Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species

Bioinformatics
Leyi WeiQuan Zou

Abstract

As one of important epigenetic modifications, DNA N4-methylcytosine (4mC) is recently shown to play crucial roles in restriction-modification systems. For better understanding of their functional mechanisms, it is fundamentally important to identify 4mC modification. Machine learning methods have recently emerged as an effective and efficient approach for the high-throughput identification of 4mC sites, although high predictive error rates are still challenging for existing methods. Therefore, it is highly desirable to develop a computational method to more accurately identify m4C sites. In this study, we propose a machine learning based predictor, namely 4mcPred-SVM, for the genome-wide detection of DNA 4mC sites. In this predictor, we present a new feature representation algorithm that sufficiently exploits sequence-based information. To improve the feature representation ability, we use a two-step feature optimization strategy, thereby obtaining the most representative features. Using the resulting features and Support Vector Machine (SVM), we adaptively train the optimal models for different species. Comparative results on benchmark datasets from six species indicate that our predictor is able to achieve generally better pe...Continue Reading

References

Mar 1, 1987·Journal of Bacteriology·M EhrlichC W Gehrke
Feb 1, 1995·Current Opinion in Structural Biology·X Cheng
Jan 14, 2005·Journal of Cellular Physiology·Maria Irene ScaranoMaurizio D'Esposito
May 11, 2010·Nature Methods·Benjamin A FlusbergStephen W Turner
Oct 24, 2013·Bioinformatics·Mingjun WangJiangning Song
Sep 23, 2014·Briefings in Functional Genomics·Pei LiQuan Zou
Feb 22, 2017·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Leyi WeiQuan Zou
Mar 24, 2017·Briefings in Bioinformatics·Bingqiang LiuQin Ma
Nov 11, 2017·Journal of Chemical Information and Modeling·Yijie DingFei Guo
Mar 15, 2018·Methods in Molecular Biology·Yungang Xu, Xiaobo Zhou
Jul 11, 2018·International Journal of Biological Sciences·Hua TangHao Lin
Jul 25, 2018·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ran SuLeyi Wei
Aug 14, 2018·Briefings in Bioinformatics·Adam McDermaidQin Ma
Aug 17, 2018·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hui YangHao Lin

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Citations

Jul 2, 2020·Briefings in Bioinformatics·Quanzhong LiuFuyi Li
May 28, 2019·Frontiers in Genetics·Ke HanChunyu Wang
Mar 17, 2020·Frontiers in Bioengineering and Biotechnology·Zhibin LvQuan Zou
Mar 27, 2020·Frontiers in Genetics·Feng ZengLan Yao
May 7, 2020·Frontiers in Bioengineering and Biotechnology·Rao Zeng, Minghong Liao
Dec 7, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Lei XuChi-Chang Chang
Dec 6, 2019·International Journal of Molecular Sciences·Jiacheng WangLei Deng
Jul 14, 2020·Current Genomics·Rajiv G GovindarajBalachandran Manavalan
Apr 25, 2019·International Journal of Molecular Sciences·Vinothini BoopathiDeok-Chun Yang
Dec 15, 2020·Briefings in Functional Genomics·Chunyan AoQuan Zou
Apr 24, 2020·Computational and Structural Biotechnology Journal·Md Mehedi HasanHiroyuki Kurata
Dec 10, 2020·Computational and Mathematical Methods in Medicine·Yanjuan LiXiaoyan Liu
Nov 25, 2020·Molecular Therapy. Nucleic Acids·Balachandran ManavalanGwang Lee
Mar 19, 2021·SAR and QSAR in Environmental Research·Y YaoY Liang
Mar 25, 2021·Briefings in Functional Genomics·Lei XuBo Gao
Apr 10, 2021·Interdisciplinary Sciences, Computational Life Sciences·Tian XueHuijuan Qiao
Apr 20, 2021·Computational and Structural Biotechnology Journal·Jhabindra KhanalKil To Chong
Jun 2, 2021·BMC Bioinformatics·Yuqing QianFei Guo

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