An Improved Algorithm for Estimating the Distribution of RNA-related Genomic Features

Jinge Wu; Lihan Zhang; Yuanzhe Weng; Jia Meng; Jionglong Su; Yue Wang

doi:10.1145/3403782.3403785

An Improved Algorithm for Estimating the Distribution of RNA-related Genomic Features

Jinge Wu, Lihan Zhang, Yuanzhe Weng, Jia Meng, Jionglong Su, Yue Wang^*

^*Corresponding author for this work

Xi'an Jiaotong-Liverpool University

Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review

Abstract

In this paper, we look into the correction on the ambiguities in the conversion between genome-based coordinates and RNA-based coordinates. An improved algorithm for estimating the distribution of RNA-related genomic features is proposed based on our previous article, 'Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features'. It applies Expectation Maximization algorithm to estimate RNA-related genomic features using iterations. After each iteration, the proportion of the real distribution coordinates is increased, and the result is closer to the real distribution, demonstrating validity and effectiveness of our proposed method.

Original language	English
Title of host publication	Proceedings of the 4th International Conference on Biological Information and Biomedical Engineering, BIBE 2020
Editors	Weimiao Yu, Chengyu Liu
Publisher	Association for Computing Machinery
ISBN (Electronic)	9781450377096
DOIs	https://doi.org/10.1145/3403782.3403785
Publication status	Published - 21 Jul 2020
Event	4th International Conference on Biological Information and Biomedical Engineering, BIBE 2020 - Chengdu, China Duration: 21 Jul 2020 → 23 Jul 2020

Publication series

Name	ACM International Conference Proceeding Series

Conference

Conference	4th International Conference on Biological Information and Biomedical Engineering, BIBE 2020
Country/Territory	China
City	Chengdu
Period	21/07/20 → 23/07/20

Keywords

Computational transcriptomics
Expectation Maximization algorithm
RNA-related genomic features
Simulation

Access to Document

10.1145/3403782.3403785

Cite this

Wu, J., Zhang, L., Weng, Y., Meng, J., Su, J., & Wang, Y. (2020). An Improved Algorithm for Estimating the Distribution of RNA-related Genomic Features. In W. Yu, & C. Liu (Eds.), Proceedings of the 4th International Conference on Biological Information and Biomedical Engineering, BIBE 2020 (ACM International Conference Proceeding Series). Association for Computing Machinery. https://doi.org/10.1145/3403782.3403785

Wu, Jinge ; Zhang, Lihan ; Weng, Yuanzhe et al. / An Improved Algorithm for Estimating the Distribution of RNA-related Genomic Features. Proceedings of the 4th International Conference on Biological Information and Biomedical Engineering, BIBE 2020. editor / Weimiao Yu ; Chengyu Liu. Association for Computing Machinery, 2020. (ACM International Conference Proceeding Series).

@inproceedings{5092c3366b6b4cffa161dc68348015b2,

title = "An Improved Algorithm for Estimating the Distribution of RNA-related Genomic Features",

abstract = "In this paper, we look into the correction on the ambiguities in the conversion between genome-based coordinates and RNA-based coordinates. An improved algorithm for estimating the distribution of RNA-related genomic features is proposed based on our previous article, 'Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features'. It applies Expectation Maximization algorithm to estimate RNA-related genomic features using iterations. After each iteration, the proportion of the real distribution coordinates is increased, and the result is closer to the real distribution, demonstrating validity and effectiveness of our proposed method.",

keywords = "Computational transcriptomics, Expectation Maximization algorithm, RNA-related genomic features, Simulation",

author = "Jinge Wu and Lihan Zhang and Yuanzhe Weng and Jia Meng and Jionglong Su and Yue Wang",

note = "Publisher Copyright: {\textcopyright} 2020 ACM.; 4th International Conference on Biological Information and Biomedical Engineering, BIBE 2020 ; Conference date: 21-07-2020 Through 23-07-2020",

year = "2020",

month = jul,

day = "21",

doi = "10.1145/3403782.3403785",

language = "English",

series = "ACM International Conference Proceeding Series",

publisher = "Association for Computing Machinery",

editor = "Weimiao Yu and Chengyu Liu",

booktitle = "Proceedings of the 4th International Conference on Biological Information and Biomedical Engineering, BIBE 2020",

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Wu, J, Zhang, L, Weng, Y, Meng, J , Su, J & Wang, Y 2020, An Improved Algorithm for Estimating the Distribution of RNA-related Genomic Features. in W Yu & C Liu (eds), Proceedings of the 4th International Conference on Biological Information and Biomedical Engineering, BIBE 2020. ACM International Conference Proceeding Series, Association for Computing Machinery, 4th International Conference on Biological Information and Biomedical Engineering, BIBE 2020, Chengdu, China, 21/07/20. https://doi.org/10.1145/3403782.3403785

An Improved Algorithm for Estimating the Distribution of RNA-related Genomic Features. / Wu, Jinge; Zhang, Lihan; Weng, Yuanzhe et al.
Proceedings of the 4th International Conference on Biological Information and Biomedical Engineering, BIBE 2020. ed. / Weimiao Yu; Chengyu Liu. Association for Computing Machinery, 2020. (ACM International Conference Proceeding Series).

Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review

TY - GEN

T1 - An Improved Algorithm for Estimating the Distribution of RNA-related Genomic Features

AU - Wu, Jinge

AU - Zhang, Lihan

AU - Weng, Yuanzhe

AU - Meng, Jia

AU - Su, Jionglong

AU - Wang, Yue

PY - 2020/7/21

Y1 - 2020/7/21

N2 - In this paper, we look into the correction on the ambiguities in the conversion between genome-based coordinates and RNA-based coordinates. An improved algorithm for estimating the distribution of RNA-related genomic features is proposed based on our previous article, 'Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features'. It applies Expectation Maximization algorithm to estimate RNA-related genomic features using iterations. After each iteration, the proportion of the real distribution coordinates is increased, and the result is closer to the real distribution, demonstrating validity and effectiveness of our proposed method.

AB - In this paper, we look into the correction on the ambiguities in the conversion between genome-based coordinates and RNA-based coordinates. An improved algorithm for estimating the distribution of RNA-related genomic features is proposed based on our previous article, 'Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features'. It applies Expectation Maximization algorithm to estimate RNA-related genomic features using iterations. After each iteration, the proportion of the real distribution coordinates is increased, and the result is closer to the real distribution, demonstrating validity and effectiveness of our proposed method.

KW - Computational transcriptomics

KW - Expectation Maximization algorithm

KW - RNA-related genomic features

KW - Simulation

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U2 - 10.1145/3403782.3403785

DO - 10.1145/3403782.3403785

M3 - Conference Proceeding

AN - SCOPUS:85123042174

T3 - ACM International Conference Proceeding Series

BT - Proceedings of the 4th International Conference on Biological Information and Biomedical Engineering, BIBE 2020

A2 - Yu, Weimiao

A2 - Liu, Chengyu

PB - Association for Computing Machinery

T2 - 4th International Conference on Biological Information and Biomedical Engineering, BIBE 2020

Y2 - 21 July 2020 through 23 July 2020

ER -

Wu J, Zhang L, Weng Y, Meng J , Su J, Wang Y. An Improved Algorithm for Estimating the Distribution of RNA-related Genomic Features. In Yu W, Liu C, editors, Proceedings of the 4th International Conference on Biological Information and Biomedical Engineering, BIBE 2020. Association for Computing Machinery. 2020. (ACM International Conference Proceeding Series). doi: 10.1145/3403782.3403785

An Improved Algorithm for Estimating the Distribution of RNA-related Genomic Features

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