A Guide to Teaching Data Science. - Stephanie C. Hicks; Rafael A. Irizarry (CoRR, 2016)

12 Grand Challenges in Single-Cell Data Science. - David Laehnemann; Johannes Köster; Ewa Szczurek; Davis J. McCarthy; Stephanie C. Hicks; Mark D. Robinson; Catalina A. Vallejos; Niko Beerenwinkel; Kieran R. Campbell; Ahmed Mahfouz; Luca Pinello; Pavel Skums; et al. (PeerJ Prepr., 2019)

TreeSummarizedExperiment: a S4 class for data with hierarchical structure. - Ruizhu Huang; Charlotte Soneson; Felix G. M. Ernst; Kevin C. Rue-Albrecht; Guangchuang Yu; Stephanie C. Hicks; Mark D. Robinson (F1000Research, 2020)

Fast and memory-efficient scRNA-seq k-means clustering with various distances. - Daniel N. Baker; Nathan Dyjack; Vladimir Braverman; Stephanie C. Hicks; Ben Langmead (BCB, 2021)

mbkmeans: Fast clustering for single cell data using mini-batch k-means. - Stephanie C. Hicks; Ruoxi Liu; Yuwei Ni; Elizabeth Purdom; Davide Risso (PLoS Comput. Biol., 2021)

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. - Ariel A. Hippen; Matias M. Falco; Lukas M. Weber; Erdogan Pekcan Erkan; Kaiyang Zhang; Jennifer Anne Doherty; Anna Vähärautio; Casey S. Greene; Stephanie C. Hicks (PLoS Comput. Biol., 2021)

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. - Dario Righelli; Lukas M. Weber; Helena L. Crowell; Brenda Pardo; Leonardo Collado-Torres; Shila Ghazanfar; Aaron T. L. Lun; Stephanie C. Hicks; Davide Risso (Bioinform., 2022)

Addressing the mean-correlation relationship in co-expression analysis. - Yi Wang 097; Stephanie C. Hicks; Kasper D. Hansen (PLoS Comput. Biol., 2022)

Design Principles for Data Analysis. - Lucy D'Agostino McGowan; Roger D. Peng; Stephanie C. Hicks (J. Comput. Graph. Stat., 2023)