BIAS: Bioinformatics Integrated Application Software. - Greg Finak; N. Godin; Michael T. Hallett; François Pepin; Z. Rajabi; V. Srivastava; Z. Tang (Bioinform., 2005)

Merging Mixture Components for Cell Population Identification in Flow Cytometry. - Greg Finak; Ali Bashashati; Ryan Remy Brinkman; Raphael Gottardo (Adv. Bioinformatics, 2009)

Optimizing Transformations for Automated, High Throughput Analysis of Flow Cytometry Data. - Greg Finak; Juan-Manuel Perez; Andrew Weng; Raphael Gottardo (BMC Bioinform., 2010)

QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data. - Greg Finak; Wenxin Jiang 002; Jorge Pardo; Adam Asare; Raphael Gottardo (BMC Bioinform., 2012)

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. - Andrew McDavid; Greg Finak; Pratip K. Chattopadhyay; Maria Dominguez; Laurie Lamoreaux; Steven S. Ma; Mario Roederer; Raphael Gottardo (Bioinform., 2013)

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis. - Greg Finak; Jacob Frelinger; Wenxin Jiang 002; Evan W. Newell; John Ramey; Mark M. Davis; Spyros A. Kalams; Stephen C. De Rosa; Raphael Gottardo (PLoS Comput. Biol., 2014)

Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells. - Andrew McDavid; Lucas Dennis; Patrick Danaher; Greg Finak; Michael Krouse; Alice Wang; Philippa Webster; Joseph Beechem; Raphael Gottardo (PLoS Comput. Biol., 2014)

flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification. - Mehrnoush Malek; Mohammad Jafar Taghiyar; Lauren Chong; Greg Finak; Raphael Gottardo; Ryan Remy Brinkman (Bioinform., 2015)

ggCyto: next generation open-source visualization software for cytometry. - Phu Van; Wenxin Jiang 002; Raphael Gottardo; Greg Finak (Bioinform., 2018)

Selective Clustering Annotated using Modes of Projections. - Evan Greene; Greg Finak; Raphael Gottardo (CoRR, 2018)

New interpretable machine-learning method for single-cell data reveals correlates of clinical response to cancer immunotherapy. - Evan Greene; Greg Finak; Leonard A. D'Amico; Nina Bhardwaj; Candice D. Church; Chihiro Morishima; Nirasha Ramchurren; Janis M. Taube; Paul T. Nghiem; Martin A. Cheever; Steven P. Fling; Raphael Gottardo (Patterns, 2021)

A General Framework for Comparing Embedding Visualizations Across Class-Label Hierarchies. - Trevor Manz; Fritz Lekschas; Evan Greene; Greg Finak; Nils Gehlenborg (IEEE Trans. Vis. Comput. Graph., 2025)