FlyVar: a database for genetic variation in Drosophila melanogaster. - Fei Wang 017; Lichun Jiang; Yong Chen 016; Nele A. Haelterman; Hugo J. Bellen; Rui Chen 013 (Database J. Biol. Databases Curation, 2015)

SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data. - Yong Chen 016; Li Zhao; Yi Wang; Ming Cao 005; Violet Gelowani; Mingchu Xu; Smriti A. Agrawal; Yumei Li 007; Stephen P. Daiger; Richard A. Gibbs; Fei Wang 017; Rui Chen 013 (BMC Bioinform., 2017)

A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data. - Shupeng Gui; Andrew P. Rice; Rui Chen 013; Liang Wu; Ji Liu 002; Hongyu Miao 001 (BMC Bioinform., 2017)

Stratified Test Alleviates Batch Effects in Single-Cell Data. - Shaoheng Liang; Qingnan Liang; Rui Chen 013; Ken Chen 001 (AlCoB, 2020)

Stratified Test Accurately Identifies Differentially Expressed Genes Under Batch Effects in Single-Cell Data. - Shaoheng Liang; Qingnan Liang; Rui Chen 013; Ken Chen 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)