Publications

You can visit ResearchGate or Google Scholar for details.

^# Co-first authors; * Co-corresponding authors

2024

• Yang Zhang, Ting Yang, Yu Yang, Dongsheng Xu, Yucheng Hu, Shuo Zhang, Nanchao Luo^*, Lin Ning^*, Liping Ren^*.siRNAEfficacyDB: An experimentally supported small interfering RNA efficacy database. IET systems biology.
• Tianyuan Liu, Xianrun Pan, Liping Ren, Xiucai Ye^*, Kai Zheng^*, Yang Zhang^*.Mapping autophagy-related membrane contact site proteins and complexes with AutoMCS Navigator. Autophagy.20 (11), 2593-2595
• Yuncong Zhang^#, Yu Yang^#, Liping Ren^#, Meixiao Zhan, Taoping Sun^*, Quan Zou^*, Yang Zhang^*.Predicting intercellular communication based on metabolite-related ligand-receptor interactions with MRCLinkdb. BMC biology. 22 (1), 152
• Yi Xu^#, Tianyuan Liu^#, Yu Yang, Juanjuan Kang, Liping Ren^*, Hui Ding^*, Yang Zhang^*.ACVPred: Enhanced prediction of anti-coronavirus peptides by transfer learning combined with data augmentation. Future Generation Computer Systems.
• Tianyuan Liu, Huiyuan Qiao, Zixu Wang, Xinyan Yang, Xianrun Pan, Yu Yang, Xiucai Ye^*, Tetsuya Sakurai, Hao Lin^*, Yang Zhang^*. CodLncScape Provides a Self-Enriching Framework for the Systematic Collection and Exploration of Coding LncRNAs. Advanced Science. 11: e2400009.
• Tianyuan Liu, Junyang Huang, Delun Luo, Liping Ren, Lin Ning, Jian Huang^*, Hao Lin^*, Yang Zhang^*. Cm-siRPred: Predicting chemically modified siRNA efficiency based on multi-view learning strategy. International Journal of Biological Macromolecules. 264, 130638.
• Liping Ren, Danni Huang, Hongjiang Liu, Lin Ning, Peiling Cai, Xiaolong Yu, Yang Zhang, Nanchao Luo, Hao Lin, Jinsong Su^*, Yinghui Zhang^*.Applications of single-cell omics and spatial transcriptomics technologies in gastric cancer. Oncology Letters. 27 (4), 1-19.
• Xianrun Pan^#, Liping Ren^#, Yu Yang, Yi Xu, Lin Ning, Yibing Zhang, Huaichao Luo^*, Quan Zou^*, Yang Zhang^*.MCSdb, a database of proteins residing in membrane contact sites. Scientific Data. 11 (1), 281.
• Hasan Zulfiqar^#, Zhiling Guo^#, Ramala Masood Ahmad, Zahoor Ahmed, Peiling CAI, Xiang Chen, Yang Zhang^*, Zheng Shi^*, Hao Lin^*.Deep-STP: A Deep Learning-Based Approach to Predict Snake Toxin Proteins by Using Word Embeddings.Frontiers in Medicine. 10, 1291352.
• Yang Zhang, Caiqi Liu, Mujiexin Liu, Tianyuan Liu, Hao Lin^*, Cheng-Bing Huang^*, Lin Ning^*.Attention is all you need: utilizing attention in AI-enabled drug discovery. Briefings in Bioinformatics. 25 (1), bbad467.

2023

• Xueqin Xie, Changchun Wu, Yuduo Hao, Tianyu Wang, Yuhe Yang, Peiling Cai, Yang Zhang, Jian Huang, Kejun Deng^*, Dan Yan^*, Hao Lin^*.Benefits and risks of drug combination therapy for diabetes mellitus and its complications: a comprehensive review. Frontiers in Endocrinology.. 14, 1301093.
• Liping Ren^#, Lin Ning^#, Yu Yang, Ting Yang, Xinyu Li, Shanshan Tan, Peixin Ge, Shun Li, Nanchao Luo^*, Pei Tao^*, Yang Zhang^*. MetaboliteCOVID: A manually curated database of metabolite markers for COVID-19. Computers in Biology and Medicine. 167, 107661.
• Xidan Zou^#, Liping Ren^#, Peiling Cai, Yang Zhang, Hui Ding, Kejun Deng, Xiaolong Yu^*, Hao Lin^*, Chengbing Huang^*. Accurately identifying hemagglutinin using sequence information and machine learning methods. Frontiers in Medicine. 10, 1281880.
• Yang Zhang, Xianrun Pan, Tianyu Shi, Zhifeng Gu, Zhaochang Yang, Minghao Liu, Yi Xu, Yu Yang, Liping Ren, Xiaoming Song^*, Hao Lin^*, Kejun Deng^*.P450Rdb: A manually curated database of reactions catalyzed by cytochrome P450 enzymes. Journal of Advanced Research.
• Liping Ren, Xianrun Pan, Lin Ning, Di Gong, Jian Huang, Kejun Deng, Lei Xie, Yang Zhang.Construction of a combined hypoxia-related genes model for hepatocellular carcinoma prognosis. Current Computer-Aided Drug Design. 19 (2), 150-161.
• Yu-Fei Zhang^#, Yu-Hao Wang^#, Zhi-Feng Gu, Xian-Run Pan, Jian Li, Hui Ding^*, Yang Zhang^*, Ke-Jun Deng^*.Bitter-RF: A random forest machine model for recognizing bitter peptides.Frontiers in Medicine. 10, 1052923.

2022

• Liping Ren^#, Yi Xu^#, Lin Ning^#, Xianrun Pan, Yuchen Li, Qi Zhao, Bo Pang, Jian Huang^*, Kejun Deng^*, Yang Zhang^*.TCM2COVID: A resource of anti-COVID-19 traditional Chinese medicine with effects and mechanisms. Imeta. 1 (4), e42.
• Zijie Sun^#, Qinlai Huang^#, Yuhe Yang, Shihao Li, Hao Lv, Yang Zhang, Hao Lin^*, Lin Ning^*. PSnoD: identifying potential snoRNA-disease associations based on bounded nuclear norm regularization. Briefings in Bioinformatics. 23 (4), bbac240.
• Liping Ren, Xiaoxia Wen, Mujiexin Liu, Yao Xiao, Ping Leng, Huaichao Luo, Pei Tao^*, Lei Xie^*. Comprehensive Analysis of the Molecular Characteristics and Prognosis value of AT II-associated Genes in Non-small Cell Lung Cancer. Computational and Mathematical Methods in Medicine. 2022 (1), 3106688.
• Anteneh M Birga, Liping Ren, Huaichao Luo^*, Yang Zhang^*, Jian Huang^*. Prediction of new risk genes and potential drugs for rheumatoid arthritis from multiomics data. Computational and Mathematical Methods in Medicine. 2022 (1), 6783659.
• Hao Lv^#, Yang Zhang^#, Jia-Shu Wang, Shi-Shi Yuan, Zi-Jie Sun, Fu-Ying Dao, Zheng-Xing Guan, Hao Lin^*, Ke-Jun Deng^*. iRice-MS: An integrated XGBoost model for detecting multitype post-translational modification sites in rice. Briefings in Bioinformatics. 23 (1), bbab486.

2021

• Hao Lv, Lei Shi, Joshua William Berkenpas, Fu-Ying Dao, Hasan Zulfiqar, Hui Ding, Yang Zhang^*, Liming Yang^*, Renzhi Cao^*. Application of artificial intelligence and machine learning for COVID-19 drug discovery and vaccine design Briefings in Bioinformatics. 22 (6), bbab320.
• Yang Zhang^{#, *}, Tianyuan Liu^#, Xuesong Hu^#, Mei Wang, Jing Wang, Bohao Zou, Puwen Tan, Tianyu Cui, Yiying Dou, Lin Ning, Yan Huang, Shuan Rao, Dong Wang^*, Xiaoyang Zhao^*. CellCall: Integrating paired ligand-receptor and transcription factor activities for cell-cell communication. Nucleic Acids Research. 49 (15), 8520-8534.
• Yan Huang^#, Jing Wang^#, Yue Zhao^#, Huafeng Wang, Tianyuan Liu, Yuhe Li, Tianyu Cui, Weiyi Li, Yige Feng, Jiaxin Luo, Jiaqi Gong, Lin Ning, Yong Zhang^*, Dong Wang^*, Yang Zhang^*. cncRNAdb: a manually curated resource of experimentally supported RNAs with both protein-coding and noncoding function. Nucleic Acids Research. 49 (D1), D65-D70.
• Yang Zhang^#, Tianyuan Liu^#, Jing Wang^#, Bohao Zou, Le Li, Linhui Yao, Kechen Chen, Lin Ning, Bingyi Wu^*, Xiaoyang Zhao^*, Dong Wang^*. Cellinker: a platform of ligand-receptor interactions for intercellular communication analysis. Bioinformatics. 37 (14), 2025-2032.

2020

• Tian-yuan Liu^#, Yun-cong Zhang^#, Yun-qing Lin^#, Yong-fei Hu, Yang Zhang, Dong Wang^*, Yan Wang^*, Lin Ning^*. Exploration of invasive mechanisms via global ncRNA-associated virus-host crosstalk. Genomics. 112 (2), 1643-1650.

2019

• Puwen Tan, Yue Ren, Yuncong Zhang, Yunqing Lin, Tianyu Cui, Yan Huang, Yang Zhang, Lin Ning, Jia Yu, Shuai Gao, Dong Wang, He Huang^*. Dissecting dynamic expression of autophagy-related genes during human fetal digestive tract development via single-cell RNA sequencing. Autophagy. 15 (11), 2019-2021.
• Yang Zhang, Tianyuan Liu, Liqun Chen, Jinxurong Yang, Jiayi Yin, Yuncong Zhang, Zhixi Yun, Hao Xu, Lin Ning, Fengbiao Guo, Yongshuai Jiang, Hao Lin, Dong Wang^*, Yan Huang^*, Jian Huang^*. RIscoper: a tool for RNA-RNA interaction extraction from the literature. Bioinformatics. 35 (17), 3199-3202.
• Yang Zhang, Zheng Zhang, Dong Wang, Jianzhen Xu, Yanhui Li, Hong Wang, Jin Li, Shaowen Mo, Yuncong Zhang, Yunqing Lin, Xiuzhao Fan, Enmin Li, Jian Huang, Huihui Fan, Ying Yi. Multidimensional Integration Analysis of Autophagy-related Modules in Colorectal Cancer. Letters in Organic Chemistry. 16 (4), 340-346.