Mass Cytometry: Single Cells, Many Features von Spitzer, Matthew H., Nolan, Garry P.

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Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development von Bendall, Sean C., Davis, Kara L., Amir, El-ad David, Tadmor, Michelle D., Simonds, Erin F., Chen, Tiffany J., Shenfeld, Daniel K., Nolan, Garry P., Pe’er, Dana

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Metal-isotope-tagged monoclonal antibodies for high-dimensional mass cytometry von Han, Guojun, Spitzer, Matthew H., Bendall, Sean C., Fantl, Wendy J., Nolan, Garry P.

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Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8 + T Cell Phenotypes von Newell, Evan W., Sigal, Natalia, Bendall, Sean C., Nolan, Garry P., Davis, Mark M.

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Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front von Schürch, Christian M., Bhate, Salil S., Barlow, Graham L., Phillips, Darci J., Noti, Luca, Zlobec, Inti, Chu, Pauline, Black, Sarah, Demeter, Janos, McIlwain, David R., Kinoshita, Shigemi, Samusik, Nikolay, Goltsev, Yury, Nolan, Garry P.

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Single-cell mass cytometry reveals distinct populations of brain myeloid cells in mouse neuroinflammation and neurodegeneration models von Ajami, Bahareh, Samusik, Nikolay, Wieghofer, Peter, Ho, Peggy P., Crotti, Andrea, Bjornson, Zach, Prinz, Marco, Fantl, Wendy J., Nolan, Garry P., Steinman, Lawrence

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Automated identification of stratifying signatures in cellular subpopulations von Bruggner, Robert V, Bodenmiller, Bernd, Dill, David L, Tibshirani, Robert J, Nolan, Garry P

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Three-dimensional intact-tissue sequencing of single-cell transcriptional states von Wang, Xiao, Allen, William E, Wright, Matthew A, Sylwestrak, Emily L, Samusik, Nikolay, Vesuna, Sam, Evans, Kathryn, Liu, Cindy, Ramakrishnan, Charu, Liu, Jia, Nolan, Garry P, Bava, Felice-Alessio, Deisseroth, Karl

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A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry von Zunder, Eli R., Lujan, Ernesto, Goltsev, Yury, Wernig, Marius, Nolan, Garry P.

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Structural Linkage between Ligand Discrimination and Receptor Activation by Type I Interferons von Thomas, Christoph, Moraga, Ignacio, Levin, Doron, Krutzik, Peter O., Podoplelova, Yulia, Trejo, Angelica, Lee, Choongho, Yarden, Ganit, Vleck, Susan E., Glenn, Jeffrey S., Nolan, Garry P., Piehler, Jacob, Schreiber, Gideon, Garcia, K. Christopher

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Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma von Ji, Andrew L., Rubin, Adam J., Thrane, Kim, Jiang, Sizun, Reynolds, David L., Meyers, Robin M., Guo, Margaret G., George, Benson M., Mollbrink, Annelie, Bergenstråhle, Joseph, Larsson, Ludvig, Bai, Yunhao, Zhu, Bokai, Bhaduri, Aparna, Meyers, Jordan M., Rovira-Clavé, Xavier, Hollmig, S. Tyler, Aasi, Sumaira Z., Nolan, Garry P., Lundeberg, Joakim, Khavari, Paul A.

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High-Dimensional Phenotypic Mapping of Human Dendritic Cells Reveals Interindividual Variation and Tissue Specialization von Alcántara-Hernández, Marcela, Leylek, Rebecca, Wagar, Lisa E., Engleman, Edgar G., Keler, Tibor, Marinkovich, M. Peter, Davis, Mark M., Nolan, Garry P., Idoyaga, Juliana

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Highly multiplexed simultaneous detection of RNAs and proteins in single cells von Frei, Andreas P, Bava, Felice-Alessio, Zunder, Eli R, Hsieh, Elena W Y, Chen, Shih-Yu, Nolan, Garry P, Gherardini, Pier Federico

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Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis von Levine, Jacob H., Simonds, Erin F., Bendall, Sean C., Davis, Kara L., Amir, El-ad D., Tadmor, Michelle D., Litvin, Oren, Fienberg, Harris G., Jager, Astraea, Zunder, Eli R., Finck, Rachel, Gedman, Amanda L., Radtke, Ina, Downing, James R., Pe’er, Dana, Nolan, Garry P.

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Computational solutions to large-scale data management and analysis von Schadt, Eric E, Linderman, Michael D, Sorenson, Jon, Lee, Lawrence, Nolan, Garry P

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viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia von Amir, El-ad David, Davis, Kara L, Tadmor, Michelle D, Simonds, Erin F, Levine, Jacob H, Bendall, Sean C, Shenfeld, Daniel K, Krishnaswamy, Smita, Nolan, Garry P, Pe'er, Dana

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Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data von Hickey, John W., Tan, Yuqi, Nolan, Garry P., Goltsev, Yury

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Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma von Phillips, Darci, Matusiak, Magdalena, Gutierrez, Belén Rivero, Bhate, Salil S., Barlow, Graham L., Jiang, Sizun, Demeter, Janos, Smythe, Kimberly S., Pierce, Robert H., Fling, Steven P., Ramchurren, Nirasha, Cheever, Martin A., Goltsev, Yury, West, Robert B., Khodadoust, Michael S., Kim, Youn H., Schürch, Christian M., Nolan, Garry P.

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CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images von Lee, Michael Y, Bedia, Jacob S, Bhate, Salil S, Barlow, Graham L, Phillips, Darci, Fantl, Wendy J, Nolan, Garry P, Schürch, Christian M

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Organization of the human intestine at single-cell resolution von Hickey, John W., Becker, Winston R., Nevins, Stephanie A., Horning, Aaron, Perez, Almudena Espin, Zhu, Chenchen, Zhu, Bokai, Wei, Bei, Chiu, Roxanne, Chen, Derek C., Cotter, Daniel L., Esplin, Edward D., Weimer, Annika K., Caraccio, Chiara, Venkataraaman, Vishal, Schürch, Christian M., Black, Sarah, Brbić, Maria, Cao, Kaidi, Chen, Shuxiao, Zhang, Weiruo, Monte, Emma, Zhang, Nancy R., Ma, Zongming, Leskovec, Jure, Zhang, Zhengyan, Lin, Shin, Longacre, Teri, Plevritis, Sylvia K., Lin, Yiing, Nolan, Garry P., Greenleaf, William J., Snyder, Michael

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