DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data. - Chengzhong Ye; Terence P. Speed; Agus Salim (Bioinform., 2019)

Genomic Language Models: Opportunities and Challenges. - Gonzalo Benegas; Chengzhong Ye; Carlos Albors; Jianan Canal Li; Yun S. Song (CoRR, 2024)

A Phylogenetic Approach to Genomic Language Modeling. - Carlos Albors; Jianan Canal Li; Gonzalo Benegas; Chengzhong Ye; Yun S. Song (RECOMB, 2025)