Block-based characterization of protease specificity from substrate sequence profile. - Enfeng Qi; Dongyu Wang; Bo Gao; Yang Li 089; Guojun Li (BMC Bioinform., 2017)

An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data. - Bingqiang Liu; Jinyu Yang; Yang Li 089; Adam McDermaid; Qin Ma 003 (Briefings Bioinform., 2018)

MiMod: A New Algorithm for Mining Biological Network Modules. - Yang Li 089; Bingqiang Liu; Jing Li; Guojun Li (IEEE Access, 2019)

ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery. - Yang Li 089; Pengyu Ni; Shaoqiang Zhang; Guojun Li; Zhengchang Su (Bioinform., 2019)

scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data. - Haocheng Gu; Hao Cheng; Anjun Ma; Yang Li 089; Juexin Wang; Dong Xu 002; Qin Ma 003 (Bioinform., 2022)

Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data. - Yang Li 089; Anjun Ma; Yizhong Wang; Qi Guo; Cankun Wang; Hongjun Fu; Bingqiang Liu; Qin Ma 003 (Briefings Bioinform., 2024)

CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq. - Yizhong Wang; Yang Li 089; Cankun Wang; Chan-Wang Jerry Lio; Qin Ma 003; Bingqiang Liu (Briefings Bioinform., 2024)

A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data. - Yang Li 089; Yizhong Wang; Cankun Wang; Anjun Ma; Qin Ma 003; Bingqiang Liu (Patterns, 2024)