XG-PseU: an eXtreme Gradient Boosting based method for identifying pseudouridine sites.

Molecular Genetics and Genomics : MGG
Kewei LiuHao Lin

Abstract

As one of the most popular post-transcriptional modifications, pseudouridine (Ψ) participates in a series of biological processes. Therefore, the efficient detection of pseudouridine sites is very important in revealing its functions in biological processes. Although experimental techniques have been proposed for identifying Ψ sites at single-base resolution, they are still labor intensive and expensive. Recently, to fill the experimental method's gap, computational methods have been proposed for identifying Ψ sites. However, their performances are still unsatisfactory. In this paper, we proposed an eXtreme Gradient Boosting (xgboost)-based method, called XG-PseU, to identify Ψ sites based on the optimal features obtained using the forward feature selection together with increment feature selection method. Our results demonstrated that XG-PseU is superior or at least complementary to existing methods for identifying pseudouridine sites. Finally, a freely available online web server for XG-PseU was established at http://www.bioml.cn/. We wish that XG-PseU will become a useful tool for computationally identifying Ψ sites.

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Citations

Mar 17, 2020·Frontiers in Bioengineering and Biotechnology·Zhibin LvQuan Zou
Jun 23, 2020·Evolutionary Bioinformatics Online·Bowen SongZhen Wei
Mar 15, 2020·Interdisciplinary Sciences, Computational Life Sciences·Yashuang MuXiaodong Liu
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Nov 25, 2020·Molecular Therapy. Nucleic Acids·Yue BiJiangning Song
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Jul 3, 2021·Mathematical Biosciences and Engineering : MBE·Hasan ZulfiqarRenzhi Cao
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Aug 28, 2021·International Journal of Molecular Sciences·Phasit CharoenkwanWatshara Shoombuatong
Dec 7, 2021·Frontiers in Genetics·Jujuan ZhuangSize Chen

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Methods Mentioned

BETA
CeU-Seq
feature extraction

Software Mentioned

CNN
Xgboost
iRNA
eXtreme Boosting
PseU
XG
iPseU
mathop
PPUS
PseUI

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