CyTOF: We have mass appeal. The technology backed by 1,000+ publications.

CyTOF® is the only high-parameter single-cell analysis system vetted by more than 1,000 publications. Covering a wide spectrum of diseases and research applications, this collection of studies demonstrates the versatility and proven performance of mass cytometry for translational and clinical research around the world.

Explore the publications by research area using the links to the right.

Bibliography

Browse our complete catalog of over 1,000 CyTOF related publications to see how Helios™ and mass cytometry empower researchers to make breakthrough discoveries in basic, translational and clinical research. Download Now

Mass Cytometry Publications Trending Now

Take a look at the issues of Mass Cytometry Publications Trending Now, a quarterly anthology series covering the most recent and impactful publications that help expand our understanding of human health and disease

Nov 2020 issue On recent applications of mass cytometry to vaccine development for infectious diseases. July 2020 issue On use of mass cytometry in COVID-19 disease research studies to date March 2020 issue On high-dimensional functional assessment of health vs. disease December 2019 issue On use of mass cytometry in clinical trials September 2019 issue On key publications from 2019

• Overview

  Number of papers per research area as of January, 2021

  Number of cumulative papers as of January, 2021

• Recent

  • Two subsets of stem-like CD8 + memory T cell progenitors with distinct fate commitments in humans
    Galletti, G., Simone, G.D., Mazza, E.M.C. Nature Immunology (2020): doi: 10.1038/s41590-020-0791-5
  • Th17-inducing autologous dendritic cell vaccination promotes antigen-specific cellular and humoral immunity in ovarian cancer patients
    Block, M. S., Dietz, A.B., Gustafson, M.P. Nature Communications (2020): doi.org/10.1038/s41467-020-18962-z
  • Glioma stem-like cells can be targeted in boron neutron capture therapy with boronophenylalanine
    Kondo, N., Hikida, M., Nakada , M. Cancers (2020): doi.org/10.3390/cancers12103040
  • Application of an activity-based probe to determine proteolytic activity of cell surface cathepsin G by mass cytometry data acquisition
    Gärtner, F., Knippschild, U., Burster, T. ACS Omega (2020): doi.org/10.1021/acsomega.0c04092
  • Salmonella enterica serovar Typhi exposure elicits ex vivo cell-type-specific epigenetic changes in human gut cells
    Sztein, M.B., Bafford, A.C., Salerno-Goncalves, R. Scientific Reports (2020): doi.org/10.1101/cshperspect.a029546
  • Agile workflow for interactive analysis of mass cytometry data
    Casado, J., Lehtonen, O., Rantanen, V. Bioinformatics (2020): DOI: 10.1093/bioinformatics/btaa946

• Research Areas

  • Biomarker Screening

    • Single-cell peripheral immunoprofiling of Alzheimer’s and Parkinson’s diseases
      Phongpreecha, T., Fernandez, R., Mrdjen, D. Science Advances (2020): DOI: 10.1126/sciadv.abd5575
    • 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

    • Prediction of functional markers of mass cytometry data via deep learning
      Solís-Lemus, C., Ma, X., HostetterII, M. Statistical Modeling in Biomedical Research (2021): 95-104
    • SwiftReg cluster registration automatically reduces flow cytometry data variability including batch effects.
      Rebhahn, J.A., Quataert, S.A., Sharma, G. Communications Biology (2021): doi.org/10.5281/zenodo.3733491
    • Brick plots: an intuitive platform for visualizing multiparametric immunophenotyped cell clusters
      Norton, S.E., Leman, J. K. H., Khong, T. BMC Bioinformatics (2021): doi.org/10.1186/s12859-020-3469-y
    • The Extended Polydimensional Immunome Characterization (EPIC) web-based reference and discovery tool for cytometry data
      Yeo, J.G., Wasser, M., Albani, S. Nature Biotechnology (2020): 679–684
    • Single-cell profiling of Ebola virus disease in vivo reveals viral and host dynamics
      Kratochv´ıl, M., Hunewald, O., Heirendt, L. GigaScience (2020): DOI: 10.1093/gigascience/giaa127
    • Integration of mechanistic immunological knowledge into a machine learning pipeline improves predictions
      Culos, A., Tsai, A. S., Aghaeepour, N. Nature Machine Intelligence (2020): 619–628
    • Uncovering the key dimensions of high-throughput biomolecular data using deep learning
      Zhang, S., Li, X., Lin, Q. Nucleic Acid Research (2020): 56
    • Learning pathway dynamics from single‐cell proteomic data: a comparative study
      Verrou, K.M., Tsamardinos, L., Papoutsoglou, G. Cytometry Part A (2020): doi.org/10.1002/cyto.a.23976
    • VoPo leverages cellular heterogeneity for predictive modeling of single-cell data
      Stanley, N., Stelzer, I.A., Aghaeepour, N. Nature Communications (2020): doi.org/10.1182/bloodadvances.2020001565
    • Visualizing Structure and Transitions for Biological Data Exploration
      Moon, K.R., van Dijk, D., Wang, Z. et al. Cell (2018): 1,482–92
    • 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): 1,283–94
    • High‐dimensional data analysis algorithms yield comparable results for mass cytometry and spectral flow cytometry data
      Ferrer-Font, L., Mayer, J.U., Old, S. Cytometry Part A (2020): 824–31
    • 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
    • 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

    • Partial absence of PD‐1 expression by tumor‐infiltrating EBV‐specific CD8+ T cells in EBV‐driven lymphoepithelioma‐like carcinoma
      Simoni, Y., Becht, E., Li, S. Clinical & Translational Immunology (2021): doi.org/10.1002/cti2.1175
    • High‐dimensional analyses reveal a distinct role of T‐cell subsets in the immune microenvironment of gastric cancer
      Wang, M., Huang, Y. K., Kong, J. CH. Clinical Translational Immunology (2021): doi: 10.1002/cti2.1127
    • Identification of the immune checkpoint signature of multiple myeloma using mass cytometry‐based single‐cell analysis
      Wang, J., Zheng, Y., Tu, C. Clinical & Translational Immunology (2021): doi.org/10.1002/cti2.1132
    • Integrated RNA Sequencing and Single-Cell Mass Cytometry Reveal a Novel Role of LncRNA HOXA-AS2 in Tumorigenesis and Stemness of Hepatocellular Carcinoma
      Lu, Q., Gao, J., Tang, S. OncoTargets and Therapy (2020): doi: 10.2147/OTT.S272717
    • The identification and functional analysis of CD8+PD-1+CD161+ T cells in hepatocellular carcinoma
      Li, Z., Zheng, B., Qiu, X. npj Precision Oncology (2020): doi.org/10.17632/ttccnvj
    • The PD-1 expression balance between effector and regulatory T cells predicts the clinical efficacy of PD-1 blockade therapies
      Kumagai, S., Togashi, Y., Kamada, T. Nature Immunology (2020): DOI: 10.1038/s41590-020-0769-3
    • IL-31 induces antitumor immunity in breast carcinoma
      Kan, T., Feldman, E., Timaner, M. Journal for ImmunoTherapy of Cancer (2020): doi.org/10.1136/jitc-2020-001010
    • Interleukin-17–induced neutrophil extracellular traps mediate resistance to checkpoint blockade in pancreatic cancer
      Zhang, Y., Chandra, V., Sanchez, E. R. Journal of Experimental Medicine (2020): doi.org/10.1084/jem.20190354
    • Metabolic reprograming via deletion of CISH in human iPSC-derived NK cells promotes in vivo persistence and enhances anti-tumor activity
      Zhu, H., Blum, R.H., Bernareggi, D. Cell Stem Cell (2020): DOI: 10.1016/j.stem.2020.05.008
    • Cellular immunotherapy with multiple infusions of in vitro-expanded haploidentical natural killer cells after autologous transplantation for patients with plasma cell myeloma
      Tschan-Plessl, A., Kalberer, C.P., Wieboldt, R. Cytotherapy (2020): doi.org/10.1016/j.jcyt.2020.09.009
    • Personalized cytokine-directed therapy with tocilizumab for refractory immune checkpoint inhibitor–related cholangiohepatitis
      Moi, L., Bouchaab, H., Mederos, N. Journal of Thoracic Oncology (2020): DOI: 10.1016/j.jtho.2020.09.007
    • Ex vivo enrichment of PRAME antigen‐specific T cells for adoptive immunotherapy using CD137 activation marker selection
      Lee, K.H., Gowrishankar , K., Street , J. Clinical & Translational Immunology (2020): doi.org/10.1002/cti2.1200
    • Long-term survival of patients with stage III colon cancer treated with VRP-CEA(6D), an alphavirus vector that increases the CD8+ effector memory T cell to Treg ratio
      Crosby, E.J., Hobeika, A. C., Niedzwiecki, D. Journal for ImmunoTherapy of Cancer (2020): doi.org/10.1136/jitc-2020-001662
    • Lack of myeloid cell infiltration as an acquired resistance strategy to immunotherapy
      Beyranvand, E.N., Labrie, C., Abdulrahman, Z. The Lancet Rheumatology (2020): doi.org/10.1136/jitc-2020-001326
    • Charge-altering releasable transporters enable phenotypic manipulation of natural killer cells for cancer immunotherapy
      Wilk, A.J., Vergara, R., Haabeth, O.A.W. Blood (2020): doi.org/10.1182/bloodadvances.2020002355
    • Neoadjuvant PD-L1 plus CTLA-4 blockade in patients with cisplatin-ineligible operable high-risk urothelial carcinoma
      Gao, J., Sharma, P., Navai, N. Nature Medicine (2020): doi.org/10.1038/s41591-020-1086-y
    • "Blockade of EGFR improves responsiveness to PD-1 blockade in EGFR-mutated non–small cell lung cancer"
      Sugiyama, E., Togashi, Y., Takeuchi, Y. Science Immunology (2020): DOI: 10.1126/sciimmunol.aav3937
    • Reversible suppression of T cell function in the bone marrow microenvironment of acute myeloid leukemia
      Lamble, A.J., Kosaka, Y., Laderas, T. PNAS (2020): doi.org/10.1073/pnas.1916206117
    • Adoptive cell therapy in combination with checkpoint inhibitors in ovarian cancer
      Kverneland, A.H., Pedersen, M., Nielsen, M. Oncotarget (2020): doi: 10.18632/oncotarget.27604
    • Viral status, immune microenvironment and immunological response to checkpoint inhibitors in hepatocellular carcinoma
      Ho, W.J., Danilova, L., Lim, S.U. Journal for ImmunoTherapy of Cancer (2020): doi.org/10.1136/jitc-2019-000394
    • 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. Journal of Pathology (2020): 420–39
    • A peripheral immune signature of responsiveness to PD-1 blockade in patients with classical Hodgkin lymphoma
      Cader, F.Z., Xu, X., Goh, W.L. Nature Medicine (2020): 1,468–79
    • Multidimensional analyses of donor memory-like NK cells reveal new associations with response after adoptive immunotherapy for leukemia
      Berrien-Elliot, M., Cashen, A.F., Cubitt, C.C. Cancer Discovery (2020): DOI: 10.1158/2159-8290.CD-20-0312
    • 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): 609–17
    • 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): 2,217–33
    • Natural killer cells as a potential biomarker for predicting immunotherapy efficacy in patients with non-small cell lung cancer
      Cho, Y-H., Choi, M. G., Kim, D. H. Targeted Oncology (2020): 241–7
    • CAR-modified memory-like NK cells exhibit potent responses to NK-resistant lymphomas
      Gang, M., Marin, N.D., Wong, P. Blood (2020): DOI: 10.1182/blood.2020006619
    • Deep immune profiling of patients treated with lenalidomide and dexamethasone with or without daratumumab
      Casneuf, T., Adams III, H. C., Abraham, Y. Leukemia (2020): doi.org/10.1038/s41375-020-0855-4
    • Phase 1 Study of combinatorial sorafenib, G-CSF, and plerixafor treatment in relapsed/refractory, FLT3-ITD-mutated acute myelogenous leukemia patients
      Borthakur, G.,Zeng, Z.,Cortes, J. E. American Journal of Hematology (2020): DOI: 10.1002/ajh.25943
    • 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
    • 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
    • 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

    • Autoantibody-positive healthy individuals with lower lupus risk display a unique immune endotype
      Slight-Webb, S., Smith, M., Bylinska, A. Journal of Allergy and Clinical Immunology (2021): DOI: 10.1016/j.jaci.2020.04.047
    • Deep phenotyping by mass cytometry and single Ccell RNA-sequencing reveals LYN regulated signaling profiles underlying monocyte subset heterogeneity and lifespan
      Roberts, M.E., Barvalia, M., Silva, J. A. F. D. Circulation Research (2021): DOI: 10.1161/CIRCRESAHA.119.315708
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      Mukai, K., Gaudenzio, N., Gupta, S. et al. Journal of Allergy and Clinical Immunology (2017): 889–99.e11
    • Novel Resolvin D2 Receptor Axis in Infectious Inflammation
      Chiang, N., de la Rosa, X., Libreros, S. et al. Journal of Immunology (2017): 842–51
    • Combining Flow and Mass Cytometry in the Search for Biomarkers in Chronic Graft-versus-Host Disease
      Stikvoort, A., Chen, Y., Rådestad, E. et al. Frontiers in Immunology (2017): 717
    • Immune Checkpoint Function of CD85j in CD8 T Cell Differentiation and Aging
      Gustafson, C.E., Qi, Q., Hutter-Saunders, J. et al. Frontiers in Immunology (2017): 692
    • Interferon Gamma Induces Changes in Natural Killer (NK) Cell Ligand Expression and Alters NK Cell-Mediated Lysis of Pediatric Cancer Cell Lines
      Aquino-López, A., Senyukov, V.V., Vlasic, Z. et al. Frontiers in Immunology (2017): 391
    • Dissecting the Molecular Mechanisms of the Tropism of Varicella-Zoster Virus for Human T Cells
      Sen, N., Arvin, A.M. Journal of Virology (2016): 3,284–7
    • Multiparameter analysis of stimulated human peripheral blood mononuclear cells: a comparison of mass and fluorescence cytometry
      Nicholas, K.J., Greenplate, A.R., Flaherty, D.K. et al. Cytometry Part A (2015): 271–80
    • Regulation of adaptive NK cells and CD8 T cells by HLA-C correlates with allogeneic hematopoietic cell transplantation and with cytomegalovirus reactivation
      Horowitz, A., Guethlein, L.A., Nemat-Gorgani, N. et al. Journal of Immunology (2015): 4,524–36
    • Age‐related aspects of human IgM+ B cell heterogeneity
      Martin, V., Wu, Y.C., Kipling, D., Dunn-Walters, D.K. Annals of the New York Academy of Sciences (2015): 153–63
    • Implementing mass cytometry at the bedside to study the immunological basis of human diseases: distinctive immune features in patients with a history of term or preterm birth
      Gaudillière, B., Ganio, E.A., Tingle, M. et al. Cytometry, Part A (2015): 817–29
    • Application of mass cytometry (CyTOF®) for functional and phenotypic analysis of natural killer cells
      Kay, A.W., Strauss-Albee, D.M., Blish, C.A. Methods in Molecular Biology (2016): 13–26
    • Single-cell states versus single-cell atlases—two classes of heterogeneity that differ in meaning and method
      Janes, K.A. Current Opinion in Biotechnology (2016): 120–5
    • Mapping the diversity of follicular helper T cells in human blood and tonsils using high-dimensional mass cytometry analysis
      Wong, M.T., Chen, J., Narayanan, S. et al. Cell Reports (2015): 1,822–33
    • Cutting Edge: Redox Signaling Hypersensitivity Distinguishes Human Germinal Center B Cells
      Polikowsky, H.G., Wogsland, C.E., Diggins, K.E. et al. Journal of Immunology (2015): 1,364–7
    • Single-cell systems-level analysis of human Toll-like receptor activation defines a chemokine signature in patients with systemic lupus erythematosus
      O'Gorman, W.E., Hsieh, E.W., Savig, E.S. et al. Journal of Allergy and Clinical Immunology (2015): 1,326–36
    • Phenotypic complexity of the human regulatory T cell compartment revealed by mass cytometry
      Mason, G.M., Lowe, K., Melchiotti, R. et al. The Journal of Immunology (2015): 2,030–7
    • A small molecule screen for enhanced homing of systemically infused cells
      Levy, O., Mortensen, L.J., Boquet, G. et al. Cell Reports (2015): 1,261–8
    • Phenotype and function of nasal dendritic cells
      Lee, H., Ruane, D., Law, K. et al. Mucosal Immunology (2015): 1,083–98
    • Beneficial Effects of CpG-Oligodeoxynucleotide Treatment on Trauma and Secondary Lung Infection
      Wanke-Jellinek, L., Keegan, J.W., Dolan, J.W. et al. The Journal of Immunology (2016): 767–77
    • Mass Cytometry of the Human Mucosal Immune System Identifies Tissue- and Disease-Associated Immune Subsets
      van Unen, V., Li, N., Molendijk, I. et al. Immunity (2016): 1,227–39
    • A High-Dimensional Atlas of Human T Cell Diversity Reveals Tissue-Specific Trafficking and Cytokine Signature
      Wong, M.T., Ong, D.E., Lim, F.S, et al. Immunity (2016): 442–56
    • Mass cytometry profiling the response of basophils and the complete peripheral blood compartment to peanut
      Tordesillas, L., Rahman, A.H., Hartmann, B.M. et al. Journal of Allergy and Clinical Immunology (2016): 1741–4.e9
    • Cytometry by time-of-flight immunophenotyping identifies a blood Sjögren's signature correlating with disease activity and glandular inflammation
      Mingueneau, M., Boudaoud, S., Haskett, S. et al. The Journal of Allergy and Clinical Immunology (2016): 1,809–21
    • Increased lymphocyte apoptosis in mouse models of colitis upon ABT-737 treatment is dependent upon BIM expression
      Lutz, C., Mozaffari, M., Tosevski, V. et al. Clinical and Experimental Immunology (2015): 343–56
    • Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum
      Bendall, S.C., Simonds, E.F., Qiu, P. et al. Science (2011): 687–96
    • Human CD4+ lymphocytes for antigen quantification: characterization using conventional flow cytometry and mass cytometry
      Wang, L., Abbasi, F., Ornatsky, O. et al. Cytometry, Part A (2012): 567–75
    • The transcriptional landscape of αβ T cell differentiation
      Mingueneau, M., Kreslavsky, T., Gray, D. et al. Nature Immunology (2013): 619–32
    • Genetic and environmental determinants of human NK cell diversity revealed by mass cytometry
      Horowitz, A., Strauss-Albee, D.M., Leipold, M. et al. Science Translational Medicine (2013): 208ra145
    • Antigen-dependent integration of opposing proximal TCR-signaling cascades determines the functional fate of T lymphocytes
      Wolchinsky, R., Hod-Marco, M., Oved, K. et al. Journal of Immunology (2014): 2,109–19
    • Clinical recovery from surgery correlates with single-cell immune signatures
      Gaudillière, B., Fragiadakis, G.K., Bruggner, R.V. et al. Science Translational Medicine (2014): 255ra131
    • Single-cell mass cytometry analysis of human tonsil T cell remodeling by varicella zoster virus
      Sen, N., Mukherjee, G., Sen, A. et al. Cell Reports (2014): 633–45
    • CD161 defines a transcriptional and functional phenotype across distinct human T cell lineages
      Fergusson, J.R., Smith, K.E., Fleming, V.M. et al. Cell Reports (2014): 1,075–88
    • Human skin is protected by four functionally and phenotypically discrete populations of resident and recirculating memory T cells
      Watanabe, R., Gehad, A., Yang, C. et al. Science Translational Medicine (2015): 279ra39
    • Pregnancy Does Not Attenuate the Antibody or Plasmablast Response to Inactivated Influenza Vaccine
      Kay, A.W., Bayless, N.L., Fukuyama, J. et al. The Journal of Infectious Diseases (2015): 861–70
    • Single-cell trajectory projection uncovers progression and regulatory coordination in human B cell development
      Bendall, S.C., Davis, K.L., Amir, E.D. et al. Cell (2014): 714–25
    • Adenoviral Vector Vaccination Induces a Conserved Program of CD8+ T Cell Memory Differentiation in Mouse and Man
      Bolinger, B., Sims, S., Swadling, L. et al. Cell Reports (2015): 1,578–88
    • Large-Scale and Comprehensive Immune Profiling and Functional Analysis of Normal Human Aging
      Whiting, C.C., Siebert, J., Newman, A.M. et al. PLoS One (2015): e0133627
    • Expansion of inflammatory innate lymphoid cells in patients with common variable immune deficiency
      Cols, M., Rahman, A., Maglione, P.J. et al. Journal of Allergy and Clinical Immunology (2016): 1,206–15
    • Reversibility of Defective Hematopoiesis Caused by Telomere Shortening in Telomerase Knockout Mice
      Raval, A., Behbehani, G.K., Nguyen, L.X.T. et al. PLoS One (2015): e0131722
    • Deep Profiling Human T Cell Heterogeneity by Mass Cytometry
      Cheng, Y., Newell, E.W. Advances in Immunology (2016): 101–34
    • Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states
      Furman, D., Chang, J., Lartigue, L. et al. Nature Medicine (2017): 174–84
    • Mass spectrometry goes with the flow: mass cytometry and its potentials in regenerative medicine
      Agnetti, G. Circulation: Cardiovascular Genetics (2012): 379–80
    • New tools for classification and monitoring of autoimmune diseases
      Maecker, H.T., Lindstrom, T.M., Robinson, W.H. et al. Nature Reviews Rheumatology (2012): 317–28
    • Human Innate Lymphoid Cell Subsets Possess Tissue-Type Based Heterogeneity in Phenotype and Frequency
      Simoni, Y., Fehlings, M., Kløverpris, H.N. et al. Immunity (2016): 148–61
    • Novel tools for primary immunodeficiency diagnosis: making a case for deep profiling
      Hsieh, E.W., Hernandez, J.D. Current Opinion in Allergy and Clinical Immunology (2016): 549–56
    • The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome
      Gury-BenAri, M., Thaiss, C.A., Serafini, N. et al. Cell (2016): 1,231–46
    • Deep phenotyping of Tregs identifies an immune signature for idiopathic aplastic anemia and predicts response to treatment
      Kordasti, S., Costantini, B., Seidl, T. et al. Blood (2016): 1,193–205
    • Unsupervised High-Dimensional Analysis Aligns Dendritic Cells across Tissues and Species
      Guilliams, M., Dutertre, C.A., Scott, C.L. et al. Immunity (2016): 669–84
    • Wild immunology assessed by multidimensional mass cytometry
      Japp, A.S., Hoffmann, K., Schlickeiser, S. et al. Cytometry Part A (2016): 85–95
    • Mass cytometry analytical approaches reveal cytokine-induced changes in natural killer cells
      Vendrame, E., Fukuyama, J., Strauss-Albee, D.M. et al. Cytometry Part B Clinical Cytometry (2016): 57–67
    • Comprehensive mass cytometry analysis of cell cycle, activation and coinhibitory receptors expression in CD4 T cells from healthy and HIV-infected individuals
      Corneau, A., Cosma, A., Even, S. et al. Cytometry Part B Clinical Cytometry (2016): 21–32
    • Isolation and high-dimensional phenotyping of gastrointestinal immune cells
      David, B.A., Rubino, S., Moreira, T.G. et al. Immunology (2016): 56–70
    • Lymphocyte enrichment using CD81-targeted immunoaffinity matrix
      Pelák, O., Kužílková, D., Thürner, D., et al. Cytometry Part A (2017): 62–72
    • Activation of the reward system boosts innate and adaptive immunity
      Ben-Shaanan, T.L., Azulay-Debby, H., Dubovik, T., et al. Nature Medicine (2016): 940–4
    • Impact of the microbial derived short chain fatty acid propionate on host susceptibility to bacterial and fungal infections in vivo
      Ciarlo, E., Heinonen, T., Herderschee, J. et al. Scientific Reports (2016): 37,944
    • Identification of Novel CD4+ T Cell Subsets in the Target Tissue of Sjögren’s Syndrome and Their Differential Regulation by the Lymphotoxin/LIGHT Signaling Axis
      Haskett, S., Ding, J., Zhang, W. et al. Journal of Immunology (2016): 1,600,407
    • Technological advances transforming rheumatology
      Robinson, W.H., Mao, R. Nature Reviews Rheumatology (2015): 626–8
    • Biomarkers to guide clinical therapeutics in rheumatology?
      Robinson, W.H., Mao, R. Current Opinion in Rheumatology (2016): 168–75
    • La couleur du métal Brève introduction à la cytométrie de masse (Fr.)
      Cosma, A., Le Grand, R. Médecine/sciences (2011): 1,072–4
    • NK Cells in HIV Disease
      Scully, E., Alter, G. Current HIV/AIDS Reports (2016): 85–94
    • Human NK Cell Diversity in Viral Infection: Ramifications of Ramification
      Strauss-Albee, D.M., Blish, C.A. Frontiers in Immunology (2016): 66
    • Coordinated regulation of natural killer receptor expression in the maturing human immune system
      Strauss-Albee, D.M., Horowitz, A., Parham, P., Blish, C.A. Journal of Immunology (2014): 4,871–9
    • Challenges and Promise for the Development of Human Immune Monitoring
      Shen-Orr, S.S. Rambam Maimonides Medical Journal (2012): e0023
    • Guardians of the Gut – Murine Intestinal Macrophages and Dendritic Cells
      Gross, M., Salame, T.M., Jung, S. Frontiers in Immunology (2015): 254

  • Immunophenotyping

    • Maternal obesity is associated with phenotypic alterations in fetal immune cells by single‐cell mass cytometry
      Enninga, E.A.L., Jang, J. S., Hur, B. American Journal of Reproductive Immunology (2020): doi.org/10.1111/aji.13358
    • 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): 1,893–908.e4
    • Mapping of γ/δ T cells reveals Vδ2+ T cells resistance to senescence
      Xu, W., Monaco, G., Wong, E.H.. et al. EBioMedicine (2019): 44–58
    • Pitfalls in the characterization of circulating and tissue-resident human γδ T cells
      Beucke, N., Wesch, D., Oberg, H.-H., et al Journal of Leukocyte Biology (2020): 1,097-105
    • Inherent immune cell variation within colonic segments presents challenges for clinical trial design
      Tyler, C.J., Guzman, M. Lundborg, L.R. et al. Journal of Crohn's and Colitis (2020): doi: 10.1093/ecco-jcc/jjaa067
    • 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
    • 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
    • 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

    • Dysregulation of the immune response affects the outcome of critical COVID‐19 patients
      Wei, L.L., Wang, W.J., Chen, D.X. Journal of Medical Virology (2021): doi.org/10.1002/jmv.26181
    • Down-regulated gene expression spectrum and immune responses changed during the disease progression in COVID-19 patients
      Ouyang, Y., Yin, J., Wang, W. Clinical Infectious Disease (2021): DOI: 10.1093/cid/ciaa462
    • The inhibition of IL-2/IL-2R gives rise to CD8+ T cell and lymphocyte decrease through JAK1-STAT5 in critical patients with COVID-19 pneumonia
      Shi, H., Wang, W., Yin, J. Cell Death & Disease (2021): doi.org/10.1101/2020.02.10.20021832
    • Cutting edge: characterization of human tissue-resident memory T Cells at different infection sites in patients with tuberculosis
      Yang, Q. , Zhang, M., Chen, Q. Journal of Immunology (2020): DOI: 10.4049/jimmunol.1901326
    • Modulation of cell surface receptor expression by modified vaccinia virus Ankara in leukocytes of healthy and HIV-infected individuals
      Leite Pereira, A., Jouhault, Q., Lopez, E. M. Frontiers in Immunology (2020): doi.org/10.3389/fimmu.2020.02096
    • Immunologic timeline of Ebola virus disease and recovery in humans
      McElroy, A.K., Akondy, R. S., Mcllwain, D. R. JCI Insight (2020): doi.org/10.1172/jci.insight.137260DS1
    • A network of immune and microbial modifications underlies viral persistence in the gastrointestinal tract
      Macleod, B.L., Elsaesser, H. J., Snell, L. M. Journal of Experimental Medicine (2020): doi.org/10.1084/jem.20191473
    • HIV efficiently infects T cells from the endometrium and remodels them to promote systemic viral spread
      Ma, T., Luo, X., George, A. F. eLife (2020): DOI: 10.7554/eLife.55487
    • Single-cell profiling of Ebola virus disease in vivo reveals viral and host dynamics
      Kotliar, D., Lin, A. E., Logue, J. Cell (2020): doi.org/10.1016/j.cell.2020.10.002
    • Multidimensional proteomic approach of endothelial progenitors demonstrate expression of KDR restricted to CD19 cells
      Guerin, C.L., Guyonnet, L., Goudot, G. Stem Cell Reviews and Reports (2020): doi.org/10.1016/j.cell.2020.09.034
    • Mapping systemic inflammation and antibody responses in multisystem inflammatory syndrome in children (MIS-C)
      Gruber, C., Patel, R. S., Trachtman, R. Cell (2020): doi.org/10.1016/j.cell.2020.09.034
    • The potential role of immune alteration in the cancer–COVID19 equation—a prospective longitudinal study
      Goshen-Lago, T., Szwarcwort-Cohen, M., Benguigui, M. Cancers (2020): doi.org/10.3390/cancers12092421
    • Ontogeny of different subsets of yellow fever virus-specific circulatory CXCR5+ CD4+ T cells after yellow fever vaccination
      DeGottardi, Q., Gates, T. J., Yang, J. Scientific Reports (2020): doi.org/10.1002/cyto.a.22348
    • Natural killer cell phenotype is altered in HIV-exposed seronegative women
      Zhao, N.Q., Vendrame, E., Ferreira, A. M. PLOS One (2020): doi.org/10.1371/journal.pone.0238347
    • Treated HIV infection alters phenotype but not HIV-specific function of peripheral blood natural killer cells
      Zhao, N.Q., Ferreira, A. M., Grant, P. M. Frontiers in Immunology (2020): doi: 10.3389/fimmu.2020.00829
    • Unbiased profiling reveals compartmentalization of unconventional T-cells within the intestinal mucosa irrespective of HIV infection
      Magnoumba, M., Singh, A., Ogongo, P. Frontiers in Immunology (2020): doi: 10.1038/ni.3298
    • Vi-vaccinations induce heterogeneous plasma cell responses that associate with protection from typhoid fever
      Cross, D.L., Verheul, M. K., Leipold, M. D. Frontiers in Immunology (2020): doi: 10.1093/cid/cis359
    • Metformin enhances anti-mycobacterial responses by educating CD8+ T-cell immunometabolic circuits
      Bohme, J., Martinez, N., Li, S. Nature Communications (2020): doi.org/10.1101/2020.03.06.978791.
    • Altered immune response to the annual influenza A vaccine in patients with myeloproliferative neoplasms
      Alimam, S., Timms , J.A., Harrison, C.N. British Journal of Haematology (2020): doi.org/10.1111/bjh.17096
    • High-dimensional single-cell analysis reveals the immune characteristics of COVID-19
      Shi, W., Liu, X., Ma, P. American Journal of Physiology (2020): doi.org/10.1152/ajplung.00355.2020
    • Mass cytometry analysis of the NK cell receptor–ligand repertoire reveals unique differences between dengue-infected children and adults
      McKechnie, J.L., Beltrán, Davis., Ferreira, A-M. M. ImmunoHorizons (2020): doi.org/10.4049/immunohorizons.2000074
    • Augmenting emergency granulopoiesis with CpG conditioned mesenchymal stromal cells in murine neutropenic sepsis
      Ng, J., Guo, F., Marneth, A.E. Blood Advances (2020): doi.org/10.1182/bloodadvances.2020002556
    • Salmonella enterica serovar Typhi exposure elicits ex vivo cell-type-specific epigenetic changes in human gut cells
      Sztein, M.B., Bafford, A.C., Salerno-Goncalves, R. Scientific Reports (2020): doi.org/10.1101/cshperspect.a029546
    • 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. Transplantation (2020): DOI: 10.1097/TP.0000000000003130
    • IRF5 promotes influenza-induced inflammatory responses in human iPSC-derived myeloid cells and murine models
      Forbester, J.L., Clement, M., Wellington, D. Journal of Virology (2020): e00121-20
    • T-bet+ memory B vells link to local cross-reactive IgG upon human rhinovirus infection
      Eccles, J.D., Turner, R.B., Kirk, N.A. Cell Reports (2020): doi.org/10.1016/j.celrep.2019.12.027
    • Systems-level immunomonitoring from acute to recovery phase of severe COVID-19
      Rodriguez, L., Pekkarinen, P. T., Lakshmikanth, T. Cell Reports Medicine (2020): doi.org/10.1016/j.xcrm.2020.100078
    • A human circulating immune cell landscape in aging and COVID-19
      Zheng, Y., Liu, X., Le, W. Protein & Cell (2020): doi.org/10.1007/s13238-020-00762-2
    • Complex autoinflammatory syndrome unveils fundamental principles of JAK1 kinase transcriptional and biochemical function
      Gruber, C.N., Calis, J. J. A., Buta, S. Immunity (2020): doi.org/10.1016/j.immuni.2020.07.006
    • Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans
      Arunachalam, P.S., Wimmers, F., Mok, C. K. P. Science (2020): DOI: 10.1126/science.abc6261
    • Rapidly expanded partially HLA DRB1–matched fungus-specific T cells mediate in vitro and in vivo antifungal activity
      Castellellano-González, G., McGuire, H.M., Luciani, F. Blood Advances (2020): doi.org/10.1182/bloodadvances.2020001565
    • Genetically detoxified pertussis toxin displays near identical structure to its wild-type and exhibits robust immunogenicity.
      Ausar, S.F., Zhu, S., Duprez, J. Communications Biology (2020): doi.org/10.1038/s42003-020-01153-3
    • Suppressive myeloid cells are a hallmark of severe COVID-19
      Schulte-Shrepping, J., Reusch, N., Paclik, D. Cell (2020): doi.org/10.1016/j.cell.2020.08.001
    • Programing of an intravascular immune firewall by the gut microbiota protects against pathogen dissemination during infection
      McDonald, B., Zucoloto, A.Z., Yu, I.L. Cell Host & Microbe (2020): DOI: 10.1016/j.chom.2020.07.014
    • High-dimensional immune profiling by mass cytometry revealed immunosuppression and dysfunction of immunity in COVID-19 patients
      Wang, W., Su, B., Pang, L. Cellular & Molecular Immunology (2020): doi.org/10.1016/S1473-3099
    • SARS-CoV-2-specific T cells exhibit unique features characterized by robust helper function, lack of terminal differentiation, and high proliferative potential
      Neidleman, J., Luo, X., Frouard, J. Cell Reports Medicine (2020): doi: 10.1016/j.xcrm.2020.100081
    • Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients
      Hadjadj, J., Yatim, N., Barnabei, L. Science (2020): DOI: 10.1126/science.abc6027
    • Immunocyte single cell analysis of vaccine‐induced narcolepsy
      Lind, A., Salami, F., Landtblom, A.M. European Journal of Immunology (2020): doi.org/10.1002/eji.202048633
    • 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
    • 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
    • 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
      Hamlin, R.E., Rahman, A., Pak, T.R. et al. Journal of Clinical Investigation Insight (2017): e92424
    • 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
      Napolitani, G., Kurupati, P., Teng, K.W.W. et al. Nature Immunology (2018): doi: 10.1038/s41590-018-0133-z
    • Identification and characterization of HIV-specific resident memory CD8+ T cells in human lymphoid tissue
      Buggert, M., Nguyen, S., Salgado-Montes de Oca, G. et al. Science Immunology (2018): doi: 10.1126/sciimmunol.aar4526
    • High-Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune-Checkpoint Cancer Therapy
      Gubin, M.M., Esaulova, E., Ward, J.P. et al. Cell (2018): doi: 10.1016/j.cell.2018.09.030
    • 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

    • Multiplexed probing of proteolytic enzymes using mass cytometry-compatible activity-based probes
      Poreba, M., Groborz , K. M., Rut, W. Journal of American Chemical Society (2021): DOI: 10.1021/jacs.0c06762
    • High-throughput mass cytometry staining for immunophenotyping clinical samples
      Thrash, E.M., Kleinsteuber, K., Hathaway, E. S. STAR Protocols (2021): doi.org/10.1016/j.xpro.2020.100055
    • Toward high‐dimensional single‐cell analysis of graphene oxide biological impact: tracking on immune cells by single‐cell mass cytometry
      Orrecchioni, M., Bordoni, V., Fuoco, C. Small (2021): DOI: 10.1002/smll.202000123
    • High-throughput single-cell analysis of exosome mediated dual drug delivery, in vivo fate and synergistic tumor therapy
      Wang, J., Li, G., Tu, C. Nanoscale (2021): DOI: 10.1039/d0nr02344b
    • Training novices in generation and analysis of high‐dimensional human cell phospho‐flow cytometry data
      Roe, C.E., Hayes, M. J., Barone, S. M. Current Protocols in Cytometry (2021): DOI: 10.1002/cpcy.71
    • Immunophenotyping and intracellular staining of fixed whole blood for mass cytometry (CyTOF)
      Kowli, S., Maecker, H. Bio-101 (2020): DOI:10.21769/BioProtoc.5004
    • Effects of processing conditions on stability of immune analytes in human blood
      Gottfried-Blackmore, A., Rubin, S. J. S., Bai, L. Scientific Reports (2020): doi.org/10.1038/s41598-020-74274-8
    • Tantalum oxide nanoparticle-based mass tag for mass cytometry
      Zhang, Y., Zabinyakov, N., Majonis, D. Analytical Chemistry (2020): doi: 10.1021/acs.analchem.9b04970
    • Heterogenous Internalization of Nanoparticles at Ultra-Trace Concentration in Environmental Individual Unicellular Organisms Unveiled by Single-Cell Mass Cytometry
      Wu, Q., Shi, J., Ji, X. ACS Nano (2020): DOI: 10.1021/acsnano.0c03587
    • Application of an activity-based probe to determine proteolytic activity of cell surface cathepsin G by mass cytometry data acquisition
      Gärtner, F., Knippschild, U., Burster, T. ACS Omega (2020): doi.org/10.1021/acsomega.0c04092
    • Loading of metal isotope-containing intercalators for mass cytometry-based high-throughput quantitation of exosome uptake at the single-cell level
      Wang, J., Tu, C., Zhang, H. Biomaterials (2020): DOI: 10.1016/j.biomaterials.2020.120152
    • Graphene, other carbon nanomaterials and the immune system: toward nanoimmunity-by-design
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      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

    • Exploration of the personalized immune checkpoint atlas of plasma cell dyscrasias patients using high‑dimensional single‑cell analysis
      Tu, C., Zheng, Y., Zhang, H. Oncology Reports (2021): 224-240
    • TBL1XR1 mutations drive extranodal lymphoma by inducing a pro-tumorigenic memory fate
      Venturutti, L., Teater, M., Zhai, A. Cell (2021): doi.org/10.1016/j.cell.2020.05.049
    • The use of single cell mass cytometry to define the molecular mechanisms of Varicella-Zoster virus lymphotropism
      Sen, N., Mukherjee, G., Arvin, A.M. Frontiers in Microbiology (2020): doi.org/10.3389/fmicb.2020.01224
    • PAI-1-dependent inactivation of SMAD4-modulated junction and adhesion complex in obese endometrial cancer
      Lin, L.L., Kost, E. R., Lin, C. L. Cell Reports (2020): doi.org/10.17632/5ywmdd6fnd.1)
    • SFPQ depletion Is synthetically lethal with BRAFV600E in colorectal cancer cells
      Klotz-Noack, K., Klinger, B., Rivera, M. Cell Reports (2020): DOI: 10.1016/j.celrep.2020.108184
    • Immune phenotyping of diverse syngeneic murine brain tumors identifies immunologically distinct types
      Khalsa, J.K., Cheng, N., Keegan, J. Nature Communications (2020): doi: 10.1038/s41467-020-17704-5
    • The Gustatory Sensory G-Protein GNAT3 Suppresses Pancreatic Cancer Progression in Mice
      Hoffman, M. T, Kemp, S. B., Salas-Escabillas, D. J. Cellular and molecular gastroenterology and hepatology (2020): doi.org/10.1016/j.jcmgh.2020.08.011
    • The Temperature-Dependent Effectiveness of Platinum-Based Drugs Mitomycin-C and 5-FU during Hyperthermic Intraperitoneal Chemotherapy
      Helderman, R., Loke, D.R., Verhoeff, J. Cells (2020): doi.org/10.3390/cells9081775
    • CyTOF mass cytometry reveals phenotypically distinct human blood neutrophil populations differentially correlated with melanoma stage
      Zhu, Y.P., Eggert, T., Araujo, D.j. Journal for ImmunoTherapy of Cancer (2020): doi.org/10.1136/jitc-2019-000473
    • Cancers from novel Pole-mutant mouse models provide insights into polymerase-mediated hypermutagenesis and immune checkpoint blockade
      Galati, M.A., Hodel, K.P., Gams, M.S. Cancer Research (2020): DOI: 10.1158/0008-5472.CAN-20-0624
    • UBC9 coordinates inflammation affecting development of bladder cancer
      Huang, X., Tao, Y., Gao, J. Scientific Reports (2020): doi.org/10.3322/caac.21387
    • Glioma stem-like cells can be targeted in boron neutron capture therapy with boronophenylalanine
      Kondo, N., Hikida, M., Nakada , M. Cancers (2020): doi.org/10.3390/cancers12103040
    • Th17-inducing autologous dendritic cell vaccination promotes antigen-specific cellular and humoral immunity in ovarian cancer patients
      Block, M. S., Dietz, A.B., Gustafson, M.P. Nature Communications (2020): doi.org/10.1038/s41467-020-18962-z
    • Method for the analysis of the tumor microenvironment by mass cytometry: application to chronic lymphocytic leukemia
      Gonder, S., Botana, I.F., Wierz, M. Frontiers in Immunology (2020): doi: 10.1182/blood-2010-05-284984
    • Multimodal mapping of the tumor and peripheral blood immune landscape in human pancreatic cancer
      Steele, N.G., Carpenter, E.S., Magliano, M.P.D. Nature Cancer (2020): doi.org/10.1038/s43018-020-00121-4
    • CNS-native myeloid cells drive immune suppression in the brain metastatic niche through Cxcl10
      Guldner, I.H., Wang, Q., Yang, L. Cell (2020): DOI: 10.1016/j.cell.2020.09.064
    • Phenotype molding of T cells in colorectal cancer by single‐cell analysis
      Di, J., Liu, M., Fan, Y. International Journal of Cancer (2020): DOI: 10.1002/ijc.32856
    • Mass cytometry identifies expansion of double positive and exhausted T cell subsets in the tumour microenvironment of patients with POEMS syndrome
      Kourelis, T.V., Jevremovic, D., Jessen, E. British Journal of Haematology (2020): DOI: 10.1111/bjh.16522
    • Radiation induces iatrogenic immunosuppression by indirectly affecting hematopoiesis in bone marrow
      Kapoor, V., Collins, A., Griffith, K. Oncotarget (2020): doi.org/10.18632/oncotarget.27564
    • Loss of myeloid BMPR1a alters differentiation and reduces mouse prostate cancer growth
      Ihle, C.L., Straign, D.M., Provera, M.D. Frontiers in Oncology (2020): doi.org/10.3389/fonc.2020.00357
    • High dimensional mass cytometry analysis reveals characteristics of the immunosuppressive microenvironment in diffuse astrocytomas
      Fu, W., Wang, W., Li, H. Frontiers in Oncology (2020): doi: 10.3389/fonc.2020.00078
    • Tumor-targeted pH-low insertion peptide delivery of theranostic gadolinium nanoparticles for image-guided nanoparticle-enhanced radiation therapy
      Liu, W., Deacon, J., yan, H. Translational Oncology (2020): DOI: 10.1016/j.tranon.2020.100839
    • Single-Cell Mapping of Human Brain Cancer Reveals Tumor-Specific Instruction of Tissue-Invading Leukocytes
      Friebel, E., Kapolou, K., Unger, S. Cell (2020): DOI: 10.1016/j.cell.2020.04.055
    • EFHD2 contributes to non-small cell lung cancer cisplatin resistance by the activation of NOX4-ROS-ABCC1 axis
      Fan, C-C., Tsai, S-T., Lin, C-Y. Redox Biology (2020): doi.org/10.1016/j.redox.2020.101571
    • Glioblastomas exploit truncated O-linked glycans for local and distant immune modulation via the macrophage galactose-type lectin
      Dusoswa, S.A., Verhoeff, J., Abels, E. PNAS (2020): DOI: 10.1073/pnas.1907921117
    • Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy
      Brodin, P. Nature Communications (2020): 11
    • Hepatocellular carcinoma cells upregulate PVRL1, stabilizing PVR and inhibiting the cytotoxic T-cell response via TIGIT to mediate tumor resistance to PD1 inhibitors in mice
      Chiu, D.K., Yuen, V. W., Cheu, J. W. Gastroenterology (2020): DOI: 10.1053/j.gastro.2020.03.074
    • Systemic dysfunction and plasticity of the immune macro environment in cancer models
      Allen, B. M.,Hiam, K. J., Burnett C. E. Nature Medicine (2020): DOI: 10.1038/s41591-020-0892-6
    • 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
    • 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
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    • Cholesterol esterification inhibition and imatinib treatment synergistically inhibit growth of BCR-ABL mutation-independent resistant chronic myelogenous leukemia
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    • Discovery of human cell selective effector molecules using single cell multiplexed activity metabolomics
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    • Macrophages orchestrate breast cancer early dissemination and metastasis
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    • Apatinib exhibits anti-leukemia activity in preclinical models of acute lymphoblastic leukemia
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    • 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
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    • 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
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    • 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
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    • Checkpoint blockade immunotherapy reshapes the high-dimensional phenotypic heterogeneity of murine intratumoural neoantigen-specific CD8+ T cells
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    • 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
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    • Novel BET protein proteolysis-targeting chimera exerts superior lethal activity than bromodomain inhibitor (BETi) against post-myeloproliferative neoplasm secondary (s) AML cells
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    • Colony Lysate Arrays for Proteomic Profiling of Drug-Tolerant Persisters of Cancer Cell
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    • Mass cytometry analysis reveals hyperactive NF Kappa B signaling in myelofibrosis and secondary acute myeloid leukemia
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    • Phenotypic and functional characterization of a bortezomib-resistant multiple myeloma cell line by flow and mass cytometry
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    • PARP inhibitor upregulates PD-L1 expression and enhances cancer-associated immunosuppression
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    • Cytokine-induced memory-like natural killer cells exhibit enhanced responses against myeloid leukemia
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    • The novel BMI-1 inhibitor PTC596 downregulates MCL-1 and induces p53-independent mitochondrial apoptosis in acute myeloid leukemia progenitor cells
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    • Overexpression of the human antigen R suppresses the immediate paradoxical proliferation of melanoma cell subpopulations in response to suboptimal BRAF inhibition
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    • Unraveling cell populations in tumors by single-cell mass cytometry
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    • Eradication of CML stem cells
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    • NRASG12V oncogene facilitates self-renewal in a murine model of acute myelogenous leukemia
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    • Dasatinib changes immune cell profiles concomitant with reduced tumor growth in several murine solid tumor models
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    • Mutant IDH1 Downregulates ATM and Alters DNA Repair and Sensitivity to DNA Damage Independent of TET2
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    • PD-1 marks dysfunctional regulatory T cells in malignant gliomas
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    • Single-cell measurement of the uptake, intratumoral distribution and cell cycle effects of cisplatin using mass cytometry
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    • Mass cytometry analysis shows that a novel memory phenotype B cell is expanded in multiple myeloma
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    • Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis
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    • Myelodysplastic Syndrome Revealed by Systems Immunology in a Melanoma Patient Undergoing Anti-PD-1 Therapy
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    • High-Dimensional Analysis of Acute Myeloid Leukemia Reveals Phenotypic Changes in Persistent Cells during Induction Therapy
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    • Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks
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  • Review

    • Progress and applications of mass cytometry in sketching immune landscapes
      Zhang, T., Warden, A. R., Li, Y. Clinical and Translational Medicine (2020): doi.org/10.1002/ctm2.206
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    • Use of mass cytometry to profile human T cell exhaustion
      Winkler, F., Bengsch, B. Frontiers in Immunology (2020): doi.org/10.3389/fimmu.2019.03039
    • Recent advances in single-cell ultra-trace analysis
      Wei, X., Lu, Y., Zhang, X. TrAC Trends in Analytical Chemistry (2020): doi.org/10.1016/j.trac.2020.115886
    • The use of single cell mass cytometry to define the molecular mechanisms of Varicella-Zoster virus lymphotropism
      Sen, N., Mukherjee, G., Arvin, A.M. Frontiers in Microbiology (2020): doi.org/10.3389/fmicb.2020.01224
    • Key steps and methods in the experimental design and data analysis of highly multi-parametric flow and mass cytometry
      Paulina Rybakowska ,Marta E.Alarcón-Riquelme, Concepción Marañón Computational and Structural Biotechnology Journal (2020): https://doi.org/10.1016/j.csbj.2020.03.024
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      Adeeb H Rahman, Dirk Homann Current Opinion in Endocrinology, Diabetes and Obesity (2020): DOI: 10.1097/MED.0000000000000549
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      Kaitlin C O'Boyle, Takuya Ohtani, Sasikanth Manne Methods in Molecular Biology (2020): DOI: 10.1007/978-1-0716-0266-9_1
    • Microglia heterogeneity in the single-cell era
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    • Recent Advances in Computer-Assisted Algorithms for Cell Subtype Identification of Cytometry Data
      Liu, P., Liu, S., Fang, Y. Frontiers in Cell and Developmental Biology (2020): doi.org/10.3389/fcell.2020.00234
    • The role of single-cell technology in the study and control of infectious diseases
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    • Mass Cytometry of Hematopoietic Cells
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    • The use and limitations of single‐cell mass cytometry for studying human microglia function
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    • Mass cytometry—A tool for the curious Networking in Berlin
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    • Technologies for assessing vaccine responses in the very young
      Brodin, P. Current Opinion in Immunology (2020): doi.org/10.1016/j.coi.2020.03.011
    • 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
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      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
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      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
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      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):
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    • 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
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      Smith, E.A. and Hodges, H.C. Trends in Cancer (2019): 411-425
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    • The role of proteomics in assessing beta-cell dysfunction and death in type 1 diabetes
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    • Appreciating what’s unique about every stem cell
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      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
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      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

    • Mass cytometry reveals immune signatures associated with cytomegalovirus (CMV) control in recipients of allogeneic haemopoietic stem cell transplant and CMV-specific T cells
      McGuire, H.M., Rizzetto, I., Withers, B. P. Clinical & Translational Immunology (2020): doi: 10.1002/cti2.1149
    • Mesenchymal stem cells alleviate LPS-induced acute lung injury by inhibiting the proinflammatory function of Ly6C+ CD8+ T cells
      Zhu, J., Feng, B., Xu, Y. Cell Death & Disease (2020): doi.org/10.1038/s41419-020-03036-1
    • Activation of the receptor tyrosine kinase RET improves long-term hematopoietic stem cell outgrowth and potency
      Grey, W., R, Chauhan.,Piganeau, M. Blood (2020): DOI: 10.1182/blood.2020006302
    • 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
    • High-resolution myogenic lineage mapping by single-cell mass cytometry
      Porpiglia, E., Samusik, N., Van Ho, A.T. et al. Nature Cell Biology (2017): 558–67
    • A continuous molecular roadmap to iPSC reprogramming through progression analysis of single-cell mass cytometry
      Zunder, E.R., Lujan, E., Goltsev, Y. et al. Cell Stem Cell (2015): 323–37
    • Early reprogramming regulators identified by prospective isolation and mass cytometry
      Lujan, E., Zunder, E.R., Ng, Y.H. et al. Nature (2015): 352–6
    • Cell expansion during directed differentiation of stem cells toward the hepatic lineage
      Raju, R., Chau, D., Cho, D.S. et al. Stem Cells and Development (2016): 274–84
    • Distinct signaling programs control human hematopoietic stem cell survival and proliferation
      Knapp, D.J., Hammond, C.A., Aghaeepour, N. et al. Blood (2016): 307–18
    • Combination Of Mass Cytometry and Imaging Analysis Reveals Origin, Location, and Functional Repopulation of Liver Myeloid Cells in Mice
      David, B.A., Rezende, R.M., Antunes, M.M. et al. Gastroenterology (2016): 1,176–91
    • High-dimensional analysis of the murine myeloid cell system
      Becher, B., Schlitzer, A., Chen, J. et al. Nature Immunology (2014): 1,181–9
    • Low-dose IL-2 selectively activates subsets of CD4+ Tregs and NK cells
      Hirakawa, M., Matos, T., Liu, H. et al. JCI Insight (2016): e89278
    • Studying hematopoiesis using single-cell technologies
      Ye, F., Huang, W., Guo, G. Journal of Hematology and Oncology (2017): 27

  • Other

    • Single-cell analyses of colon and blood reveal distinct immune cell signatures of ulcerative colitis and Crohn’s disease
      Mitsialis, V., Wall, S., Liu, P. Gastroenterology (2021): DOI: 10.1053/j.gastro.2020.04.074
    • Immune cells in the placental villi contribute to intra-amniotic inflammation
      Toothaker, J.M., Presicce, P., Cappelletti, M. Frontiers in Immunology (2021): 28-30
    • A distinct GM-CSF+ T helper cell subset requires T-bet to adopt a TH1 phenotype and promote neuroinflammation
      Rasouli, J., Casella, G., Yoshimura, S. Science Immunology (2020): DOI: 10.1126/sciimmunol.aba9953
    • Naive CD8+ T cells expressing CD95 increase human cardiovascular disease severity
      Padgett, L.E., Dinh, H. Q., Wu, R. Arteriosclerosis, Thrombosis, and Vascular Biology (2020): doi/suppl/10.1161/ATVBAHA.120.315106.
    • Monogenic inflammatory bowel disease: It's never too late to make a diagnosis
      Vardi, I., Chermesh, I., Werner, L. Frontiers in Immunology (2020): doi.org/10.3389/fimmu.2020.01775
    • IgG3+ B cells are associated with the development of multiple sclerosis
      Marsh-Wakefield, Ashhurst, T., Trend, S. Clinical & Translational Immunology (2020): doi.org/10.1002/cti2.1133
    • Systematic Study of the Immune Components after Ischemic Stroke Using CyTOF Techniques
      Li, Y., Wang, Y, Yao, Y. Journal of Immunology Research (2020): doi.org/10.1155/2020/9132410
    • Hypothalamic circuitry underlying stress-induced insomnia and peripheral immunosuppression
      Li, S.B., Borniger, J. C., Yamaguchi, H. Science Advances (2020): DOI: 10.1126/sciadv.abc2590
    • Single-cell mass cytometry of microglia in major depressive disorder reveals a non-inflammatory phenotype with increased homeostatic marker expression
      Bottcher, C., Fernández-Zapata, C., Snijders, G. J. L. Translational Psychiatry (2020): doi.org/10.1038/s41380-019-0516-z
    • Soluble PD-L1 improved direct ARDS by reducing monocyte-derived macrophages
      Xu, J., Wang, J., Wang, X. Cell Death and Disease (2020): doi.org/10.1038/s41419-020-03139-9
    • Visualizing dynamic changes at the maternal-fetal interface throughout human pregnancy by mass cytometry
      van der Zwan, A., Beyrend, G., Laban, S. Frontiers in Immunology (2020): doi.org/10.3389/fimmu.2020.571300
    • Mesenchymal stromal cell-derived extracellular vesicle therapy prevents preeclamptic physiology through intrauterine immunomodulation
      Taglauer, E.S, Wills, G. R., Reis, M. Biology of Reproduction (2020): DOI: 10.1093/biolre/ioaa198
    • Endothelial p300 promotes portal hypertension and hepatic fibrosis through CCL2‐mediated angiocrine signaling
      Gao, J., Wei, B., Liu, M. Hepatology (2020): doi.org/10.1136/jitc-2020-001662
    • Sirolimus for treatment of patients with inclusion body myositis: a randomised, double-blind, placebo-controlled, proof-of-concept, phase 2b trial
      Benveniste, O., Horgel, J. Y., Belin, L. The Lancet Rheumatology (2020): doi.org/10.1016/S2665-9913(20)30280-0
    • Immune phenotyping of Erdheim-Chester disease through mass cytometry highlights decreased proportion of non-classical monocytes and increased proportion of Th17 cells
      Zhang, Y., Zabinyakov, N., Majonis, D. Papo, M., Corneau , A., Robin, B. (2020): DOI: 10.1136/annrheumdis-2020-217316
    • Lower PDL1/2 and AXL expression on lung myeloid cells suggests inflammatory bias in smoking and COPD
      Vasudevan, S., Vásquez , J.J., Chen, W. American Journal of Respiratory Cell and Molecular Biology (2020): DOI: 10.1165/rcmb.2020-0085OC
    • Safety and feasibility of hematopoietic progenitor stem cell collection by mobilization with plerixafor followed by apheresis versus bone marrow harvest in patients with sickle cell disease in the multi-center HGB-206 trial
      Tisdale, J.F., Pierciey Jr, F.J., Bonner, M. American Journal of Hematology (2020): DOI: 10.1002/ajh.25867
    • Blood natural killer cell deficiency reveals an immunotherapy strategy for atopic dermatitis
      Mack, M.R., Brestoff, J.R., Trier, A.M. Science Translational Medicine (2020): DOI: 10.1126/scitranslmed.aay1005
    • Cellular census of human fibrosis defines functionally distinct stromal cell types and states
      Layton, T.B., Williams, L., McCann, F. Nature Communications (2020): doi.org/10.1038/s41467-020-16264-y
    • The Intermucosal Connection between the Mouth and Gut in Commensal Pathobiont-Driven Colitis
      Kitamoto, S., Jiao, Y., Hayashi, A. Cell (2020): doi.org/10.1016/j.cell.2020.05.048
    • Pediatric burn survivors have long-term immune dysfunction with diminished vaccine response
      Johnson, B.Z., McAlister, S., McGuire, H.M. Frontiers in Immunology (2020): DOI: 10.1002/eji.202048531
    • Mass cytometry analysis reveals a distinct immune environment in peritoneal fluid in endometriosis: a characterisation study
      Guo, M., Bafligil, C., Tapmeier, T. BMC Medicine (2020): 3
    • Single-cell mass cytometry reveals cross-talk between inflammation-dampening and inflammation-amplifying cells in osteoarthritic cartilage
      Grandi, F.C., Baskar, R., Smeriglio, P. Science Advances (2020): eaay5352.
    • Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer’s disease
      Gate, D., Saligrama, N., Leventhal, O. Nature (2020): 399–404
    • An RTEL1 mutation links to infantile-onset ulcerative colitis and severe immunodeficiency
      Ziv, A., Werner, L., Konnikova, L. Journal of Clinical Immunology (2020): DOI: 10.1007/s10875-020-00829-z
    • TLR2 Dimerization Blockade Allows Generation of Homeostatic Intestinal Macrophages under Acute Colitis Challenge
      Gross-Vered, M., Zarmi, B., Humphries, F. Journal of Immunology (2020): DOI: 10.4049/jimmunol.1900470
    • The Proximal Airway Is a Reservoir for Adaptive Immunologic Memory in Idiopathic Subglottic Stenosis
      Gelbard, A., Wanjalla, C., Wootten, C.T. The Laryngoscope (2020): DOI: 10.1002/lary.28840
    • Costimulation blockade disrupts CD4+ T cell memory pathways and uncouples their link to decline in β-cell function in type 1 diabetes
      Eichmann, M., Baptista, R., Ellis, R.J. Jounal of Immunology (2020): DOI: 10.4049/jimmunol.1901439
    • C9orf72 suppresses systemic and neural inflammation induced by gut bacteria
      Burberry, A., Cuoto, A., Smith, K.S. Nature (2020): 89–94
    • Characterization of pulmonary immune responses to hyperoxia by high-dimensional mass cytometry analyses
      Hanidziar, D., Nakahori, Y., Cahill, L.A. et al. Scientific Reports (2020): 4677.
    • Wearing-off at the end of natalizumab dosing intervals is associated with low receptor occupancy
      Bringeland, G.H., Blaser, N., Myhr, K.-M. et al. Neurology Neuroimmunology & Neuroinflammation (2020): doi: 10.1212/NXI.0000000000000678.
    • 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
    • Mass cytometry studies of patients with autoimmune endocrine diseases reveal distinct disease-specific alterations in immune cell subsets
      Magnusson, L., Barcenilla, H., Pihl, M. et al. Frontiers in Immunology (2020): doi: 10.3389/fimmu.2020.00288.
    • Smooth muscle cell reprogramming in aortic aneurysms
      Chen, P.-Y., Qin, L., Li, G. et al. Cell Stem Cell (2020): 542-557.
    • Th17 reprogramming of T cells in systemic juvenile idiopathic arthritis
      Henderson, L.A., Hoyt, K.J., Lee, P.Y. et al. Journal of Clinical Investigation Insight (2020): e132508.
    • Circulating factors in trauma plasma activate specific human immune cell subsets
      Cahill, L.A., Guo, F., Nguyen, J. et al. Injury (2020): 819-829.
    • Cell-type-specific signaling networks in heterocellular organoids
      Qin, X., Sufi, J., Vlckova, P. et al. Nature Methods (2020): 335-342.
    • Deep phenotyping of urinary leukocytes by mass cytometry reveals a leukocyte signature for early and non-invasive prediction of response to treatment in active lupus nephritis
      Bertolo, M., Baumgart, S., Durek, P. et al. Frontiers in Immunology (2020): doi:10.3389/fimmu.2020.00256
    • Tumor necrosis factor-related apoptosis-inducing ligand receptor deficiency promotes the ductular reaction, macrophage accumulation, and hepatic fibrosis in the Mdr2 -/- mouse
      Krishnan, A., Katsumi, T., Guicciardi, M.E. et al. American Journal of Pathology (2020): 30135-8
    • Targeted apoptosis of ductular reactive cells reduces hepatic fibrosis in a mouse model of cholestasis
      Azad, A.I., Krishnan, A., Troop, L. et al. Hepatology (2020): doi: 10.1002/hep.31211.
    • 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
    • Rheumatoid arthritis patients display B-cell dysregulation already in the naïve repertoire consistent with defects in B-cell tolerance
      Wang, Y., Lloyd, K.A., Melas, I., et al. Scientific Reports (2019): 19995
    • Leptin induces TNFα-dependent inflammation in acquired generalized lipodystrophy and combined Crohn’s disease
      Ziegler, J.F., Böttcher, C., Letizia, M., et al. Nature Communications (2019): 5629
    • A novel immature natural killer cell subpopulation predicts relapse after cord blood transplantation
      Li, L., Chen, H., Marin, D., et al. Transplantation (2019): 4,117–4,130
    • PD-1H (VISTA)–mediated suppression of autoimmunity in systemic and cutaneous lupus erythematosus
      Han, X., Vesely, M.D., Yang, W., et al. Science Translational Medicine (2019): eaax1159.
    • Sphingosine-1-phosphate lyase inhibition alters the S1P gradient and ameliorates Crohn’s-like Ileitis by suppressing thymocyte maturation
      Karuppuchamy, T., Tyler, C.J., Lundborg, L.R., et al. Inflammatory Bowel Diseases (2020): 216-228
    • Immunome perturbation is present in patients with juvenile idiopathic arthritis who are in remission and will relapse upon anti-TNFα withdrawal
      Leong, J.Y., Chen, P., Yeo, J.G. et al. Annals of the Rheumatic Diseases (2019): 1,712-1,721
    • Anti‐TNF treatment negatively regulates human CD4+ T‐cell activation and maturation in vitro, but does not confer an anergic or suppressive phenotype
      Povoleri, G.M., Lalnunhlimi, S., Steel, K.J.A., et al. European Journal of Immunology (2019): DOI: 10.1002/eji.201948190
    • Defective glycosylation and multisystem abnormalities characterize the primary immunodeficiency XMEN disease
      Ravell, J.C., Matsuda-Lennikov, M., Chauvin, S.D., et al. Journal of Clinical Investigation (2019): 507-522
    • TRAIL-induced variation of cell signaling states provides nonheritable resistance to apoptosis
      Baskar, R., Fienberg, H.G., Khair, Z., et al. Life Science Alliance (2019): DOI: 10.26508/lsa.201900554
    • Applicability, safety and biological activity of regulatory T cell therapy in liver transplantation
      Sánchez–Fueyo, A., Whitehouse, G., Grageda, N., et al. American Journal of Transplantation (2019): DOI: 10.1111/ajt.15700
    • Trisomy 21 dysregulates T cell lineages toward an autoimmunity-prone state associated with interferon hyperactivity
      Araya, P., Waugh, K.A., Sullivan, K.D. et al. Proceedings of the National Academy of Sciences of the United States of America (2019): 24,231-24,241
    • Characterization of phenotypes and functional activities of leukocytes from rheumatoid arthritis patients by mass cytometry
      Pereira, A.L., Bitoun, S., Paoletti, A. et al. Frontiers in Immunology (2019): doi: 10.3389/fimmu.2019.02384
    • Anti-inflammatory mechanisms of the novel cytokine interleukin-38 in allergic asthma
      Sun, X., Hou, T., Cheung, E. et al. Cellular & Molecular Immunology (2019): doi: 10.1038/s41423-019-0300-7
    • Single-cell analysis of Crohn's disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy
      Martin, J.C., Chang, C., Boschetti, G. et al. Cell (2019): 1,493–1,508.e20
    • Lung endothelial cell antigen cross-presentation to CD8+T cells drives malaria-associated lung injury
      Claser, C., Teng Nguee, S.Y., Balachander, A. et al. Nature Communications (2019): 4241
    • PD-1hi CXCR5- T peripheral helper cells promote B cells responses in lupus via MAF and IL-21.
      Bocharnikov, A.V., Keegan, J., Wacleche, V.S. et al. JCI Insight (2019): 130062
    • Multiplexed imaging of immune cells in staged multiple sclerosis lesions by mass cytometry
      Ramaglia, V., Sheikh-Mohamed, S., Legg, K. et al. eLife (2019): e48051
    • Immunomodulatory effect of mesenchymal stem cells in chemical-induced liver injury: a high-dimensional analysis
      Liu, J., Feng, B., Xu, Y. et al. Stem Cell Research & Therapy (2019): 262
    • Transcriptomic analysis and High dimensional phenotypic mapping of mononuclear phagocytes in mesenteric lymph nodes reveal differences between ulcerative colitis and Crohn’s disease
      Chapuy, L, Bsat, M., Rubio, M. et al. Journal of Crohn's and Colitis (2019): doi: 10.1093/ecco-jcc/jjz156.
    • A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry
      Damond, N., Engler, S., Zanotelli, V.R.T. et al. Cell Metabolism (2019): doi: 10.1016/j.cmet.2018.11.014
    • Reversal of epigenetic aging and immunosenescent trends in humans
      Fahy, G.M., Brooke, R.T., Watson, J.P. et al. Aging Cell (2019): doi: 10.1111/acel.13028
    • Integrin and transcriptomic profiles identify a distinctive synovial CD8+ T cell subpopulation in spondyloarthritis.
      Qaiyum, Z., Gracey, E., Yao, Y. et al. Annals of the Rheumatic Diseases (2019): doi: 10.1136/annrheumdis-2019-215349
    • Common variable immunodeficiency-associated endotoxemia promotes early commitment to the T follicular lineage
      Le Coz, C., Bengsch, B., Khanna, C. et al. Journal of Allergy and Clinical Immunology (2019): doi: 10.1016/j.jaci.2019.08.007
    • Cytometry by Time of Flight identifies distinct signatures in patients with systemic sclerosis, systemic lupus erythematosus and Sjögrens syndrome
      van der Kroef, M., van den Hoogen, L.L., Mertens, J.S. et al. European Journal of Immunology (2019): doi: 10.1002/eji.201948129.
    • High-dimensional analysis reveals a pathogenic role of inflammatory monocytes in experimental diffuse alveolar hemorrhage
      Lee, P.Y., Nelson-Maney, N., Huang, Y. et al. JCI Insight (2019): e129703.
    • Integrin β1-enriched extracellular vesicles mediate monocyte adhesion and promote liver inflammation in murine NASH
      Guo, Q., Furuta, K., Lucien, F. et al. Journal of Hepatology (2019): doi: 10.1016/j.jhep.2019.07.019.
    • Expansion of luminal progenitor cells in the aging mouse and human prostate
      Crowell, P.D., Fox, J.J., Hashimoto, T. et al. Cell Reports (2019): doi: 10.1016/j.celrep.2019.07.007
    • Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry
      Zhang, F., Wei, K., Slowikowski, K. et al. Nature Immunology (2019): 928-942.
    • Mycophenolate mofetil reduces STAT3 phosphorylation in systemic lupus erythematosus patients
      Slight-Webb, S., Guthridge, J.M., Chakravarty, E.F. et al. JCI Insight (2019): e124575.
    • Infliximab–tumor necrosis factor complexes elicit formation of anti-drug antibodies
      Bar-Yoseph, H., Pressman, S., Blatt, A. et al. Gastroenterology (2019): 41201-8
    • Mass cytometry reveals an impairment of B cell homeostasis in anti-synthetase syndrome
      Dzangué-Tchoupou, G., Allenbach, Y., Preuße, C. et al. Journal of Neuroimmunology (2019): 212-215.
    • GM-CSF and CXCR4 define a T helper cell singature in multiple sclerosis
      Galli, E., Hartmann, F.J., Schreiner, B. et al. Nature Medicine (2019): 1,290-1,300
    • An integrated framework using high-dimensional mass cytometry and fluorescent flow cytometry identifies discrete B cell subsets in patients with red meat allergy
      Cox, K.M., Commins, S.P., Capaldo, B.J. et al. Clinical & Experimental Allergy (2018): 615-625
    • Imaging Mass Cytometry and single-cell genomics reveals differential depletion and repletion of B-cell populations following ofatumumab treatment in cynomolgus monkeys
      Theil,D., Smith,P., Huck, C. et al. Frontiers in Immunology (2019): 1,340
    • Unifying mechanism for different fibrotic diseases
      Wernig, G., Chen, S.Y., van Neste, C. et al. Proceedings of the National Academy of Sciences of the United States of Americ (2017): 4,757-4,762
    • Mass cytometry identifies a distinct monocyte cytokine signature shared by clinically heterogeneous pediatric SLE patients
      O'Gorman, W.E., Kong, D.S., Balboni, I.M. et al. Journal of Autoimmunity (2017): 74-89
    • The oxysterol synthesising enzyme CH25H contributes to the development of intestinal fibrosis
      Raselli, T., Wyss, A., Gonzalez Alvarado, M.N. et al. Journal of Crohn's and Colitis (2019): doi: 10.1093/ecco-jcc/jjz039
    • Systemic immunologic consequences of chronic periodontitis
      Gaudilliere, D.K., Culos, A., Djebali, K. et al. Journal of Dental Research (2019): doi: 10.1177/0022034519857714.
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