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    1. Cell Biology

    Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites

    Adam J Reid, Arthur M Talman ... Mara KN Lawniczak
    Plasmodium parasite transcription shifts dramatically along asexual development, and transmission stages variably express important immune evasion genes, suggesting much interesting biology has until now been hidden by bulk analyses.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila

    Evan Witt, Sigi Benjamin ... Li Zhao
    Single-cell RNA-sequencing and germline substitutions provide novel insights into how testis is a hotspot for evolutionary innovation of genes, expression, and mutation at the single-cell level.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    scRNA-Seq reveals distinct stem cell populations that drive hair cell regeneration after loss of Fgf and Notch signaling

    Mark E Lush, Daniel C Diaz ... Tatjana Piotrowski
    Several support cell populations balance progenitor maintenance with differentiation in zebrafish lateral line sensory organs.
    1. Medicine

    A single-cell atlas depicting the cellular and molecular features in human anterior cruciate ligamental degeneration: A single cell combined spatial transcriptomics study

    Runze Yang, Tianhao Xu ... Weili Fu
    Single-cell combined spatial transcriptomics provides the molecular foundation for investigating how ligamental cell identities, biochemical functions, and interactions contributed to the ligamental degeneration process.
    1. Genetics and Genomics
    2. Immunology and Inflammation

    Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation

    Hyeogsun Kwon, Mubasher Mohammed ... Ryan C Smith
    Single-cell RNA-seq analysis reveals an increased complexity of mosquito hemocytes, enabling the functional and molecular characterization of immune cell sub-populations in Anopheles gambiae.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    RNA splicing programs define tissue compartments and cell types at single-cell resolution

    Julia Eve Olivieri, Roozbeh Dehghannasiri ... Julia Salzman
    Comprehensive analysis of alternative splicing from human droplet-based scRNA-seq data identifies genes with regulated splicing conserved in mouse and mouse lemur.
    1. Computational and Systems Biology
    2. Developmental Biology

    Discovering sparse transcription factor codes for cell states and state transitions during development

    Leon A Furchtgott, Samuel Melton ... Sharad Ramanathan
    Sparse patterns in gene expression allow simultaneous discovery of cell states, lineage relationships and key genes controlling developmental decisions.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host–pathogen dynamics in lymphoblastoid cell lines

    Elliott D SoRelle, Joanne Dai ... Micah A Luftig
    Single-cell RNA sequencing highlights the influence of host–pathogen interactions and stochasticity on transcriptional and phenotypic variance in lymphoblastoid cell lines derived from Epstein–Barr virus-infected primary B cells.
    1. Cell Biology
    2. Computational and Systems Biology

    Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury

    Nona Farbehi, Ralph Patrick ... Richard P Harvey
    Comprehensive scRNA-seq analysis of cardiac stromal cells in healthy and injured hearts reveals novel cell types and non-linear cell dynamics, providing new insights into cardiac inflammation, fibrosis and repair.
    1. Immunology and Inflammation

    Integrative analysis of scRNA-seq and scATAC-seq revealed transit-amplifying thymic epithelial cells expressing autoimmune regulator

    Takahisa Miyao, Maki Miyauchi ... Taishin Akiyama
    The combination of single-cell analysis and cell fate mapping studies evidenced the presence of AIRE-expressing transit-amplifying thymic epithelial cells, which differentiate into mature medullary thymic epithelial cells expressing tissue-specific antigens.