Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network. - Dorjsuren Battogtokh; Shihoko Kojima; John J. Tyson (PLoS Comput. Biol., 2018)

Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression. - Xiangyu Yao; Shihoko Kojima; Jing Chen 029 (PLoS Comput. Biol., 2020)

Correction: Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression. - Xiangyu Yao; Shihoko Kojima; Jing Chen 029 (PLoS Comput. Biol., 2021)

Leveraging Machine Learning for Predicting Circadian Transcription in mRNAs and lncRNAs. - Lin Miao; Krishna Vamsi Dhulipalla; Sanchari Kundu; Bokun Zheng; Song Li; Shihoko Kojima (BIBM, 2024)