We, at CytoGenie.org, would like to acknowledge the below publications and it’s authors, referenced in the development of AutoGate and relevant User Guides.
♠ Two physically, functionally, and developmentally distinct peritoneal macrophage subsets
Eliver Eid Bou Ghosn, Alexandra A. Cassado, Gregory R. Govoni, Takeshi Fukuhara, Yang Yang, Denise M. Monack, Karina R. Bortoluci, Sandro R. Almeida, Leonard A. Herzenberg, & Leonore A. Herzenberg
♠ UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction
Leland McInnes Tutte Institute for Mathematics and Computing, John Healy Tutte Institute for Mathematics and Computing & James Melville
♠ Dimensionality reduction for visualizing single-cell data using UMAP
Etienne Becht Leland McInnes, John Healy, Charles-Antoine Dutertre, Immanuel W H Kwok, Lai Guan Ng, Florent Ginhoux & Evan W Newell
♠ Automatic Clustering of Flow Cytometry Data with Density-Based Merging
Guenther Walther, Noah Zimmerman, Wayne Moore, David Parks, Stephen Meehan, Ilana Belitskaya, Jinhui Pan, & Leonore Herzenberg
♠ Earth Mover’s Distance (EMD) : A True Metric for Comparing Biomarker Expression Levels in Cell Populations
Darya Y. Orlova, Noah Zimmerman, Stephen Meehan, Connor Meehan, Jeffrey Waters, Eliver E. B. Ghosn, Alexander Filatenkov, Gleb A. Kolyagin, Yael Gernez, Shanel Tsuda, Wayne Moore, Richard B. Moss, Leonore A. Herzenberg & Guenther Walther
♠ QFMatch: multidimensional flow and mass cytometry samples alignment
Darya Y. Orlova, Stephen Meehan, David Parks, Wayne A. Moore, Connor Meehan, Qian Zhao, Eliver E. B. Ghosn, Leonore A. Herzenberg & Guenther Walther
♠ Automated subset identification and characterization pipeline for multidimensional flow and mass cytometry data clustering and visualization
Stephen Meehan, Gleb A. Kolyagin, David Parks, Justin Youngyunpipatkul, Leonore A. Herzenberg, Guenther Walther, Eliver E.B. Ghosn & Darya Y. Orlova
♠ Automated mapping of phenotype space with single-cell data
Samusik N, Good Z, Spitzer MH, Davis KL & Nolan GP
♠ Comparison of CyTOF assays across sites: Results of a six-center pilot study
Michael D. Leipold, Gerlinde Obermoser, Craig Fenwick, Katja Kleinstuber, Narges Rashidi, John P. McNevind, Allison N. Naue, Lisa E. Wagare, Virginie Rozot, Mark M. Davise, Stephen DeRosa, Giuseppe Pantaleo, Thomas J. Scriba, Bruce D. Walker, Lars R. Olsen & Holden T. Maecker
♠ Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses
Shadi Toghi Eshghi, Amelia Au-Yeung, Chikara Takahash, Christopher R. Bolen, Maclean N. Nyachienga, Sean P. Lear, Cherie Green, W. Rodney Mathews & William E. O’Gorman
♠ OMIP-047: High-Dimensional Phenotypic Characterization of B Cells
Thomas Liechti, Huldrych F. Gu€nthard, Alexandra Trkola
♠ OMIP-044: 28-Color Immunophenotyping of the Human Dendritic Cell Compartment
Florian Mair & Martin Prlic