| Optimization of metabolomic data processing using NOREVA J Fu, Y Zhang, Y Wang, H Zhang, J Liu, J Tang, Q Yang, H Sun, W Qiu, ... Nature protocols 17 (1), 129-151, 2022 | 160 | 2022 |
| DrugMAP: molecular atlas and pharma-information of all drugs F Li, J Yin, M Lu, M Mou, Z Li, Z Zeng, Y Tan, S Wang, X Chu, H Dai, ... Nucleic acids research 51 (D1), D1288-D1299, 2023 | 72 | 2023 |
| PFmulDL: a novel strategy enabling multi-class and multi-label protein function annotation by integrating diverse deep learning methods W Xia, L Zheng, J Fang, F Li, Y Zhou, Z Zeng, B Zhang, Z Li, H Li, F Zhu Computers in Biology and Medicine 145, 105465, 2022 | 65 | 2022 |
| SYNBIP: synthetic binding proteins for research, diagnosis and therapy X Wang, F Li, W Qiu, B Xu, Y Li, X Lian, H Yu, Z Zhang, J Wang, Z Li, ... Nucleic acids research 50 (D1), D560-D570, 2022 | 62 | 2022 |
| ConSIG: consistent discovery of molecular signature from OMIC data F Li, J Yin, M Lu, Q Yang, Z Zeng, B Zhang, Z Li, Y Qiu, H Dai, Y Chen, ... Briefings in bioinformatics 23 (4), bbac253, 2022 | 58 | 2022 |
| PROFEAT update: a protein features web server with added facility to compute network descriptors for studying omics-derived networks P Zhang, L Tao, X Zeng, C Qin, SY Chen, F Zhu, SY Yang, ZR Li, ... Journal of molecular biology 429 (3), 416-425, 2017 | 45 | 2017 |
| NPCDR: natural product-based drug combination and its disease-specific molecular regulation X Sun, Y Zhang, Y Zhou, X Lian, L Yan, T Pan, T Jin, H Xie, Z Liang, ... Nucleic acids research 50 (D1), D1324-D1333, 2022 | 38 | 2022 |
| AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding L Zheng, S Shi, M Lu, P Fang, Z Pan, H Zhang, Z Zhou, H Zhang, M Mou, ... Genome biology 25 (1), 41, 2024 | 33 | 2024 |
| A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder Y Wang, Z Pan, M Mou, W Xia, H Zhang, H Zhang, J Liu, L Zheng, Y Luo, ... Nucleic acids research 51 (21), e110-e110, 2023 | 33 | 2023 |
| ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA H Zhang, Y Wang, Z Pan, X Sun, M Mou, B Zhang, Z Li, H Li, F Zhu Briefings in bioinformatics 23 (6), bbac411, 2022 | 28 | 2022 |
| Using artificial intelligence to document the hidden RNA virosphere X Hou, Y He, P Fang, SQ Mei, Z Xu, WC Wu, JH Tian, S Zhang, ZY Zeng, ... Cell 187 (24), 6929-6942. e16, 2024 | 25 | 2024 |
| MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics L Zheng, S Shi, X Sun, M Lu, Y Liao, S Zhu, H Zhang, Z Pan, P Fang, ... Briefings in bioinformatics 25 (2), bbae006, 2024 | 19 | 2024 |
| KG-MTT-BERT: Knowledge graph enhanced BERT for multi-type medical text classification Y He, C Wang, S Zhang, N Li, Z Li, Z Zeng arXiv preprint arXiv:2210.03970, 2022 | 17 | 2022 |
| Artificial intelligence redefines RNA virus discovery M Shi, X Hou, Y He, P Fang, SQ Mei, Z Xu, WC Wu, J Tian, S Zhang, ... | 14 | 2023 |
| Biological activities of drug inactive ingredients C Zhang, M Mou, Y Zhou, W Zhang, X Lian, S Shi, M Lu, H Sun, F Li, ... Briefings in Bioinformatics 23 (5), bbac160, 2022 | 13 | 2022 |
| REGLIV: molecular regulation data of diverse living systems facilitating current multiomics research S Zhang, X Sun, M Mou, K Amahong, H Sun, W Zhang, S Shi, Z Li, J Gao, ... Computers in Biology and Medicine 148, 105825, 2022 | 11 | 2022 |
| LucaOne: Generalized Biological Foundation Model with Unified Nucleic Acid and Protein Language Y He, P Fang, Y Shan, Y Pan, Y Wei, Y Chen, Y Chen, Y Liu, Z Zeng, ... bioRxiv, 2024.05. 10.592927, 2024 | 6 | 2024 |
| BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow Q Xin, Q Kong, H Ji, Y Shen, Y Liu, Y Sun, Z Zhang, Z Li, X Xia, B Deng, ... bioRxiv, 2024.05. 22.595240, 2024 | 3 | 2024 |
| Feature, Function, and Information of Drug Transporter–Related Databases J Yin, F Li, Z Li, L Yu, F Zhu, S Zeng Drug Metabolism and Disposition 50 (1), 76-85, 2022 | 3 | 2022 |
| AnnoPRO: an Innovative Strategy for Protein Function Annotation based on Image-like Protein Representation and Multimodal Deep Learning L Zheng, S Shi, P Fang, H Zhang, Z Pan, S Huang, W Xia, H Li, Z Zeng, ... bioRxiv, 2023.05. 13.540619, 2023 | 1 | 2023 |
