Production of a Preliminary Quality Control Pipeline for Single Nuclei RNA-Seq and Its Application in the Analysis of Cell Type Diversity of Post-Mortem Human Brain Neocortex. - Brian D. Aevermann; Jamison M. McCorrison; Pratap Venepally; Rebecca D. Hodge; Trygve E. Bakken; Jeremy A. Miller; Mark Novotny; Danny N. Tran; Francisco Diez-Fuertes; Lena Christiansen; Fan Zhang; Frank Steemers; et al. (PSB, 2017)

Cell type discovery and representation in the era of high-content single cell phenotyping. - Trygve E. Bakken; Lindsay G. Cowell; Brian D. Aevermann; Mark Novotny; Rebecca D. Hodge; Jeremy A. Miller; Alexandra Lee; Ivan Chang; Jamison M. McCorrison; Bali Pulendran; Yu Qian; Nicholas J. Schork; et al. (BMC Bioinform., 2017)

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test. - Yun Zhang 021; Brian D. Aevermann; Trygve E. Bakken; Jeremy A. Miller; Rebecca D. Hodge; Ed S. Lein; Richard H. Scheuermann (Briefings Bioinform., 2021)

Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets. - Jia Zhao; Gefei Wang; Jingsi Ming; Zhixiang Lin; Yang Wang; Snigdha Agarwal; Aditi Agrawal; Ahmad Al-Moujahed; Alina Alam; Megan A. Albertelli; Paul Allegakoen; Thomas Ambrosi; et al. (Nat. Comput. Sci., 2022)

Cytosplore Simian Viewer: Visual Exploration for Multi-Species Single-Cell RNA Sequencing Data. - Soumyadeep Basu; Jeroen Eggermont; Thomas Kroes; Nikolas Jorstad; Trygve E. Bakken; Ed S. Lein; Boudewijn P. F. Lelieveldt; Thomas Höllt (VCBM, 2023)

Cytosplore EvoViewer: Visual Analytics of Conserved Evolutionary Patterns in multi-species single-cell sequencing data. - Soumyadeep Basu; Morgan Wirthlin; Jeroen Eggermont; Thomas Kroes; Boudewijn P. F. Lelieveldt; Ed S. Lein; Trygve E. Bakken; Thomas Höllt (PacificVis, 2025)