Single-cell transcriptome sequencing: recent advances and remaining challenges

RNA-Seq: a revolutionary tool for transcriptomics

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Circular RNAs are a large class of animal RNAs with regulatory potency

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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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MicroRNAs: small RNAs with a big role in gene regulation

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

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

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Spatially resolved, highly multiplexed RNA profiling in single cells

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Detecting and characterizing circular RNAs

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Tumour evolution inferred by single-cell sequencing

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Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

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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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Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

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RNA sequencing: advances, challenges and opportunities

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

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

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viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

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The Technology and Biology of Single-Cell RNA Sequencing

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Bayesian approach to single-cell differential expression analysis

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Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

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

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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 transcriptomics reveals bimodality in expression and splicing in immune cells

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Quantitative single-cell RNA-seq with unique molecular identifiers

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Computational and analytical challenges in single-cell transcriptomics

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

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

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

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Counting absolute numbers of molecules using unique molecular identifiers

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A Brief Review on the Mechanisms of miRNA Regulation

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

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Accounting for technical noise in single-cell RNA-seq experiments

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Highly Multiplexed Subcellular RNA Sequencing in Situ

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Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

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Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

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In situ sequencing for RNA analysis in preserved tissue and cells

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Mammalian genes are transcribed with widely different bursting kinetics

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Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

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

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Single-cell RNA-seq: advances and future challenges

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Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

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

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Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury

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How to infer gene networks from expression profiles

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

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Validation of noise models for single-cell transcriptomics

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Synthetic spike-in standards for RNA-seq experiments

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In the right place at the right time: visualizing and understanding mRNA localization

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Advances and Applications of Single-Cell Sequencing Technologies

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ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis

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Mosaic Copy Number Variation in Human Neurons

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Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain

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Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

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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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Integrated genome and transcriptome sequencing of the same cell

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Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

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From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

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Single-cell systems biology by super-resolution imaging and combinatorial labeling

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Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

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Combinatorial labeling of single cells for gene expression cytometry

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Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons

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Genomewide characterization of non-polyadenylated RNAs

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

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RNA-sequencing from single nuclei

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Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

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

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Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments

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

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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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High‐throughput sequencing for biology and medicine

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Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

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Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

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Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing

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Single-Cell Transcriptome Analyses Reveal Signals to Activate Dormant Neural Stem Cells

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Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments

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Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis

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Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

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DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

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Review on statistical methods for gene network reconstruction using expression data

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