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

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

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

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

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

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