Immune monitoring using mass cytometry and related high-dimensional imaging approaches

Parallel analysis of tri-molecular biosynthesis with cell identity and function in single cells

(2019) Samuel C. Kimmey et al.   Nature Communications

Multiplexed profiling of RNA and protein expression signatures in individual cells using flow or mass cytometry

(2019) Andrew D. Duckworth et al.   Nature Protocols

Distinct phenotype of CD4+ T cells driving celiac disease identified in multiple autoimmune conditions

(2019) Asbjørn Christophersen et al.   NATURE MEDICINE

Proliferation tracing with single-cell mass cytometry optimizes generation of stem cell memory-like T cells

(2019) Zinaida Good et al.   NATURE BIOTECHNOLOGY

A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry

(2019) Nicolas Damond et al.   Cell Metabolism

Multiplexed In Situ Imaging Mass Cytometry Analysis of the Human Endocrine Pancreas and Immune System in Type 1 Diabetes

(2019) Yue J. Wang et al.   Cell Metabolism

A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer

(2019) Johanna Wagner et al.   CELL

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Deep learning for cellular image analysis

(2019) Erick Moen et al.   NATURE METHODS

GM-CSF and CXCR4 define a T helper cell signature in multiple sclerosis

(2019) Edoardo Galli et al.   NATURE MEDICINE

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy

(2019) Felix J. Hartmann et al.   Cell Reports

Immunome perturbation is present in patients with juvenile idiopathic arthritis who are in remission and will relapse upon anti-TNFα withdrawal

(2019) Jing Yao Leong et al.   ANNALS OF THE RHEUMATIC DISEASES

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

(2019) Andrea Cossarizza et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure

(2019) Leeat Keren et al.   Science Advances

Rebooting Human Immunology

(2018) Mark M. Davis et al.   Annual Review of Immunology

GateFinder: projection-based gating strategy optimization for flow and mass cytometry

(2018) Nima Aghaeepour et al.   BIOINFORMATICS

Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging

(2018) Peggie Cheung et al.   CELL

High-Dimensional Single-Cell Mapping of Central Nervous System Immune Cells Reveals Distinct Myeloid Subsets in Health, Aging, and Disease

(2018) Dunja Mrdjen et al.   IMMUNITY

Comparison of CyTOF assays across sites: Results of a six-center pilot study

(2018) Michael D. Leipold et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Ruthenium counterstaining for imaging mass cytometry

(2018) Raúl Catena et al.   JOURNAL OF PATHOLOGY

Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse

(2018) Zinaida Good et al.   NATURE MEDICINE

Targeting B Cells and Plasma Cells in Autoimmune Diseases

(2018) Katharina Hofmann et al.   Frontiers in Immunology

Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry

(2018) Stéphane Chevrier et al.   Cell Systems

Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks

(2018) Hyunghoon Cho et al.   Cell Systems

Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry

(2018) Daniel Schulz et al.   Cell Systems

Rheumatoid arthritis

(2018) Josef S. Smolen et al.   Nature Reviews Disease Primers

Microneedle-based device for the one-step painless collection of capillary blood samples

(2018) Timothy M. Blicharz et al.   Nature Biomedical Engineering

Stereotypic Immune System Development in Newborn Children

(2018) Axel Olin et al.   CELL

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

(2018) Yury Goltsev et al.   CELL

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

(2018) Leeat Keren et al.   CELL

Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates

(2018) Yannick Simoni et al.   NATURE

CDeep3M—Plug-and-Play cloud-based deep learning for image segmentation

(2018) Matthias G. Haberl et al.   NATURE METHODS

Metal-isotope-tagged monoclonal antibodies for high-dimensional mass cytometry

(2018) Guojun Han et al.   Nature Protocols

MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data

(2018) Zicheng Hu et al.   Cell Reports

Deep Learning in Image Cytometry: A Review

(2018) Anindya Gupta et al.   CYTOMETRY PART A

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

U-Net: deep learning for cell counting, detection, and morphometry

(2018) Thorsten Falk et al.   NATURE METHODS

A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links

(2018) Helle Krogh Pedersen et al.   Nature Protocols

New insights into the genetics and epigenetics of systemic sclerosis

(2018) Chiara Angiolilli et al.   Nature Reviews Rheumatology

Cell and fluid sampling microneedle patches for monitoring skin-resident immunity

(2018) Anasuya Mandal et al.   Science Translational Medicine

Mixed-effects association of single cells identifies an expanded effector CD4+ T cell subset in rheumatoid arthritis

(2018) Chamith Y. Fonseka et al.   Science Translational Medicine

B cell alterations during BAFF inhibition with belimumab in SLE

(2018) Daniel Ramsköld et al.   EBioMedicine

Approximated and User Steerable tSNE for Progressive Visual Analytics

(2017) Nicola Pezzotti et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Mass cytometry identifies a distinct monocyte cytokine signature shared by clinically heterogeneous pediatric SLE patients

(2017) W.E. O'Gorman et al.   JOURNAL OF AUTOIMMUNITY

Pathologically expanded peripheral T helper cell subset drives B cells in rheumatoid arthritis

(2017) Deepak A. Rao et al.   NATURE

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

(2017) Denis Schapiro et al.   NATURE METHODS

Image Data Resource: a bioimage data integration and publication platform

(2017) Eleanor Williams et al.   NATURE METHODS

Testing for differential abundance in mass cytometry data

(2017) Aaron T L Lun et al.   NATURE METHODS

Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types

(2017) Vincent van Unen et al.   Nature Communications

Sensitive detection of rare disease-associated cell subsets via representation learning

(2017) Eirini Arvaniti et al.   Nature Communications

Discerning Risk of Disease Transition in Relatives of Systemic Lupus Erythematosus Patients Utilizing Soluble Mediators and Clinical Features

(2017) Melissa E. Munroe et al.   Arthritis & Rheumatology

More Is Better: Recent Progress in Multi-Omics Data Integration Methods

(2017) Sijia Huang et al.   Frontiers in Genetics

CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets

(2016) David Dao et al.   BIOINFORMATICS

Mass Cytometry: Single Cells, Many Features

(2016) Matthew H. Spitzer et al.   CELL

Biomarkers to guide clinical therapeutics in rheumatology?

(2016) William H. Robinson et al.   CURRENT OPINION IN RHEUMATOLOGY

Standardization and quality control for high-dimensional mass cytometry studies of human samples

(2016) Katja Kleinsteuber et al.   CYTOMETRY PART A

Mass cytometry panel optimization through the designed distribution of signal interference

(2016) Chikara Takahashi et al.   CYTOMETRY PART A

Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data

(2016) Lukas M. Weber et al.   CYTOMETRY PART A

Cytometry by time-of-flight immunophenotyping identifies a blood Sjögren's signature correlating with disease activity and glandular inflammation

(2016) Michael Mingueneau et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

High-dimensional single-cell analysis reveals the immune signature of narcolepsy

(2016) Felix J. Hartmann et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Simian Immunodeficiency Virus-Producing Cells in Follicles Are Partially Suppressed by CD8 + Cells In Vivo

(2016) Shengbin Li et al.   JOURNAL OF VIROLOGY

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Mass cytometry: blessed with the curse of dimensionality

(2016) Evan W Newell et al.   NATURE IMMUNOLOGY

Automated mapping of phenotype space with single-cell data

(2016) Nikolay Samusik et al.   NATURE METHODS

Highly multiplexed simultaneous detection of RNAs and proteins in single cells

(2016) Andreas P Frei et al.   NATURE METHODS

New insights into the immunopathogenesis of systemic lupus erythematosus

(2016) George C. Tsokos et al.   Nature Reviews Rheumatology

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

(2016) David A. Van Valen et al.   PLoS Computational Biology

Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications

(2016) Bernd Bodenmiller   Cell Systems

Sjögren syndrome

(2016) Pilar Brito-Zerón et al.   Nature Reviews Disease Primers

Systemic lupus erythematosus

(2016) Arvind Kaul et al.   Nature Reviews Disease Primers

Epigenetics in autoimmune diseases: Pathogenesis and prospects for therapy

(2015) Zimu Zhang et al.   AUTOIMMUNITY REVIEWS

Quantifying Memory CD8 T Cells Reveals Regionalization of Immunosurveillance

(2015) Elizabeth M. Steinert et al.   CELL

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry

(2015) Eli R. Zunder et al.   Cell Stem Cell

A CD45-based barcoding approach to multiplex mass-cytometry (CyTOF)

(2015) Liyun Lai et al.   CYTOMETRY PART A

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

(2015) Sofie Van Gassen et al.   CYTOMETRY PART A

Platinum-conjugated antibodies for application in mass cytometry

(2015) Henrik E. Mei et al.   CYTOMETRY PART A

The end of gating? An introduction to automated analysis of high dimensional cytometry data

(2015) Florian Mair et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Single-cell systems-level analysis of human Toll-like receptor activation defines a chemokine signature in patients with systemic lupus erythematosus

(2015) William E. O'Gorman et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Age-Associated B Cells: A T-bet–Dependent Effector with Roles in Protective and Pathogenic Immunity

(2015) Kira Rubtsova et al.   JOURNAL OF IMMUNOLOGY

Fine-Needle Aspiration Biopsy of the Lymph Node: A Novel Tool for the Monitoring of Immune Responses after Skin Antigen Delivery

(2015) Danijela Tatovic et al.   JOURNAL OF IMMUNOLOGY

Algorithmic Tools for Mining High-Dimensional Cytometry Data

(2015) Cariad Chester et al.   JOURNAL OF IMMUNOLOGY

Barcoding of Live Human Peripheral Blood Mononuclear Cells for Multiplexed Mass Cytometry

(2015) Henrik E. Mei et al.   JOURNAL OF IMMUNOLOGY

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

(2015) Eli R Zunder et al.   Nature Protocols

Technological advances transforming rheumatology

(2015) William H. Robinson et al.   Nature Reviews Rheumatology

Immune cell profiling to guide therapeutic decisions in rheumatic diseases

(2015) Joerg Ermann et al.   Nature Reviews Rheumatology

An interactive reference framework for modeling a dynamic immune system

(2015) M. H. Spitzer et al.   SCIENCE

Human NK cell repertoire diversity reflects immune experience and correlates with viral susceptibility

(2015) Dara M. Strauss-Albee et al.   Science Translational Medicine

Mass cytometry as a platform for the discovery of cellular biomarkers to guide effective rheumatic disease therapy

(2015) Nitya Nair et al.   ARTHRITIS RESEARCH & THERAPY

Identification of Hypoxic Cells Using an Organotellurium Tag Compatible with Mass Cytometry

(2014) Landon J. Edgar et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

TNF and TNF-receptors: From mediators of cell death and inflammation to therapeutic giants – past, present and future

(2014) Lisa M. Sedger et al.   CYTOKINE & GROWTH FACTOR REVIEWS

Autoimmune disease in the epigenetic era: how has epigenetics changed our understanding of disease and how can we expect the field to evolve?

(2014) Matlock A Jeffries et al.   Expert Review of Clinical Immunology

ImmPort: disseminating data to the public for the future of immunology

(2014) Sanchita Bhattacharya et al.   IMMUNOLOGIC RESEARCH

Single-cell measurement of the uptake, intratumoral distribution and cell cycle effects of cisplatin using mass cytometry

(2014) Qing Chang et al.   INTERNATIONAL JOURNAL OF CANCER

Characterizing and Diminishing Autofluorescence in Formalin-fixed Paraffin-embedded Human Respiratory Tissue

(2014) A. Sally Davis et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells

(2014) Evan W Newell et al.   NATURE BIOTECHNOLOGY

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

Automated identification of stratifying signatures in cellular subpopulations

(2014) Robert V. Bruggner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conditional density-based analysis of T cell signaling in single-cell data

(2014) S. Krishnaswamy et al.   SCIENCE

IL-17 and GM-CSF Expression Are Antagonistically Regulated by Human T Helper Cells

(2014) R. Noster et al.   Science Translational Medicine

Clinical recovery from surgery correlates with single-cell immune signatures

(2014) B. Gaudilliere et al.   Science Translational Medicine

Multiple sclerosis-associated IL2RA polymorphism controls GM-CSF production in human TH cells

(2014) Felix J. Hartmann et al.   Nature Communications

Sjögren's Syndrome

(2013) Clio P. Mavragani et al.   Annual Review of Pathology-Mechanisms of Disease

Normalization of mass cytometry data with bead standards

(2013) Rachel Finck et al.   CYTOMETRY PART A

Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization

(2013) Evan W Newell et al.   NATURE BIOTECHNOLOGY

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue

(2013) M. J. Gerdes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A platinum-based covalent viability reagent for single-cell mass cytometry

(2012) Harris G. Fienberg et al.   CYTOMETRY PART A

FlowRepository: A resource of annotated flow cytometry datasets associated with peer-reviewed publications

(2012) Josef Spidlen et al.   CYTOMETRY PART A

Single-cell mass cytometry adapted to measurements of the cell cycle

(2012) Gregory K. Behbehani et al.   CYTOMETRY PART A

Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8+ T Cell Phenotypes

(2012) Evan W. Newell et al.   IMMUNITY

Histo-Cytometry: A Method for Highly Multiplex Quantitative Tissue Imaging Analysis Applied to Dendritic Cell Subset Microanatomy in Lymph Nodes

(2012) Michael Y. Gerner et al.   IMMUNITY

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

(2012) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

A deep profiler's guide to cytometry

(2012) Sean C. Bendall et al.   TRENDS IN IMMUNOLOGY

A B-cell subset uniquely responsive to innate stimuli accumulates in aged mice

(2011) Y. Hao et al.   BLOOD

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Synthesis of a Functional Metal-Chelating Polymer and Steps toward Quantitative Mass Cytometry Bioassays

(2010) Daniel Majonis et al.   ANALYTICAL CHEMISTRY

Epitope spreading of the anti-citrullinated protein antibody response occurs before disease onset and is associated with the disease course of early arthritis

(2010) D. van der Woude et al.   ANNALS OF THE RHEUMATIC DISEASES

Optimizing transformations for automated, high throughput analysis of flow cytometry data

(2010) Greg Finak et al.   BMC BIOINFORMATICS

Good cell, bad cell: Flow cytometry reveals T-cell subsets important in HIV disease

(2010) Pratip K. Chattopadhyay et al.   CYTOMETRY PART A

Highly multiparametric analysis by mass cytometry

(2010) Olga Ornatsky et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY

Study of Cell Antigens and Intracellular DNA by Identification of Element-Containing Labels and Metallointercalators Using Inductively Coupled Plasma Mass Spectrometry

(2008) O. I. Ornatsky et al.   ANALYTICAL CHEMISTRY

MIFlowCyt: The minimum information about a flow cytometry experiment

(2008) Jamie A. Lee et al.   CYTOMETRY PART A

A Prescription for Human Immunology

(2008) Mark M. Davis   IMMUNITY

Development of analytical methods for multiplex bio-assay with inductively coupled plasma mass spectrometry

(2008) Olga I. Ornatsky et al.   JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY