The SPADE algorithm was originally developed by Peng Qiu in Sylvia Plevritis' lab in collaboration with Garry P. Nolan's laboratory to visualize and analyze high-dimensional flow cytometry data, and especially data collected with the CyToF mass cytometer. SPADE and its use is described in the following publications/abstracts:
- Peng Qiu, Erin F. Simonds, Sean C. Bendall, Kenneth D. Gibbs Jr., Robert V. Bruggner, Michael D. Linderman, Karen Sachs, Garry P. Nolan, Sylvia K. Plevritis, "Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE", Nature Biotechnology, 2011.
- Sean C. Bendall, Erin F. Simonds, Peng Qiu, El-ad D. Amir, Peter O. Krutzik, Rachel Finck, Robert V. Bruggner, Rachel Melamed, Angelica Trejo, Olga I. Ornatsky, Robert S. Balderas, Sylvia K. Plevritis, Karen Sachs, Dana Pe’er, Scott D. Tanner, Garry P. Nolan, "Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum", Science, 332 (6030): 687-696.
- Michael D. Linderman, Erin F. Simonds, Peng Qiu, Zach Bjornson, Nikesh Kotecha, Teresa H. Meng, Sylvia Plrevritis, Garry P. Nolan, "Algorithmically recoving the hematopoietic lineage from high-dimensional cytometry data using SPADE", Congress of the Intl. Society for Advancement of Cytometry, 2010.
SPADE was implemented in Garry P. Nolan's Laboratory by Michael Linderman, Erin Simonds, Zach Bjornson, Robert Bruggner and Ketaki Sheode. The SPADE Cytoscape plugin includes code generously supplied by Cytobank under the AGPL license. SPADE is in wide use within the Nolan Laboratory as stand-alone tool and as part of the Cytobank online single-cell analysis platform.
Tools for visualizing and analyzing high-dimensional flow cytometry data is an important and vibrant area of research. The above publication has a rich related work section that situates SPADE in the context of other advances tools in this field, including probability state modeling with Gemstone, SAMSpectral (Zare, et al., BMC Bioinformatics, 2010.) and many others.