Single-Cell Analysis

• 

  Subject Areas on Research

  • 3D traction stresses activate protease-dependent invasion of cancer cells. 
  • A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology. 
  • A Microfluidic System with Surface Patterning for Investigating Cavitation Bubble(s)-Cell Interaction and the Resultant Bioeffects at the Single-cell Level. 
  • A Single-Cell Assay for Time Lapse Studies of Exosome Secretion and Cell Behaviors. 
  • A multimodal cell census and atlas of the mammalian primary motor cortex. 
  • A multimodal micro-optrode combining field and single unit recording, multispectral detection and photolabeling capabilities. 
  • A noisy linear map underlies oscillations in cell size and gene expression in bacteria. 
  • A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. 
  • A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins. 
  • A single peptide-major histocompatibility complex ligand triggers digital cytokine secretion in CD4(+) T cells. 
  • A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. 
  • A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain. 
  • A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. 
  • A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. 
  • A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics. 
  • Activation of Piezo1 mechanosensitive ion channel in HEK293T cells by 30 MHz vertically deployed surface acoustic waves. 
  • Adaptation and selection shape clonal evolution of tumors during residual disease and recurrence. 
  • An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma. 
  • An acoustofluidic trap and transfer approach for organizing a high density single cell array. 
  • Archaeal cells share common size control with bacteria despite noisier growth and division. 
  • BEARscc determines robustness of single-cell clusters using simulated technical replicates. 
  • CD28 costimulation drives tumor-infiltrating T cell glycolysis to promote inflammation. 
  • COMPASS identifies T-cell subsets correlated with clinical outcomes. 
  • COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. 
  • CRISPR-based methods for high-throughput annotation of regulatory DNA. 
  • Cell membrane deformation and bioeffects produced by tandem bubble-induced jetting flow. 
  • Cell-Type-Specific Analysis of Molecular Pathology in Autism Identifies Common Genes and Pathways Affected Across Neocortical Regions. 
  • Cellular crosstalk regulates the aqueous humor outflow pathway and provides new targets for glaucoma therapies. 
  • Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. 
  • Clonal analysis of human anti-V3 monoclonal antibodies selected by a V3 tetramer. 
  • Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering. 
  • Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor. 
  • Comparative cellular analysis of motor cortex in human, marmoset and mouse. 
  • Comprehensive functional genomic resource and integrative model for the human brain. 
  • Contribution of adipogenesis to healthy adipose tissue expansion in obesity. 
  • Contribution of plasma cells and B cells to hidradenitis suppurativa pathogenesis. 
  • Cortical interneurons that specialize in disinhibitory control. 
  • Cytological and genetic consequences for the progeny of a mitotic catastrophe provoked by Topoisomerase II deficiency. 
  • DNA methylation atlas of the mouse brain at single-cell resolution. 
  • Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. 
  • Detection of differentially abundant cell subpopulations in scRNA-seq data. 
  • Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo. 
  • Discordance between GLP-1R gene and protein expression in mouse pancreatic islet cells. 
  • Dissecting the human kidney allograft transcriptome: single-cell RNA sequencing. 
  • Distinct behavioural and network correlates of two interneuron types in prefrontal cortex. 
  • Division of labour between Myc and G1 cyclins in cell cycle commitment and pace control. 
  • Emerging approaches and technologies in transplantation: the potential game changers. 
  • Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution. 
  • Estimation of immune cell content in tumor using single-cell RNA-seq reference data. 
  • Expanded Genomic Profiling of Circulating Tumor Cells in Metastatic Breast Cancer Patients to Assess Biomarker Status and Biology Over Time (CALGB 40502 and CALGB 40503, Alliance). 
  • Expanding studies of chromosome structure and function in the era of T2T genomics. 
  • Extracellular caspase-6 drives murine inflammatory pain via microglial TNF-α secretion. 
  • FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows. 
  • Genetic Single Neuron Anatomy Reveals Fine Granularity of Cortical Axo-Axonic Cells. 
  • Hemoglobin consumption by P. falciparum in individual erythrocytes imaged via quantitative phase spectroscopy. 
  • Heterogeneity of human prostate carcinoma-associated fibroblasts implicates a role for subpopulations in myeloid cell recruitment. 
  • High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity. 
  • High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing. 
  • High-content image informatics of the structural nuclear protein NuMA parses trajectories for stem/progenitor cell lineages and oncogenic transformation. 
  • High-resolution, noninvasive longitudinal live imaging of immune responses. 
  • Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. 
  • Human distal lung maps and lineage hierarchies reveal a bipotent progenitor. 
  • Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult mice. 
  • Identifying gene expression from single cells to single genes. 
  • Immature excitatory neurons develop during adolescence in the human amygdala. 
  • In Toto Imaging of Dynamic Osteoblast Behaviors in Regenerating Skeletal Bone. 
  • Integrative functional genomic analysis of human brain development and neuropsychiatric risks. 
  • Keratin Profiling by Single-Cell RNA-Sequencing Identifies Human Prostate Stem Cell Lineage Hierarchy and Cancer Stem-Like Cells. 
  • Latent transcriptional variations of individual Plasmodium falciparum uncovered by single-cell RNA-seq and fluorescence imaging. 
  • Lessons from single-cell transcriptome analysis of oxygen-sensing cells. 
  • Long-primed germinal centres with enduring affinity maturation and clonal migration. 
  • Long-term growth data of Escherichia coli at a single-cell level. 
  • Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19. 
  • MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics. 
  • MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate. 
  • Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments. 
  • Massively parallel quantification of phenotypic heterogeneity in single-cell drug responses. 
  • Metabolism in the tumor microenvironment: insights from single-cell analysis. 
  • Methodologies for Following EMT In Vivo at Single Cell Resolution. 
  • Molecular taxonomy of human ocular outflow tissues defined by single-cell transcriptomics. 
  • Monitoring Tissue Regeneration at Single-Cell Resolution. 
  • Monocyte-derived transcriptome signature indicates antibody-dependent cellular phagocytosis as a potential mechanism of vaccine-induced protection against HIV-1. 
  • Morphological diversity of single neurons in molecularly defined cell types. 
  • Moving into the cell: single-molecule studies of molecular motors in complex environments. 
  • Multimodal Single-Cell Analysis Reveals Physiological Maturation in the Developing Human Neocortex. 
  • Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas. 
  • NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data. 
  • NanoSIMS single cell analyses reveal the contrasting nitrogen sources for small phytoplankton. 
  • Neurotoxic microglia promote TDP-43 proteinopathy in progranulin deficiency. 
  • Organoid single cell profiling identifies a transcriptional signature of glomerular disease. 
  • Origins and Proliferative States of Human Oligodendrocyte Precursor Cells. 
  • Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients. 
  • Probing Computation in the Primate Visual System at Single-Cone Resolution. 
  • Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT. 
  • RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data. 
  • Recapitulation and Modulation of the Cellular Architecture of a User-Chosen Cell of Interest Using Cell-Derived, Biomimetic Patterning. 
  • Region-Specific Differences in Morphometric Features and Synaptic Colocalization of Astrocytes During Development. 
  • SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues. 
  • SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. 
  • Self-renewing endometrial epithelial organoids of the human uterus. 
  • Semiochemical responsive olfactory sensory neurons are sexually dimorphic and plastic. 
  • Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains. 
  • Single Cell Analysis of Stored Red Blood Cells Using Ultra-High Throughput Holographic Cytometry. 
  • Single Cell Chemical Cytometry of Akt Activity in Rheumatoid Arthritis and Normal Fibroblast-like Synoviocytes in Response to Tumor Necrosis Factor α. 
  • Single cell RNA-seq reveals profound transcriptional similarity between Barrett's oesophagus and oesophageal submucosal glands. 
  • Single cell analysis of cribriform prostate cancer reveals cell intrinsic and tumor microenvironmental pathways of aggressive disease. 
  • Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy. 
  • Single cell transcriptomics of mouse kidney transplants reveals a myeloid cell pathway for transplant rejection. 
  • Single neurons may encode simultaneous stimuli by switching between activity patterns. 
  • Single-Cell Analysis Reveals Distinct Gene Expression and Heterogeneity in Male and Female Plasmodium falciparum Gametocytes. 
  • Single-Cell Analysis Reveals Distinct Immune and Smooth Muscle Cell Populations that Contribute to Chronic Thromboembolic Pulmonary Hypertension. 
  • Single-Cell Analysis of Quiescent HIV Infection Reveals Host Transcriptional Profiles that Regulate Proviral Latency. 
  • Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells. 
  • Single-Cell RNA Sequencing Identifies Yes-Associated Protein 1-Dependent Hepatic Mesothelial Progenitors in Fibrolamellar Carcinoma. 
  • Single-Cell Transcriptional Heterogeneity of Neutrophils During Acute Pulmonary Cryptococcus neoformans Infection. 
  • Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer. 
  • Single-Cell-Based High-Throughput Ig and TCR Repertoire Sequencing Analysis in Rhesus Macaques. 
  • Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression. 
  • Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. 
  • Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection. 
  • Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines. 
  • Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. 
  • Single-cell analyses reveal increased intratumoral heterogeneity after the onset of therapy resistance in small-cell lung cancer. 
  • Single-cell analysis by mass cytometry reveals metabolic states of early-activated CD8+ T cells during the primary immune response. 
  • Single-cell analysis of cell identity in the Arabidopsis root apical meristem: insights and opportunities. 
  • Single-cell analysis of immune cell transcriptome during HIV-1 infection and therapy. 
  • Single-cell analysis of olfactory neurogenesis and differentiation in adult humans. 
  • Single-cell analysis uncovers that metabolic reprogramming by ErbB2 signaling is essential for cardiomyocyte proliferation in the regenerating heart. 
  • Single-cell genomics identifies cell type-specific molecular changes in autism. 
  • Single-cell imaging of T cell immunotherapy responses in vivo. 
  • Single-cell imaging of human cancer xenografts using adult immunodeficient zebrafish. 
  • Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. 
  • Single-cell monitoring using fiberoptic nanosensors. 
  • Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration. 
  • Single-cell redox imaging demonstrates a distinctive response of dopaminergic neurons to oxidative insults. 
  • Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla. 
  • Single-cell transcriptomic analysis of the immune cell landscape in the aged mouse brain after ischemic stroke. 
  • The Future is Now: Gene Expression Dynamics at Single Cell Resolution. 
  • The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. 
  • The role of single-cell analyses in understanding cell lineage commitment. 
  • Thinking outside the gate: single-cell assessments in multiple dimensions. 
  • Tracing Self-Reactive B Cells in Normal Mice. 
  • Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing. 
  • Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers. 
  • Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma. 
  • Triiodothyronine and dexamethasone alter potassium channel expression and promote electrophysiological maturation of human-induced pluripotent stem cell-derived cardiomyocytes. 
  • Tumor heterogeneity. 
  • Type V Collagen in Scar Tissue Regulates the Size of Scar after Heart Injury. 
  • Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. 
  • Urinary Single-Cell Profiling Captures the Cellular Diversity of the Kidney. 
  • scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. 
  • scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells. 
  • κ-Opioid receptors in the central amygdala regulate ethanol actions at presynaptic GABAergic sites. 
• 

  Keywords of People

  • Ferrari, Guido, Professor in Surgery, Molecular Genetics and Microbiology
  • Ji, Zhicheng, Assistant Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics