Genome-Wide Analysis of the Association of Transposable Elements with Gene Regulation Suggests that Alu Elements Have the Largest Overall Regulatory Impact. - Lu Zeng; Stephen M. Pederson; Danfeng Cao; Zhipeng Qu; Zhiqiang Hu; David L. Adelson; Chaochun Wei (J. Comput. Biol., 2018)

strandCheckR: An R package for quantifying and removing double strand sequences for strand-specific RNA-seq. - Thu-Hien To; Stephen M. Pederson (J. Open Source Softw., 2019)

ngsReports: a Bioconductor package for managing FastQC reports and other NGS related log files. - Christopher M. Ward; Thu-Hien To; Stephen M. Pederson (Bioinform., 2020)

Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. - Lachlan Baer; Karissa Barthelson; John H. Postlethwait; David L. Adelson; Stephen M. Pederson; Michael Lardelli (PLoS Comput. Biol., 2024)