A kinetic-dynamic model for regulatory RNA processing

Sher Singh; Hsiu Yi Ou Yang; Mei Ying Chen; Sung Liang Yu

doi:10.1016/j.jbiotec.2006.07.034

A kinetic-dynamic model for regulatory RNA processing

Sher Singh, Hsiu Yi Ou Yang, Mei Ying Chen, Sung Liang Yu^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

5 Citations (Scopus)

Abstract

A kinetic-dynamic model was proposed to simulate RNA processing by determining four essential reaction rates, including the rates of transcription, pre-mRNA turnover, pre-mRNA splicing, and mRNA decay. A family competition evolutionary algorithm (FCEA) was adapted herein to approximate these rates. Several artificial datasets were used to verify the correctness and robustness of the FCEA. The model was finally applied on time series data of yeast prp4-l mutant cells for determination of rates of RNA processing. Based on the FCEA, the model indicated that the pre-mRNA splicing was decreased in the mutant cells as well as the possible effects on transcription, pre-mRNA turnover, and mRNA decay, which was consistent with surveyed literature.

Original language	English
Pages (from-to)	488-495
Number of pages	8
Journal	Journal of Biotechnology
Volume	127
Issue number	3
DOIs	https://doi.org/10.1016/j.jbiotec.2006.07.034
Publication status	Published - 2007 Jan 10
Externally published	Yes

Keywords

FC_adaptive
FCEA
Kinetic-dynamic model
Pre-mRNA splicing

ASJC Scopus subject areas

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology

Access to Document

10.1016/j.jbiotec.2006.07.034

Cite this

@article{752bf83e15bc4a9ca50676fe879d3a9c,

title = "A kinetic-dynamic model for regulatory RNA processing",

abstract = "A kinetic-dynamic model was proposed to simulate RNA processing by determining four essential reaction rates, including the rates of transcription, pre-mRNA turnover, pre-mRNA splicing, and mRNA decay. A family competition evolutionary algorithm (FCEA) was adapted herein to approximate these rates. Several artificial datasets were used to verify the correctness and robustness of the FCEA. The model was finally applied on time series data of yeast prp4-l mutant cells for determination of rates of RNA processing. Based on the FCEA, the model indicated that the pre-mRNA splicing was decreased in the mutant cells as well as the possible effects on transcription, pre-mRNA turnover, and mRNA decay, which was consistent with surveyed literature.",

keywords = "FC_adaptive, FCEA, Kinetic-dynamic model, Pre-mRNA splicing",

author = "Sher Singh and Yang, {Hsiu Yi Ou} and Chen, {Mei Ying} and Yu, {Sung Liang}",

note = "Funding Information: This research was supported by the National Taiwan University Center for Genomic Medicine (NTUCGM) Research Fund.",

year = "2007",

month = jan,

day = "10",

doi = "10.1016/j.jbiotec.2006.07.034",

language = "English",

volume = "127",

pages = "488--495",

journal = "Journal of Biotechnology",

issn = "0168-1656",

publisher = "Elsevier",

number = "3",

}

TY - JOUR

T1 - A kinetic-dynamic model for regulatory RNA processing

AU - Singh, Sher

AU - Yang, Hsiu Yi Ou

AU - Chen, Mei Ying

AU - Yu, Sung Liang

N1 - Funding Information: This research was supported by the National Taiwan University Center for Genomic Medicine (NTUCGM) Research Fund.

PY - 2007/1/10

Y1 - 2007/1/10

N2 - A kinetic-dynamic model was proposed to simulate RNA processing by determining four essential reaction rates, including the rates of transcription, pre-mRNA turnover, pre-mRNA splicing, and mRNA decay. A family competition evolutionary algorithm (FCEA) was adapted herein to approximate these rates. Several artificial datasets were used to verify the correctness and robustness of the FCEA. The model was finally applied on time series data of yeast prp4-l mutant cells for determination of rates of RNA processing. Based on the FCEA, the model indicated that the pre-mRNA splicing was decreased in the mutant cells as well as the possible effects on transcription, pre-mRNA turnover, and mRNA decay, which was consistent with surveyed literature.

AB - A kinetic-dynamic model was proposed to simulate RNA processing by determining four essential reaction rates, including the rates of transcription, pre-mRNA turnover, pre-mRNA splicing, and mRNA decay. A family competition evolutionary algorithm (FCEA) was adapted herein to approximate these rates. Several artificial datasets were used to verify the correctness and robustness of the FCEA. The model was finally applied on time series data of yeast prp4-l mutant cells for determination of rates of RNA processing. Based on the FCEA, the model indicated that the pre-mRNA splicing was decreased in the mutant cells as well as the possible effects on transcription, pre-mRNA turnover, and mRNA decay, which was consistent with surveyed literature.

KW - FC_adaptive

KW - FCEA

KW - Kinetic-dynamic model

KW - Pre-mRNA splicing

UR - http://www.scopus.com/inward/record.url?scp=37849189528&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=37849189528&partnerID=8YFLogxK

U2 - 10.1016/j.jbiotec.2006.07.034

DO - 10.1016/j.jbiotec.2006.07.034

M3 - Article

C2 - 16978727

AN - SCOPUS:37849189528

SN - 0168-1656

VL - 127

SP - 488

EP - 495

JO - Journal of Biotechnology

JF - Journal of Biotechnology

IS - 3

ER -

A kinetic-dynamic model for regulatory RNA processing

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this