CyTOF & Helios Publications

As we celebrate 10 years of unrivaled leadership in deep cell profiling and single-tube cytometry, we introduce a new quarterly anthology series that will cover the most recent and impactful publications that help expand our understanding of human health and disease.

Take a look at the issues of Mass Cytometry Publications Trending Now below to see how the mass cytometry community uses CyTOF® technology across the sciences to power its findings and drive development of new innovations.

Mass Cytometry Publications Trending Now NEW! March issue On high-dimensional functional assessment of health vs. disease December issue On use of mass cytometry in clinical trials September issue On key publications from the first half of 2019

Browse our complete catalog of over 900 CyTOF related publications to see how Helios™ and mass cytometry empower researchers to make breakthrough discoveries in basic, translational and clinical research.

• Overview

  Number of papers per research area as of July, 2020

  Number of cumulative papers as of July, 2020

• Recent

  • Transplantation of ACE2- mesenchymal stem cells improves the outcome of patients with COVID-19 pneumonia
    Leng, Z., Zhu, R., Hou, W. et al. Aging and Disease (2020): 216–228
  • IRF5 promotes influenza-induced inflammatory responses in human iPSC-derived myeloid cells and murine models
    Forbester, J.L., Clement, M., Wellington, D. et al. Journal of Virology (2020): DOI: 10.1128/JVI.00121-20
  • Multiplexed single-cell morphometry for hematopathology diagnostics
    Tsai, A.G., Glass, D.R., Juntilla, M. et al. Nature Methods (2020): 408–17
  • Autoreactive CD8+ T cell exhaustion distinguishes subjects with slow type 1 diabetes progression
    Wiedeman, A.E., Muir, V.S., Rasasco, M.G. et al. Journal of Clinical Investigation (2020): 480–90
  • Uncovering axes of variation among single-cell cancer specimens
    Chen, W.S., Zivanovic, N., van Dijk, D. et al. Nature Methods (2020): 302–10
  • Mass cytometry reveals cellular fingerprint associated with IgE+ peanut tolerance and allergy in early life
    Neeland, M.R., Andorf, S., Manohar, M. et al. Nature Communications (2020): 1091

• Research Areas

  • Biomarker Screening

    • CD8+T-bet+ cells as a predominant biomarker for inclusion body myositis
      Dzangué-Tchoupou, G., Mariampillai, K., Bolko, L. et al. Autoimmunity Reviews (2019): 325–33
    • A high-sensitivity lanthanide nanoparticle reporter for mass cytometry: tests on microgels as a proxy for cells
      Lin, W., Hou, Y., Lu, Y. et al. Langmuir (2014): 3,142–53
    • Mass cytometry identifies distinct lung CD4+ T cell patterns in Löfgren’s syndrome and non-Löfgren’s syndrome sarcoidosis
      Kaiser, Y., Lakshmikanth, T., Chen, Y., et al. Frontiers in Immunology (2017): 1,130
    • High dimensional immune biomarkers demonstrate differences in phenotypes and endotypes in food allergy and asthma
      Chinthrajah, R.S., Purington, N., Sampath, V. et al. Annals of Allergy, Asthma, and Immunology (2018): 117–9.e1
    • A frameshift in CSF2RB predominant among Ashkenazi Jews increases risk for Crohn's disease and reduces monocyte signaling via GM-CSF
      Chuang, L.S., Villaverde, N., Hui, K.Y. et al. Gastroenterology (2016): 710–723.e2
    • Distinct predictive biomarker candidates for response to anti-CTLA-4 and anti-PD-1 immunotherapy in melanoma patients
      Subrahmanyam, P.B., Dong, Z., Gusenleitner, D. et al. Journal for ImmunoTherapy of Cancer (2018): 18
    • A time to amaze, a time to settle down, and a time to discover
      Cosma, A. Cytometry Part A (2015): 795–6
    • Immune cell profiling to guide therapeutic decisions in rheumatic diseases
      Ermann, J., Rao, D.A., Teslovich, N.C. et al. Nature Reviews Rheumatology (2015): 541–51
    • Signaling effects of sodium hydrosulfide in healthy donor peripheral blood mononuclear cells
      Sulen, A., Gullaksen, S.E., Bader, L. et al. Pharmacological Research (2016): 216–27

  • Data Analysis Methods

    • Uncovering axes of variation among single-cell cancer specimens
      Chen, W.S., Zivanovic, N., van Dijk, D. et al. Nature Methods (2020): 302–10
    • FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets
      Ko, M.E., Williams, C.M., Fread, K.I. et al. Nature Protocols (2020): 398-420.
    • Stabilized reconstruction of signaling networks from single-cell cue-response data
      Kumar, S., Lun, X-K., Bodenmiller, B. et al. Scientific Reports (2020): 1233
    • Structure-preserving visualisation of high dimensional single-cell datasets
      Szubert, B., Cole, J.E., Monaco, C. et al. Scientific Reports (2019): 8914
    • Cell cycle analysis and relevance for single-cell gating in mass cytometry
      Rein, I.D., Notø, H. Ø., Bostad, M. et al. Cytometry Part A (2020): DOI: 10.1002/cyto.a.23926
    • CytoFA: Automated gating of mass cytometry data via robust skew factor analyzers
      Lee, S.X. Advances in Knowledge Discovery and Data Mining. Lecture Notes in Computer Science (2019): 514–25
    • Learning single‐cell distances from cytometry data
      Nguyen, B., Rubbens, P., Kerckhof, F.M. et al. Cytometry Part A (2019): 782–91
    • Visualizing structure and transitions in high-dimensional biological data
      Moon, K.R., van Dijk, D., Wang, Z. et al. Nature Biotechnology (2019): 1,482–92
    • Computational analysis of high-dimensional mass cytometry data from clinical tissue samples
      Norton, S. and Kemp, R. Mass Cytometry: Methods and Protocols (2019): 295–307
    • Exploring single-cell data with deep multitasking neural networks
      Amodio, M., van Dijk, D., Srinivasan, K., et al. Nature Methods (2019): 1,139–45
    • Analysis of high-dimensional phenotype data generated by mass cytometry or high-dimensional flow cytometry
      Cirovic, B., Katzmarski, N., and Schlitzer, A. Mass Cytometry: Methods and Protocols (2019): 281–94
    • SCENERY: a web application for (causal) network reconstruction from cytometry data
      Papoutsoglou, G., Athineou G., Lagani, V. et al. Nucleic Acids Research (2017): W270–W275
    • Automated data cleanup for mass cytometry
      Bagwell, C.B., Inokuma, M., Hunsberger, B., et al. Cytometry Part A (2019): 184–198
    • Modeling cell-cell interactions from spatial molecular data with spatial variance component analysis
      Arnol, D., Schapiro, D., Bodenmiller, B. et al. Cell Reports (2019): P202–211.E6
    • Visualization and quantification of high-dimensional cytometry data using Cytofast and the upstream clustering methods FlowSOM and Cytosplore
      Beyrend, G., Stam, K., Ossendorp, F. et al. Journal of Visual Experiments (2019): DOI: 10.3791/60525
    • HiPPO and PANDA: Two bioinformatics tools to support analysis of mass cytometry data
      Pirrò, S., Spada, F., Gadaleta, E. et al. Journal of Computational Biology (2019): DOI: 10.1089/cmb.2019.0384
    • A comparison framework and guideline of clustering methods for mass cytometry data
      Liu, X., Song, W., Wong, B.Y., et al. Genome Biology (2019): 297
    • Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets
      Belkina, A.C., Ciccolella, C.O., Anno, R., et al. Nature Communications (2019): 5415
    • Challenges in the multivariate analysis of mass cytometry data: The effect of randomization
      Papoutsoglou, G., Lagani, V., Schmidt, A., et al. Cytometry Part A (2019): DOI: 10.1002/cyto.a.23908
    • Acquisition, processing, and quality control of mass cytometry data
      Lee, B.H. and Rahman, A.H. Mass Cytometry: Methods and Protocols (2019): 13–31
    • Supervised machine learning with CITRUS for single cell biomarker discovery
      Polikowsky, H.G. and Drake, K.A. Mass Cytometry: Methods and Protocols (2019): 309–32
    • Analysis of mass cytometry data
      Pederson, C.B. and Olsen, L.R. Mass Cytometry: Methods and Protocols (2019): 267–79
    • Automated cell type discovery and classification through knowledge transfer
      Lee, H.C., Kosoy, R., Becker, C.E. et al. Bioinformatics (2017): 1,689–95
    • CytoNorm: A normalization algorithm for cytometry data
      Van Gas, S., Gaudilliere, B., Angst , M.S. et al. Cytometry Part A (2019): doi: 10.1002/cyto.a.23904
    • Minimizing Batch Effects in Mass Cytometry Data
      Schuyler, R.P., Jackson, C., Garcia-Perez, J.E. et al. Frontiers in Immunology (2019): doi: 10.3389/fimmu.2019.02367
    • Predicting cell populations in single cell mass cytometry data
      Abdelaal, T., van Unen, V., Höllt T. et al. Cytometry Part A (2019): 769–81
    • Computational approaches for characterizing the tumor immune microenvironment
      Liu, C.C., Steen, C.B., and Newman, A.M. Immunology (2019): 70–84
    • SCINA: A semi-supervised subtyping algorithm of single cells and bulk samples
      Zhang, Z., Luo, D., Zhong, X. et al. Genes (2019): 531
    • A novel, five-marker alternative to CD16-CD14 gating to identify the three human monocyte subsets
      Ong, S.M., Teng, K., Newell, E. et al. Frontiers in Immunology (2019): 1,761
    • Methods for analyzing tellurium Imaging Mass Cytometry data
      Bassan, J. and Nitz, M. PLoS One (2019): e0221714
    • VOLARE: visual analysis of disease-associated microbiome-immune system interplay
      Siebert, J.C., Preston Neff, C., Schneider, J.M. et al. BMC Bioinformatics (2019): 432
    • Improving the t-SNE algorithms for cytometry and other technologies: Cen-Se′ mapping
      Bagwell, C.B., Bray, C.M., Herbert, D.J. et al. Journal of Biometrics & Biostatistics (2019): 430
    • diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering
      Weber, L.M., Nowicka, M., Soneson, C. et al. Communications Biology (2019): 183
    • ImaCytE: Visual exploration of cellular microenvironments for Imaging Mass Cytometry data
      Somarakis, A., van Unen, V., Koning, F. et al. IEEE Transactions on Visualization and Computer Graphics (2019): doi: 10.1109/TVCG.2019.2931299.
    • Advanced imaging technology applications in cytology
      Pantanowitz, L., Preffer, F., Wilbur, D.C. Nature Communications (2018): 5–14
    • Mass synaptometry: High-dimensional multi parametric assay for single synapses
      Gajera, C.R., Fernandez, R., Postupna, N. et al. Journal of Neuroscience Methods (2018): 73–83
    • histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data
      Schapiro, D., Jackson, H.W., Raghuraman, S. et al. Nature Methods (2017): 873–6
    • Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data
      Fernandez, N.F., Gundersen, G.W., Rahman, A. et al. Scientific Data (2017): 170151
    • CytoBinning: immunological insights from multi-dimensional data
      Shen, Y., Chaigne-Delalande, B., Lee, R.W.J. et al. PLoS One (2018): e0205291
    • Compensation of signal spillover in suspension and Imaging Mass Cytometry
      Chevrier, S., Crowell, H.L., Zanotelli, V.R.T. et al. Cell Systems (2018): 612–20
    • Automated subset identification and characterization pipeline for multidimensional flow and mass cytometry data clustering and visualization
      Meehan, S., Kolyagin, G.A., Parks, D. et al. Nature Communications Biology (2019): 229
    • Quantitative comparison of conventional and t-SNE-guided gating analyses treatment in cynomolgus monkeys
      Eshgi, S.T., Au-Yeung, A., Takahashi, C. et al. Frontiers in Immunology (2019): 1,194
    • Development of a comprehensive antibody staining database using a standardized analytics pipeline
      Amir, E.D., Lee, B., Badoual, P. et al. Frontiers in Immunology (2019): 1,315
    • CyTOFmerge: Integrating mass cytometry data across multiple panels
      Abdelaal, T., Höllt T., van Unen, V. et al. Bioinformatics (2019): btz180
    • Robust prediction of clinical outcomes using cytometry data
      Hu, Z., Glicksberg, B.S., Butte, A.J. Bioinformatics (2018): 1,197–203
    • ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data
      Sidhom, J.W., Theodros, D., Murter, B. et al. Journal of Visualized Experiments (2019): doi: 10.3791/57473.
    • CytoBackBone: an algorithm for merging of phenotypic information from different cytometric profiles
      Pereira, A.L., Lambotte, O., Le Grand, R. et al. Bioinformatics (2019): btz212
    • High throughput automated analysis of big flow cytometry data
      Rahim, A., Meskas, J., Drissler, S. et al. Methods (2018): 164–76
    • GateFinder: projection-based strategy optimization for flow and mass cytometry.
      Aghaeepour, N., Simonds, E.F., Knapp D.J.H.F. et al. Bioinformatics (2018): 4,131–3
    • QFMatch: multidimensional flow and mass cytometry samples alignment
      Orlova, D.Y., Meehan, S., Parks D. et al. Scientific Reports (2018): 3,291
    • Cytosplore: interactive immune cell phenotyping for large single-cell datasets
      Höllt, T., Pezzotti, N., van Unen, V. et al. Computer Graphics Forum (2016): 171–80
    • A roadmap towards personalized immunology
      Delhalle, S., Bode, S.F.N., Balling, R. et al. Systems Biology and Applications (2018): 9
    • Cytofast: A workflow for visual and quantitative analysis of flow and mass cytometry data to discover immune signatures and correlations
      Beyrend, G., Stam, K., Höllt, T. et al. Computational and Structural Biotechnology Journal (2018): 435–42
    • Dimensionality reduction for visualizing single-cell data using UMAP
      Becht, E., McInnes, L., Healy, J. et al. Nature Biotechnology (2018): 38–44
    • Single-cell epigenetics - Chromatin modification atlas unveiled by mass cytometry
      Cheung, P., Vallania, F., Dvorak, M. et al. Clinical Immunology (2018): 40–8
    • MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data
      Hu, Z., Jujjavarapu, C., Hughey, J.J. et al. Cell Reports (2018): 1,377–88
    • Unsupervised trajectory analysis of single-cell RNA-seq and imaging data reveals alternate tuft cell origins in the gut
      Pollyea, D.A., Stevens, B.M., Jones, C.L. et al. Cell Systems (2018): 37–51
    • CytoML for cross-platform cytometry data sharing
      Finak, G., Jiang, W., Gottardo, R. Cytometry Part A: Journal of the ISAC (2018): 1,189–96
    • Removal of batch effects using distribution-matching residual networks
      Shaham, U., Stanton, K.P., Zhao, J. et al. Bioinformatics (2017): 2,539–46
    • Mixed-effects association of single cells identifies an expanded effector CD4+ T cell subset in rheumatoid arthritis
      Fonseka, C.Y., Rao, D.A., Teslovich, N.C. et al. Science Translational Medicine (2018): eaaq0305
    • Sensitive detection of rare disease-associated cell subsets via representation learning
      Arvaniti, E., Claassen, M. Nature Communications (2017): doi: 10.1007/s12094-018-02004-8
    • Multiparametric analysis of colorectal cancer immune responses
      Leman, J.K.H., Sandford, S.K., Rhodes, J.L. et al. World Journal of Gastroenterology (2018): 2,995-3,005
    • Learning time-varying information flow from single-cell epithelial to mesenchymal transition data
      Krishnaswamy, S., Zivanovic, N., Sharma, R. et al. PLoS One (2018): e0203389
    • Continuous Immune Cell Differentiation Inferred From Single-Cell Measurements Following Allogeneic Stem Cell Transplantation
      Chen, Y., Lakshmikanth, T., Olin, A. et al. Frontiers in Molecular Biosciences (2018): 81
    • Average Overlap Frequency: a simple metric to evaluate staining quality and community identification in high dimensional mass cytometry experiments
      Amir, E.D., Guo, X.V., Mayovska, O. et al. Journal of Immunological Methods (2018): 20–29
    • Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE
      Qiu, P., Simonds, E.F., Bendall, S.C. et al. Nature Biotechnology (2011): 886–91
    • Bayesian hierarchical models for protein networks in single-cell mass cytometry
      Mitra, R., Müller, P., Qiu, P. et al. Cancer Informatics (2014): 79–89
    • Cytofkit: a bioconductor package for an integrated mass cytometry data analysis pipeline
      Chen, H., Lau, M.C., Wong, M.T. et al. PLoS Computational Biology (2016): e1005112
    • ImmPort, toward repurposing of open access immunological assay data for translational and clinical research
      Bhattacharya, S., Dunn, P., Thomas, C.G. et al. Scientific Data (2018): 180,015
    • Alternatives to current flow cytometry data analysis for clinical and research studies
      Gondhalekar, C., Rajwa, B., Patsekin, V. et al. Methods (2018): 113–29
    • Generating quantitative cell identity labels with marker enrichment modeling (MEM)
      Diggins, K.E., Gandelman, J.S., Roe, C.E. et al. Current Protocols in Cytometry (2018): 10.21.1–28
    • CellCycleTRACER accounts for cell cycle and volume in mass cytometry data
      Rapsomaniki, M.A., Lun, X.K., Woerner, S. et al. Nature Communications (2018): 632
    • Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data
      Weber, L.M., Robinson, M.D. Cytometry Part A (2016): 1,084–96
    • Gating mass cytometry data by deep learning
      Li, H., Shaham, U., Stanton, K.P. et al. Bioinformatics (2017): 3,423–30
    • Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks
      Li, Y.H., Li, D., Samusik, N. et al. PLoS Computational Biology (2017): e1005875
    • A computational approach for phenotypic comparisons of cell populations in high-dimensional cytometry data
      Platon, L., Pejoski, D., Gautreau, G. et al. Methods (2017): 66–75
    • Automated identification of stratifying signatures in cellular subpopulations
      Bruggner, R.V., Bodenmiller, B., Dill, D.L. et al. Proceedings of the National Academy of Sciences of the United States of America (2014): E2770–E2777
    • OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis
      Finak, G., Frelinger, J., Jiang, W. et al. PLoS Computational Biology (2014): e1003806
    • Conditional density-based analysis of T cell signaling in single-cell data
      Krishnaswamy, S., Spitzer, M.H., Mingueneau, M. et al. Science (2014): 1,250,689
    • Unsupervised trajectory analysis of single-cell RNA-seq and imaging data reveals alternative tuft cell origins in the gut
      Herring, C.A., Banerjee, A., McKinley, E.T. et al. Cell Systems (2018): 37–51.e9
    • Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types
      Van Unen, V., Höllt, T., Pezzotti, N. et al. Nature Communications (2017): 1,740
    • CyteGuide: visual guidance for hierarchical single-cell analysis
      Holt, T., Pezzotti, N., van Unen, V. et al. IEEE Transactions on Visualization and Computer Graphics (2018): 739–48
    • A beginner's guide to analyzing and visualizing mass cytometry data
      Kimball, A.K., Oko, L.M., Bullock, B.L. et al. Journal of Immunology (2018): 3–22
    • Integrated inference and analysis of regulatory networks from multi-level measurements
      Poultney, C.S., Greenfield, A., Bonneau, R. Methods in Cell Biology (2012): 19–56
    • RchyOptimyx: cellular hierarchy optimization for flow cytometry
      Aghaeepour, N., Jalali, A., O'Neill, K. et al. Cytometry, Part A (2012): 1,022–30
    • Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE)
      Shekhar, K., Brodin, P., Davis, M.M. et al. Proceedings of the National Academy of Sciences (2014): 202–7
    • Enhanced flowType/RchyOptimyx: a BioConductor pipeline for discovery in high-dimensional cytometry data
      O'Neill, K., Jalali, A., Aghaeepour, N. et al. Bioinformatics (2014): 1,329–30
    • FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data
      Van Gassen, S., Callebaut, B., Van Helden, M.J. et al. Cytometry Part A (2015): 636–45
    • An Interactive Reference Framework for Modeling a Dynamic Immune System
      Spitzer, M.H., Gherardini, P.F., Fragiadakis, G.K. et al. Science (2015): 1,259,425
    • immunoClust—An automated analysis pipeline for the identification of immunophenotypic signatures in high-dimensional cytometric datasets
      Sörensen, T., Baumgart, S., Durek, P. et al. Cytometry, Part A (2015): 603–15
    • NetworkPainter: dynamic intracellular pathway animation in Cytobank
      Karr, J.K., Guturu, H., Chen, E.Y. et al. BMC Bioinformatics (2015): 172
    • Computationally efficient multidimensional analysis of complex flow cytometry data using second order polynomial histograms
      Zaunders, J., Jing, J., Leipold, M. et al. Cytometry, Part A (2015): 44–58
    • Processing, visualising and reconstructing network models from single-cell data
      Woodhouse, S., Moignard, V., Göttgens, B., Fisher, J. Immunology and Cell Biology (2015): 256–65
    • Wishbone identifies bifurcating developmental trajectories from single-cell data
      Setty, M., Tadmor, M.D., Reich-Zeliger, S. et al. Nature Biotechnology (2016): 637–45
    • Automated mapping of phenotype space with single-cell data
      Samusik, N., Good, Z., Spitzer, M.H. et al. Nature Methods (2016): 493–6
    • Computational flow cytometry: helping to make sense of high-dimensional immunology data
      Saeys, Y., Gassen, S.V., Lambrecht, B.N. Nature Reviews Immunology (2016): 449–62
    • The end of gating? An introduction to automated analysis of high dimensional cytometry data
      Mair, F., Hartmann, F.J., Mrdjen et al. European Journal of Immunology (2015): 34–43
    • Mapping the effects of drugs on the immune system
      Kidd, B.A., Wroblewska, A., Boland, M.R. et al. Nature Biotechnology (2015): 47–54
    • densityCut: an efficient and versatile topological approach for automatic clustering of biological data
      Ding, J., Shah, S., Condon, A. Bioinformatics (2016): 2,567–76
    • Categorical Analysis of Human T Cell Heterogeneity with One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding
      Cheng, Y., Wong, M.T., van der Maaten, L., Newell, E.W. Journal of Immunology (2016): 924–32
    • AirLab: a cloud-based platform to manage and share antibody-based single-cell research
      Catena, R., Özcan, A., Jacobs, A. et al. Genome Biology (2016): 142
    • destiny: diffusion maps for large-scale single-cell data in R
      Angerer, P., Haghverdi, L., Büttner, M. et al. Bioinformatics (2016): 1,241–3
    • Visualization and cellular hierarchy inference of single-cell data using SPADE
      Anchang, B., Hart, T.D., Bendall, S.C. et al. Nature Protocols (2016): 1,264–79
    • Predicting Causal Relationships from Biological Data: Applying Automated Causal Discovery on Mass Cytometry Data of Human Immune Cells
      Triantafillou, S., Lagani, V., Heinze-Deml, C. et al. Scientific Reports (2017): 12,724
    • Toward deterministic and semiautomated SPADE analysis
      Qiu, P. Cytometry Part A (2017): 281–9
    • CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
      Nowicka, M., Krieg, C., Weber, L.M. et al. F1000 Research (2017): 748
    • Cluster stability in the analysis of mass cytometry data
      Melchiotti, R., Gracio, F., Kordasti, S. et al. Cytometry Part A (2017): 73–84
    • Testing for differential abundance in mass cytometry data
      Lun, A.T.L., Richard, A.C., Marioni, J.C. Nature Methods (2017): 707–9
    • SPADEVizR: an R package for visualization, analysis and integration of SPADE results
      Gautreau, G., Pejoski, D., Le Grand, R. et al. Bioinformatics (2017): 779–81
    • Characterizing cell subsets in heterogeneous tissues using marker enrichment modeling
      Diggins, K.E., Greenplate, A.R., Leelatian, N. et al. Nature Methods (2017): 275-8
    • Exploring Glucocorticoid Receptor Agonists Mechanism of Action through Mass Cytometry and Radial Visualizations
      Abraham, Y., Gerrits, B., Ludwig, M.G. et al. Cytometry Part B Clinical Cytometry (2016): 42–56

  • Immuno-oncology

    • Pretreatment innate cell populations and CD4 T cells in blood are associated with response to immune checkpoint blockade in melanoma patients
      Pirozyan, M.R., McGuire, H.M., Emran, A.A. et al. Frontiers in Immunology (2020): doi: 10.3389/fimmu.2020.00372.
    • Combination of PD1 inhibitor and OX40 agonist induces tumor rejection and immune memory in mouse models of pancreatic cancer
      Ma, Y., Li, J., Wang, H. et al. Gastroenterology (2020): 30339-5.
    • Multipanel mass cytometry reveals anti–PD-1 therapy–mediated B and T cell compartment remodeling in tumor-draining lymph nodes
      Ho, W.J., Yarchoan, M., Charmsaz, S. et al. Journal of Clinical Investigation Insight (2020): e132286
    • Persistence of adoptively transferred T cells with a kinetically engineered IL-2 receptor agonist
      Parisi, G., Saco, J.D., Salazar, F.B. et al. Nature Communications (2020): 660
    • Combined inhibition of MDM2 and Bcr-Abl tyrosine kinase targets chronic myeloid leukemia stem/progenitor cells in a murine model
      Carter, B.Z., Mak, P.Y., Mu, H. et al. Haematologica (2019): haematol.2019.219261
    • Potent efficacy of MCL-1 inhibitor-based therapies in preclinical models of mantle cell lymphoma
      Dengler, M.A., Teh, C.E., Thijssen, R., et al. Oncogene (2019): 2,009–23
    • Multi-panel mass cytometry reveals anti-PD1 therapy-mediated B and T cell compartment remodeling in tumor-draining lymph nodes
      Ho, W.J., Yarchoan, M., Charmsaz, S., et al. JCI Insight (2019): 132286
    • Loss of BAP1 expression is associated with an immunosuppressive microenvironment in uveal melanoma, with implications for immunotherapy development
      Figueiredo, C.R., Kalirai, H., Sacco, J.J. et al. Journal of Pathology (2020): 420–39
    • Deep profiling of apoptotic pathways with mass cytometry identifies a synergistic drug combination for killing myeloma cells
      Teh, C.E., Gong, J-N., Segal, D. et al. Cell Death & Differentiation (2020): DOI: 10.1038/s41418-020-0498-z
    • B cells and tertiary lymphoid structures promote immunotherapy response
      Helmink, B.A., Reddy, S.M., Gao, J. et al. Nature (2020): 549–55
    • Single-cell proteomic profiling identifies combined AXL and JAK1 inhibition as a novel therapeutic strategy for lung cancer
      Taverna, J.A., Hung, C-N., DeArmond, D.T. et al. Cancer Research (2020): DOI: 10.1158/0008-5472.CAN-19-3183
    • Single-cell immune competency signatures associate with survival in phase 2 GVAX and CRS-207 randomized studies in metastatic pancreatic cancer patients
      Nair, N., Chen, S-Y., Lemmens, E. et al. Cancer Immunology Research (2020): DOI: 10.1158/2326-6066.CIR-19-0650
    • A novel GUCY2C-CD3 T cell engaging bispecific construct (PF-07062119) for the treatment of gastrointestinal cancers
      Mathur, D., Root, A.R., Bugaj-Gaweda, B. et al. Clinical Cancer Research (2020): DOI: 10.1158/1078-0432.CCR-19-3275
    • AXL targeting abrogates autophagic flux and induces immunogenic cell death in drug resistant cancer cells
      Lotsberg, M.L., Wnuk-Lipinska, K., Terry, S. et al. Journal of Thoracic Oncology (2020): DOI: 10.1016/j.jtho.2020.01.015
    • Macrophage Syk–PI3Kγ inhibits antitumor immunity: SRX3207, a novel dual Syk–PI3K inhibitory chemotype relieves tumor immunosuppression
      Joshi, S., Liu, K.X., Zulcic,M. et al. Molecular Cancer Therapeutics (2020): DOI: 10.1158/1535-7163.MCT-19-0947
    • Modulation of phospho-proteins by interferon-alpha and valproic acid in acute myeloid leukemia
      Forthun, R.B., Hellesoy, M., Sulen, A. et al. Journal of Cancer Research and Clinical Oncology (2019): 1,729–49
    • Expression analysis and significance of PD-1, LAG-3, and TIM-3 in human non-small cell lung cancer using spatially resolved and multiparametric single-cell analysis
      Datar, I., Sanmamed, M.F., Wang, J. et al. Clinical Cancer Research (2019): 4663–73
    • Systemic clinical tumor regressions and potentiation of PD1 blockade with in situ vaccination
      Hammerich, L., Marron, T.U., Upadhyay, R. et al. Nature Medicine (2019): 814–24
    • CD4+ T-cell immunity in the peripheral blood correlates with response to anti-PD-1 therapy
      Kagamu, H., Kitano, S., Yamaguchi, O. et al. Cancer Immunology Research (2019): 334–44
    • Immune profiling of human tumors identifies CD73 as a combinatorial target in glioblastoma
      Goswami, S., Walle, T., Cornish, A.E., et al. Nature Medicine (2019): 39–46
    • PAK4 inhibition improves PD-1 blockade immunotherapy
      Abril-Rodriguez, G., Torrejon, D.Y., Liu, W., et al. Nature Cancer (2019): 46–58
    • The potential application of PD1 blockade therapy for early stage biliary tract cancer
      Umemoto, K., Togashi, Y., Arai, Y., et al. International Immunology (2019): doi: 10.1093/intimm/dxz080
    • KRAS-IRF2 axis drives immune suppression and immune therapy resistance in colorectal cancer
      Liao, W., Overman, M.J., Boutin, A.T., et al. Cancer Cell (2019): 559-572.e7
    • Immune activation underlies a sustained clinical response to Yttrium-90 radioembolisation in hepatocellular carcinoma
      Chew, V., Lee, Y.H., Nasir, N.J.M. et al. Gut (2018): 335–46
    • Switchable CAR-T cells mediate remission in metastatic pancreatic ductal adenocarcinoma
      Raj, D., Yang, M.H., Rodgers, D. et al. Gut (2018): 1052–64
    • Idarubicin, cytarabine, and nivolumab in patients with newly diagnosed acute myeloid leukaemia or high-risk myelodysplastic syndrome: a single-arm, phase 2 study
      Ravandi, F., Assi, R., Daver, N. et al. The Lancet Haematology (2019): e480–8
    • Systemic immunity is required for effective cancer immunotherapy
      Spitzer, M.H., Carmi, Y., Reticker-Flynn, N.E. et al. Cell (2017): 487–502.e15
    • Multiplexed (18-Plex) Measurement of Signaling Targets and Cytotoxic T Cells in Trastuzumab-Treated Patients using Imaging Mass Cytometry
      Carvajal-Hausdorf, D.E., Patsenker, J., Stanton, K.P. et al. Clinical Cancer Research (2019): 3,054–62
    • Engineering γδT cells limits tonic signaling associated with chimeric antigen receptors
      Fisher, J., Sharma, R., Don, D.W. et al. Science Signaling (2019): eaax1872
    • Phase I/II trial of the CXCR4 inhibitor plerixafor in combination with bortezomib as a chemosensitization strategy in relapsed/refractory multiple myeloma
      Ghobrial, I.M., Liu, C.J., Zavidij, O. et al. American Journal of Hematology (2019): 1,244–53
    • In vivo CRISPR screening in CD8 T cells with AAV–Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma
      Ye, L., Park, J.J., Dong, M.B. et al. Nature Biotechnology (2019): 1,302–13
    • Pembrolizumab for anaplastic thyroid cancer: a case study
      Aghajani, M.J., Cooper, A., McGuire, H. et al. Cancer Immunology, Immunotherapy (2019): 1–14
    • Combination anti–CTLA-4 plus anti–PD-1 checkpoint blockade utilizes cellular mechanisms partially distinct from monotherapies
      Wei, S.C., Anang, N.A.S., Sharma, R. et al. Proceedings of the National Academy of Sciences of the United States of America (2019): 22,699–709
    • Metronomic capecitabine as an immune modulator in glioblastoma patients reduces myeloid-derived suppressor cells
      Peereboom, D.M., Alban, T.J., Grabowski, M.M. et al. JCI Insight (2019): 130,748
    • Role of CXCR3 signaling in response to anti-PD-1 therapy
      Han, X., Wang, Y., Sun, J. et al. EBioMedicine (2019): 30,589–594.
    • Tumor-intrinsic response to IFNγ shapes the tumor microenvironment and anti–PD-1 response in NSCLC
      Bullock, B.L., Kimball, A.K., Poczobutt, J.M. et al. Life Science Alliance (2019): e201900328
    • Mass cytometry dissects T cell heterogeneity in the immune tumor microenvironment of common dysproteinemias at diagnosis and after first line therapies
      Kourelis, T.V., Villasboas, J.C., Jessen, E. et al. Blood Cancer Journal (2019): 72
    • PD-L1 blockade engages tumor-infiltrating lymphocytes to co-express targetable activating and inhibitory receptors
      Beyrend, G., van der Gracht, E., Yilmaz, A. et al. Journal for ImmunoTherapy of Cancer (2019): 217
    • Fibrinogen-like Protein 1 Is a Major Immune Inhibitory Ligand of LAG-3
      Wang, J., Sanmamed, M.F., Datar, I. et al. Cell (2018): 334–47
    • The anatomical location shapes the immune infiltrate in tumors of same etiology and affects survival
      Santegoets, S.J., van Ham, V.J., Ehsan, I. et al. Clinical Cancer Research (2018): 240–52
    • CSF1R inhibitors exhibit anti-tumor activity in acute myeloid leukemia by blocking paracrine signals from support cells
      Edwards, D.K., Watanabe-Smith, K., Rofelty, A. et al. Blood (2018): 588–99
    • High-parameter mass cytometry evaluation of relapsed/refractory multiple myeloma patients treated with daratumumab demonstrates immune modulation as a novel mechanism of action
      Adams, H.C., Stevenart, F., Krejcik, J. et al. Cytometry Part A: Journal of the ISAC (2019): 279–289
    • A pilot trial of the combination of transgenic NY-ESO-1-reactive adoptive transfer therapy with dendritic cell vaccination with or without ipilimumab
      Nowicki, T.S., Berent-Moaz, B., Cheung-Lau, G. et al. Clinical Cancer Research (2019): 2,096–2,108.
    • Concomitant targeting of BCL2 with venetoclax and MAPK signaling with cobimetinib in acute myeloid leukemia models
      Han, L., Zhang, Q., Dail, M. et al. Haematologica (2019): doi: 10.3324/haematol.2018.205534.
    • A novel combination of chemotherapy and immunotherapy controls tumor growth in mice with a human immune system
      Burlion, A., Ramos, R.N., Pukar, K.C. et al. OncoImmunology (2019): 1,596,005.
    • Anti-CTLA-4 immunotherapy does not deplete FOXP3+ regulatory T cells (Tregs) in human cancers
      Sharma, A., Subudhi, S.K., Blando, J. et al. Clinical Cancer Research (2018): 3,468
    • Characterizing human head and neck tumors and cancer cell lines with mass cytometry
      Brodie, T.M., Tosevski, V., Medová, M. Cytometry Part A: Journal of the ISAC (2018): 406–10
    • The FGFR1 V561M Gatekeeper Mutation Drives AZD4547 Resistance Through STAT3 Activation and EMT
      Ryan, M.R., Sohl, C.D., Luo, B. et al. Molecular Cancer Research (2018): 532–43
    • Prevalence and Cellular Distribution of Novel Immune Checkpoint Targets Across Longitudinal Specimens in Treatment-naïve Melanoma Patients: Implications for Clinical Trials
      Edwards, J., Tasker, A., Pires da Silva, I. et al. Clinical Cancer Research (2019): 3,247–58
    • Multidimensional analyses reveal distinct immune microenvironment in hepatitis B virus-related hepatocellular carcinoma
      Lim, C.J., Lee, Y.H., Pan, L. et al. Gut (2018): 916–27
    • A Pilot Trial of the Combination of Transgenic NY-ESO-1-reactive Adoptive Cellular Therapy with Dendritic Cell Vaccination With or Without Ipilimumab
      Nowicki, T.S., Berent-Maoz, B., Cheung-Lau, G.C. et al. Clinical Cancer Research (2018): 2,096–108
    • Comparison of immune infiltrates in melanoma and pancreatic cancer highlights VISTA as a potential target in pancreatic cancer
      Blando, J., Sharma, A., Higa, M.G. et al. Proceedings of the National Academy of Sciences (2019): 1,692–7
    • Neoadjuvant anti-PD-1 immunotherapy promotes a survival benefit with intratumoral and systemic immune responses in recurrent glioblastoma
      Cloughesy, T.F., Mochizuki, A.Y., Orpilla, J.R. et al. Nature Medicine (2019): 477–86
    • Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy
      Gide, T.N., Quek, C., Menzies, A.M. et al. Cancer Cell (2019): 238–55.e6
    • Clonal Deletion of Tumor-Specific T Cells by Interferon-γ Confers Therapeutic Resistance to Combination Immune Checkpoint Blockade
      Pai, C.S., Huang, J.T., Lu, X. et al. Immunity (2019): 477–92
    • The Combination of MEK inhibitor with Immunomodulatory Antibodies Targeting PD-1 and PD-L1 Results in Prolonged Survival in Kras/p53-Driven Lung Cancer
      Lee, J.W., Zhang, Y., Eoh, K.J. et al. Journal of Thoracic Oncology (2019): 1,046–60
    • BETP degradation simultaneously targets acute myelogenous leukemia stem cells and the microenvironment
      Piya, S., Mu, H., Bhattacharya, S. et al. Journal of Clinical Investigation (2019): 120,654
    • Siglec-15 as an immune suppressor and potential target for normalization cancer immunotherapy
      Wang, J., Sun, J., Liu, L.N. et al. Nature Medicine (2019): 656–66
    • Targeting DDR2 enhances tumor response to anti–PD-1 immunotherapy
      Tu, M.M., Lee, F.Y.F., Jones, R.T. et al. Science Advances (2019): eaav2437
    • MET Inhibitors Promote Liver Tumor Evasion of the Immune Response by Stabilizing PDL1
      Li, H., Li, C.W., Li, X. et al. Gastroenterology (2019): 1,848-61
    • Tumor microenvironment modulation enhances immunologic benefit of chemoradiotherapy
      Hanoteau, A., Newton, J.M., Krupar, R. et al. Journal of ImmunoTherapy for Cancer (2019): doi: 10.1186/s40425-018-0485-9.
    • Macrophage migration inhibitory factor regulates U1-snRNP immune complex mediated activation of the NLRP3 inflammasome
      Shin, M.S., Kang, Y., Wahl, E.R. et al. Arthritis and Rheumatology (2018): 109–20
    • High-Dimensional Phenotyping Identifies Age-Emergent Cells in Human Mammary Epithelia
      Pelissier Vatter, F. A., Schapiro, D., Chang, H. et al. Cell Reports (2018): 1,205–19
    • Genetic Inactivation of CD33 in Hematopoietic Stem Cells to Enable CAR T Cell Immunotherapy for Acute Myeloid Leukemia
      Kim, M.Y., Yu, K.R., Kenderian, S.S. et al. Cell (2018): 1,439–53
    • SRC/ABL inhibition disrupts CRLF2-driven signaling to induce cell death in B-cell acute lymphoblastic leukemia
      Sarno, J., Savino, A.M., Buracchi, C. et al. Oncotarget (2018): 22,872–85
    • Anti-PD-1-induced high-grade hepatitis associated with corticosteroid-resistant T cells: a case report
      McGuire, H.M., Shklovskaya, E., Trevillian, P.R. et al. Cancer Immunology, Immunotherapy (2018): 563–73
    • Disruption of Wnt/β-Catenin Exerts Antileukemia Activity and Synergizes with FLT3 Inhibition in FLT3-Mutant Acute Myeloid Leukemia
      Jiang, X., Mak, P.Y., Mu, H. et al. Clinical Cancer Research (2018): 2,417–29
    • Dual PD1/LAG3 immune checkpoint blockade limits tumor development in a murine model of chronic lymphocytic leukemia
      Wierz, M., Pierson, S., Guyonnet, L. et al. Blood (2018): 1,617–21
    • Dynamic molecular monitoring reveals that SWI-SNF mutations mediate resistance to ibrutinib plus venetoclax in mantle cell lymphoma
      Agarwal, R., Chan, Y.C., Tam, C.S. et al. Nature Medicine (2018): 119–29
    • NKG2A Blockade Potentiates CD8 T Cell Immunity Induced by Cancer Vaccines
      van Montfoort, N., Borst, L., Korrer, M.J. et al. Cell (2018): 1,744–55
    • Venetoclax with azacitidine disrupts energy metabolism and targets leukemia stem cells in patients with acute myeloid leukemia
      Pollyea, D.A., Stevens, B.M., Jones, C.L. et al. Nature Medicine (2018): 1,859–66
    • Tumor-specific MHC-II expression drives a unique pattern of resistance to immunotherapy via LAG-3/FCRL6 engagement
      Johnson, D.B., Nixon, M.J., Wang, Y. et al. JCI Insight (2018): e120360
    • Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
      Azizi, E., Carr, A.J., Plitas, G. et al. Cell (2018): 1,293–308
    • Melanoma Immunotherapy: Next-Generation Biomarkers
      Hogan, S.A., Levesque, M.P., Cheng, P.F. Frontiers in Oncology (2018): 178
    • High-dimensional mass cytometry analysis revealed microenvironment complexity in chronic lymphocytic leukemia
      Wierz, M., Janji, B., Berchem, G. et al. OncoImmunology (2018): e1465167
    • Global immune fingerprinting in glioblastoma patient peripheral blood reveals immune-suppression signatures associated with prognosis
      Alban, T.J., Alvarado, A.G., Sorensen, M.D. et al. JCI Insight (2018): e122264
    • Mass cytometry of Hodgkin lymphoma reveals a CD4+ regulatory T-cell-rich and exhausted T-effector microenvironment
      Cader, F.Z., Schackmann, R.C.J., Hu, X. et al. Blood (2018): 825–36
    • T cell-directed IL-17 production by lung granular γδ T cells is coordinated by a novel IL-2 and IL-1β circuit
      Ménoret, A., Buturla, J.A., Xu, M.M. et al. Mucosal Immunology (2018): doi: 10.1038/s41385-018-0037-0
    • Resistance to radiotherapy and PD-L1 blockade is mediated by TIM-3 upregulation and regulatory T-cell infiltration
      Oweida, A., Hararah, M., Phan, A.V. et al. Clinical Cancer Research (2018): DOI: 10.1158/1078-0432.CCR-18-1038
    • Eradication of Triple-Negative Breast Cancer Cells by Targeting Glycosylated PD-L1
      Li, C.W., Lim, S.O., Chung, E.M. et al. Cancer Cell (2018): 187–201.e10
    • Functional screening of FGFR4-driven tumorigenesis identifies PI3K/mTOR inhibition as a therapeutic strategy in rhabdomyosarcoma
      McKinnon, T., Venier, R., Yohe, M. et al. Oncogene (2018): 2,630–44
    • Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse
      Good, Z., Sarno, J., Jager, A. et al. Nature Medicine (2018): 474–83
    • Sensitive and frequent identification of high avidity neo-epitope specific CD8+ T cells in immunotherapy-naive ovarian cancer
      Bobisse, S., Genolet, R., Roberti, A. et al. Nature Communications (2018): 1,092
    • Integrated functional and mass spectrometry-based flow cytometric phenotyping to describe the immune microenvironment in acute myeloid leukemia
      Lamble, A.J., Dietz, M., Laderas, T. et al. Journal of Immunological Methods (2017): 44–52
    • Clinical response to PD-1 blockade correlates with a sub-fraction of peripheral central memory CD4+ T cells in patients with malignant melanoma
      Takeuchi, Y., Tanemura, A., Tada, Y. et al. International Immunology (2018): 13–22
    • High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy
      Krieg, C., Nowicka, M., Guglietta, S. et al. Nature Medicine (2018): 144–53
    • Comprehensive immunoproteogenomic analyses of malignant pleural mesothelioma
      Lee, H.S., Jang, H.J., Choi, J.M. et al. Journal of Clinical Investigation Insight (2018): e98575
    • Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates
      Simoni, Y., Becht, E., Fehlings, M. et al. Nature (2018): 575–9
    • Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells
      Bengsch, B., Ohtani, T., Khan, O. et al. Immunity (2018): 1,029–45
    • Commonly occurring cell subsets in high-grade serous ovarian tumors identified by single-cell mass cytometry
      Gonzalez, V.D., Samusik, N., Chen, T.J. et al. Cell Reports (2018): 1,875–88
    • Technology to watch in 2018: boosting cancer vaccines
      Mardis, E. Nature (2018): 532
    • Immunotherapy-induced sarcoidosis in patients with melanoma treated with PD-1 checkpoint inhibitors: Case series and immunophenotypic analysis
      Lomax, A.J., McGuire, H.M., McNeil, C. et al. International Journal of Rheumatic Diseases (2017): 1,277–85
    • Delineation of an immunosuppressive gradient in hepatocellular carcinoma using high-dimensional proteomic and transcriptomic analyses
      Chew, V., Lai, L., Pan, L. et al. Proceedings of the National Academy of Sciences of the United States of America (2017): E5900–9
    • T-cell invigoration to tumour burden ratio associated with anti-PD-1 response
      Huang, A.C., Postow, M.A., Orlowski, R.J. et al. Nature (2017): 60–5
    • Mitochondrial dysregulation and glycolytic insufficiency functionally impair CD8 T cells infiltrating human renal cell carcinoma
      Siska, P.J., Beckerman, K.E., Mason, F.M. et al. JCI Insight (2017): e93411
    • VISTA is an inhibitory immune checkpoint that is increased after ipilimumab therapy in patients with prostate cancer
      Gao, J., Ward, J.F., Pettaway, C.A. et al. Nature Medicine (2017): 551–5
    • Natural Killer Defective Maturation Is Associated with Adverse Clinical Outcome in Patients with Acute Myeloid Leukemia
      Chretien, A.S., Fauriat, C., Orlanducci, F. et al. Frontiers in Immunology (2017): 573
    • An immune atlas of clear cell renal cell carcinoma
      Chevrier, S., Levine, J.H., Zanotelli, V.R.T. et al. Cell (2017): 736–49
    • Systems immune monitoring in cancer therapy
      Greenplate, A.R., Johnson, D.B., Ferrell, P.B. Jr., Irish, J.M. European Journal of Cancer (2016): 77–84
    • Combined targeting of BCL-2 and BCR-ABL tyrosine kinase eradicates chronic myeloid leukemia stem cells
      Carter, B.Z., Mak, P.Y., Mu, H. et al. Science Translational Medicine (2016): 355ra117

  • Immunology

    • Activation of the TLR signaling pathway in CD8+ T cells counteracts liver endothelial cell-induced T cell tolerance
      Zhang, E., Yan, H., Li, Q. et al. Cellular & Molecular Immunology (2019): 774–6
    • Negative Co-stimulation Constrains T Cell Differentiation by Imposing Boundaries on Possible Cell States
      Wei, S.C., Sharma, R., Anang, N.A.S. et al. Immunity (2019): P1084–98.E10
    • Quantifying the dynamics of hematopoiesis by in vivo IdU pulse-chase, mass cytometry, and mathematical modeling
      Erez, A., Mukherjee, R., and Altan-Bonnet, G. Cytometry Part A (2019): 1,075–84
    • Integrated cross-species analysis identifies a conserved transitional dendritic cell population
      Leylek, R., Alcántara-Hernández, M., Lanzar, Z., et al. Cell Reports (2019): 3,736–50.E8
    • Notch controls urothelial integrity in the mouse bladder
      Paraskevopoulou, V., Bonis, V., Dionellis, V.S. et al. JCI Insight (2020): e133232
    • T-cell exhaustion correlates with improved outcomes in kidney transplant recipients
      Fribourg, M., Anderson, L., Fischman, C. et al. Kidney International (2019): 436–49
    • Subsets of ILC3−ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues
      Cella, M., Gamini, R., Secca, C. et al. Nature Immunology (2019): 980–91
    • Complex mammalian-like haematopoietic system found in a colonial chordate
      Rosental, B., Kowarsky, M., Seita, J. et al. Nature (2018): 425–9
    • Spatiotemporal segregation of human marginal zone and memory B cell populations in lymphoid tissue
      Zhao, Y., Uduman, M., Siu, J.H.Y. et al. Nature Communications (2018): 3,857
    • A genome-wide transcriptomic analysis of protein-coding genes in human blood cells
      Uhlen, M., Karlsson, M.J., Zhong, W., et al. Science (2019): eaax9198
    • Multidimensional analyses of proinsulin peptide-specific regulatory T cells induced by tolerogenic dendritic cells
      Suwandi, J.S., Laban, S., Vass, K., et al. Journal of Autoimmunity (2019): 102361
    • Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy
      Ghaemi, M.S., DiGiulio, D.B., Kévin Contrepois, K. et al. Bioinformatics (2019): 95–103
    • Plasmacytoid dendritic cells develop from Ly6D+ lymphoid progenitors distinct from the myeloid lineage
      Dress, R.J., Dutertre, C.A., Giladi, A. et al. Nature Immunology (2019): 852–64
    • Single-cell mass cytometry reveals in vivo immunological response to surgical biomaterials
      Wu, H., Han, S., Wu, B. et al. Applied Materials Today (2019): 169–78
    • Analysis of the murine bone marrow hematopoietic system using mass and flow cytometry
      Ashhurst, T.M., Cox, D.A., Smith, A.L. et al. Mass Cytometry: Methods and Protocols (2019): 159–92
    • Picturing polarized myeloid phagocytes and regulatory cells by mass cytometry
      Roussel, M., Bartkowiak, T. and Irish, J.M. Mass Cytometry: Methods and Protocols (2019): 217–26
    • Development of a 2-dimensional atlas of the human kidney with Imaging Mass Cytometry
      Singh, N., Avigan, Z.M., Kliegel, J.A. et al. JCI Insight (2019): e129477
    • Single-cell analysis of human mononuclear phagocytes reveals subset-defining markers and identifies circulating inflammatory dendritic cells
      Dutertre, C.A., Becht, E., Irac, S.E. et al. Immunity (2019): 30,334–6.
    • Mass cytometry reveals species-specific differences and a new level of complexity for immune cells in the prostate
      Fox, J.J., Navarro, H.I., Hashimoto, T. et al. American Journal of Clinical and Experimental Urology (2019): 281–96.
    • Spatiotemporal immune zonation of the human kidney
      Stewart, B.J., Ferdinand, J.R., Young, M.D. et al. Science (2019): 1,461–6
    • Highly multiplexed Imaging Mass Cytometry allows visualization of tumor and immune cell interactions of the tumor microenvironment in FFPE tissue sections
      Singh, M., Chaudhry, P., Gerdtsson, E. et al. Blood (2017): 2,751
    • Dietary intake regulates the circulating inflammatory monocyte pool
      Jordan, S., Tung, N., Casanova-Acebes, M. et al. Cell (2019): 1,102–14
    • Maturation of the Human Intestinal Immune System Occurs Early in Fetal Development
      Stras, S.F., Werner. L., Toothaker, J.M. et al. Developmental Cell (2019): 357–73.e5
    • Decoding human fetal liver haematopoiesis
      Popescu, D.M, Botting, R.A., Stephenson, E. et al. Nature (2019): 365–71
    • Early-life compartmentalization of immune cells in human fetal tissues revealed by high-dimensional mass cytometry
      Li, N., van Unen, V., Guo, N. et al. Frontiers in Immunology (2019): 1,932
    • Increased T cell differentiation and cytolytic function in Bangladeshi compared to American children
      Wagar, L.E., Bolen, C.R., Sigal, N. et al. Frontiers in Immunology (2019): doi: 10.3389/fimmu.2019.02239
    • Circulating B cells with memory and antibody-secreting phenotypes are detectable in pediatric kidney transplant recipients before the development of antibody-mediated rejection
      Fischman, C., Fribourg, M., Ginevri, F. et al. Transplantation Direct (2019): e481
    • Effect of CTLA4-Ig (abatacept) treatment on T cells and B cells in peripheral blood of patients with polymyositis and dermatomyositis
      Tang, Q., Ramsköld, D., Krystufkova, O. et al. Scandinavian Journal of Immunology (2018): 89
    • Differential control of human Treg and effector T cells in tumor immunity by Fc-engineered anti-CTLA-4 antibody
      Ha, D., Tanaka, A., Kibayashi, T. et al. PNAS (2018): 609–18
    • Human regulatory T cells undergo self-inflicted damage via granzyme pathways upon activation
      Sula Karreci, E., Eskandari, S.K., Dotiwala, F. et al. JCI Insight (2017): e91599
    • T cells expressing chimeric antigen receptor promote immune tolerance
      Pierini, A., Iliopoulou, B.P., Peiris, H. et al. JCI Insight (2017): e92865
    • In silico modeling identifies CD45 as a regulator of IL-2 synergy in the NKG2D-mediated activation of immature human NK cells
      Mukherjee, S., Jensen, H., Stewart, W. et al. Science Signaling (2017): eaai9062
    • Identification and analysis of islet antigen-specific CD8+ T cells with T cell libraries
      Ogura, H., Preston-Hurlburt, P., Perdigoto, A.L. et al. Journal of Immunology (2018): 1,662–70
    • Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry
      Oetjen, K.A., Lindblad, K.E., Goswami, M. et al. JCI Insight (2018): e124928
    • Gene regulatory programs conferring phenotypic identities to human NK cells
      Collins, P.L., Cella, M., Porter, S.I. et al. Cell (2018): 348-360.e12
    • Opposing Roles of Dendritic Cell Subsets in Experimental GN
      Brähler, S., Zinselmeyer, B.H., Raju, S. et al. Journal of the American Society of Nephrology (2018): 138–54
    • CD44 variant isoform 9 emerges in response to injury and contributes to the regeneration of the gastric epithelium
      Bertaux-Skeirik, N., Wunderlich, M., Teal, E. et al. Journal of Pathology (2017): 463–75
    • Preparation of whole bone marrow for mass cytometry analysis of neutrophil-lineage cells
      Zhu, Y.P., Padgett, L., Dinh, H.Q. et al. Journal of Visual Experiments (2019): doi: 10.3791/59617.
    • Mass cytometry reveals systemic and local immune signatures that distinguish inflammatory bowel diseases
      Rubin, S.J.S., Bai, L., Haileselassie, Y. et al. Nature Communications (2019): 2686
    • Direct CD137 costimulation of CD8 T cells promotes retention and innate-like function within nascent atherogenic foci
      Xu, M.M., Ménoret, A., Nicolas, S.E. et al. American Journal of Physiology Heart and Circulatory Physiology (2019): H1,480–H1,494.
    • Fibro-adipogenic progenitors of dystrophic mice are insensitive to NOTCH regulation of adipogenesis
      Marinkovic, M., Fuoco, C., Sacco, F. et al. Life Science Alliance (2019): e201900437
    • JunB regulates homeostasis and suppressive functions of effector regulatory T cells
      Koizumi, S.-I., Sasaki,D., Hsieh,T.H. et al. Nature Communications (2018): 5,344
    • Fetal-derived macrophages dominate in adult mammary glands
      Jäppinen, N., Félix, I., Lokka, E. et al. Nature Communications (2019): 281
    • The time-dependent shift in the hepatic graft and recipient macrophage pool following liver transplantation
      Huang, H., Zhang, X., Zhang, C. et al. Cellular & Molecular Immunology (2019): doi:10.1038/s41423-019-0253-x.
    • Differential dynamics of the maternal immune system in healthy pregnancy and preeclampsia
      Han, X., Ghaemi, M.S., Ando, K. et al. Frontiers in Immunology (2019): 1,305
    • Human Lymph Nodes Maintain TCF-1hi Memory T Cells with High Functional Potential and Clonal Diversity throughout Life
      Miron, M., Kumar, B.V., Meng, W. et al. Journal of Immunology (2018): 2,132–40
    • High-dimensional single-cell proteomics analysis identifies immune checkpoint signatures and therapeutic targets in ulcerative colitis
      Fuchs, S., Sawas, N., Staedler, N. et al. European Journal of Immunology (2018): 462–75
    • Penalized Supervised Star Plots: Example Application in Influenza-Specific CD4+ T Cells
      Holmes, T.H., Subrahmanyam, P.B., Wang, W. et al. Viral Immunology (2019): 102–9
    • Human Germinal Center B Cells Differ from Naïve and Memory B Cells in CD40 Expression and CD40L-Induced Signaling Response
      Huse, K., Wogsland, C.E., Polikowsky, H.G. et al. Cytometry Part A (2019): 442–9
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    • Clinical recovery from surgery correlates with single-cell immune signatures
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  • Immunophenotyping

    • Distinctive phenotypes and functions of innate lymphoid cells in human decidua during early pregnancy
      Huhn, O., Ivarsson, M.A., Gardner, L. et al. Nature Communications (2020): 381
    • Mapping of γ/δ T cells reveals Vδ2+ T cells resistance to senescence
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    • Multi-parameter immune profling of peripheral blood mononuclear cells by multiplexed single-cell mass cytometry in patients with early multiple sclerosis
      Böttcher, C., Fernández-Zapata, C., Schlickeiser, S. et al. Scientific Reports (2019): 19471
    • T-cell phenotyping uncovers systemic features of atopic dermatitis and psoriasis
      Farrera, C., Melchiotti, R., Petrov, N., et al. Journal of Allergy and Clinical Immunology (2019): 31623–9
    • Multi‐site reproducibility of a human immunophenotyping assay in whole blood and peripheral blood mononuclear cells preparations using CyTOF technology coupled with Maxpar Pathsetter, an automated data analysis system
      Bagwell, C.B., Hunsberger, B., Hill, B., et al. Cytometry Part B Clinical Cytometry (2019): DOI: 10.1002/cyto.b.21858
    • Distinguishing human peripheral blood CD16+ myeloid cells based on phenotypic characteristics
      Fromm, P.D., Silveira, P.A., Hsu, J.L., et al. Journal of Leukocyte Biology (2019): 323-339
    • Mass cytometry reveals global immune remodeling with multi-lineage hypersensitivity to Type I interferon in Down syndrome
      Waugh, K.A., Araya, P., Pandey, A., et al. Cell Reports (2019): 1,893-1,908.e4
    • A high-resolution mass cytometry analysis reveals a delay of cytokines production after TLR4 or TLR7/8 engagements in HIV-1 infected humans
      Leite Pereira, A., Tchitchek, N., Marcos Lopez, E. et al. Cytokine (2018): 97–105
    • Single-cell immune landscape of human atherosclerotic plaques
      Fernandez, D.M., Rahman, A.H., Fernandez, N.F. et al. Nature Medicine (2019): 1,576–88
    • Short-term sleep deprivation in mice induces B cell migration to the brain compartment
      Korin, B., Avraham, S., Azulay-Debby, H. et al. Sleep (2019): doi:10.1093/sleep/zsz222
    • Practical limitations of monocyte subset repartitioning by multiparametric flow cytometry in chronic myelomonocytic leukemia
      Pophali, P.A., Timm, M.M., Mangaonkar, A.A. et al. Blood Cancer Journal (2019): 65
    • Laboratory mice born to wild mice have natural microbiota and model human immune responses
      Rosshart, S.P., Herz, J., Vassalo, B.G. et al. Science (2019): DOI: 10.1126/science.aaw4361
    • Human microglia regional heterogeneity and phenotypes determined by multiplexed single-cell mass cytometry
      Böttcher, C., Schlickeiser, S., Sneeboer, M.A.M. et al. Nature Neuroscience (2018): 78-90
    • High-dimensional single-cell analysis reveals the immune signature of narcolepsy
      Hartmann, F.J., Bernard-Valnet, R., Quériault, C. et al. Journal of Experimental Medicine (2017): 2,621–33
    • High-Dimensional Single-Cell Mapping of Central Nervous System Immune Cells Reveals Distinct Myeloid Subsets in Health, Aging, and Disease
      Mrdjen, D., Pavlovic, A., Hartmann, F.J. et al. Immunity (2018): 380–95
    • Comprehensive immune monitoring of clinical trials to advance human immunotherapy
      Hartmann, F.J., Babdor, J., Gherardini, P.F. et al. Cell Reports (2019): 819-831.E4
    • A unique presentation of infantile-onset colitis and eosinophilic disease without recurrent infections resulting from a novel homozygous CARMIL2 variant
      Kurolap, A., Adiv, O.E., Konnikova, L. et al. Journal of Clinical Immunology (2019): 430-439
    • Validation of CyTOF® against flow cytometry for immunological studies and monitoring of human cancer clinical trials
      Gadalla, R., Noamani, B., MacLeod, B.L. et al. Frontiers in Oncology (2019): 415
    • OMIP-054: Broad Immune Phenotyping of Innate and Adaptive Leukocytes in the Brain, Spleen, and Bone Marrow of an Orthotopic Murine Glioblastoma Model by Mass Cytometry
      Dusoswa, S.A., Verhoeff, J., Garcia-Vallejo, J.J. Cytometry Part A (2019): 422-6
    • Expansion and activation of distinct central memory T lymphocyte subsets in complex regional pain syndrome
      Russo, M.A., Fiore, N.T., van Vreden, C. et al. Journal of Neuroinflammation (2019): doi: 10.1186/s12974-019-1449-9
    • Systems-level immune monitoring by mass cytometry
      Lakshmikanth, T., Brodin, P. Methods in Molecular Biology (2019): doi: 10.1007/978-1-4939-8979-9_3
    • A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring
      Alpert ,A., Pickman, Y., Leipold M. et al. Nature Medicine (2019): 487-95
    • Human Monocyte Heterogeneity as Revealed by High-Dimensional Mass Cytometry
      Hamers, A.A.J., Dinh, H.Q., Thomas, G.D. et al. Arteriosclerosis, Thrombosis, and Vascular Biology (2019): 25–36
    • Maturing human CD127+ CCR7+ PDL1+ dendritic cells express AIRE in the absence of tissue restricted antigens
      Fergusson, J.R., Morgan, M., Bruchard, M. et al. Frontiers in Immunology (2018): doi: 10.3389/fimmu.2018.02902
    • Heterogeneity of circulating CD8 T-cells specific to islet, neo-antigen and virus in patients with type 1 diabetes mellitus
      Laban, S., Suwandi, J.S., van Unen, V. et al. PLoS One (2018): e0200818
    • CD56 Expression Marks Human Group 2 Innate Lymphoid Cell Divergence from a Shared NK Cell and Group 3 Innate Lymphoid Cell Developmental Pathway
      Chen, L., Youssef, Y., Robinson, C. et al. Immunity (2018): 464-76
    • Single-cell Analysis of Immunophenotype and Cytokine Production in Peripheral Whole Blood via Mass Cytometry
      Baxter, R.M., Kong, D.S., Garcia-Perez, J.E. et al. Journal of Visualized Experiments (2018): doi: 10.3791/57780
    • Circulating Endothelial Progenitor Cells Present an Inflammatory Phenotype and Function in Patients With Alcoholic Liver Cirrhosis
      Kaur, S., Seghal, R., Shastry, S.M. et al. Frontiers in Physiology (2018): doi: 10.3389/fphys.2018.00556
    • Single-cell RNA sequencing to explore immune cell heterogeneity
      Papalexi, E., Satija, R. Nature Reviews Immunology (2018): 35-45
    • Deep Profiling of the CD8+ T cell Compartment identifies Activated cell subsets and Multifunctional Responses Associated with Control of Cytomegalovirus Viremia
      Ferreira, V.H., Kumar, D., Humar, A. Transplantation (2018): doi: 10.1097/TP.0000000000002373
    • Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging
      Cheung, P., Vallania, F., Warsinske, H.C. et al. Cell (2018): 1,385-97
    • Single-cell analysis identifies a CD33+ subset of human cord blood cells with high regenerative potential
      Knapp, D.J.H.F., Hammond, C.A., Hui, T. et al. Nature Cell Biology (2018): 710-20
    • Cytometry TOF identifies alveolar macrophage subtypes in acute respiratory distress syndrome
      Morrell, E.D., Wiedeman, A., Long, S.A. et al. JCI Insight (2018): doi: 10.1172/jci.insight.99281
    • Prime and Boost Vaccination Elicit a Distinct Innate Myeloid Cell Immune Response
      Palgen, J.L., Tchitchek, N., Elhmouzi-Younes, J. et al. Scientific Reports (2018): https://doi.org/10.1038/s41598-018-21222-2
    • Proteomic approaches for novel systemic lupus erythematosus (SLE) drug discovery
      Li, Y., Wu, T. Expert Opinion on Drug Discovery (2018): 765-77
    • Immune cell census in murine atherosclerosis: cytometry by time of flight illuminates vascular myeloid cell diversity
      Cole, J.E., Park, I., Ahern, D. et al. Cardiovascular Research (2018): 1,360–71
    • Identity and Diversity of Human Peripheral Th and T Regulatory Cells Defined by Single-Cell Mass Cytometry
      Kunicki, M.A., Amaya Hernandez, L.C., Davis, K.L. et al. Journal of Immunology (2018): 336–46
    • Atlas of the immune cell repertoire in mouse atherosclerosis defined by single-cell RNA-sequencing and mass cytometry
      Winkels, H., Ehinger, E., Vassallo, M. et al. Circulation Research (2018): CIRCRESAHA-117
    • Deep Immune Profiling of an Arginine-Enriched Nutritional Intervention in Patients Undergoing Surgery
      Aghaeepour, N., Kin, C., Ganio, E.A. et al. Journal of Immunology (2017): 2,171–80
    • Single-cell mass cytometry reveals distinct populations of brain myeloid cells in mouse neuroinflammation and neurodegeneration models
      Ajami, B., Samusik, N., Wieghofer, P. et al. Nature Neuroscience (2018): 541–51
    • MAIT cell clonal expansion and TCR repertoire shaping in human volunteers challenged with Salmonella Paratyphi A
      Howson, L.J., Napolitani, G., Shepherd, D. et al. Nature Communications (2018): 253
    • The receptor repertoire and functional profile of follicular T cells in HIV-infected lymph nodes
      Wendel, B.S., Del Alcazar, D., He, C. et al. Science Immunology (2018): eaan8884
    • Mass cytometry analysis of immune cells in the brain
      Korin, B., Dubovik, T., Rolls, A. Nature Protocols (2018): 377–91
    • Mass cytometry reveals innate lymphoid cell differentiation pathways in the human fetal intestine
      Li, N., van Unen, V., Höllt, T. et al. Journal of Experimental Medicine (2018): 1,383–96
    • Broad immune monitoring and profiling of T cell subsets with mass cytometry
      Brodie, T.M., Tosevski, V. Methods in Molecular Biology (2018): 67–82
    • Application of phospho-CyTOF® to characterize immune activation in patients with sickle cell disease in an ex vivo model of thrombosis
      Glassberg, J., Rahman, A.H., Zafar, M. et al. Journal of Immunological Methods (2017): 11–19
    • CyTOF® measurement of immunocompetence across major immune cell types
      Subrahmanyam, P.B., Maecker, H.T. Current Protocols in Cytometry (2017): 9.54.1–12
    • SCREENING: CyTOF®—the next generation of cell detection
      Cheung, R.K., Utz, P.J. Nature Reviews Rheumatology (2011): 502–3
    • OMIP-034: Comprehensive immune phenotyping of human peripheral leukocytes by mass cytometry for monitoring immunomodulatory therapies
      Baumgart, S., Peddinghaus, A., Schulte-Wrede, U. et al. Cytometry Part A (2016): 34–8
    • In depth comparative phenotyping of blood innate myeloid leukocytes from healthy humans and macaques using mass cytometry
      Elhmouzi-Younes, J., Palgen, J.L., Tchitchek, N. et al. Cytometry Part A (2017): 969–82
    • Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses
      Lavin, Y., Kobayashi, S., Leader, A. et al. Cell (2017): 750-65
    • Continuous immunotypes describe human immune variation and predict diverse responses
      Kaczorowski, K.J., Shekhar, K., Nkulikiyimfura, D. et al. Proceedings of the National Academy of Sciences of the United States of America (2017): E6,097–106
    • Multiparameter single cell profiling of airway inflammatory cells
      Yao, Y., Welp, T., Liu, Q. et al. Cytometry Part B, Clinical Cytometry (2016): 12–20
    • Applying mass cytometry to the analysis of lymphoid populations in transplantation
      Krams, S.M., Schaffert, S., Lau, A.H., Martinez O.M. American Journal of Transplantation (2016): 1,992–9
    • Mass cytometry reveals a distinct immunoprofile of operational tolerance in pediatric liver transplantation
      Lau, A.H., Vitalone, M.J., Hass, K. et al. Pediatric Transplantation (2016): 1,072–80
    • Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy
      Fragiadakis, G.K., Baca, Q.J., Gherardini, P.F. et al. The Journal of Immunology (2016): 4,482–92
    • Emerging single-cell technologies in immunology
      Herderschee, J., Fenwick, C., Pantaleo, G. et al. Journal of Leukocyte Biology (2015): 23–32
    • Highly multiparametric analysis by mass cytometry
      Ornatsky, O., Bandura, D., Baranov, V. et al. Journal of Immunological Methods (2010): 1–20
    • Mass cytometry: single cells, many features
      Spitzer, M.H., Nolan, G.P. Cell (2016): 780–91
    • Patient-specific immune states before surgery are strong correlates of surgical recovery
      Fragiadakis, G.K., Gaudillière, B., Ganio, E.A. et al. Anesthesiology (2015): 1,241–55
    • Mass cytometry as a platform for the discovery of cellular biomarkers to guide effective rheumatic disease therapy
      Nair, N., Mei, H.E., Chen, S.Y. et al. Arthritis Research & Therapy (2015): 127
    • Variation in the human immune system is largely driven by non-heritable influences.
      Brodin, P., Jojic, V., Gao, T. et al. Cell (2015): 37–47
    • Distinct immunologic changes in vivo following combination versus individual PD-1 or CTLA-4 checkpoint blockade in human cancer
      Dhodapkar, K., Verma, R., Sznol, M. et al. Journal for ImmunoTherapy of Cancer (2014): O7
    • Combination therapy with anti-CTLA4 and anti-PD1 leads to distinct immunologic changes in-vivo
      Das, R., Verma, R., Sznol, M. et al. Journal of Immunology (2015): 950–9
    • Human NK cell repertoire diversity reflects immune experience and correlates with viral susceptibility
      Strauss-Albee, D.M., Fukuyama, J., Liang, E.C. et al. Science Translational Medicine (2015): 297ra115
    • Decoupling of Tumor-Initiating Activity from Stable Immunophenotype In HoxA9-Meis1 Driven AML
      Gibbs, K.D., Jager, A., Crespo, O. et al. Cell Stem Cell (2013): 210–7
    • Multicenter Systems Analysis of Human Blood Reveals Immature Neutrophils in Males and During Pregnancy
      Blazkova, J., Gupta, S., Liu, Y. et al. Journal of Immunology (2017): 2,479–88
    • Targeting YAP-dependent MDSC infiltration impairs tumor progression
      Wang, G., Lu, X., Dey, P. et al. Cancer Discovery (2016): 80–95
    • Immune Profiles to Predict Response to Desensitization Therapy in Highly HLA-Sensitized Kidney Transplant Candidates
      Yabu, J.M., Siebert, J.C., Maecker, H.T. PLoS One (2016): e0153355
    • Protein networks and activation of lymphocytes
      Helou, Y.A., Salomon, A.R. Current Opinion in Immunology (2015): 78–85
    • Characterization of lung infection-induced TCRγδ T cell phenotypes by CyTOF mass cytometry
      Wanke-Jellinek, L., Keegan, J.W., Dolan, J.W., Lederer, J.A. Journal of Leukocyte Biology (2015): 483–93
    • Characterizing Phenotypes and Signaling Networks of Single Human Cells by Mass Cytometry
      Leelatian, N., Diggins, K.E., Irish, J.M. Methods in Molecular Biology (2015): 99–113
    • New technologies for autoimmune disease monitoring
      Maecker, H.T., Nolan, G.P., Fathman, C.G. Current Opinion in Endocrinology, Diabetes and Obesity (2010): 322–8

  • Infectious Disease/Microbiology

    • Comprehensive immunoprofiling of pediatric Zika reveals key role for monocytes in the acute phase and no effect of prior dengue virus infection
      Michlmayr, D., Kim, E.-Y., Rahman, A.H. et al. Cell Reports (2020): 107569.
    • Innate and secondary humoral responses are improved by increasing the time between MVA vaccine immunizations
      Palgen, J.-L., Tchitchek, N., Rodriguez-Pozo, A. et al. npj Vaccines (2020): 24.
    • Effects of hepatitis B surface antigen on virus-specific and global T cells in patients with chronic HBV infection
      Le Bert, N., Gill, U.S., Hong, M. et al. Gastroenterology (2020): 30492-3.
    • Transplantation of ACE2- mesenchymal stem cells improves the outcome of patients with COVID-19 pneumonia
      Leng, Z., Zhu, R., Hou, W. et al. Aging and Disease (2020): 216–228
    • Single cell immune profiling of dengue virus patients reveals intact immune responses to Zika virus with enrichment of innate immune signatures
      Zhao, Y., Amodio, M., Vander Wyk, B. et al. PLOS Neglected Tropical Diseases (2020): DOI: 10.1371/journal.pntd.0008112
    • Mapping the extent of heterogeneity of human CCR5+ CD4 T-cells in peripheral blood and lymph nodes
      Zaunders, J., Munier, C.M.L., McGuire, H. et al. AIDS (2020): DOI: 10.1097/QAD.0000000000002503
    • TIGIT is upregulated by HIV-1 infection and marks a highly functional adaptive and mature subset of natural killer cells
      Vendrame, E., Seiler, C., Ranganath, T. et al. AIDS (2020): DOI: 10.1097/QAD.0000000000002488
    • The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system
      Tomic, A., Tomic, I., Dekker, C.L. et al. Scientific Data (2019): 214
    • Zika virus mucosal infection provides protective immunity
      Martínez, L.E., Garcia, G. Jr., Contreras, D. et al. Journal of Virology (2020): DOI: 10.1128/JVI.00067-20
    • Innate and adaptive immune correlates of chronic and self-limiting Epstein-Barr Virus (EBV) DNAemia in solid-organ transplant recipients
      Ferreira, V.H., Batist, J., Humar, A. et al. Transplantation (2020): DOI: 10.1097/TP.0000000000003130
    • Helminth infections drive heterogeneity in human type 2 and regulatory cells
      de Ruiter, K., Jochems, S.P., Tahapary, D.L. et al. Science Translational Medicine (2020): DOI: 10.1126/scitranslmed.aaw3703
    • IRF5 promotes influenza-induced inflammatory responses in human iPSC-derived myeloid cells and murine models
      Forbester, J.L., Clement, M., Wellington, D. et al. Journal of Virology (2020): DOI: 10.1128/JVI.00121-20
    • B cell profiling in malaria reveals expansion and remodelling of CD11c+ B cell subsets
      Sundling, C., Rönnberg, C., Yman, V. et al. JCI Insight (2019): 126492
    • Molecular signatures of dengue virus-specific IL-10/IFN-γ co-producing CD4 T cells and their association with dengue disease
      Tian, Y., Seumois, G., De-Oliveira-Pinto, L.M. et al. Cell Reports (2019): 4482-4495.e4
    • Large-scale HLA tetramer tracking of T cells during dengue infection reveals broad acute activation and differentiation into two memory cell fates
      Chng, M.H.Y., Lim, M.Q., Rouers, A., et al. Immunity (2019): 1,119-1,135.e5
    • Mass cytometry analysis reveals complex cell-state modifications of blood myeloid cells during HIV infection
      Coindre, S., Tchitchek, N., Alaoui, L. et al. Frontiers in Immunology (2019): doi: 10.3389/fimmu.2019.02677
    • A multi-cohort study of the immune factors associated with M. tuberculosis infection outcomes
      Roy Chowdhury, R., Vallania, F., Yang, Q. et al. Nature (2018): 644–48
    • Dengue-specific CD8+ T cell subsets display specialized transcriptomic and TCR profiles
      Tian, Y., Babor, M., Lane, J. et al. Journal of Clinical Investigation (2019): 1,727–41
    • Pregnancy-induced alterations in NK cell phenotype and function
      Le Gars, M., Seiler, C., Kay, A.W. et al. Frontiers in Immunology (2019): 10.3389/fimmu.2019.02469
    • Characterization of leukocytes from HIV-ART patients using combined cytometric profiles of 72 cell markers
      Pereira, A.L., Tchitchek, N., Lambotte, O. et al. Frontiers in Immunology (2019): 1,777
    • Lymph node migratory dendritic cells modulate HIV-1 transcription through PD-1 engagement
      Banga, R., Rebecchini, C., Procopio, F.A. et al. PLOS Pathogens (2019): 10.1371/journal.ppat.1007918
    • Individual liver plasmacytoid dendritic cells are capable of producing IFNα and multiple additional cytokines during chronic HCV infection
      Doyle, E.H., Rahman, A., Aloman, C. et al. PLOS Pathogens (2019): doi: 10.1371/journal.ppat.1007935
    • Innate and adaptive nasal mucosal immune responses following experimental human pneumococcal colonization
      Jochems, S.P., de Ruiter, K., Solórzano, C. et al. Journal of Clinical Investigation (2019): doi: 10.1172/JCI128865
    • Differential induction of IFN-α and modulation of CD112 and CD54 expression govern the magnitude of NK cell IFN-γ response to influenza A viruses
      Kronstad, L.M., Seiler, C., Vergara, R. et al. Journal of Immunology (2018): 2,117-2,131
    • An optimized and validated method for isolation and characterization of lymphocytes from HIV+ human gut biopsies
      Trapecar, M., Khan, S., Roan, N.R., et al. AIDS Research and Human Retroviruses (2017): S31–S39.
    • Host sirtuin 1 regulates mycobacterial immunopathogenesis and represents a therapeutic target against tuberculosis
      Cheung, C.Y., Gutierrez, N.M., Marzuki, M.B. et al. Science Immunology (2017): eaaj1789
    • Life-threatening primary varicella zoster virus infection with haemophagocytic lymphohistiocytosis-like disease in GATA2 haploinsufficiency accompanied by expansion of double negative T-lymphocyte
      Prader, S., Felber, M., Volkmer, B. et al. Frontiers in Immunology (2018): doi: 10.3389/fimmu.2018.02766
    • Mass cytometry reveals the immaturity of circulating neutrophils during SIV infection
      Lemaitre,J., Cosma, A., Desjardins, D. et al. Journal of Innate Immunity (2019): doi: 10.1159/000499841
    • PD1+CCR2+CD8+ T cells infiltrate the central nervous system during acute Japanese Encephalitis Virus infection
      Zhang, F., Qi, L., Li, X. et al. Virologica Sinica (2019): 1-11
    • Altered monocyte and NK cell phenotypes correlate with post-trauma infection
      Seshadri, A., Brat, G.A., Yorkgitis, B.K. et al. Journal of Trauma and Acute Care Surgery (2019): doi: 10.1097/TA.0000000000002264
    • Human natural killer cells mediate adaptive immunity to viral antigens
      Nikzad, R., Angelo, L.S., Aviles-Padilla, K. et al. Journal of Science Immunology (2019): eaat8116
    • Distinct phenotype and function of circulating Vδ1+ and Vδ2+ γδT-cells in acute and chronic hepatitis B
      Chang, K.M, Traum, D., Park, J.J. et al. PLOS Pathogens (2019): e1007715
    • Aedes aegypti AgBR1 antibodies modulate early Zika virus infection of mice
      Uraki, R., Hastings, A.K., Marin-Lopez, A. et al. Nature Microbiology (2019): doi: 10.1038/s41564-019-0385-x
    • Diversity of Salmonella Typhi-responsive CD4 and CD8 T cells before and after Ty21a typhoid vaccination in children and adults
      Rudolph, M.E., McArthur, M.A., Magder, L.S. et al. International Immunology (2019): doi: 10.1093/intimm/dxz011
    • Age-Associated Heterogeneity of Ty21a-Induced T Cell Responses to HLA-E Restricted Salmonella Typhi Antigen Presentation
      Rudolph, M.E., McArthur, M.A., Magder, L.S. et al. Frontiers in Immunology (2019): doi: 10.3389/fimmu.2019.00257
    • Identification of NK Cell Subpopulations That Differentiate HIV-Infected Subject Cohorts with Diverse Levels of Virus Control
      Pohlmeyer, C.W., Gonzalez, V.D., Irrinki, A. et al. Journal of Virology (2019): doi: 10.1128/JVI.01790-18
    • A functional subset of CD8+ T cells during chronic exhaustion is defined by SIRPα expression
      Myers, L.M., Tal, M.C., Torrez Dulgeroff, L.B. et al. Nature Communications (2019): 794
    • Upregulation of Chitinase I in alveolar macrophages of HIV-infected smokers
      Logue, E.C., Neff, C.P., Mack, D.G. et al. Journal of Immunology (2019): 1,363-72
    • Metformin alters human host responses to Mycobacterium tuberculosis in healthy subjects
      Lachmandas, E., Eckold, C., Böhme, J. et al. Journal of Infectious Diseases (2019): doi: 10.1093/infdis/jiz064
    • High-Dimensional Characterization of IL-10 Production and IL-10–Dependent Regulation during Primary Gammaherpesvirus Infection
      Kimball, A.K., Oko, L.M., Kaspar, R.E. et al. ImmunoHorizons (2019): 94-109
    • Multifactorial heterogeneity of virus-specific T cells and association with the progression of human chronic hepatitis B infection
      Cheng, Y., Zhu, Y.O., Becht, E. et al. Science Immunology (2019): doi: 10.1126/sciimmunol.aau6905
    • Mass cytometry identifies distinct CD4+ T cell clusters distinguishing HIV-1-infected patients according to antiretroviral therapy initiation
      Bekele, Y., Lakshmikanth, T., Chen, Y. et al. JCI Insight (2019): doi: 10.1172/jci.insight.125442
    • Allogeneic BK Virus-Specific T Cells for Progressive Multifocal Leukoencephalopathy
      Muftuoglu, M., Olson, A., Marin, D. et al. New England Journal of Medicine (2018): 1,443–51
    • CD32+ and PD-1+ Lymph Node CD4 T Cells Support Persistent HIV-1 Transcription in Treated Aviremic Individuals
      Noto, A., Procopio, F.A., Banga, R. et al. Cell (2018): doi: 10.1128/JVI.00901-18
    • IL-15 regulates susceptibility of CD4+ T cells to HIV infection
      Manganaro, L. Hong, P., Hernandez, M.M. et al. PNAS (2018): E9659-67
    • Identification of functionally primitive and immunophenotypically distinct subpopulations in secondary acute myeloid leukemia by mass cytometry
      Bandyopadhyay, S., Fowles, J.S., Yu, L. et al. Cytometry Part B: Clinical Cytometry (2018): doi: 10.1002/cyto.b.21743
    • Identification of enhanced IFN-γ signaling in polyarticular juvenile idiopathic arthritis with mass cytometry
      Throm, A.A., Moncrieffe, H., Orandi, A.B. et al. JCI Insight (2018): e121544
    • Application and utility of mass cytometry in vaccine development
      Reeves, P.M., Sluder, A.E., Paul, S.R. et al. FASEB Journal (2018): 5–15
    • Anti-α4β7 therapy targets lymphoid aggregates in the gastrointestinal tract of HIV-1–infected individuals
      Uzzan, M., Tokuyama, M., Rosenstein, A.K. et al. Science Translational Medicine (2019): 461
    • A large, international study on post-transplant glomerular diseases: the TANGO project
      Uffing, A., José Pérez-Sáez, M., La Manna, G. et al. BMC Nephrology (2018): 229
    • Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases
      Michlmayr, D., Pak, T.R., Rahman, A.H. et al. Molecular Systems Biology (2018): e7862
    • Role of immune aging in susceptibility to West Nile virus
      Yao, Y., Montgomery, R.R. Methods in Molecular Biology (2016): 235–47
    • The natural killer cell response to West Nile virus in young and old individuals with or without a prior history of infection
      Yao, Y., Strauss-Albee, D.M., Zhou, J.Q. et al. PLoS One (2017): e0172625
    • Impact of CD4+ T Cell Responses on Clinical Outcome following Oral Administration of Wild-Type Enterotoxigenic Escherichia coli in Humans
      McArthur, M.A., Chen, W.H., Magder, L. et al. PLoS Neglected Tropical Diseases (2017): e0005291
    • Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization
      Newell, E.W., Sigal, N., Nair, N. et al. Nature Biotechnology (2013): 623–9
    • The Split Virus Influenza Vaccine rapidly activates immune cells through Fcγ receptors
      O'Gorman, W.E., Huang, H., Wei, Y.L. et al. Vaccine (2014): 5,989–97
    • High-dimensional immune profiling of total and rotavirus VP6-specific intestinal and circulating B cells by mass cytometry
      Nair, N., Newell, E.W., Vollmers, C. et al. Mucosal Immunology (2015): 68–82
    • Activation of Salmonella Typhi-Specific Regulatory T Cells in Typhoid Disease in a Wild-Type S. Typhi Challenge Model
      McArthur, M.A., Fresnay, S., Magder, L.S. et al. PLoS Pathogens (2015): e1004914
    • Brief Report: Chikungunya viral arthritis in the United States: A mimic of seronegative rheumatoid arthritis
      Miner, J.J., Aw Yeang, H.X., Fox, J.M. et al. Arthritis and Rheumatology (2015): 1,214–20
    • A human vaccine strategy based on chimpanzee adenoviral and MVA vectors that primes, boosts, and sustains functional HCV-specific T cell memory
      Swadling, L., Capone, S., Antrobus, R.D. et al. Science Translational Medicine (2014): 261ra153
    • Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes
      Newell, E.W., Sigal, N., Bendall, S.C. et al. Immunity (2012): 142–52
    • Identification of vaccine-altered circulating B cell phenotypes using mass cytometry and a two-step clustering analysis
      Pejoski, D., Tchitchek, N., Rodriguez, P. A. et al. The Journal of Immunology (2016): 4,814–31
    • FHL2 Regulates Natural Killer Cell Development and Activation during Streptococcus pneumoniae Infection
      Baranek, T., Morello, E., Valayer, A. et al. Frontiers in Immunology (2017): 123
    • Single cell mass cytometry reveals remodeling of human T cell phenotypes by varicella zoster virus
      Sen, N., Mukherjee, G., Arvin, A.M. Methods (2015): 85–94
    • High-dimensional CyTOF® analysis of dengue virus-infected human DCs reveals distinct viral signatures
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    • Hepatitis B virus–specific T cells associate with viral control upon nucleos(t)ide-analogue therapy discontinuation
      Rivino, L., Le Bert, N., Gill, U.S. et al. Journal of Clinical Investigation (2018): 668–81
    • Mass cytometric analysis of HIV entry, replication, and remodeling in tissue CD4+ T cells
      Cavrois, M., Banerjee, T., Mukherjee, G. et al. Cell Reports (2017): 984–98
    • Baseline immune profile by CyTOF can predict response to an investigational adjuvanted vaccine in elderly adults
      Lingblom, C.M.D., Kowli, S., Swaminathan, N. et al. Journal of Translational Medicine (2018): 153
    • Adaptive NKG2C+CD57+ Natural Killer Cell and Tim-3 Expression During Viral Infections
      Kared, H., Martelli, S., Tan, S.W. et al. Frontiers in Immunology (2018): 686
    • Mass Cytometry Analysis Reveals the Landscape and Dynamics of CD32a+ CD4+ T Cells From Early HIV Infection to Effective cART
      Coindre, S., Tchichek, N., Alaoui, L. et al. Frontiers in Immunology (2018): doi: 10.3389/fimmu.2018.01217
    • In-depth phenotypic characterization of reticulocyte maturation using mass cytometry
      Thomson-Luque, R., Wang, C., Ntumngia, F.B. et al. Blood Cells, Molecules, and Diseases (2018): 22-33
    • Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses
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    • High-Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune-Checkpoint Cancer Therapy
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    • Pushing the frontiers of T-cell vaccines: accurate measurement of human T-cell responses
      Saade, F., Gorski, S.A., Petrovsky, N. Expert Review of Vaccines (2012): 1,459–70

  • Liquid Biopsy

    • Multiplex protein detection on circulating tumor cells from liquid biopsies using Imaging Mass Cytometry
      Gerdtsson, E., Pore, M., Thiele, J.A. et al. Convergent Science Physical Oncology (2018): 015002

  • Method Development

    • Engineering of nebulized metal–phenolic capsules for controlled pulmonary deposition for controlled pulmonary deposition
      Ju, Y., Cortez-Jugo, C., Chen, J. et al. Advanced Science (2020): 1902650.
    • Mass cytometry and single‐cell RNA‐seq profiling of the heterogeneity in human peripheral blood mononuclear cells interacting with silver nanoparticles
      Ha, M.K., Kwon, S.J., Choi, J.-S. et al. Small (2020): e1907674.
    • Mass cytometric study on the heterogeneity in cellular association and cytotoxicity of silver nanoparticles in primary human immune cells
      Ha, M.K., Choi, J.-S., Kwon, S.J. et al. Environmental Science: Nano (2020): 1102-1114.
    • A carrier strategy for mass cytometry analysis of small numbers of cells
      Jia, X., Zhou, X., Zheng, H. et al. Methods in Molecular Biology (2020): 21-33
    • Metal-encoded polystyrene microbeads as a mass cytometry calibration/normalization standard covering channels from yttrium (89 amu) to bismuth (209 amu)
      Liu, J., Jarzabek, J., Majonis, D. et al. Analytical Chemistry (2020): 999-1,006
    • Macromolecular approach for targeted radioimmunotherapy in non-Hodgkin's lymphoma
      Hee, C., Ho, D., Karton, A., et al. Chemical Communications (2019): 14,506-14,509
    • Signal amplification for Imaging Mass Cytometry
      Rana, R., Gómez-Biagi, R.F., Bassan, J., et al. Bioconjugate Chemistry (2019): 2,805-2,810
    • Ratiometric Barcoding for Mass Cytometry
      Wu, X., DeGottardi, Q., Wu, I.C. et al. Analytical Chemistry (2018): 10,688–94
    • Quantifying Heterogeneity of Individual Organelles in Mixed Populations via Mass Cytometry
      Brown, H.M.G., Arriaga, E.A. Analytical Chemistry (2018): 13,315–21
    • Method for tagging antibodies with metals for mass cytometry experiments
      Chang, S.G. and Guidos, C.J. Mass Cytometry: Methods and Protocols (2019): 47–54
    • Multiplexed profiling of RNA and protein expression signatures in individual cells using flow or mass cytometry
      Duckworth, A.D., Gherardini, P.F., Sykorova, M. et al. Nature Protocols (2019): 901–20
    • Quantitative measurement of cell-nanoparticle interactions using mass cytometry
      Mitchell, A.J., Ivask, A., and Ju, Y. Mass Cytometry: Methods and Protocol (2019): 227–41
    • Lanthanide nanoparticles for high sensitivity multiparameter single cell analysis
      Pichaandi, J., Zhao, G., Bouzekri, A. et al. Chemical Science (2019): 2,965–74
    • Scalable conjugation and characterization of immunoglobulins with stable mass isotope reporters for single-cell mass cytometry analysis
      Hartmann, F.J., Simonds, E.F., Vivanco, N. et al. Mass Cytometry: Methods and Protocols (2019): 55–81
    • Significant interference in mass cytometry from medicinal iodine in human lung
      Keller, B.C., Presti, R.M., Byers, D.E. et al. American Journal of Respiratory Cell and Molecular Biology (2016): 150–1
    • Surface barcoding of live PBMC for multiplexed mass cytometry
      Schulz, A.R. and Mei, H.E. Mass Cytometry: Methods and Protocols (2019): 93–108
    • Automated cell processing for mass cytometry experiments
      Mikes, J., Olin, A., Lakshmikanth, T. et al. Mass Cytometry: Methods and Protocols (2019): 111–23
    • Clickable and High-Sensitivity Metal-Containing Tags for Mass Cytometry
      Allo, B., Lou, X., Bouzekri, A.. et al. Bioconjugate Chemistry (2018): 2,028–38
    • High-parameter immune profiling with CyTOF
      Sahaf, B., Rahman, A., Maecker, H.T. et al. Biomarkers for Immunotherapy of Cancer (2019): 351–68.
    • Live cell barcoding for efficient analysis of small samples by mass cytometry
      Wagar, L.E. Mass Cytometry: Methods and Protocols (2019): 125–35
    • A β-galactosidase probe for the detection of cellular senescence by mass cytometry
      Lumba, M.A., Willis, L.M., Santra, S. et al. Organic & Biomolecular Chemistry (2017): 6,388–92
    • Titration of mass cytometry reagents
      van Vreden, C., Niewold, P., McGuire, H.M. et al. Mass Cytometry: Methods and Protocols (2019): 83–92
    • Simultaneous determination of proteins using an element-tagged immunoassay coupled with ICP-MS detection
      Quinn, Z.A., Baranov, V.I., Tanner, S.D. et al. Journal of Analytical Atomic Spectrometry (2002): 892–96
    • Multiplex MHC class I tetramer combined with intranuclear staining by mass cytometry
      Simoni, Y., Fehlings, M., and Newell, E.W. Mass Cytometry: Methods and Protocols (2019): 147–58.
    • Single-Cell Mass Cytometry of Archived Human Epithelial Tissue for Decoding Cancer Signaling Pathways
      Scurrah, C.R., Simmons, A.J., Lau, K.S. Methods in Molecular Biology (2018): 215–29
    • Mass cytometry enables absolute and fast quantification of silver nanoparticle uptake at the single cell level
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    • Immunophenotyping by mass cytometry
      Behbehani, G.K. Methods in Molecular Biology (2019): 31–51
    • Platelet surface marker analysis by mass cytometry
      Blair, T.A. and Frelinger, A.L. Platelets (2019): 1–8
    • Staining of phosphorylated signalling markers protocol for mass cytometry
      Shinko, D., Ashhurst, T.M., McGuire, H.M. et al. Mass Cytometry: Methods and Protocols (2019): 139–46
    • Whole blood preservation methods alter chemokine receptor detection in mass cytometry experiments
      Sakkestad, S.T., Skavland, J., and Hanevik, K. Journal of Immunological Methods (2019): doi: 10.1016/j.jim.2019.112673
    • A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter‐Instrument Variability of the Helios Mass Cytometer
      Lee, B.H., Kelly, G., Bradford, S. et al. Cytometry Part A (2019): 1,019–30
    • Highly stable and inert complexation of Indium(III) by reinforced cyclam dipicolinate and a bifunctional derivative for bead encoding in mass cytometry
      Grenier, L., Beyler, M., Platas-Iglesias, C. et al. Chemistry (2019): doi: 10.1002/chem.201903969
    • DNA-conjugated gold nanoparticles as high-mass probes in Imaging Mass Cytometry
      Malile, B., Brkic, J., Bouzekri, A. et al. ACS Applied Bio Materials (2019): doi: 10.1021/acsabm.9b00574
    • A metal-chelating polymer for chelating zirconium and its use in mass cytometry
      Cho, H., Liu, P., Pichaandi, J. et al. European Polymer Journal (2019): doi: 10.1016/j.eurpolymj.2019.08.002
    • Glutathione might attenuate cadmium-induced liver oxidative stress and hepatic stellate cell activation
      Ren, L., Qi, K., Zhang, L. et al. Biological Trace Element Research (2019): 443-452.
    • Multidimensional profiling of drug‐treated cells by Imaging Mass Cytometry
      Bouzekri, A., Esch, A., and Ornatsky, O. FEBS Open Bio (2019): doi:10.1002/2211-5463.12692
    • An updated debarcoding tool for mass cytometry with cell type-specific and cell sample-specific stringency adjustment
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    • Analytical figures of merit for a novel tissue imaging system
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    • Single cell level quantification of nanoparticle-cell interactions using mass cytometry
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    • Self-assembled nanoparticles from phenolic derivatives for cancer therapy
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    • Imaging Mass Cytometry
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    • Ruthenium Counterstaining for Imaging Mass Cytometry
      Catena, R., Montuenga, L.M., Bodenmiller, B. Journal of Pathology (2018): 479–84
    • Multiplexed protease assays using element-tagged substrates
      Lathia, U.S., Ornatsky, O., Baranov, V., Nitz, M. Analytical Biochemistry (2011): 157–9
    • Development of inductively coupled plasma-mass spectrometry-based protease assays
      Lathia, U.S., Ornatsky, O., Baranov, V., Nitz, M. Analytical Biochemistry (2010): 93–8
    • ICP-MS-based multiplex profiling of glycoproteins using lectins conjugated to lanthanide-chelating polymers
      Leipold, M.D., Herrera, I., Ornatsky, O. et al. Journal of Proteome Research (2009): 443–9
    • Mass cytometric cell cycle analysis
      Behbehani, G. Mass Cytometry: Methods and Protocols (2019): 193-215
    • Unlabeled competitor antibody to reduce nonlinear signal spillover in mass cytometry
      Sekhri,P., Kim, M.Y., and Behbehani,G.K. Cytometry Part A (2019): doi: 10.1002/cyto.a.23793
    • Stabilizing antibody cocktails for mass cytometry
      Schulz,A.R., Baumgart,S., Schulze,J. et al. Cytometry Part A (2019): doi: 10.1002/cyto.a.23781.
    • Evaluation of mass cytometry in the clinical laboratory
      Ravkov, E.V., Charlton,C.M., Barker, A.P. et al. Cytometry Part B Clinical Cytometry (2019): doi:10.1002/cyto.b.21791
    • Titrating complex mass cytometry panels
      Gullaksen, S.E., Bader, L., Hellesoy, M. et al. Cytometry Part A (2019): doi: 10.1002/cyto.a.23751
    • Isolation and staining of mouse skin keratinocytes for cell cycle specific analysis of cellular protein expression by mass cytometry
      Fernandez, J. and Torchia, E.C. Journal of Visual Experiments (2019): doi:10.3791/59353
    • Osmium-labeled microspheres for bead-based assays in mass cytometry
      Budzinski, L., Schulz, A.R., Baumgart, S. et al. Journal of Immunology (2019): 3,103–3,112
    • TePhe, a tellurium-containing phenylalanine mimic, allows monitoring of protein synthesis in vivo with mass cytometry
      Bassan, J., Willis, L.M. Vellanki, R.N. et al. Proceedings of the National Academy of Sciences (2019): doi: 10.1073/pnas.1821151116
    • Proliferation tracing with single-cell mass cytometry optimizes generation of stem cell memory-like T cells
      Good, Z., Borges, L., Vivanco Gonzalez, N. et al. Nature Biotechnology (2019): 259–66
    • The anatomy of single cell mass cytometry data
      Olsen, L.R., Leipold, M.D., Pedersen, C.B. et al. Cytometry Part A: Journal of the ISAC (2018): 156–72
    • Isotopologous Organotellurium Probes Reveal Dynamic Hypoxia In Vivo with Cellular Resolution
      Edgar, L.J., Vellanki, R.N., McKee, T.D. et al Angewandte Chemie International Edition (2016): 13,159–63
    • In-Depth Characterization of Monocyte-Derived Macrophages using a Mass Cytometry-Based Phagocytosis Assay
      Schulz, D., Severin, Y., Zanotelli, V.R.T. et al. Scientific Reports (2019): 1,925
    • Parallel analysis of tri-molecular biosynthesis with cell identity and function in single cells
      Kimmey, S.C., Borges, L., Baskar, R. et al. Nature Communications (2019):
    • Implementation of Mass Cytometry for Immunoprofiling of Patients with Solid Tumors
      Poláková, I., Pelák, O., Thürner, D. et al. Journal of Immunology Research (2019): doi: 10.1155/2019/6705949
    • A mass-ratiometry-based CD45 barcoding methods for mass cytometry detection
      Meng, H., Warden, A., Zhang, L. et al. SLAS Technology (2019): doi: 10.1177/2472630319834057
    • Optimization of Receptor Occupancy Assays in Mass Cytometry: Standardization Across Channels with QSC Beads
      Bringeland, G.H., Bader, L., Blaser, N. et al. Cytometry Part A (2019): 314-22
    • Metal-isotope-tagged monoclonal antibodies for high-dimensional mass cytometry
      Han, G., Spitzer, M.H., Bendall, S.C. et al. Nature Protocols (2018): 2,121-48
    • Single-Cell Protein Assays: A Review
      Fan, B., Wang, J., Xu, Y. et al. Methods in Molecular Biology (2018): 293-309
    • Mass Spectrometry Imaging and Integration with Other Imaging Modalities for Greater Molecular Understanding of Biological Tissues
      Porta Siegel, T., Hamm, G., Bunch, J. et al. Molecular Imaging and Technology (2018): 888-901
    • Effect of storage time and temperature on cell cycle analysis by mass cytometry
      Devine, R.D., Sekhri, P., Behbehani, G.K. Cytometry Part A: Journal of the ISAC (2018): 1,141-9
    • Methods for high-dimensonal analysis of cells dissociated from cyropreserved synovial tissue
      Donlin, L., Rao, D., Wei, K. et al. Arthritis Research and Therapy (2018): 139
    • Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens
      Wroblewska, A., Dhainaut, M., Ben-Zvi, B. et al. Cell (2018): doi: 10.1016/j.cell.2018.09.022
    • Development of a click-chemistry reagent compatible with mass cytometry
      Shaklee, J., Srivastava, K., Brown, H. et al. Scientific Reports (2018): 6,657
    • Lanthanide-coordinated semiconducting polymer dots used for flow cytometry and mass cytometry
      Wu, X., DeGottardi, Q., Wu, I.C. et al. Angewandte Chemie (2017): 14,908–12
    • Cell cycle analysis by mass cytometry
      Behbehani, G.K. Methods in Molecular Biology (2017): 105–24
    • Synthetically modified viral capsids as versatile carriers for use in antibody-based cell targeting
      ElSohly, A.M., Netirojjanakul, C., Aanei, I.L. et al. Bioconjugate Chemistry (2015): 1,590–6
    • Mass cytometric analysis reveals viable activated caspase-3+ luminal progenitors in the normal adult human mammary gland
      Knapp, D.J.H.F., Kannan, N., Pellacani, D. et al. Cell Reports (2017): 1,116–26
    • A Universal Live Cell Barcoding-Platform for Multiplexed Human Single Cell Analysis
      Hartmann, F.J., Simonds, E.F., Bendall, S.C. Scientific Reports (2018): 10,770
    • Tellurium-based mass cytometry barcode for live and fixed cells
      Willis, L.M., Park, H., Watson, M.W.L. et al. Cytometry Part A: Journal of the ISAC (2018): doi: 10.1002/cyto.a.23495
    • Simultaneous Detection of Protein and mRNA in Jurkat and KG-1a Cells by Mass Cytometry
      Mavropoulos, A., Allo, B., He, M. et al. Cytometry Part A (2017): 1,200–8
    • Advances in Proteomic Techniques for Cytokine Analysis: Focus on Melanoma Research
      Skalnikova, H.K., Cizkova, J., Cervenka, J. et al. International Journal of Molecular Sciences (2017): 2,697
    • Multiplex peptide-MHC tetramer staining using mass cytometry for deep analysis of the influenza-specific T-cell response in mice
      Fehlings, M., Chakarov, S., Simoni, Y. et al. Journal of Immunological Methods (2017): 30–6
    • Aptamer-facilitated mass cytometry
      Mironov, G.G., Bouzekri, A., Watson, J. et al. Analytical and Bioanalytical Chemistry (2018): 3,047–51
    • Comparison of CyTOF^® assays across sites: results of a six-center pilot study
      Leipold, M.D., Obermoser, G., Fenwick, C. et al. Journal of Immunological Methods (2018): 37–43
    • Engineered Tumor-Targeted T Cells Mediate Enhanced Anti-Tumor Efficacy Both Directly and through Activation of the Endogenous Immune System
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    • Phenotyping of live human PBMC using CyTOF® mass cytometry
      Leipold, M.D., Maecker, H.T. Bio-protocol (2015): e1382
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    • Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-α-induced apoptosis in vivo
      Simmons, A.J., Banerjee, A., McKinley, E.T. et al. Molecular Systems Biology (2015): 835
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    • CyTOF® mass cytometry for click proliferation assays
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    • CyTOF® supports efficient detection of immune cell subsets from small samples
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    • An optimized method to measure human FOXP3+ regulatory T cells from multiple tissue types using mass cytometry
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    • xCell: digitally portraying the tissue cellular heterogeneity landscape
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    • High-throughput quantitation of inorganic nanoparticle biodistribution at the single-cell level using mass cytometry
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    • Analysis of Signaling Networks at the Single-Cell Level Using Mass Cytometry
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      Guo, Y., Baumgart, S., Stärk, H.J. et al. Frontiers in Microbiology (2017): 1,326
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    • Highly multiplexed simultaneous detection of RNAs and proteins in single cells
      Frei, A.P., Bava, F.A., Zunder, E.R. et al. Nature Methods (2016): 269–75
    • Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm
      Zunder, E.R., Finck, R., Amir, el-A.D. et al. Nature Protocols (2015): 316–33
    • Organotellurium scaffolds for mass cytometry reagent development
      Park, H., Edgar, L.J., Lumba, M.A. et al. Organic and Biomolecular Chemistry (2015): 7,027–33
    • Barcoding of live human peripheral blood mononuclear cells for multiplexed mass cytometry
      Mei, H.E., Leipold, M.D., Schulz, A.R. et al. Journal of Immunology (2015): 2,022–31
    • Evaluating the efficiency of isotope transmission for improved panel design and a comparison of the detection sensitivities of mass cytometer instruments
      Tricot, S., Meyrand, M., Sammicheli, C. et al. Cytometry, Part A (2015): 357–68
    • Identification of hypoxic cells using an organotellurium tag compatible with mass cytometry
      Edgar, L.J., Vellanki, R.N., Halupa, A. et al. Angewandte Chemie (2014): 11,473–7
    • Metal-Containing Polystyrene Beads as Standards for Mass Cytometry
      Abdelrahman, A.I., Ornatsky, O., Bandura, D. et al. Journal of Analytical Atomic Spectrometry (2010): 260–8
    • Metal-chelating polymers by anionic ring-opening polymerization and their use in quantitative mass cytometry
      Illy, N., Majonis, D., Herrera, I. et al. Biomacromolecules (2012): 2,359–69
    • A platinum-based covalent viability reagent for single-cell mass cytometry
      Fienberg, H.G., Simonds, E.F., Fantl, W.J. et al. Cytometry, Part A (2012): 467–75
    • Flow cytometer with mass spectrometer detection for massively multiplexed single-cell biomarker assay
      Tanner, S.D., Bandura, D.R., Ornatsky, O. et al. Pure and Applied Chemistry (2008): 2,627–41
    • Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining
      Behbehani, G.K., Thom, C., Zunder, E.R. et al. Cytometry, Part A (2014): 1,011–9
    • Normalization of mass cytometry data with bead standards
      Finck, R., Simonds, E.F., Jager, A. et al. Cytometry, Part A (2013): 483–94
    • Single-cell mass cytometry adapted to measurements of the cell cycle
      Behbehani, G.K., Bendall, S.C., Clutter, M.R. et al. Cytometry, Part A (2012): 552–66
    • Improving lanthanide nanocrystal colloidal stability in competitive aqueous buffer solutions using multivalent PEG-phosphonate ligands
      Cao, P., Tong, L., Hou, Y. et al. Langmuir (2012): 12,861–70
    • Effect of pendant group structure on the hydrolytic stability of polyaspartamide polymers under physiological conditions
      Lu, Y., Chau, M., Boyle, A.J. et al. Biomacromolecules (2012): 1,296–306
    • Development of mass cytometry methods for bacterial discrimination
      Leipold, M.D., Ornatsky, O., Baranov, V. et al. Analytical Biochemistry (2011): 1–8
    • Synthesis and mass cytometric analysis of lanthanide-encoded polyelectrolyte microgels
      Lin, W., Ma, X., Qian, J. et al. Langmuir (2011): 7,265–75
    • Surface Functionalization Methods to Enhance Bioconjugation in Metal-Labeled Polystyrene Particles
      Abdelrahman, A.I., Thickett, S.C., Liang, Y. et al. Macromolecules (2011): 4,801–13
    • Element-tagged immunoassay with ICP-MS detection: evaluation and comparison to conventional immunoassays
      Razumienko, E., Ornatsky, O., Kinach, R. et al. Journal of Immunological Methods (2008): 56–63
    • Development of analytical methods for multiplex bio-assay with inductively coupled plasma mass spectrometry
      Ornatsky, O.I., Kinach, R., Bandura, D.R. et al. Journal of Analytical Atomic Spectrometry (2008): 463–9
    • Biocompatible Hybrid Nanogels
      Pich, A., Zhang, F., Shen, L. et al. Small (2008): 2,171–5
    • Multiple cellular antigen detection by ICP-MS
      Ornatsky, O., Baranov, V.I., Bandura, D.R. et al. Journal of Immunological Methods (2006): 68–76
    • Polymer-Based Elemental Tags for Sensitive Bioassays
      Lou, X., Zhang, G., Herrera, I. et al. Angewandte Chemie (2007): 6,111–4
    • Study of cell antigens and intracellular DNA by identification of element-containing labels and metallointercalators using inductively coupled plasma mass spectrometry
      Ornatsky, O.I., Lou, X., Nitz, M. et al. Analytical Chemistry (2008): 2,539–47
    • Lanthanide-containing polymer nanoparticles for biological tagging applications: nonspecific endocytosis and cell adhesion
      Vancaeyzeele, C., Ornatsky, O., Baranov, V. et al. Journal of the American Chemical Society (2007): 13,653–60
    • Synthesis of Uniform NaLnF4 (Ln: Sm to Ho) Nanoparticles for Mass Cytometry
      Tong, L., Lu, E., Pichaandi, J. et al. Journal of Physical Chemistry (2016): 6,269–80
    • Single cell analysis of human tissues and solid tumors with mass cytometry
      Leelatian, N., Doxie, D.B., Greenplate, A.R. et al. Cytometry, Part B (2017): 68–78
    • Barcoding of live human PBMC for multiplexed mass cytometry
      Mei, H.E., Leipold, M.D., Schulz, A.R. et al. The Journal of Immunology (2015): 2,022–31
    • Standardization and quality control for high-dimensional mass cytometry studies of human samples
      Kleinsteuber, K., Corleis, B., Rashidi, N. et al. Cytometry Part A (2016): 903–13
    • Lanthanide-containing polymer microspheres by multiple-stage dispersion polymerization for highly multiplexed bioassays
      Abdelrahman, A.I., Dai, S., Thickett, S.C. et al. Journal of the American Chemical Society (2009): 15,276–83
    • Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry
      Bandura, D.R., Baranov, V.I., Ornatsky, O.I. et al. Analytical Chemistry (2009): 6,813–22
    • Hybrid Imaging Labels: Providing the Link Between Mass Spectrometry-Based Molecular Pathology and Theranostics
      Buckle, T., van der Wal, S., van Malderen, S.J.M. et al. Theranostics (2017): 624–33
    • Brief introduction to mass cytometry
      Cosma, A., Le Grand, R. Medecine/Sciences (2011): 1,072–4
    • Multiparameter Phenotyping of Human PBMCs Using Mass Cytometry
      Leipold, M.D., Newell, E.W., Maecker, H.T. Methods in Molecular Biology (2015): 81–95
    • Enhanced multiplexing in mass cytometry using osmium and ruthenium tetroxide species
      Catena, R., Özcan, A., Zivanovic, N., Bodenmiller, B. Cytometry Part A (2016): 491–7
    • Single-cell gene expression profiling and cell state dynamics: collecting data, correlating data points and connecting the dots
      Marr, C., Zhou, J.X., Huang, S. Current Opinion in Biotechnology (2016): 207–14
    • The potential for elemental analysis in biotechnology
      Baranov, V.I., Quinn, Z.A., Bandura, D.R., Tanner, S.D. Journal of Analytical Atomic Spectrometry (2002): 1,148–52
    • The numerology of T cell functional diversity
      Haining, W.N. Immunity (2012): 10–2
    • A Deep Profiler’s Guide to Cytometry
      Bendall, S.C., Nolan, G.P., Roederer, M., Chattopadhyay, P.K. Trends in Immunology (2012): 323–32
    • Multiplex bio-assay with inductively coupled plasma mass spectrometry: Towards a massively multivariate single-cell technology
      Tanner, S.D., Ornatsky, O., Bandura, D.R., Baranov, V.I. Spectrochimica Acta Part B: Atomic Spectroscopy (2007): 188–95
    • The synthesis and characterization of lanthanide-encoded poly(styrene-co-methacrylic acid) microspheres
      Liang, Y., Abdelrahman, A.I., Baranov, V., Winnik, M.A. Polymer (2011): 5,040–52
    • Curious results with palladium- and platinum-carrying polymers in mass cytometry bioassays and an unexpected application as a dead cell stain
      Majonis, D., Ornatsky, O., Kinach, R., Winnik, M.A. Biomacromolecules (2011): 3,997–4,010
    • The release and extraction of lanthanide ions from metal-encoded poly (styrene-co-methacrylic acid) microspheres
      Liang, Y., Abdelrahman, A.I., Baranov, V., Winnik, M.A. Polymer (2012): 998–1,004
    • A sensitive and quantitative element-tagged immunoassay with ICPMS detection
      Baranov, V.I., Quinn, Z., Bandura, T.R., Tanner, S.D. Analytical Chemistry (2002): 1,629–36
    • Mass cytometry: protocol for daily tuning and running cell samples on a CyTOF mass cytometer
      Leipold, M.D., Maecker, H.T. Journal of Visualized Experiments (2012): e4398
    • Platinum-conjugated antibodies for application in mass cytometry
      Mei, H.E., Leipold, M.D., Maecker, H.T. Cytometry, Part A (2015): 292–300
    • Single-cell methods
      de Souza, N. Nature Methods (2012): 35
    • Immune monitoring technology primer: flow and mass cytometry
      Maecker, H.T., Harari, A. Journal for ImmunoTherapy of Cancer (2015): 44
    • Dual-purpose polymer labels for fluorescent and mass cytometric affinity bioassays
      Majonis, D., Ornatsky, O., Weinrich, D., Winnik, M.A. Biomacromolecules (2013): 1,503–13

  • Neurology

    • Mapping microglia states in the human brain through the integration of high-dimensional techniques
      Sankowski, R., Böttcher, C., Masuda, T., et al. Nature Neuroscience (2019): 2,098-2,110
    • The landscape of myeloid and astrocyte phenotypes in acute multiple sclerosis lesions
      Park, C., Ponath, G., Levine-Ritterman, M. et al. Acta Neuropathologica Communications (2019): 130
    • Pro-inflammatory, IL-17 pathways dominate the architecture of the immunome in pediatric refractory epilepsy
      Kumar, P., Shih, D.C.W., Lim, A. et al. JCI Insight (2019): doi: 10.1172/jci.insight.126337

  • Oncology

    • Organoid cultures from normal and cancer-prone human breast tissues preserve complex epithelial lineages
      Rosenbluth, J.M., Schackmann, R.C.J., Gray, G.K. et al. Nature Communications (2020): 1711.
    • Imaging mass cytometry and multiplatform genomics define the phenogenomic landscape of breast cancer
      Ali, H.R., Jackson, H.W., Zanotelli, Z.R.T. et al. Nature Cancer (2020): 163-175.
    • Mass cytometry defines distinct immune profile in germinal center B-cell lymphomas
      Roussel, M., Lhomme, F., Roe, C.E. et al. Cancer Immunology Immunotherapy (2020): 407-420.
    • The single-cell pathology landscape of breast cancer
      Jackson, H.W., Fischer, J.R., Zanotelli, V.R. et al. Nature (2020): 615-620.
    • Immune cell repertoires in breast cancer patients after adjuvant chemotherapy
      Gustafson, C.E., Jadhav, R., Cao, W. et al. JCI Insight (2020): e134569.
    • Multiplexed single-cell morphometry for hematopathology diagnostics
      Tsai, A.G., Glass, D.R., Juntilla, M. et al. Nature Methods (2020): 408–17
    • High dimensional mass cytometry analysis reveals characteristics of the immunosuppressive microenvironment in diffuse astrocytomas
      Fu, W., Wang, W., Li, H. et al. Frontiers in Oncology (2020): doi: 10.3389/fonc.2020.00078
    • Profiling myelodysplastic syndromes by mass cytometry demonstrates abnormal progenitor cell phenotype and demonstrates abnormal progenitor cell phenotype and differentiation
      Behbehani, G.K., Finck, R., Samusik, N. et al. Cytometry Part B Clinical Cytometry (2020): 131-145.
    • Regulatory T cell depletion alters the tumor microenvironment and accelerates pancreatic carcinogenesis
      Zhang, Y., Lazarus, J., Steele, N.G. et al. Cancer Discovery (2020): doi: 10.1158/2159-8290.
    • Circulating neutrophil subsets in advanced lung cancer patients exhibit unique immune signature and relate to prognosis
      Shaul, M.E., Eyal, O., Guglietta, S. et al. FASEB Journal (2020): 4204-4218
    • IGLV3-21*01 is an inherited risk factor for CLL through the acquisition of a single-point mutation enabling autonomous BCR signaling
      Maity, P.C., Bilal, M., Koning, M.T. et al. Proceedings of the National Academy of Sciences of the United States of America (2020): 4320-4327
    • Cancer-associated fibroblasts promote immunosuppression by inducing ROS-generating monocytic MDSCs in lung squamous cell carcinoma
      Xiang, H., Ramil, C.P., Hai, J. et al. Cancer Immunology Research (2020): 436-450
    • Apatinib exhibits cytotoxicity toward leukemia cells by targeting VEGFR2-mediated prosurvival signaling and angiogenesis
      Deng, M., Zha, J., Zhao, H. et al. Experimental Cell Research (2020): 111934.
    • Phenotyping of tumor infiltrating immune cells using mass-cytometry (CyTOF)
      Maby, P., Corneau, A., and Galon, J. Methods in Enzymology (2020): 339-368
    • Single cell mass cytometry revealed the immunomodulatory effect of cisplatin via downregulation of splenic CD44+, IL-17A+ MDSCs and promotion of circulating IFN-γ+ myeloid cells in the 4T1 metastatic breast cancer model
      Balog, J.A., Hackler, L., Kovács, A.K., et al. International Journal of Molecular Sciences (2019): doi: 10.3390/ijms21010170
    • High‐dimensional single‐cell proteomics analysis reveals the landscape of immune cells and stem‐like cells in renal tumors
      Li, Z., Hu, J., Qin, Z., et al. Journal of Clinical Laboratory Analysis (2019): e23155
    • GCN2 drives macrophage and MDSC function and immunosuppression in the tumor microenvironment
      Halaby, M.J., Hezaveh, K., Lamorte, S., et al. Science Immunology (2019): eaax8189
    • Mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution
      Karacosta, L.G., Anchang, B., Ignatiadis, N. et al. Nature Communications (2019): 5587
    • Targeting the MET receptor tyrosine kinase as a strategy for radiosensitization in loco-regionally advanced head and neck squamous cell carcinoma
      Nisa, L., Francica, P., Giger, R., et al. Molecular Cancer Therapeutics (2019): DOI: 10.1158/1535-7163.MCT-18-1274
    • Application value of CyTOF 2 mass cytometer technology at single-cell level in human gastric cancer cells
      Han, S., Jiang, X., Sun, X-F., et al. Exprimental Cell Research (2019): 111568
    • Mass cytometry reveals a sustained reduction in CD16+ natural killer cells following chemotherapy in colorectal cancer patients
      Shinko, D., McGuire, H.M., Diakos, C.I. et al. Frontiers in Immunology (2019): doi: 10.3389/fimmu.2019.02584
    • Single cell phenotypic profiling of 27 DLBCL cases reveals marked intertumoral and intratumoral heterogeneity
      Nissen, M.D., Kusakabe, M., Wang X. et al. Cytometry Part A (2019): doi: 10.1002/cyto.a.23919
    • A 40-Marker Panel for High Dimensional Characterization of Cancer Immune Microenvironments by Imaging Mass Cytometry
      Ijsselsteijn, M.E., van der Breggen, R., Fariña Sarasqueta, A. et al. Frontiers in Immunology (2019): doi: 10.3389/fimmu.2019.02534
    • High-efficiency CRISPR induction of t(9;11) chromosomal translocations and acute leukemias in human blood stem cells
      Jeong, J., Jager, A., Domizi, P. et al. Blood Advances (2019): 2,825–35
    • Perturbed myoepithelial cell differentiation in BRCA mutation carriers and in ductal carcinoma in situ
      Ding, L., Su, Y., Fassl, A. et al. Nature Communications (2019): 4182
    • Single cell mass cytometry of non-small cell lung cancer cells reveals complexity of in vivo and three-dimensional models over the Petri-dish
      Alföldi, R., Balog, J.A.,, Farago, N. et al. Cells (2019): 1,093
    • Targeting myeloid-derived suppressor cells in combination with primary mammary tumor resection reduces metastatic growth in the lungs
      Bosiljcic, M., Cederberg, R.A., Hamilton, M.J. et al. Breast Cancer Research (2019): 103
    • Skin platinum deposition in colorectal cancer patients following oxaliplatin-based therapy
      Cao, Y., Chang, Q., Zhang, W. et al. Cancer Chemotherapy and Pharmacology (2019): 1-6
    • Cell type-dependent differential activation of ERK by oncogenic KRAS in colon cancer and intestinal epithelium
      Brandt, R., Sell, T., Lüthen, M. et al. Nature Communications (2019): doi: 10.1038/s41467-019-10954-y
    • Mass cytometry discovers two discrete subsets of CD39-Treg which discriminate MGUS from Multiple Myeloma
      Marsh-Wakefield, F., Kruzins, A., McGuire, H.M. et al. Frontiers in Immunology (2019): doi: 10.3389/fimmu.2019.01596
    • Immunocyte profiling using single-cell mass cytometry reveals EpCAM+ CD4+ T cells abnormal in colon cancer
      Zhang, T., Lv, J., Tan, Z. et al. Frontiers in Immunology (2019): doi: 10.3389/fimmu.2019.01571
    • Cross-species single-cell analysis of pancreatic ductal adenocarcinoma reveals antigen-presenting cancer-associated fibroblasts
      Elyada, E., Bolisetty, M., Laise, P. et al. Cancer Discovery (2019): doi: 10.1158/2159-8290.CD-19-0094.
    • Deubiquitination and stabilization of PD-L1 by CSN5
      Lim, S.O., Li, C.W., Xia, W. et al. Cancer Cell (2016): 925-939
    • Biodistribution of cisplatin revealed by imaging mass cytometry identifies extensive collagen binding in tumor and normal tissues
      Chang, Q., Ornatsky, O.I., Siddiqui, I. et al. Scientific Reports (2016): 36,641
    • Single-cell mass cytometry of acute myeloid leukemia and leukemia stem/progenitor cells
      Zeng, Z., Konopleva, M., Andreeff, M. Methods in Molecular Biology (2017): 75–86
    • Establishing high dimensional immune signatures from peripheral blood via mass cytometry in a discovery cohort of stage IV melanoma patients
      Wistuba-Hamprecht, K., Martens, A., Weide, B. et al. Journal of Immunology (2017): 927-936
    • Targeting P-selectin blocks neuroblastoma growth
      Nolo, R., Herbrich, S., Rao, A. et al. Oncotarget (2017): 86,657-86,670
    • Characterization of phosphorus content of biological samples by ICP-DRC-MS: potential tool for cancer research
      Bandura, D.R., Ornatsky, O.I., Liao, L. Journal of Analytical Atomic Spectrometry (2004): 96–100
    • Messenger RNA Detection in Leukemia Cell lines by Novel Metal-Tagged in situ Hybridization using Inductively Coupled Plasma Mass Spectrometry
      Ornatsky, O., Baranov, V.I., Bandura, D.R. et al. Translational Oncogenomics (2006): 1–9
    • Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry
      Schulz, D., Zanotelli, V.R.T., Fischer, J.R. et al. Cell Systems (2018): 25–36
    • Characterization of TRKA signaling in acute myeloid leukemia
      Herbrich, S.M., Kannan, S., Nolo, R.M. et al. Oncotarget (2018): 30,092–105
    • Thrombomodulin expressing monocytes are associated with low risk features in myelodysplastic syndromes and dampen excessive immune activation
      van Leeuwen-Kerkhoff, N., Westers, T.M., Poddighe, P.J. et al. Haematologica (2019): doi: 10.3324/haematol.2019.219303
    • Intramucosal inoculation of squamous cell carcinoma cells in mice for tumor immune profiling and treatment response assessment
      Oweida, A.J., Bhatia, S., Van Court, B. et al. Journal of Visual Experiments (2019): doi: 10.3791/59195.
    • Stromal microenvironment shapes the intratumoral architecture of pancreatic cancer
      Ligorio,M., Sil, S., Malagon-Lopez, J. et al. Cell (2019): 160-175.E27
    • High-dimensional cytometric analysis of colorectal cancer reveals novel mediators of antitumour immunity
      de Vries, N., van Unen, V., Ijsselsteijn, M.E. et al. Gut (2019): doi: 10.1136/gutjnl-2019-318672
    • Mass cytometric functional profiling of acute myeloid leukemia defines cell-cycle and immunophenotypic properties that correlate with known responses to therapy
      Behbehani, G.K., Samusik, N., Bjornson, Z.B. et al. Cancer Discovery (2015): 988–1,003
    • A single-cell atlas of the tumor and immune ecosystem of human breast cancer
      Wagner, J., Rapsomaniki, M.A., Chevrier, S. et al. Cell (2019): 1,330-45
    • High-resolution imaging and single-cell analysis via laser ablation-inductively coupled plasma-mass spectrometry for the determination of membranous receptor expression levels in breast cancer cell lines using receptor-specific hybrid tracers
      Van Acker, T., Buckle, T., Van Malderen, S.J.M. et al. Analytica Chimica Acta (2019): 45-53
    • Control of tumor-associated macrophages and T cells in glioblastoma via AHR and CD39
      Takenaka, M.C., Gabriely, G., Rothhammer, V. et al. Nature Neuroscience (2019): 729-740
    • Analysis of the human kinome and phosphatome by mass cytometry reveals overexpression-induced effects on cancer-related signaling
      Lun, X.K., Szklarczyk, D., Gábor, A. et al. Molecular Cell (2019): 1086-1102.E5
    • The critical role of dysregulated RhoB signaling pathway in radioresistance of colorectal cancer
      Liu, N., Cui, W., Jiang, X. et al. International Journal of Radiation Oncology*Biology*Physics (2019): doi: 10.1016/j.ijrobp.2019.04.021
    • Early alterations in stem-like/marrow-resident T cells and innate and myeloid cells in preneoplastic gammopathy
      Bailur, J.K., McCachren, S.S., Doxie, D.B. et al. JCI Insight (2019): 127807
    • Mass Cytometry Analysis Reveals that Specific Intratumoral CD4+ T Cell Subsets Correlate with Patient Survival in Follicular Lymphoma
      Yang, Z.Z., Kim, H.J., Villasboas, J.C. et al. Cell Reports (2019): doi: 10.1016/j.celrep.2019.01.085
    • Cytometric analysis of cell suspension generated by cavitron ultrasonic surgical aspirator in pediatric brain tumors
      Vaskova, M., Tichy, M., Zamecnik, J. et al. Journal of Neuro-Oncology (2019): 15-25
    • High-Dimensional Mass Cytometric Analysis Reveals an Increase in Effector Regulatory T Cells as a Distinguishing Feature of Colorectal Tumors
      Norton, S.E., Ward-Hartstonge, K.A., McCall, J.L. et al. Journal of Immunology (2019): 1,871-84
    • The Coincidence Between Increasing Age, Immunosuppression, and the Incidence of Patients With Glioblastoma
      Ladomersky, E., Scholtens, D.M., Kocherginsky, M. et al. Frontiers in Pharmacology (2019): doi: 10.3389/fphar.2019.00200
    • Computational Immune Monitoring Reveals Abnormal Double-Negative T Cells Present across Human Tumor Types
      Greenplate, A.R., McClanahan, D.D., Oberholtzer, B.K. et al. Cancer Immunology Research (2019): 86-99
    • IL-8 and CXCR1 expression is associated with cancer stem cell-like properties of clear cell renal cancer
      Corrò, C., Healy, M.E., Engler, S. et al. Journal of Pathology (2019): doi: 10.1002/path.5267
    • Expression of PD-1 by T cells in malignant glioma patients reflects exhaustion and activation
      Davidson, T.B., Lee, A.H., Hsu, M. et al. Cliniical Cancer Research (2018): doi: 10.1158/1078-0432.CCR-18-1176
    • Cdh1 and Pik3ca Mutations Cooperate to Induce Immune-Related Invasive Lobular Carcinoma of the Breast
      An, Y., Adams, J.R., Hollern, D.P. et al. Cell Reports (2018): 702–14
    • Antigen-mediated regulation in monoclonal gammopathies and myeloma
      Nair, S., Sng, J., Boddupalli, C.S. et al. JCI Insight (2018): doi: 10.1172/jci.insight.98259
    • Targeting small molecule drugs to T cells with antibody-directed cell-penetrating gold nanoparticles
      Yang, Y.S., Moynihan, K.D., Bekdemir, A. et al. Biomaterials Science (2018): 240-52
    • Intratumoral HPV16-Specific T Cells Constitute a Type I-Oriented Tumor Microenvironment to Improve Survival in HPV16-Driven Oropharyngeal Cancer
      Welters, M.J.P., Ma., W., Santegoets, S.J.A.M. et al. Clinical Cancer Research (2018): 634-47
    • EPH Profiling of BTIC Populations in Glioblastoma Multiforme Using CyTOF
      Hu, A.X., Adams, J.J., Vora, P. et al. Brain Tumor Stem Cells (2018): 155-68
    • DRUG-NEM: Optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity
      Anchang, B., Davis, K.L., Fienberg, H.G. et al. PNAS (2018): E4294–303
    • Activation of the Receptor Tyrosine Kinase AXL Regulates the Immune Microenvironment in Glioblastoma
      Sadahiro, H., Kang, K.D., Gibson, J.T. et al. Cancer Research (2018): 3,002-13
    • Co-targeting ephrin receptor tyrosine kinases A2 and A3 in cancer stem cells reduces growth of recurrent glioblastoma
      Qazi, M.A., Vora, P., Venugopal, C. et al. Cancer Research (2018): doi: 10.1158/0008-5472.CAN-18-0267
    • Ovarian cancer cells cisplatin sensitization agents selected by mass cytometry target ABCC2 inhibition
      Comsa, E., Nguyen, K.A., Loghin, F. et al. Future Medicinal Chemistry (2018): 1,349-60
    • Regulatory T cells in ovarian cancer are characterized by a highly activated phenotype distinct from that in melanoma
      Toker, A., Nguyen, L.T., Stone, S.C. et al. Clinical Cancer Research (2018): DOI: 10.1158/1078-0432.CCR-18-0554
    • BRAF and MEK inhibitor therapy eliminates Nestin-expressing melanoma cells in human tumors
      Doxie, D.B., Greenplate, A.R., Gandelman, J.S. et al. Pigment Cell and Melanoma Research (2018): doi: 10.1111/pcmr.12712
    • Clonal diversity revealed by morphoproteomic and copy number profiles of single prostate cancer cells at diagnosis
      Malihi, P.D., Morikado, M., Welter, L. et al. Convergent Science Physical Oncology (2018): doi: 10.1088/2057-1739/aaa00b
    • Combined inhibition of β-catenin and Bcr-Abl synergistically targets tyrosine kinase inhibitor-resistant blast crisis chronic myeloid leukemia blasts and progenitors in vitro and in vivo
      Zhou, H., Mak, P.Y., Mu, H. et al. Leukemia (2017): 2,065–74
    • High-dimensional single cell mapping of cerium distribution in the lung immune microenvironment of an active smoker
      Rahman, A.H., Lavin, Y., Kobayashi, S. et al. Cytometry Part B: Clinical Cytometry (2017): doi: 10.1002/cyto.b.21545
    • Cholesterol esterification inhibition and imatinib treatment synergistically inhibit growth of BCR-ABL mutation-independent resistant chronic myelogenous leukemia
      Bandyopadhyay, S., Li, J., Traer, E. et al. PLoS One (2017): e0179558
    • Discovery of human cell selective effector molecules using single cell multiplexed activity metabolomics
      Earl, D.C., Ferrell, P.B. Jr., Leelatian, N. et al. Nature Communications (2018): 39
    • Macrophages orchestrate breast cancer early dissemination and metastasis
      Linde, N., Casanova-Acebes, M., Sosa, M.S. et al. Nature Communications (2018): 21
    • Apatinib exhibits anti-leukemia activity in preclinical models of acute lymphoblastic leukemia
      Deng, M., Zha, J., Jiang, Z. et al. Journal of Translational Medicine (2018): 47
    • Recent advances and opportunities in proteomic analyses of tumour heterogeneity
      Bateman, N.W., Conrads, T.P. The Journal of Pathology (2018): 628–37
    • SOX11 augments BCR signaling to drive MCL-like tumor development
      Kuo, P.Y., Jatiani, S.S., Rahman, A.H. et al. Blood (2018): 2,247–55
    • Deep Profiling of the Immune System of Multiple Myeloma Patients Using Cytometry by Time-of-Flight (CyTOF)
      Smets, T., Stevenaert, F., Adams, H. et al. Methods in Molecular Biology (2018): 47–54
    • Single-cell mass cytometry reveals intracellular survival/proliferative signaling in FLT3-ITD-mutated AML stem/progenitor cells
      Han, L., Qiu, P., Zeng, Z. et al. Cytometry, Part A (2015): 346–56
    • Defining Renal Neoplastic Disease, One Cell at a Time: Mass Cytometry, a New Tool for the Study of Kidney Biology and Disease
      Nelson, P.J., Kretzler, M. American Journal of Kidney Diseases (2017): 758–61
    • Pregnane X receptor is associated with unfavorable survival and induces chemotherapeutic resistance by transcriptional activating multidrug resistance-related protein 3 in colorectal cancer
      Dong, Y., Wang, Z., Xie, G.F. et al. Molecular Cancer (2017): 71
    • Checkpoint blockade immunotherapy reshapes the high-dimensional phenotypic heterogeneity of murine intratumoural neoantigen-specific CD8+ T cells
      Fehlings, M., Simoni, Y., Penny, H.L. et al. Nature Communications (2017): 562
    • Single cell immune profiling by mass cytometry of newly diagnosed chronic phase chronic myeloid leukemia treated with nilotinib
      Gullaksen, S.E., Skavland, J., Gavasso, S. et al. Haematologica 1,361–7
    • Expression of LAG-3 defines exhaustion of intratumoral PD-1+ T cells and correlates with poor outcome in follicular lymphoma
      Yang, Z.Z., Kim, H.J., Villasboas, J.C. et al. Oncotarget (2017): 61,425–39
    • Novel BET protein proteolysis-targeting chimera exerts superior lethal activity than bromodomain inhibitor (BETi) against post-myeloproliferative neoplasm secondary (s) AML cells
      Saenz, D.T., Fiskus, W., Qian, Y. et al. Leukemia (2017): 1,951–61
    • Colony Lysate Arrays for Proteomic Profiling of Drug-Tolerant Persisters of Cancer Cell
      Kume, Kohei, Nishizuka, S.S. Analytical Chemistry (2017): 8,626–31
    • Mass cytometry analysis reveals hyperactive NF Kappa B signaling in myelofibrosis and secondary acute myeloid leukemia
      Fisher, D.A., Malkova, O., Engle, E.K. et al. Leukemia (2017): 1,962–74
    • Phenotypic and functional characterization of a bortezomib-resistant multiple myeloma cell line by flow and mass cytometry
      Baughn, L.B., Sachs, Z., Noble-Orcutt, K.E. et al. Leukemia and Lymphoma (2017): 1,931–40
    • PARP inhibitor upregulates PD-L1 expression and enhances cancer-associated immunosuppression
      Jiao, S., Xia, W., Yamaguchi, H. et al. Clinical Cancer Research (2017): 3,711–20
    • Cytokine-induced memory-like natural killer cells exhibit enhanced responses against myeloid leukemia
      Romee, R., Rosario, M., Berriern-Elliott, M.M. et al. Science Translational Medicine (2016): 357
    • The novel BMI-1 inhibitor PTC596 downregulates MCL-1 and induces p53-independent mitochondrial apoptosis in acute myeloid leukemia progenitor cells
      Nishida, Y., Maeda, A., Kim, M.J. et al. Blood Cancer Journal (2017): e527
    • Overexpression of the human antigen R suppresses the immediate paradoxical proliferation of melanoma cell subpopulations in response to suboptimal BRAF inhibition
      Fernandez, M., Sutterlüty‐Fall, H., Schwärzler, C. et al. Cancer Medicine (2017): 1,652–64
    • Unraveling cell populations in tumors by single-cell mass cytometry
      Di Palma S., Bodenmiller B. Current Opinion in Biotechnology (2015): 122–9
    • Eradication of CML stem cells
      Carter, B.Z., Andreeff, M. Oncoscience (2016): 313–5
    • NRASG12V oncogene facilitates self-renewal in a murine model of acute myelogenous leukemia
      Sachs, Z., LaRue, R.S., Nguyen, H.T. et al. Blood (2014): 3,274–83
    • Dasatinib changes immune cell profiles concomitant with reduced tumor growth in several murine solid tumor models
      Hekim, C., Ilander, M., Yan, J. et al. Cancer Immunology Research (2017): 157–69
    • Mutant IDH1 Downregulates ATM and Alters DNA Repair and Sensitivity to DNA Damage Independent of TET2
      Inoue, S., Li, W.Y., Tseng, A. et al. Cancer Cell (2016): 337–48
    • PD-1 marks dysfunctional regulatory T cells in malignant gliomas
      Lowther, D.E., Goods, B.A., Lucca, L.E. et al. Journal of Clinical Investigation (2016): e85935
    • Single-cell measurement of the uptake, intratumoral distribution and cell cycle effects of cisplatin using mass cytometry
      Chang, Q., Ornatsky, O.I., Koch, C.J. et al. International Journal of Cancer (2015): 1202–9
    • Mass cytometry analysis shows that a novel memory phenotype B cell is expanded in multiple myeloma
      Hansmann, L., Blum, L., Ju, C.H. et al. Cancer Immunology Research (2015): 650–60
    • Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis
      Levine, J.H., Simonds, E.F., Bendall, S.C. et al. Cell (2015): 184–97
    • Myelodysplastic Syndrome Revealed by Systems Immunology in a Melanoma Patient Undergoing Anti-PD-1 Therapy
      Greenplate, A.R., Johnson, D.B., Roussel, M. et al. Cancer Immunology Research (2016): 474–80
    • High-Dimensional Analysis of Acute Myeloid Leukemia Reveals Phenotypic Changes in Persistent Cells during Induction Therapy
      Ferrell, P.B. Jr., Diggins, K.E., Polikowsky, H.G. et al. PLoS One (2016): e0153207
    • Anti-apoptotic ARC protein confers chemoresistance by controlling leukemia-microenvironment interactions through a NFκB/IL1β signaling network
      Carter, B.Z., Mak, P.Y., Chen, Y. et al. Oncotarget (2016): 20,054–67
    • Expansion and Activation of CD103(+) Dendritic Cell Progenitors at the Tumor Site Enhances Tumor Responses to Therapeutic PD-L1 and BRAF Inhibition
      Salmon, H., Idoyaga, J., Rahman, A. et al. Immunity (2016): 924–38
    • Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks
      Simmons, A.J., Scurrah, C.R., McKinley, E.T. et al. Science Signaling (2016): rs11
    • BET protein bromodomain inhibitor-based combinations are highly active against post-myeloproliferative neoplasm secondary AML cells
      Saenz, D.T., Fiskus, W., Manshouri, T. et al. Leukemia (2016): 678–87
    • A Prospective Clinical Trial Combining Radiation Therapy With Systemic Immunotherapy in Metastatic Melanoma
      Hiniker, S.M., Reddy, S.A., Maecker, H.T. et al. International Journal of Radiation Oncology Biology Physics (2016): 578–88
    • Mass cytometry of follicular lymphoma tumors reveals intrinsic heterogeneity in proteins including HLA-DR and a deficit in non-malignant plasmablast and germinal center B cell populations
      Wogsland, C.E., Greenplate, A.R., Kolstad, A. et al. Cytometry Part B Clinical Cytometry (2016): 79–87
    • Human Melanoma-Derived Extracellular Vesicles Regulate Dendritic Cell Maturation
      Maus, R.L.G., Jakub, J.W., Nevala, W.K. et al. Frontiers in Immunology (2017): 358
    • Interlesional diversity of T cell receptors in melanoma with immune checkpoints enriched in tissue-resident memory T cells
      Boddupalli, C.S., Bar, N., Kadaveru, K. et al. JCI Insight (2016): e88955
    • Effect of cryopreservation on delineation of immune cell subpopulations in tumor specimens as determinated by multiparametric single cell mass cytometry analysis
      Kadić, E., Moniz, R.J., Huo, Y. et al. BMC Immunology (2017): 6
    • MLN0128, a novel mTOR kinase inhibitor, disrupts survival signaling and triggers apoptosis in AML and AML stem/ progenitor cells
      Zeng, Z., Wang, R.Y., Qiu, Y.H., et al. Oncotarget (2016): 55,083–97
    • NCR1 Expression Identifies Canine Natural Killer Cell Subsets with Phenotypic Similarity to Human Natural Killer Cells
      Foltz, J.A., Somanchi, S.S., Yang, Y. et al. Frontiers in Immunology (2016): 521
    • Comprehensive characterization of VISTA expression in patients with acute myeloid leukemia
      Lamble, A., Kosaka, Y., Huang, F. et al. Journal of Clinical Oncology (2016): e14546
    • Mass Cytometry: A High-Throughput Platform to Visualize the Heterogeneity of Acute Myeloid Leukemia
      Do, P., Byrd, J.C. Cancer Discovery (2015): 912–4
    • From single cells to deep phenotypes in cancer
      Bendall, S.C., Nolan, G.P. Nature Biotechnology (2012): 639–47
    • From mass cytometry to cancer prognosis
      Winter, D.R., Ledegor, G., Amit, I. Nature Biotechnology (2015): 931–2

  • Review

    • Rigor and reproducibility of cytometry practices for immuno‐oncology: a multifaceted challenge
      Laskowski, T.J., Hazen, A.L., Collazo, R.S. et al. Cytometry Part A (2020): 116-125
    • Peptide‐MHC class I and class II tetramers: From flow to mass cytometry
      Christophersen, A. HLA Immune Response Genetics (2019): DOI: 10.1111/tan.13789
    • Deciphering immunity at high plexity and resolution
      Domínguez Conde, C. and Teichmann, S. Nature Reviews Immunology (2019): 77-78
    • Immune monitoring using mass cytometry and related high-dimensional imaging approaches
      Hartmann, F.J. and Bendall, S.C. Nature Reviews Rheumatology (2020): 87-99
    • Using single-cell technologies to map the human immune system — implications for nephrology
      Stewart, B.J., Ferdinand, J.R., Clatworthy, M.R., et al. Nature Reviews Nephrology (2020): 112-128
    • WS05: How to ensure robustness and reproducibility when using mass cytometry for clinical trials
      Escobar, D.L.B., Estevam, J., Leipold, M., et al. Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2019 Conference Workshops (2019): 1,264-1,268
    • The islets of Langerhans continue to reveal their secrets
      Bonner-Wei, S. Nature Reviews Endocrinology (2019): 73-74
    • Mass cytometry imaging for the study of human diseases – applications and data analysis strategies
      Baharlou, H., Canete, N.P., Cunningham, A.L. et al. Frontiers in Immunology (2019): doi: 10.3389/fimmu.2019.02657
    • Deciphering host immunity to malaria using systems immunology
      Loiseau, C., Cooper, M.M., and Doolan, D.L. (2019): doi: 10.1111/imr.12814
    • Data-driven flow cytometry analysis
      Wang, S. and Brinkman, R.R. Mass Cytometry: Methods and Protocols (2019): 245-265
    • Proteomic tools and new insights for the study of B-cell precursor acute lymphoblastic leukemia
      Citalan-Madrid, A.F., Cabral-Pacheco, G.A., Martinez-de-Villarreal, L.E. et al. Hematology (2019): 637-650
    • Multimodal single-cell approaches shed light on T cell heterogeneity
      Nathan, A., Baglaenko, Y., Fonseka, C.Y. et al. Current Opinion in Immunology (2019): 17-25
    • Importance of multi-parametric evaluation of immune-related T-cell markers in renal cell carcinoma
      Kawashima, A., Uemura, M., and Nonomura, N. Clinical Genitourinary Cancer (2019): doi: 10.1016/j.clgc.2019.07.021.
    • Systems immunology allows a new view on human dendritic cells
      Schultze, J.L. and Aschenbrenner, A.C. Seminars in Cell & Developmental Biology (2019): 15-23.
    • Single-cell high-throughput technologies in cerebrospinal fluid research and diagnostics
      Lanz, T.V., Pröbstel, A.K., Mildenberger, I. et al. Frontiers in Immunology (2019): 1302
    • Human microglia seize the chance to be different
      Brewster, A.L. Epilepsy Currents (2019): 190-192.
    • Advancing systems immunology through data-driven statistical analysis
      Fong, L.E., Muñoz-Rojas, A.R., Miller-Jensen, K. Current Opinion in Biotechnology (2018): 109-115
    • High‐resolution interrogation of biological systems via mass cytometry
      Brown, H.M.G., Kuhns, M.M., and Arriaga, E.A. Proteomics for Biological Discovery (2019): 215-246
    • The role of systems biology approaches in determining molecular signatures for the development of more effective vaccines
      Pezeshki, A., Ovsyannikova, I.G., McKinney, B.A. et al. Expert Review of Vaccines (2019): 253-267
    • An introduction to mass cytometry: fundamentals and applications
      Tanner, S.D., Baranov, V.I., Ornatsky, O.I. et al. Cancer Immunology, Immunotherapy (2013): 955–65
    • New assays for monitoring residual HIV burden in effectively treated individuals
      Strain, M.C, Richman, D.D. Current Opinion in HIV & AIDS (2013): 106–110
    • Higher Throughput Methods of Identifying T Cell Epitopes for Studying Outcomes of Altered Antigen Processing and Presentation
      Newell, E.W. Frontiers in Immunology (2013): 430
    • Inductively coupled plasma mass spectrometry-based immunoassay: a review
      Liu, R., Wu, P., Yang, L. et al. Mass Spectrometry Reviews (2014): 373–93
    • Cracking the code of human T-cell immunity
      Harvey, C.J., Wucherpfennig, K.W. Nature Biotechnology (2013): 609–10
    • Single cell mass cytometry for analysis of immune system functional states
      Bjornson, Z.B., Nolan, G.P., Fantl, W.J. Current Opinion in Immunology (2013): 484–94
    • A practical guide to multiplexed mass cytometry
      Zivanovic, N., Jacobs, A., Bodenmiller, B. Current Topics in Microbiology and Immunology (2014): 95–109
    • High-dimensional analysis of human CD8(+) T cell phenotype, function, and antigen specificity
      Newell, E.W., Lin, W. Current Topics in Microbiology and Immunology (2013): 61–84
    • Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells
      Newell, E.W., Davis, M.M. Nature Biotechnology (2014): 149–57
    • Different subsets of natural killer T cells may vary in their roles in health and disease
      Kumar, V., Delovitch, T.L. Immunology (2014): 321–36
    • Twenty (forward looking) questions
      Hassell, L.A., Wagar, E.A. Journal of Pathology Informatics (2014): 27
    • Mass cytometry to decipher the mechanism of nongenetic drug resistance in cancer
      Fienberg, H.G., Nolan, G.P. Current Topics in Microbiology and Immunology (2014): 85–94
    • Shooting movies of signaling network dynamics with multiparametric cytometry
      Claassen, M. Current Topics in Microbiology and Immunology (2014): 177–89
    • Monitoring the Immune Competence of Cancer Patients to Predict Outcome
      Chang, S., Kohrt, H., Maecker, H.T. Cancer Immunology, Immunotherapy (2014): 713–9
    • The reconstructed natural history of type 1 diabetes mellitus
      Pozzilli, P. and Signore, A. Nature Reviews Endocrinology (2019): 256-257
    • Considerations for immunohistochemistry
      Balaji, S., Li, H., Steen, E. et al. Success in Academic Surgery: Basic Science (2019): 105-144
    • Monitoring of the immune dysfunction in cancer patients
      Santegoets, S.J.A.M., Welters, M.J.P. and van der Burg, S.H. Vaccines (Basel) (2016): 29
    • Retracing the in vivo haematopoietic tree using single-cell methods
      Perié, L. and Duffy, K.R. FEBS Letters (2016): 4,068-4,083
    • Mass cytometry: Blessed with the curse of dimensionality
      Newell, E.W. and Cheng, Y. Nature Immunology (2016): 890-895
    • High standards for high dimensional investigations
      Montgomery, R.R. Cytometry Part A (2016): 886-888
    • Single-cell proteomics: potential implications for cancer diagnostics
      Gavasso, S., Gullaksen, S.E., Skavland, J. et al. Expert Review of Molecular Diagnostics (2016): 579-589
    • Natural killer cell diversity in viral infection: Why and how much?
      Blish, C.A. Pathogens and Immunity (2016): 165-192
    • Single cell proteomics in biomedicine: high-dimensional data acquisition, visualization and analysis
      Su, Y., Shi, Q., and Wei, W. Proteomics (2017): 10
    • Regulatory myeloid cells: an underexplored continent in B-cell lymphomas
      Roussel, M., Irish, J.M., Menard, C. et al. Cancer Immunology Immunotherapy (2017): 1,103-1,111
    • Integral membrane proteins: bottom-up, top-down and structural proteomics
      Karr, U., Simonian, M. and Whitelegge, J.P. Expert Review of Proteomics (2017): 715-723
    • Current advances in highly multiplexed antibody-based single-cell proteomic measurements
      Huang, L., Michael, S.A., Chen, Y. et al. Chemistry an Asian Journal (2017): 1,680-1,691
    • How many subsets of innate lymphoid cells do we need?
      Ealey, K.N. and Koyasu, S. Immunity (2017): 10-13
    • Human immune system variation
      Brodin, P. and Davis. M.M. Nature Reviews Immunology (2017): 21-29
    • Nolan Lab Profiles Small-Molecule Inhibitors Using New Multiplexing Method for DVS Sciences' CyTOF
      Bonislawski, A. Genome Web (2012):
    • Application of single cell sequencing in cancer
      Yu, L., Zhao, H., Meng, L. et al. Single Cell Biomedicine (2018): 135-148
    • Data analysis to modeling to building theory in NK cell biology and beyond: How can computational modeling contribute?
      Das, J., and Lanier., L.L. Journal of Leukocyte Biology (2019): 1,305-1,1317.
    • Setting up mass cytometry in a shared resource lab environment
      Warth, S. and Kunkel, D. Mass Cytometry: Methods and Protocols (2019): 3-11
    • Expanding the clinical cytometry toolbox—Receptor occupancy by mass cytometry
      Huse, K. Cytometry Part A (2019): doi: 10.1002/cyto.a.23784
    • In silico methods for studying T cell biology
      Grzesik, K., Eng, K., Crauste, F. et al. International Review of Cell and Molecular Biology (2019): 265-304
    • The end of omics? High dimensional single cell analysis in precision medicine
      Galli, E., Friebel, E., Ingelfinger, F. et al. European Journal of Immunology (2019): 212-220.
    • CyTOF®: A new tool to decipher the immunomodulatory activity of daratumumab
      Castella, B., Mina, R., and Gay, F. Cytometry Part A (2019): doi: 10.1002/cyto.a.23752
    • Visualization of mass cytometry signal background to enable optimal core panel customization and signal threshold gating
      Au-Yeung, A., Takahashi, C., Mathews, W.R. et al. Mass Cytometry: Methods and Protocols (2019): 35-45
    • Diagnostic tools for inborn errors of human immunity (primary immunodeficiencies and immune dysregulatory diseases)
      Richardson, A.M., Moyer, A.M., Hasadsri, L. et al. Current Allergy and Asthma Reports (2018): 19
    • Meeting the challenges of high-dimensional single-cell data analysis in immunology
      Palit, S., Heuser, C., de Almeida, G.P. et al. Frontiers in Immunology (2019): doi: 10.3389/fimmu.2019.01515.
    • Single-cell technologies in reproductive immunology
      Vazquez, J., Ong, I.M., Stanic, A.K. et al. American Journal of Reproductive Immunology (2019): e13157
    • The spatial and genomic hierarchy of tumor ecosystems revealed by single-cell technologies
      Smith, E.A. and Hodges, H.C. Trends in Cancer (2019): 411-425
    • WS10: Best practices for development and implementation of a CyTOF® core
      Rayanki,R., Ashhurst,T.M., van Vreden, C. et al. Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops (2019): 619–621.
    • The role of proteomics in assessing beta-cell dysfunction and death in type 1 diabetes
      Nakayasu, E.S., Qian, W.J., Evans-Molina, C. et al. Expert Review of Proteomics (2019): 569-582
    • Appreciating what’s unique about every stem cell
      Kruger, R.P. Cell (2019): 1,663-1,665
    • Immunophenotyping of human peripheral blood mononuclear cells by mass cytometry
      Heck, S., Bishop, C.J. and Ellis, R.J. Methods in Molecular Biology. Single Cell Methods: Sequencing and Proteomics (2019): 285-303
    • Single-cell technologies — studying rheumatic diseases one cell at a time
      Cheung, P., Khatri, P., Utz, P.J. et al. Nature Reviews Rheumatology (2019): 340-354
    • Single-cell protein secretion detection and profiling
      Chen, Z., Chen, J.J., and Fan, R. Annual Review of Analytical Chemistry (2019): 431-449
    • Recent trends in analysis of nanoparticles in biological matrices
      Gajdosechova, Z., Zoltan Mester, Z. Analytical and Bioanalytical Chemistry (2019): 1-16
    • Immune Profiling and Precision Medicine in Systemic Lupus Erythematosus
      Nagafuchi, Y., Shoda, H., Fujio, K. Cell (2019): doi: 10.3390/cells8020140
    • Mass spectrometry and proteomics in hematology
      Rolland, D.C.M., Lim, M.S., Elenitoba-Johnson, K.S.J. Seminars in Hematology (2019): 52-7
    • Getting the Most from Your High-Dimensional Cytometry Data
      Olsen, L.R., Pedersen, C.B., Leipold, M.D. et al. Immunity (2019): 535-6
    • Single cell immune profiling in transplantation research
      Higdon, L.E., Schaffert, S., Khatri, P. et al. American Journal of Transplantation (2019): 598
    • Flow Cytometry
      Blair, T., Frelinger III, A.L., Michelson, A.D. et al. Platelets (2019): 627-51
    • Integrative diagnosis of cancer by combining CTCs and associated peripheral blood cells in liquid biopsy
      Zhang, W.W., Rong, Y., Liu, Q. et al. Clinical and Translational Oncology (2018): doi: 10.1007/s12094-018-02004-8
    • Human intestinal lymphoid tissue in time and space
      Spencer, J., Siu, J.H.Y., Montorsi, L. Mucosal Immunology (2018): doi: 10.1038/s41385-018-0120-6
    • Enabling drug discovery and development through single-cell imaging
      Pomerantz, A.K., Sari-Sarraf, F., Grove, K.J. et al. Expert Opinion on Drug Discovery (2018): 1-11
    • Beyond the message: advantages of snapshot proteomics with single-cell mass cytometry in solid tumors
      Mistry, A.M., Greenplate, A.R., Ihrie, R.A. et al. FEBS Journal (2018): doi: 10.1111/febs.14730
    • Ushering in Integrated T Cell Repertoire Profiling in Cancer
      Jiang, N., Schonnesen, A.A., Ma, K.Y. Trends in Cancer (2018): doi: 10.1016/j.trecan.2018.11.005
    • The role of automated cytometry in the new era of cancer immunotherapy
      Danova, M., Torchio, M, Comolli, G. et al. Molecular and Clinical Oncology (2018): 355-61
    • Single-Cell Resolution of T Cell Immune Responses
      Buchholz, V.R., Flossdorf, M. Advances in Immunology (2018): doi: 10.1016/bs.ai.2017.12.001
    • Heterogeneity of Metazoan Cells and Beyond: To Integrative Analysis of Cellular Populations at Single-Cell Level
      Barteneva, N.S., Vorobjev, I.A. Methods in Molecular Biology (2018): doi: 10.1007/978-1-4939-7680-5_1
    • Impact of recent innovations in the use of mass cytometry in support of drug development
      Nassar, A.F., Ogura, H., Wisnewski, A.V. Drug Discovery Today (2015): 1,169–75
    • Cytometry: Measure for measure
      Kling, J. Nature (2015): 439–43
    • Mass cytometry: a powerful tool for dissecting the immune landscape
      Simoni, Y., Chng, M.H.Y., Li, S. et al. Current Opinion in Immunology (2018): 187–96
    • Technology to watch in 2018
      Powell, K. Nature (2018):

  • Stem Cell

    • Characterization of mesoangioblast cell fate and improved promyogenic potential of a satellite cell-like subpopulation upon transplantation in dystrophic murine
      Mavoungoua, L.O., Neuenschwander, S., Pham, U. et al. Stem Cell Research (2019): 101,619
    • Mass cytometry-based single-cell analysis of human stem cell reprogramming uncovers differential regulation of specific pluripotency markers
      Im, I., Son, Y.S, Jung, K.B. et al. Journal of Biological Chemistry (2019): doi: 10.1074/jbc.RA119.009061
    • Human lymphoid organ cDC2 and macrophages play complementary roles in T follicular helper responses
      Durand, M., Walter, T., Pirnay, T. et al. Journal of Experimental Medicine (2019): 1,561-1,581
    • Stress-induced changes in bone marrow stromal cell populations revealed through single-cell protein expression mapping
      Severe, N., Karabacak, N.M., Gustafsson, K. et al. Cell Stem Cell (2019): doi: 10.1016/j.stem.2019.06.003.
    • High-dimensional single-cell cartography reveals novel skeletal muscle-resident cell populations
      Giordani, L., He, G.J., Negroni, E. et al. Molecular Cell (2019): 609-621.e6
    • Glucose metabolism drives histone acetylation landscape transitions that dictate muscle stem cell function
      Yucel, N., Wang, Y.X., Mai, T. et al. Cell Reports (2019): 3,939-3,955.E6
    • Pro-inflammatory aorta-associated macrophages are involved in embryonic development of hematopoietic stem cells
      Mariani, S.A., Li, Z., Rice, S. et al. Immunity (2019): 1439-1452.E5
    • Serial transplantation reveals a critical role for endoglin in hematopoietic stem cell quiescence
      Borges, L, Oliveira, V.K.P., Baik, J. et al. Blood (2018): doi: 10.1182/blood-2018-09-874677
    • Tumor Platinum Concentrations and Pathological Responses Following Cisplatin-Containing Chemotherapy in Gastric Cancer Patients
      Cao, Y., Chang, Q., Cabanero, M. et al. Journal of Gastrointestinal Cancer (2018): doi: 10.1007/s12029-018-0153-9
    • The impact of ischemia-reperfusion injuries on skin resident murine dendritic cells
      Goh, C.C., Evrard, M., Chong, S.Z. et al. European Journal of Immunology (2018): 1,014-9
    • Single Cell Proteomics for Molecular Targets in Lung Cancer: High-Dimensional Data Acquisition and Analysis
      Wang, Z., Zhang, X. Advances in Experimental and Medical Biology (2018): 73-87
    • Single Cell Genetics and Epigenetics in Early Embryo: From Oocyte to Blastocyst
      Wei, Y., Zhang, H., Wang, Q. et al. Advances in Experimental and Medical Biology (2018): 103-17
    • Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease
      Kinchen, J., Chen, H.H., Parikh, K. et al. Cell Reports (2018): 372-86
    • Thrombopoietin Metabolically Primes Hematopoietic Stem Cells to Megakaryocyte-Lineage Differentiation
      Nakamura-Ishizu, A., Matsumura, T., Stumpf, P.S. et al. Cell Reports (2018): 1,772-85
    • Human Intestinal Allografts Contain Functional Hematopoietic Stem and Progenitor Cells that Are Maintained by a Circulating Pool
      Fu, J., Zuber, J., Martinez, M. et al. Cell Stem Cell (2018): doi: 10.1016/j.stem.2018.11.007
    • Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis
      Churko, J.M., Garg, P., Treutlein, B. et al. Nature Communications (2018): 4,906
    • Immune and metabolic shifts during neonatal development reprogram liver identity and function
      Nakagaki, B.N., Mafra, K., de Carvalho, É. et al. Journal of Hepatology (2018): 1,2394-307
    • Mass Cytometry for the Assessment of Immune Reconstitution After Hematopoietic Stem Cell Transplantation
      Stern, L., McGuire, H., Avdic, S. et al. Frontiers in Immunology (2018): 1672
    • High-Dimensional Phenotypic Mapping of Human Dendritic Cells Reveals Interindividual Variation and Tissue Specialization
      Alcántara-Hernández M., Leylek, R., Wagar, L.E. et al. Immunity (2017): 1,037–50
    • MYB fusions and CD markers as tools for authentication and purification of cancer stem cells from salivary adenoid cystic carcinoma
      Panaccione, A., Zhang, Y., Ryan, M. et al. Stem Cell Research (2017): 160-6
    • Reconstitution of immune cell populations in multiple sclerosis patients after autologous stem cell transplantation
      Karnell, F.G., Lin, D., Motley, S. et al. Clinical and Experimental Immunology (2017): 268–78
    • Pathologically expanded peripheral T helper cell subset drives B cells in rheumatoid arthritis
      Rao, D.A., Gurish, M.F., Marshall, J.L. et al. Nature (2017): 110–4
    • Proceedings: immune tolerance and stem cell transplantation: a CIRM mini-symposium and workshop report
      Talib, S., Millan, M.T., Jorgenson, R.L., Shepard, K.A. Stem Cells Translational Medicine (2015): 4–9
    • Charting a map through the cellular reprogramming landscape
      Wen, L., Tang, F. Cell Stem Cell (2016): 215–6
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