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DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures 期刊论文
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 2024, 卷号: 23, 页码: 617-625
作者:  Qiao, Yixuan;  Yang, Rui;  Liu, Yang;  Chen, Jiaxin;  Zhao, Lianhe;  Huo, Peipei;  Wang, Zhihao;  Bu, Dechao;  Wu, Yang;  Zhao, Yi
收藏  |  浏览/下载：4/0  |  提交时间：2024/05/20
Information fusion  Deep learning  RNA -binding proteins  In vivo RNA structures  Motifs  
Benchmarking spatial clustering methods with spatially resolved transcriptomics data 期刊论文
NATURE METHODS, 2024, 页码: 25
作者:  Yuan, Zhiyuan;  Zhao, Fangyuan;  Lin, Senlin;  Zhao, Yu;  Yao, Jianhua;  Cui, Yan;  Zhang, Xiao-Yong;  Zhao, Yi
收藏  |  浏览/下载：3/0  |  提交时间：2024/05/20
Streamlining spatial omics data analysis with Pysodb 期刊论文
NATURE PROTOCOLS, 2023, 页码: 72
作者:  Lin, Senlin;  Zhao, Fangyuan;  Wu, Zihan;  Yao, Jianhua;  Zhao, Yi;  Yuan, Zhiyuan
收藏  |  浏览/下载：2/0  |  提交时间：2024/05/20
Biological knowledge graph-guided investigation of immune therapy response in cancer with graph neural network 期刊论文
BRIEFINGS IN BIOINFORMATICS, 2023, 卷号: 24, 期号: 2, 页码: 9
作者:  Zhao, Lianhe;  Qi, Xiaoning;  Chen, Yang;  Qiao, Yixuan;  Bu, Dechao;  Wu, Yang;  Luo, Yufan;  Wang, Sheng;  Zhang, Rui;  Zhao, Yi
收藏  |  浏览/下载：8/0  |  提交时间：2023/12/04
immune checkpoints inhibitors  deep learning  graph neural networks  
ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs 期刊论文
NUCLEIC ACIDS RESEARCH, 2021, 卷号: 49, 期号: W1, 页码: W459-W468
作者:  Zhang, Yuwei;  Bu, Dechao;  Huo, Peipei;  Wang, Zhihao;  Rong, Hao;  Li, Yanguo;  Liu, Jingjia;  Ye, Meng;  Wu, Yang;  Jiang, Zheng;  Liao, Qi;  Zhao, Yi
收藏  |  浏览/下载：37/0  |  提交时间：2021/12/01
FangNet: Mining herb hidden knowledge from TCM clinical effective formulas using structure network algorithm 期刊论文
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 2021, 卷号: 19, 页码: 62-71
作者:  Bu, Dechao;  Xia, Yan;  Zhang, JiaYuan;  Cao, Wanchen;  Huo, Peipei;  Wang, Zhihao;  He, Zihao;  Ding, Linyi;  Wu, Yang;  Zhang, Shan;  Gao, Kai;  Yu, He;  Liu, Tiegang;  Ding, Xia;  Gu, Xiaohong;  Zhao, Yi
收藏  |  浏览/下载：37/0  |  提交时间：2021/12/01
Formulas  Herb  Symptom  TCM  
DeepOmix: A scalable and interpretable multi-omics deep learning framework and application in cancer survival analysis 期刊论文
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 2021, 卷号: 19, 页码: 2719-2725
作者:  Zhao, Lianhe;  Dong, Qiongye;  Luo, Chunlong;  Wu, Yang;  Bu, Dechao;  Qi, Xiaoning;  Luo, Yufan;  Zhao, Yi
收藏  |  浏览/下载：43/0  |  提交时间：2021/12/01
Multi-omics  Deep learning  Survival analysis  Prognosis prediction  Interpretable model  
Identification and function annotation of long intervening noncoding RNAs 期刊论文
BRIEFINGS IN BIOINFORMATICS, 2017, 卷号: 18, 期号: 5, 页码: 789-797
作者:  Luo, Haitao;  Bu, Dechao;  Sun, Liang;  Fang, Shuangsang;  Liu, Zhiyong;  Zhao, Yi
收藏  |  浏览/下载：66/0  |  提交时间：2019/12/12
transcriptom sequencing  noncoding RNAs  gene identification  function annotation  network analysis  computational method  
NPInter v3.0: an upgraded database of noncoding RNA-associated interactions 期刊论文
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2016, 页码: 9
作者:  Hao, Yajing;  Wu, Wei;  Li, Hui;  Yuan, Jiao;  Luo, Jianjun;  Zhao, Yi;  Chen, Runsheng
收藏  |  浏览/下载：57/0  |  提交时间：2019/12/13
A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification 期刊论文
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 2011, 卷号: 35, 期号: 5, 页码: 298-307
作者:  Yu, Liang;  Gao, Lin;  Li, Kui;  Zhao, Yi;  Chiu, David K. Y.
收藏  |  浏览/下载：69/0  |  提交时间：2019/12/16
Protein-protein interaction (PPI) networks  Complexes  Degree distribution  Hierarchical agglomerative algorithm