DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures

doi:10.1016/j.csbj.2023.12.040

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	DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures
	Qiao, Yixuan 1,2; Yang, Rui 1,2; Liu, Yang 1,2; Chen, Jiaxin 1; Zhao, Lianhe 1; Huo, Peipei 1; Wang, Zhihao 1; Bu, Dechao 1; Wu, Yang 1; Zhao, Yi 1,2
	2024-12-01
发表期刊	COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
ISSN	2001-0370
卷号	23 页码:617-625
摘要	RNA -binding proteins (RBPs) are key post -transcriptional regulators, and the malfunctions of RBP-RNA binding lead to diverse human diseases. However, prediction of RBP binding sites is largely based on RNA sequence features, whereas in vivo RNA structural features based on high -throughput sequencing are rarely incorporated. Here, we designed a deep bimodal information fusion network called DeepFusion for unraveling protein -RNA interactions by incorporating structural features derived from DMS-seq data. DeepFusion integrates two submodels to extract local motif -like information and long-term context information. We show that DeepFusion performs best compared with other cutting -edge methods with only sequence inputs on two datasets. DeepFusion's performance is further improved with bimodal input after adding in vivo DMS-seq structural features. Furthermore, DeepFusion can be used for analyzing RNA degradation, demonstrating significantly different RBPbinding scores in genes with slow degradation rates versus those with rapid degradation rates. DeepFusion thus provides enhanced abilities for further analysis of functional RNAs. DeepFusion's code and data are available at http://bioinfo.org/deepfusion/.
关键词	Information fusion Deep learning RNA -binding proteins In vivo RNA structures Motifs
DOI	10.1016/j.csbj.2023.12.040
收录类别	SCI
语种	英语
资助项目	National Key R&D Program of China[2022YFC3500105] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA16021400] ; National Natural Science Foundation of China[82172864] ; National Natural Science Foundation of China[32070670] ; Innovation Fund from Institute of Computing Technology, CAS[E161080] ; Zhejiang Provincial Natural Science Foundation of China[LY21C060003] ; Beijing Natural Science Foundation Haidian Origination and Innovation Joint Fund[L222007]
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS类目	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS记录号	WOS:001154337300001
出版者	ELSEVIER
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/38384
专题	中国科学院计算技术研究所
通讯作者	Wu, Yang; Zhao, Yi
作者单位	1.Chinese Acad Sci, Res Ctr Ubiquitous Comp Syst, Inst Comp Technol, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Qiao, Yixuan,Yang, Rui,Liu, Yang,et al. DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures[J]. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL,2024,23:617-625.
APA	Qiao, Yixuan.,Yang, Rui.,Liu, Yang.,Chen, Jiaxin.,Zhao, Lianhe.,...&Zhao, Yi.(2024).DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures.COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL,23,617-625.
MLA	Qiao, Yixuan,et al."DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures".COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 23(2024):617-625.