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    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    Single-cell RNA sequencing reveals cellular and molecular heterogeneity in fibrocartilaginous enthesis formation

    Tao Zhang, Liyang Wan ... Hongbin Lu
    Single-cell RNA sequencing to delineate the comprehensive postnatal RC enthesis growth from as early as postnatal day 1 to postnatal day 56.
    1. Developmental Biology
    2. Neuroscience

    Developmental single-cell transcriptomics of hypothalamic POMC neurons reveal the genetic trajectories of multiple neuropeptidergic phenotypes

    Hui Yu, Marcelo Rubinstein, Malcolm J Low
    Single-cell transcriptomic analyses of hypothalamic POMC neurons performed at seven developmental ages revealed marked cellular heterogeneity and divergent developmental pathways into alternative neuronal phenotypes that lack POMC.
    1. Cancer Biology
    2. Computational and Systems Biology

    Signature-scoring methods developed for bulk samples are not adequate for cancer single-cell RNA sequencing data

    Nighat Noureen, Zhenqing Ye ... Siyuan Zheng
    Dropouts in single cell RNA sequencing data are associated with cell states and can affect gene signature scoring if methods do not account for them.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Systems level identification of a matrisome-associated macrophage polarisation state in multi-organ fibrosis

    John F Ouyang, Kunal Mishra ... Jacques Behmoaras
    A meta-analysis of single-cell data reveals an advanced and conserved polarisation state of SPP1+ macrophages in multiple human fibrotic tissues.
    1. Developmental Biology
    2. Evolutionary Biology

    New hypotheses of cell type diversity and novelty from orthology-driven comparative single cell and nuclei transcriptomics in echinoderms

    Anne Meyer, Carolyn Ku ... Veronica Hinman
    Understanding novel cell types and their evolutionary history is re-evaluated using single nuclei transcriptomic approaches and their inferred underlying gene regulatory networks.
    1. Chromosomes and Gene Expression
    2. Neuroscience

    Avoiding false discoveries in single-cell RNA-seq by revisiting the first Alzheimer’s disease dataset

    Alan E Murphy, Nurun Fancy, Nathan Skene
    Reanalysis reveals the impact of quality control and differential analysis methods on the discovery of disease-associated genes on the first Alzheimer's disease single-nucleus RNA-seq dataset.
    1. Computational and Systems Biology
    2. Stem Cells and Regenerative Medicine

    Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming

    Mirko Francesconi, Bruno Di Stefano ... Thomas Graf
    Variation in efficiency, speed and path during transdifferentiation and reprogramming originates from two pre-B cell subpopulations with reciprocal propensity towards each fate conversion.
    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    Coverage-dependent bias creates the appearance of binary splicing in single cells

    Carlos F Buen Abad Najar, Nir Yosef, Liana F Lareau
    Sequencing and counting RNAs from single cells can create a misleading picture of alternative splicing if too many mRNAs are lost in the process.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    Endothelial cell signature in muscle stem cells validated by VEGFA-FLT1-AKT1 axis promoting survival of muscle stem cell

    Mayank Verma, Yoko Asakura ... Atsushi Asakura
    Bulk and single-cell RNA-seq data demonstrated that muscle stem cells express low levels of canonical endothelial cell markers, including VEGFA receptors, and VEGFA-FLT1 pathway has a drastic effect on muscle stem cell survival through AKT1 in vitro and in vivo.
    1. Neuroscience

    The landscape of regulatory genes in brain-wide neuronal phenotypes of a vertebrate brain

    Hui Zhang, Haifang Wang ... Jie He
    Single-cell transcriptomes of larval zebrafish whole brain shed light on the multidimensional landscapes of transcription factors and post-transcriptional regulators in vertebrate whole-brain neuronal classification and revealed principles of how neuronal cell diversity develops and evolves.