methylation: roles in mammalian development

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Tumour evolution inferred by single-cell sequencing

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Mosaic Analysis with a Repressible Cell Marker for Studies of Gene Function in Neuronal Morphogenesis

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

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Long-Term Lymphohematopoietic Reconstitution by a Single CD34-Low/Negative Hematopoietic Stem Cell

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Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

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Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

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Single-cell RNA sequencing to explore immune cell heterogeneity

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Efficient tumour formation by single human melanoma cells

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

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High burden and pervasive positive selection of somatic mutations in normal human skin

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A single-cell survey of the small intestinal epithelium

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PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

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The Life History of 21 Breast Cancers

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A common progenitor for neurons and glia persists in rat retina late in development

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Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

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Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing

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Single-cell genome sequencing: current state of the science

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A Single-Cell Transcriptome Atlas of the Human Pancreas

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Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system

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Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

Marques, S., Zeisel, A., Codeluppi, S., van Bruggen, D., Mendanha Falcão, A., Xiao, L., Li, H., Häring, M., Hochgerner, H., Romanov, R. A., et al. (2016) · Science · doi:10.1126/science.aaf6463 · Cited by 1,246 · see citing works

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

Quantitative single-cell RNA-seq with unique molecular identifiers

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Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

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

Hashimshony, T., Senderovich, N., Avital, G., Klochendler, A., de Leeuw, Y., Anavy, L., Gennert, D., Li, S., Livak, K. J., Rozenblatt-Rosen, O., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0938-8 · Cited by 1,125 · see citing works

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

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

Haque, A., Engel, J., Teichmann, S. A., & Lönnberg, T. (2017) · Genome Medicine · doi:10.1186/s13073-017-0467-4 · Cited by 1,071 · see citing works

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

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Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

Chung, W., Eum, H. H., Lee, H.-O., Lee, K.-M., Lee, H.-B., Kim, K.-T., Ryu, H. S., Kim, S., Lee, J. E., Park, Y. H., et al. (2017) · Nature Communications · doi:10.1038/ncomms15081 · Cited by 992 · see citing works

Single-cell in situ RNA profiling by sequential hybridization

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Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition

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DNA methylation and healthy human aging

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

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Specification of tissue-resident macrophages during organogenesis

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The migration of neural crest cells to the wall of the digestive tract in avian embryo

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From haematopoietic stem cells to complex differentiation landscapes

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Clonal dynamics of native haematopoiesis

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

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Whole-organism lineage tracing by combinatorial and cumulative genome editing

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Biology of Mammalian L1 Retrotransposons

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In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

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

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The Human Cell Atlas: from vision to reality

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TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

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Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

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Clonal analysis of lineage fate in native haematopoiesis

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Mosaic Analysis with Double Markers in Mice

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De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

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Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution

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Somatic mutation in single human neurons tracks developmental and transcriptional history

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Wishbone identifies bifurcating developmental trajectories from single-cell data

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Mosaic Copy Number Variation in Human Neurons

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

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Design and Analysis of Single-Cell Sequencing Experiments

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Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

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

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Inferring tumor progression from genomic heterogeneityPreprint

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High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9Preprint

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Studying clonal dynamics in response to cancer therapy using high-complexity barcoding

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Whole-organism clone tracing using single-cell sequencing

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Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

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Synthetic recording and in situ readout of lineage information in single cells

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Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding

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T cell fate and clonality inference from single-cell transcriptomes

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Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity

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Diverse and heritable lineage imprinting of early haematopoietic progenitors

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Polylox barcoding reveals haematopoietic stem cell fates realized in vivo

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Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing

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Nuclear RNA-seq of single neurons reveals molecular signatures of activation

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Hierarchically related lineage-restricted fates of multipotent haematopoietic stem cells

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Single-cell mapping of lineage and identity in direct reprogramming

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Developmental barcoding of whole mouse via homing CRISPR

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