"Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE,” has been selected for advance online publication by Nature Biotechology.
Available online October 2, 2011, this article describes a novel method for automatically analyzing single-cell data produced from mass cytometry.
Peng Qiu, Ph.D., an assistant professor in the Department of Bioinformatics and Computational Biology, is the first author of this article that represents collaborative work with his former colleagues at Stanford University. SPADE, spanning-tree progression analysis of density-normalized events, views a single-cell cytometric dataset as a high-dimensional point cloud of cells, and uses topological methods to identify the geometry of the cloud. This geometry then reveals a distinct subpopulation of cells and a likely cellular hierarchy underlying the data. Authors: Peng Qiu, Erin F. Simonds,Sean C. Bendall, Kenneth D. Gibbs, Jr., Robert V Bruggner, Michael D. Linderman, Karen Sachs, Garry P. Nolan, and Sylvia K. Plevritis.