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Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

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The Fibroblast Growth Factor signaling pathway

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Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

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Mapping the Mouse Cell Atlas by Microwell-Seq

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Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

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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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Exponential scaling of single-cell RNA-seq in the past decade

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

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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 expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase

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

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Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures

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destiny : diffusion maps for large-scale single-cell data in R

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Identification of cell types from single-cell transcriptomes using a novel clustering method

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Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos

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Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

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Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia

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Single Cell Genomics: Advances and Future Perspectives

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

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Defining midbrain dopaminergic neuron diversity by single-cell gene expression profiling

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Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq

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Lineage specification in the mouse preimplantation embryo

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Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

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Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

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FGF4 is required for lineage restriction and salt-and-pepper distribution of primitive endoderm factors but not their initial expression in the mouse

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

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Identification of a cKit(+) colonic crypt base secretory cell that supports Lgr5(+) stem cells in mice

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NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment

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Distinct Requirements for FGFR1 and FGFR2 in Primitive Endoderm Development and Exit from Pluripotency

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Single-cell molecular analysis defines therapy response and immunophenotype of stem cell subpopulations in CML

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Lineage Establishment and Progression within the Inner Cell Mass of the Mouse Blastocyst Requires FGFR1 and FGFR2

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Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network

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A Bayesian framework for the inference of gene regulatory networks from time and pseudo-time series data

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Simultaneous deletion of the methylcytosine oxidases Tet1 and Tet3 increases transcriptome variability in early embryogenesis

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Pseudotime estimation: deconfounding single cell time series

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From tissues to cell types and back: single-cell gene expression analysis of tissue architecture

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Do all roads lead to Oct4? The emerging concepts of induced pluripotency

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Systems biology of stem cells: three useful perspectives to help overcome the paradigm of linear pathways

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TBX3 Directs Cell-Fate Decision toward Mesendoderm

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A Dynamic Role of TBX3 in the Pluripotency Circuitry

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A Sprouty4 reporter to monitor FGF/ERK signaling activity in ESCs and mice

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The Wnt/TCF7L1 transcriptional repressor axis drives primitive endoderm formation by antagonizing naive and formative pluripotency

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Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data

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3D computational reconstruction of tissues with hollow spherical morphologies using single-cell gene expression data

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cgCorrect: a method to correct for confounding cell–cell variation due to cell growth in single-cell transcriptomics

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Rie1 and Sgn1 form an RNA-binding complex that enforces the meiotic entry cell fate decision

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