Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics. - Chris Barry; Matthew T. Schmitz; Cara Argus; Jennifer M. Bolin; Mitchell D. Probasco; Ning Leng; Bret Duffin; John W. Steill; Scott Swanson; Brian E. McIntosh; Ron M. Stewart; Christina Kendziorski; et al. (PLoS Comput. Biol., 2019)

Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data. - Parker Knight; Marie-Pierre L. Gauthier; Carolina E. Pardo; Russell P. Darst; Kevin Kapadia; Hadley Browder; Eliza Morton; Alberto Riva; Michael P. Kladde; Rhonda Bacher (Bioinform., 2021)

Normalization by distributional resampling of high throughput single-cell RNA-sequencing data. - Jared Brown; Zijian Ni; Chitrasen Mohanty; Rhonda Bacher; Christina Kendziorski (Bioinform., 2021)

Data-driven assessment of dimension reduction quality for single-cell omics data. - Xiaoru Dong; Rhonda Bacher (Patterns, 2022)

Leveraging remeasured samples in biomedical studies. - Luer Zhong; Rhonda Bacher (Nat. Comput. Sci., 2023)

Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference. - Xiaoru Dong; Jack R. Leary; Chuanhao Yang; Maigan Brusko; Todd M. Brusko; Rhonda Bacher (Briefings Bioinform., 2024)