A Bayesian Approach for Identifying miRNA Targets by Combining Sequence Prediction and Expression Profiling. - Hui Liu 024; Lin Zhang 015; Shou-Jiang Gao; Yufei Huang 001 (IJCBS, 2009)

Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules. - Jia Meng 001; Shou-Jiang Gao; Yufei Huang 001 (Bioinform., 2009)

Computational prediction of MicroRNA regulatory pathways. - Dong Yue 002; Yidong Chen 002; Shou-Jiang Gao; Yufei Huang 001 (BIBM Workshops, 2010)

Improving performance of mammalian microRNA target prediction. - Hui Liu 024; Dong Yue 002; Yidong Chen 002; Shou-Jiang Gao; Yufei Huang 001 (BMC Bioinform., 2010)

Temporal clustering of gene expression patterns using short-time segments. - Nguyen T. Nguyen; Ying Ann Chiao; Yufei Huang 001; Shou-Jiang Gao; Merry Lindsey; Yidong Chen 002; Yufang Jin (Int. J. Funct. Informatics Pers. Medicine, 2012)

MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome. - Hui Liu 024; Huaizhi Wang; Zhen Wei; Songyao Zhang; Gang Hua 002; Shao-Wu Zhang 001; Lin Zhang 015; Shou-Jiang Gao; Jia Meng 001; Xing Chen 001; Yufei Huang 001 (Nucleic Acids Res., 2018)

Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods. - Song-Yao Zhang; Shaowu Zhang 001; Xiaonan Fan 001; Jia Meng 001; Yidong Chen 002; Shou-Jiang Gao; Yufei Huang 001 (PLoS Comput. Biol., 2019)

Deep learning tackles single-cell analysis - a survey of deep learning for scRNA-seq analysis. - Mario Flores; Zhentao Liu; Tinghe Zhang; Md Musaddaqui Hasib; Yu-Chiao Chiu; Zhenqing Ye; Karla Paniagua; Sumin Jo; Jianqiu Zhang 002; Shou-Jiang Gao; Yu-Fang Jin; Yidong Chen 002; et al. (Briefings Bioinform., 2022)

ReguloGPT: Harnessing GPT for End-to-End Knowledge Graph Construction of Molecular Regulatory Pathways. - Xidong Wu; Sumin Jo; Yiming Zeng 014; Arun Das 001; Tinghe Zhang; Parth Patel; Yuanjing Wei; Lei Li; Shou-Jiang Gao; Jianqiu Zhang 002; Dexter Pratt; Yu-Chiao Chiu; et al. (BHI, 2024)

Understanding YTHDF2-mediated mRNA degradation by m6A-BERT-Deg. - Tinghe Zhang; Sumin Jo; Michelle Zhang; Kai Wang; Shou-Jiang Gao; Yufei Huang 001 (Briefings Bioinform., 2024)