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Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites

Bioinformatics (Oxford, England), 2023-11, Vol.39 (11) [Peer Reviewed Journal]

The Author(s) 2023. Published by Oxford University Press. 2023 ;ISSN: 1367-4811 ;ISSN: 1367-4803 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btad627 ;PMID: 37847658

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  • Title:
    Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites
  • Author: Jiao, Shihu ; Ye, Xiucai ; Ao, Chunyan ; Sakurai, Tetsuya ; Zou, Quan ; Xu, Lei
  • Kelso, Janet
  • Subjects: Original Paper
  • Is Part Of: Bioinformatics (Oxford, England), 2023-11, Vol.39 (11)
  • Description: Abstract Motivation The rapid and extensive transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an unprecedented global health emergency, affecting millions of people and causing an immense socioeconomic impact. The identification of SARS-CoV-2 phosphorylation sites plays an important role in unraveling the complex molecular mechanisms behind infection and the resulting alterations in host cell pathways. However, currently available prediction tools for identifying these sites lack accuracy and efficiency. Results In this study, we presented a comprehensive biological function analysis of SARS-CoV-2 infection in a clonal human lung epithelial A549 cell, revealing dramatic changes in protein phosphorylation pathways in host cells. Moreover, a novel deep learning predictor called PSPred-ALE is specifically designed to identify phosphorylation sites in human host cells that are infected with SARS-CoV-2. The key idea of PSPred-ALE lies in the use of a self-adaptive learning embedding algorithm, which enables the automatic extraction of context sequential features from protein sequences. In addition, the tool uses multihead attention module that enables the capturing of global information, further improving the accuracy of predictions. Comparative analysis of features demonstrated that the self-adaptive learning embedding features are superior to hand-crafted statistical features in capturing discriminative sequence information. Benchmarking comparison shows that PSPred-ALE outperforms the state-of-the-art prediction tools and achieves robust performance. Therefore, the proposed model can effectively identify phosphorylation sites assistant the biomedical scientists in understanding the mechanism of phosphorylation in SARS-CoV-2 infection. Availability and implementation PSPred-ALE is available at https://github.com/jiaoshihu/PSPred-ALE and Zenodo (https://doi.org/10.5281/zenodo.8330277).
  • Publisher: Oxford University Press
  • Language: English
  • Identifier: ISSN: 1367-4811
    ISSN: 1367-4803
    EISSN: 1367-4811
    DOI: 10.1093/bioinformatics/btad627
    PMID: 37847658
  • Source: Oxford Journals Open Access Collection
    Journals@Ovid Open Access Journal Collection Rolling
    PubMed Central
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