Topologically inferring risk-active pathways toward precise cancer classification by directed random walk. - Wei Liu 187; Chunquan Li 002; Yanjun Xu; Haixiu Yang; Qianlan Yao; Junwei Han 003; Desi Shang; Chunlong Zhang; Fei Su; Xiaoxi Li; Yun Xiao 001; Fan Zhang; et al. (Bioinform., 2013)

Functional analysis of microRNA and transcription factor synergistic regulatory network based on identifying regulatory motifs in non-small cell lung cancer. - Ke-ning Li; Zi-hui Li; Ning Zhao; Yaoqun Xu; Yongjing Liu; Yuanshuai Zhou; Desi Shang; Fujun Qiu; Rui Zhang; Zhi-qiang Chang; Yan Xu (BMC Syst. Biol., 2013)

The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure. - Jing Li 115; Chunquan Li 002; Junwei Han 003; Chunlong Zhang; Desi Shang; Qianlan Yao; Yunpeng Zhang; Yanjun Xu; Wei Liu 187; Meng Zhou 003; Haixiu Yang; Fei Su; et al. (J. Biomed. Informatics, 2014)

Characterizing and optimizing human anticancer drug targets based on topological properties in the context of biological pathways. - Jian Zhang 084; Yan Wang 023; Desi Shang; Fulong Yu; Wei Liu 187; Yan Zhang; Chenchen Feng; Qiuyu Wang; Yanjun Xu; Yuejuan Liu; Xuefeng Bai 002; Xuecang Li; et al. (J. Biomed. Informatics, 2015)

BioM2MetDisease: a manually curated database for associations between microRNAs, metabolites, small molecules and metabolic diseases. - Yanjun Xu; Haixiu Yang; Tan Wu; Qun Dong; Zeguo Sun; Desi Shang; Feng Li; Yingqi Xu; Fei Su; Siyao Liu; Yunpeng Zhang; Xia Li 004 (Database J. Biol. Databases Curation, 2017)

RNAactDrug: a comprehensive database of RNAs associated with drug sensitivity from multi-omics data. - Qun Dong; Feng Li; Yanjun Xu; Jing Xiao; Yingqi Xu; Desi Shang; Chunlong Zhang; Haixiu Yang; Zihan Tian; Kai Mi 003; Xia Li 004; Yunpeng Zhang (Briefings Bioinform., 2020)

Identification and comprehensive characterization of lncRNAs with copy number variations and their driving transcriptional perturbed subpathways reveal functional significance for cancer. - Yanjun Xu; Tan Wu; Feng Li; Qun Dong; Jingwen Wang; Desi Shang; Yingqi Xu; Chunlong Zhang; Yiying Dou; Congxue Hu; Haixiu Yang; Xuan Zheng; et al. (Briefings Bioinform., 2020)

GREAP: a comprehensive enrichment analysis software for human genomic regions. - Yongsan Yang; Fengcui Qian; Xuecang Li; Yanyu Li; Liwei Zhou; Qiuyu Wang; Xinyuan Zhou; Jian Zhang 084; Chao Song; Zhengmin Yu; Ting Cui; Chenchen Feng; et al. (Briefings Bioinform., 2022)

TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse. - Yuexin Zhang; Chao Song; Yimeng Zhang; Yuezhu Wang; Chenchen Feng; Jiaxin Chen; Ling Wei; Qi Pan; Desi Shang; Yanbing Zhu; Jiang Zhu; Shuangsang Fang; et al. (Nucleic Acids Res., 2022)

EGTSyn: Edge-based Graph Transformer for Anti-Cancer Drug Combination Synergy Prediction. - Jie Hu; Xiaozhi Zhang; Desi Shang; Lijun Ouyang; Yue Li; Dongping Xiong (CoRR, 2023)

Characterization of the metabolic alteration-modulated tumor microenvironment mediated by TP53 mutation and hypoxia. - Kunpeng Luo; Zhipeng Qian; Yanan Jiang; Dongxu Lv; Kaibin Zhu; Jing Shao; Ying Hu; Chengqian Lv; Qianqian Huang; Yang Gao; Shizhu Jin; Desi Shang (Comput. Biol. Medicine, 2023)