MASS CYTOMETRY LITERATURE

BARCODING:

  1. Behbehani, G. K., Thom, C., Zunder, E. R., Finck, R., Gaudilliere, B., Fragiadakis, G. K., ... & Nolan, G. P. (2014). Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining. Cytometry Part A, 85(12), 1011-1019.

  2. Hartmann, F. J., Simonds, E. F., & Bendall, S. C. (2018). A universal live cell barcoding-platform for multiplexed human single cell analysis. Scientific reports, 8(1), 10770.

  3. Mei, H. E., Leipold, M. D., Schulz, A. R., Chester, C., & Maecker, H. T. (2015). Barcoding of live human peripheral blood mononuclear cells for multiplexed mass cytometry. The Journal of Immunology, 194(4), 2022-2031.

EXPERIMENTAL PROTOCOL & STAINING:

  1. Chevrier, S., Crowell, H., Zanotelli, V. R. T., Engler, S., Robinson, M. D., & Bodenmiller, B. (2017). Channel crosstalk correction in suspension and imaging mass cytometry. BioRxiv, 185744.

  2. Kleinsteuber, K., Corleis, B., Rashidi, N., Nchinda, N., Lisanti, A., Cho, J. L., ... & Walker, B. D. (2016). Standardization and quality control for high‐dimensional mass cytometry studies of human samples. Cytometry Part A, 89(10), 903-913.

  3. Leelatian, N., Doxie, D. B., Greenplate, A. R., Mobley, B. C., Lehman, J. M., Sinnaeve, J., ... & Thompson, R. C. (2017). Single cell analysis of human tissues and solid tumors with mass cytometry. Cytometry Part B: Clinical Cytometry, 92(1), 68-78.

  4. Leelatian, N., Doxie, D. B., Greenplate, A. R., Sinnaeve, J., Ihrie, R. A., & Irish, J. M. (2017). Preparing viable single cells from human tissue and tumors for cytomic analysis. Current protocols in molecular biology, 118(1), 25C-1.

  5. Leipold, M. D., Obermoser, G., Fenwick, C., Kleinstuber, K., Rashidi, N., McNevin, J. P., ... & DeRosa, S. (2018). Comparison of CyTOF assays across sites: Results of a six-center pilot study. Journal of immunological methods, 453, 37-43.

ALGORITHMS & ANALYSIS:

  1. Amir el, A. D., K. L. Davis, M. D. Tadmor, E. F. Simonds, J. H. Levine, S. C. Bendall, D. K. Shenfeld, S. Krishnaswamy, G. P. Nolan, and D. Pe'er. 2013. viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nat Biotechnol 31: 545-552.

  2. Anchang, B., T. D. Hart, S. C. Bendall, P. Qiu, Z. Bjornson, M. Linderman, G. P. Nolan, and S. K. Plevritis. 2016. Visualization and cellular hierarchy inference of single-cell data using SPADE. Nat Protoc 11: 1264-1279.

  3. Bruggner, R. V., B. Bodenmiller, D. L. Dill, R. J. Tibshirani, and G. P. Nolan. 2014. Automated identification of stratifying signatures in cellular subpopulations. Proc Natl Acad Sci U S A 111: E2770-2777.

  4. Chen, H., M. C. Lau, M. T. Wong, E. W. Newell, M. Poidinger, and J. Chen. 2016. Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline. PLoS Comput Biol 12: e1005112.

  5. Chester, C., and H. T. Maecker. 2015. Algorithmic Tools for Mining High-Dimensional Cytometry Data. J Immunol 195: 773-779.

  6. Diggins, K. E., A. R. Greenplate, N. Leelatian, C. E. Wogsland, and J. M. Irish. 2017. Characterizing cell subsets using marker enrichment modeling. Nat Methods 14: 275-278.

  7. Mair, F., F. J. Hartmann, D. Mrdjen, V. Tosevski, C. Krieg, and B. Becher. 2016. The end of gating? An introduction to automated analysis of high dimensional cytometry data. Eur J Immunol 46: 34-43.

  8. Newell, E. W., & Cheng, Y. (2016). Mass cytometry: blessed with the curse of dimensionality. Nature immunology, 17(8), 890.

  9. Qiu, P., E. F. Simonds, S. C. Bendall, K. D. Gibbs, Jr., R. V. Bruggner, M. D. Linderman, K. Sachs, G. P. Nolan, and S. K. Plevritis. 2011. Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat Biotechnol 29: 886-891.

  10. Samusik, N., Z. Good, M. H. Spitzer, K. L. Davis, and G. P. Nolan. 2016. Automated mapping of phenotype space with single-cell data. Nat Methods 13: 493-496.

  11. Spitzer, M. H., P. F. Gherardini, G. K. Fragiadakis, N. Bhattacharya, R. T. Yuan, A. N. Hotson, R. Finck, Y. Carmi, E. R. Zunder, W. J. Fantl, S. C. Bendall, E. G. Engleman, and G. P. Nolan. 2015. IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system. Science 349: 1259425.

  12. van der Maaten, L., and G. Hinton. 2008. Visualizing Data using t-SNE. J Mach Learn Res 9: 2579-2605.

  13. Van Gassen, S., B. Callebaut, M. J. Van Helden, B. N. Lambrecht, P. Demeester, T. Dhaene, and Y. Saeys. 2015. FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data. Cytometry A 87: 636-645.

  14. van Unen, V., Höllt, T., Pezzotti, N., Li, N., Reinders, M. J., Eisemann, E., ... & Lelieveldt, B. P. (2017). Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types. Nature communications, 8(1), 1740. HSNE Algorithm

STUDIES UTILIZING MASS CYTOMETRY:

  1. Bandura, D. R., V. I. Baranov, O. I. Ornatsky, A. Antonov, R. Kinach, X. Lou, S. Pavlov, S. Vorobiev, J. E. Dick, and S. D. Tanner. 2009. Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal Chem 81: 6813-6822.

  2. Becher, B., A. Schlitzer, J. Chen, F. Mair, H. R. Sumatoh, K. W. Teng, D. Low, C. Ruedl, P. Riccardi-Castagnoli, M. Poidinger, M. Greter, F. Ginhoux, and E. W. Newell. 2014. High-dimensional analysis of the murine myeloid cell system. Nat Immunol 15: 1181-1189.

  3. Bendall, S. C., E. F. Simonds, P. Qiu, A. D. Amir el, P. O. Krutzik, R. Finck, R. V. Bruggner, R. Melamed, A. Trejo, O. I. Ornatsky, R. S. Balderas, S. K. Plevritis, K. Sachs, D. Pe'er, S. D. Tanner, and G. P. Nolan. 2011. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 332: 687-696.

  4. Bendall, S. C., K. L. Davis, A. D. Amir el, M. D. Tadmor, E. F. Simonds, T. J. Chen, D. K. Shenfeld, G. P. Nolan, and D. Pe'er. 2014. Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell 157: 714-725.

  5. Gaudilliere, B., G. K. Fragiadakis, R. V. Bruggner, M. Nicolau, R. Finck, M. Tingle, J. Silva, E. A. Ganio, C. G. Yeh, W. J. Maloney, J. I. Huddleston, S. B. Goodman, M. M. Davis, S. C. Bendall, W. J. Fantl, M. S. Angst, and G. P. Nolan. 2014. Clinical recovery from surgery correlates with single-cell immune signatures. Sci Transl Med 6: 255ra131.

  6. Gedye, C. A., Hussain, A., Paterson, J., Smrke, A., Saini, H., Sirskyj, D., ... & Ho, J. (2014). Cell surface profiling using high-throughput flow cytometry: a platform for biomarker discovery and analysis of cellular heterogeneity. PloS one, 9(8), e105602.

  7. Gonzalez, V. D., Samusik, N., Chen, T. J., Savig, E. S., Aghaeepour, N., Quigley, D. A., ... & Chen, S. Y. (2018). Commonly occurring cell subsets in high-grade serous ovarian tumors identified by single-cell mass cytometry. Cell reports, 22(7), 1875-1888.

  8. Horowitz, A., D. M. Strauss-Albee, M. Leipold, J. Kubo, N. Nemat-Gorgani, O. C. Dogan, C. L. Dekker, S. Mackey, H. Maecker, G. E. Swan, M. M. Davis, P. J. Norman, L. A. Guethlein, M. Desai, P. Parham, and C. A. Blish. 2013. Genetic and environmental determinants of human NK cell diversity revealed by mass cytometry. Sci Transl Med 5: 208ra145.

  9. Lavin, Y., Kobayashi, S., Leader, A., Amir, E. A. D., Elefant, N., Bigenwald, C., ... & Meinhof, K. (2017). Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses. Cell, 169(4), 750-765.

  10. Levine, J. H., E. F. Simonds, S. C. Bendall, K. L. Davis, A. D. Amir el, M. D. Tadmor, O. Litvin, H. G. Fienberg, A. Jager, E. R. Zunder, R. Finck, A. L. Gedman, I. Radtke, J. R. Downing, D. Pe'er, and G. P. Nolan. 2015. Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell 162: 184-197.

  11. Newell, E. W., N. Sigal, S. C. Bendall, G. P. Nolan, and M. M. Davis. 2012. Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. Immunity 36: 142-152.

  12. Newell, E. W., Sigal, N., Nair, N., Kidd, B. A., Greenberg, H. B., & Davis, M. M. (2013). Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization. Nature biotechnology, 31(7), 623.

  13. Spitzer, M. H., and G. P. Nolan. 2016. Mass Cytometry: Single Cells, Many Features. Cell 165: 780-791.