Algorithmic Tools for Mining High-Dimensional Cytometry Data

No abstract is available for this paper.

• Publication year

  2015

• Venue

  Journal of Immunology

• Publication date

  2015-08-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.4049/jimmunol.1500633PMID 26188071PMCID PMC4507289
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm

  2015cited by this paper
• A continuous molecular roadmap to iPSC reprogramming through progression analysis of single-cell mass cytometry.

  2015cited by this paper
• FlowSOM: Using self‐organizing maps for visualization and interpretation of cytometry data

  2015influential reference
• Barcoding of Live Human Peripheral Blood Mononuclear Cells for Multiplexed Mass Cytometry

  2015cited by this paper
• Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.

  2014cited by this paper
• SWIFT—Scalable Clustering for Automated Identification of Rare Cell Populations in Large, High-Dimensional Flow Cytometry Datasets, Part 1: Algorithm Design

  2014cited by this paper
• Clinical recovery from surgery correlates with single-cell immune signatures

  2014cited by this paper
• Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE)

  2013cited by this paper
• viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

  2013cited by this paper
• Critical assessment of automated flow cytometry data analysis techniques

  2013cited by this paper
• Probability state modeling of memory CD8⁺ T-cell differentiation.

  2013cited by this paper
• Normalization of mass cytometry data with bead standards

  2013cited by this paper
• Barnes-Hut-SNE

  2013cited by this paper
• CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data

  2012cited by this paper
• Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes.

  2012cited by this paper
• Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

  2012cited by this paper
• Standardizing immunophenotyping for the Human Immunology Project

  2012cited by this paper
• Mass cytometry: protocol for daily tuning and running cell samples on a CyTOF mass cytometer.

  2012cited by this paper
• RchyOptimyx: Cellular hierarchy optimization for flow cytometry

  2012cited by this paper
• A deep profiler's guide to cytometry.

  2012cited by this paper
• SPICE: Exploration and analysis of post‐cytometric complex multivariate datasets

  2011cited by this paper
• Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE

  2011cited by this paper
• Data analysis in flow cytometry: The future just started

  2010cited by this paper
• Automated high-dimensional flow cytometric data analysis

  2009cited by this paper
• Development of analytical methods for multiplex bio-assay with inductively coupled plasma mass spectrometry.

  2008cited by this paper
• Visualizing Data using t-SNE

  2008cited by this paper
• Principal Component Analysis

  2002cited by this paper
• In silico prediction of protein-protein interactions in human macrophages

  2001cited by this paper
• Analysis of a complex of statistical variables into principal components.

  1933cited by this paper

• Leveraging Kappa-Lambda Signatures in a Multi-Stage Machine Learning Pipeline for B-Cell Lymphoma Detection by Flow Cytometry.

  2026cites this paper
• Evolving Approach to Clinical Cytometry for Immunodeficiencies and Other Immune Disorders.

  2025cites this paper
• Mass cytometry: exploring the immune landscape of systemic autoimmune and inflammatory diseases in the past fourteen years

  2025cites this paper
• Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating

  2024cites this paper
• Seeing or believing in hyperplexed spatial proteomics via antibodies: New and old biases for an image-based technology

  2024cites this paper
• Identifying dynamical persistent biomarker structures for rare events using modern integrative machine learning approach

  2023cites this paper
• Effect of a Fructose-Rich Diet on Gut Microbiota and Immunomodulation: Potential Factors for Multiple Sclerosis

  2023cites this paper
• Evolving Approach to Clinical Cytometry for Immunodeficiencies and Other Immune Disorders.

  2023cites this paper
• CRUSTY: a versatile web platform for the rapid analysis and visualization of high-dimensional flow cytometry data

  2023cites this paper
• Cytomulate: accurate and efficient simulation of CyTOF data

  2023cites this paper
• Building predictive disease models using extracellular vesicle microscale flow cytometry and machine learning

  2022cites this paper
• High-dimensional functional phenotyping of preclinical human CAR T cells using mass cytometry

  2022cites this paper
• Revealing new biology from multiplexed, metal-isotope-tagged, single-cell readouts.

  2022cites this paper
• Treatment with a neutrophil elastase inhibitor and ofloxacin reduces P. aeruginosa burden in a mouse model of chronic suppurative otitis media

  2021cites this paper
• A cross‐standardized flow cytometry platform to assess phenotypic stability in precursor B‐cell acute lymphoblastic leukemia (B‐ALL) xenografts

  2021cites this paper
• Advanced Flow Cytometry Analysis Algorithms for Optimizing the Detection of “Different From Normal” Immunophenotypes in Acute Myeloid Blasts

  2021cites this paper
• Mass cytometry profiling of human dendritic cells in blood and tissues

  2021cites this paper
• OMIP 078: A 31‐parameter panel for comprehensive immunophenotyping of multiple immune cells in human peripheral blood mononuclear cells

  2021cites this paper
• A cross-standardized flow cytometry platform to assess phenotypic stability in B-ALL xenografts.

  2021cites this paper
• Research Techniques Made Simple: Experimental Methodology for Imaging Mass Cytometry.

  2021cites this paper
• SCHNEL: Scalable clustering of high dimensional single-cell data

  2020cites this paper
• Single-Cell Immune Competency Signatures Associate with Survival in Phase II GVAX and CRS-207 Randomized Studies in Patients with Metastatic Pancreatic Cancer

  2020cites this paper
• Eleven grand challenges in single-cell data science

  2020cites this paper
• Neonatal Rhesus Macaques Have Distinct Immune Cell Transcriptional Profiles following HIV Envelope Immunization

  2020cites this paper
• Immune checkpoint expression by circulating helper T cells in Giant Cell Arteritis: Analyses of high dimensional flow cytometry data using t-distributed Stochastic Neigh- bor Embedding (tSNE)

  2020cites this paper
• Experimental Nanovaccine Offers Protection Against Repeat Exposures to Trypanosoma cruzi Through Activation of Polyfunctional T Cell Response

  2020cites this paper
• SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery

  2020cites this paper
• OMIP‐069: Forty‐Color Full Spectrum Flow Cytometry Panel for Deep Immunophenotyping of Major Cell Subsets in Human Peripheral Blood

  2020influential citation
• IL-7 receptor alpha defines heterogeneity and signature of human effector memory CD8+ T cells in high dimensional analysis.

  2020cites this paper
• A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry.

  2020cites this paper
• Detecting Prostate Cancer Using Pattern Recognition Neural Networks With Flow Cytometry-Based Immunophenotyping in At-Risk Men

  2020cites this paper
• Recent Advances in Computer-Assisted Algorithms for Cell Subtype Identification of Cytometry Data

  2020influential citation
• Proteomic profiling of stallion spermatozoa suggests changes in sperm metabolism and compromised redox regulation after cryopreservation.

  2020cites this paper
• Single Cell Flow Cytometry Profiling of Bronchoalveolar Lavage in Children.

  2020cites this paper
• From big flow cytometry datasets to smart diagnostic strategies: The EuroFlow approach.

  2019cites this paper
• Morphological profiling using machine learning reveals emergent subpopulations of interferon-γ-stimulated mesenchymal stromal cells that predict immunosuppression.

  2019cites this paper
• Dissecting alterations in human CD8+ T cells with aging by high-dimensional single cell mass cytometry.

  2019influential citation
• In Silico Methods for Studying T Cell Biology.

  2019cites this paper
• Non-cytotoxic Cardiac Innate Lymphoid Cells Are a Resident and Quiescent Type 2-Commited Population

  2019cites this paper
• Rosiglitazone in the thawing medium improves mitochondrial function in stallion spermatozoa through Akt phosphorylation and reduction of caspase 3

  2019cites this paper
• Feature Selection and Feature Extraction in Pattern Analysis: A Literature Review

  2019cites this paper
• Mass Cytometry: Methods and Protocols

  2019cites this paper
• Analysis of Mass Cytometry Data.

  2019cites this paper
• High-Resolution Interrogation of Biological Systems via Mass Cytometry

  2019cites this paper
• Single‐cell technologies in reproductive immunology

  2019cites this paper
• Single-cell mass cytometry reveals in vivo immunological response to surgical biomaterials

  2019cites this paper
• Rosiglitazone in the thawing medium improves mitochondrial function in stallion spermatozoa through regulating Akt phosphorylation and reduction of caspase 3

  2019cites this paper
• EuroFlow Lymphoid Screening Tube (LST) data base for automated identification of blood lymphocyte subsets.

  2019cites this paper
• High-Dimensional Immunophenotyping with Fluorescence-Based Cytometry: A Practical Guidebook.

  2019cites this paper
• Increased T Cell Differentiation and Cytolytic Function in Bangladeshi Compared to American Children

  2019cites this paper
• Relevance of Antibody Validation for Flow Cytometry

  2019cites this paper
• Immune monitoring using mass cytometry and related high-dimensional imaging approaches

  2019cites this paper
• Immunophenotyping: Methods and Protocols

  2019cites this paper
• Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

  2019cites this paper
• A computational approach for phenotypic comparisons of cell populations in high-dimensional cytometry data.

  2018cites this paper
• Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy

  2018cites this paper
• VOLARE: visual analysis of disease-associated microbiome-immune system interplay

  2018cites this paper
• PhenoGraph and viSNE facilitate the identification of abnormal T‐cell populations in routine clinical flow cytometric data

  2018cites this paper
• A Beginner’s Guide to Analyzing and Visualizing Mass Cytometry Data

  2018cites this paper
• Comparative Analysis of Linear and Nonlinear Dimension Reduction Techniques on Mass Cytometry Data

  2018cites this paper
• Data‐driven programmatic approach to analysis of basophil activation tests

  2018cites this paper
• The anatomy of single cell mass cytometry data

  2018cites this paper
• DAFi: A directed recursive data filtering and clustering approach for improving and interpreting data clustering identification of cell populations from polychromatic flow cytometry data

  2018cites this paper
• Flow Cytometry Data Preparation Guidelines for Improved Automated Phenotypic Analysis

  2018cites this paper
• Non-canonical roles of Bcl-xL in regulating mitochondrial function and morphology in pancreatic beta-cells

  2018cites this paper
• Translational Biomarkers: Application in the Clinical Development of Combination Therapies

  2018cites this paper
• Implementation and Validation of an Automated Flow Cytometry Analysis Pipeline for Human Immune Profiling

  2018cites this paper
• Comprehensive immunoproteogenomic analyses of malignant pleural mesothelioma

  2018cites this paper
• Bayesian Trees for Automated Cytometry Data Analysis

  2018cites this paper
• OMIP‐049: Analysis of Human Myelopoiesis and Myeloid Neoplasms

  2018cites this paper
• Mixed-effects association of single cells identifies an expanded effector CD4+ T cell subset in rheumatoid arthritis

  2018cites this paper
• A Universal Live Cell Barcoding-Platform for Multiplexed Human Single Cell Analysis

  2018cites this paper
• The Effect of GPRC5a on the Proliferation, Migration Ability, Chemotherapy Resistance, and Phosphorylation of GSK-3β in Pancreatic Cancer

  2018cites this paper
• Reverse Association of Single Cells to Rheumatoid Arthritis Accounting for Mixed Effects Identifies an Expanded CD27- HLA-DR+ Effector Memory CD4+ T Cell Population

  2017cites this paper
• Using Visualization of t-Distributed Stochastic Neighbor Embedding To Identify Immune Cell Subsets in Mouse Tumors

  2017cites this paper
• Sample Preparation for Mass Cytometry Analysis.

  2017cites this paper
• Application of inductively coupled plasma mass spectrometry in the quantitative analysis of biomolecules with exogenous tags: A review

  2017cites this paper
• Advances in high-dimensional mass cytometry cell and tissue analyses for translational biomarker discovery

  2017cites this paper
• DAFi: A Directed Recursive Filtering and Clustering Approach to Data-Driven Identification of Cell Populations from Polychromatic Flow Cytometry Data

  2017cites this paper
• OMIP‐034: Comprehensive immune phenotyping of human peripheral leukocytes by mass cytometry for monitoring immunomodulatory therapies

  2017cites this paper
• Stallion spermatozoa surviving freezing and thawing experience membrane depolarization and increased intracellular Na+

  2017cites this paper
• This information is current as Immune Cell Subsets in Mouse Tumors Stochastic Neighbor Embedding To Identify-Distributed t Using Visualization of

  2017cites this paper
• Guidelines for the use of flow cytometry and cell sorting in immunological studies.

  2017cites this paper
• Unsupervised learning techniques reveal heterogeneity in memory CD8+ T cell differentiation following acute, chronic and latent viral infections.

  2017cites this paper
• Rapid and Automated Analysis of Portable Flow Cytometer Data

  2017cites this paper
• Mondrian Processes for Flow Cytometry Analysis

  2017cites this paper
• Computational flow cytometry reveals that cryopreservation induces spermptosis but subpopulations of spermatozoa may experience capacitation-like changes.

  2017cites this paper
• High Dimensional Cytometry of Central Nervous System Leukocytes During Neuroinflammation.

  2017cites this paper
• A multi-laboratory comparison of blood dendritic cell populations

  2016cites this paper
• Comparison of Clustering Methods for High-Dimensional Single-Cell Flow and Mass Cytometry Data

  2016cites this paper
• Computational flow cytometry: helping to make sense of high-dimensional immunology data

  2016cites this paper
• The end of gating? An introduction to automated analysis of high dimensional cytometry data

  2016cites this paper
• Computational flow cytometry reveals that cryopreservation 1 induces spermptosis but subpopulations of spermatozoa may 2 experience capacitation like changes 3 2

  2016cites this paper
• Gating mass cytometry data by deep learning

  2016cites this paper
• DeepCyTOF: Automated Cell Classification of Mass Cytometry Data by Deep Learning and Domain Adaptation

  2016cites this paper
• Mass Cytometry: Single Cells, Many Features.

  2016cites this paper
• Identification of Vaccine-Altered Circulating B Cell Phenotypes Using Mass Cytometry and a Two-Step Clustering Analysis

  2016cites this paper
• Immune monitoring technology primer: flow and mass cytometry

  2015cites this paper