esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis. - Zheng Wei; Wei Zhang 241; Huan Fang 003; Yanda Li; Xiaowo Wang (Bioinform., 2018)

DISMIR: Deep learning-based noninvasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads. - Jiaqi Li; Lei Wei; Xianglin Zhang; Wei Zhang 241; Haochen Wang; Bixi Zhong; Zhen Xie; Hairong Lv; Xiaowo Wang (Briefings Bioinform., 2021)

cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data. - Wei Zhang 241; Lei Wei; Jiaqi Huang; Bixi Zhong; Jiaqi Li; Hanwen Xu; Shuying He; Yu Liu; Juhong Liu; Hairong Lv; Xiaowo Wang (Bioinform., 2021)

Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA. - Xianglin Zhang; Xiaodong Jia; Bixi Zhong; Lei Wei; Jiaqi Li; Wei Zhang 241; Huan Fang 003; Yanda Li; Yinying Lu; Xiaowo Wang (Briefings Bioinform., 2022)

ARIC: accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data. - Wei Zhang 241; Hanwen Xu; Rong Qiao; Bixi Zhong; Xianglin Zhang; Jin Gu; Xuegong Zhang; Lei Wei; Xiaowo Wang (Briefings Bioinform., 2022)

Deep generative modeling and clustering of single cell Hi-C data. - Qiao Liu 008; Wanwen Zeng; Wei Zhang 241; Sicheng Wang; Hongyang Chen; Rui Jiang 001; Mu Zhou; Shaoting Zhang 001 (Briefings Bioinform., 2023)

Weakly Supervised Causal Discovery Based on Fuzzy Knowledge and Complex Data Complementarity. - Wenrui Li; Wei Zhang 241; Qinghao Zhang; Xuegong Zhang; Xiaowo Wang (IEEE Trans. Fuzzy Syst., 2024)

Inferring cell-type-specific gene regulatory network from cellular transcriptomics data with GeneLink+. - Wei Zhang 241; Bowen Shao; Wenrui Li; Wenbo Guo 010; Jiaxin Lyu; Guangyi Chen; Chuanyuan Wang; Zhi-Ping Liu (Briefings Bioinform., 2025)

Simulation-guided pan-cancer analysis identifies a novel regulator of CpG island hypermethylation heterogeneity. - Xianglin Zhang; Wei Zhang 241; Jinyi Zhang; Xiuhong Lyu; Haoran Pan; Tianwei Jia; Ting Wang; Xiaowo Wang; Haiyang Guo (Briefings Bioinform., 2025)

Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data. - Wei Zhang 241; Xianglin Zhang; Qiao Liu 008; Lei Wei; Xu Qiao; Rui Gao 006; Zhiping Liu; Xiaowo Wang (Genom. Proteom. Bioinform., 2025)