Automated identification of stratifying signatures in cellular subpopulations

By Robert V. Bruggner, Bernd Bodenmiller, David L. Dill, Robert Tibshirani, Garry P. Nolan. Proceedings of the National Academy of Sciences of the United States of America, 2014

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Systemic Immunity is Required for Effective Cancer Immunotherapy (2017, unknown): “We therefore determined whether the statistical inference integrated into Citrus could, instead, be applied to Scaffold maps.”
Sensitive detection of rare disease-associated cell subsets via representation learning (2016, methodology): “The frequency of these cell subsets has been reported to be associated with AIDS-free survival in previous studies 9,10,17 .”
Computational flow cytometry: helping to make sense of high-dimensional immunology data (2016, methodology): “Several approaches exist, such as flowType–RchyOptimyx 73 (which use density base clustering), Citrus 74 (which uses hierarchical clustering) or COMPASS 75 (which uses model based clustering).”
Multivariate Computational Analysis of Gamma Delta T Cell Inhibitory Receptor Signatures Reveals the Divergence of Healthy and ART-Suppressed HIV+ Aging (2018, methodology): “Doublets, dead cells, debris, CD14+ cells, and CD19+ cells were excluded by manual gating and remaining live single non-CD14, non-CD19 events (downsampled to 10,000 events/subject) were input into the CITRUS algorithm (61).”