3CDB: a manually curated database of chromosome conformation capture data. - Xiaoxiao Yun; Lili Xia; Bixia Tang; Hui Zhang; Feifei Li 009; Zhihua Zhang 007 (Database J. Biol. Databases Curation, 2016)

Delta: a new web-based 3D genome visualization and analysis platform. - Bixia Tang; Feifei Li 009; Jing Li; Wenming Zhao; Zhihua Zhang 007 (Bioinform., 2018)

Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite. - Junfeng Liu; Ziyang An; Jianjun Luo 001; Jing Li; Feifei Li 009; Zhihua Zhang 007 (Bioinform., 2020)

DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data. - Bingxiang Xu; Xiaoli Li; Xiaomeng Gao; Yan Jia; Jing Liu; Feifei Li 009; Zhihua Zhang 007 (Briefings Bioinform., 2022)