ArticleMethods (San Diego, Calif.)2015
Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data.
Article in Methods (San Diego, Calif.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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Who cites it
96 citing papers in PubMed.
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- Trial
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- Optimal transport reveals immune perturbation and fingerprints over time in COVID-19 vaccination.Experimental biology and medicine (Maywood, N.J.) · 2025Article
- Exploring structured molecular landscape from single-cell multi-omics data by an explainable multimodal model.iScience · 2024Article
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- Characterization of CD34Cancers · 2024Article
- State-of-the-art cytometry in the search of novel biomarkers in digestive cancers.Frontiers in oncology · 2024Review
- IL-1β-mediated adaptive reprogramming of endogenous human cardiac fibroblasts to cells with immune features during fibrotic remodeling.Communications biology · 2023Article
- Intravesical oncolytic virotherapy and immunotherapy for non-muscle-invasive bladder cancer mouse model.BJU international · 2023Article
- The SWI/SNF chromatin-remodeling subunit DPF2 facilitates NRF2-dependent antiinflammatory and antioxidant gene expression.The Journal of clinical investigation · 2023Article
- Multiparameter analysis of human B lymphocytes identifies heterogeneous CD19Cytometry. Part A : the journal of the International Society for Analytical Cytology · 2023Article
- Glioma Stem Cells: Novel Data Obtained by Single-Cell Sequencing.International journal of molecular sciences · 2022Review
- Techniques for Profiling the Cellular Immune Response and Their Implications for Interventional Oncology.Cancers · 2022Review
- CD19 + CD21Clinical and experimental medicine · 2022Article
- Hematopoietic cell transplantation donor-derived memory-like NK cells functionally persist after transfer into patients with leukemia.Science translational medicine · 2022Article
- High-Dimensional Analysis Reveals Distinct Endotypes in Patients With Idiopathic Inflammatory Myopathies.Frontiers in immunology · 2022Article
36 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
The flood of high-dimensional data resulting from mass cytometry experiments that measure more than 40 features of individual cells has stimulated creation of new single cell computational biology tools. These tools draw on advances in the field of machine learning to capture multi-parametric relationships and reveal cells that are easily overlooked in traditional analysis. Here, we introduce a workflow for high dimensional mass cytometry data that emphasizes unsupervised approaches and visualizes data in both single cell and population level views. This workflow includes three central components that are common across mass cytometry analysis approaches: (1) distinguishing initial populations, (2) revealing cell subsets, and (3) characterizing subset features. In the implementation described here, viSNE, SPADE, and heatmaps were used sequentially to comprehensively characterize and compare healthy and malignant human tissue samples. The use of multiple methods helps provide a comprehensive view of results, and the largely unsupervised workflow facilitates automation and helps researchers avoid missing cell populations with unusual or unexpected phenotypes. Together, these methods develop a framework for future machine learning of cell identity.
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Registered trials
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