A hybrid stochastic model of the budding yeast cell cycle

被引：11

作者：

Ahmadian, Mansooreh ^{[1
]}

Tyson, John J. ^{[2
]}

Peccoud, Jean ^{[3
]}

Cao, Yang ^{[1
]}

机构：

[1] Virginia Tech, Dept Comp Sci, Blacksburg, VA 24061 USA

[2] Virginia Tech, Dept Biol Sci, Blacksburg, VA 24061 USA

[3] GenoFAB Inc, Ft Collins, CO USA

来源：

NPJ SYSTEMS BIOLOGY AND APPLICATIONS | 2020年 / 6卷 / 01期

基金：

美国国家科学基金会;

关键词：

MOLECULAR-MODEL; MITOTIC CONTROL; DIVISION CYCLE; SIMULATION; NOISE; DYNAMICS; FLUCTUATIONS; ANTAGONISM; MECHANISMS; NETWORK;

D O I：

10.1038/s41540-020-0126-z

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The growth and division of eukaryotic cells are regulated by complex, multi-scale networks. In this process, the mechanism of controlling cell-cycle progression has to be robust against inherent noise in the system. In this paper, a hybrid stochastic model is developed to study the effects of noise on the control mechanism of the budding yeast cell cycle. The modeling approach leverages, in a single multi-scale model, the advantages of two regimes: (1) the computational efficiency of a deterministic approach, and (2) the accuracy of stochastic simulations. Our results show that this hybrid stochastic model achieves high computational efficiency while generating simulation results that match very well with published experimental measurements.

引用

页数：10

共 50 条

[21] Multiple Layers of Phospho-Regulation Coordinate Metabolism and the Cell Cycle in Budding Yeast [J].

Zhang, Lichao ;

Winkler, Sebastian ;

Schlottmann, Fabian P. ;

Kohlbacher, Oliver ;

Elias, Josh E. ;

Skotheim, Jan M. ;

Ewald, Jennifer C. .

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY, 2019, 7

[22] A discrete inhomogeneous model for the yeast cell cycle [J].

Wardil, Lucas ;

da Silva, Jafferson Kamphorst L. .

BRAZILIAN JOURNAL OF PHYSICS, 2008, 38 (3A) :350-354

[23] Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle [J].

Liu, Zhen ;

Pu, Yang ;

Li, Fei ;

Shaffer, Clifford A. ;

Hoops, Stefan ;

Tyson, John J. ;

Cao, Yang .

JOURNAL OF CHEMICAL PHYSICS, 2012, 136 (03)

[24] Single-cell phenomics in budding yeast [J].

Ohya, Yoshikazu ;

Kimori, Yoshitaka ;

Okada, Hiroki ;

Ohnuki, Shinsuke .

MOLECULAR BIOLOGY OF THE CELL, 2015, 26 (22) :3920-3925

[25] An automaton model for the cell cycle [J].

Altinok, Atilla ;

Gonze, Didier ;

Levi, Francis ;

Goldbeter, Albert .

INTERFACE FOCUS, 2011, 1 (01) :36-47

[26] A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast [J].

Jariani, Abbas ;

Vermeersch, Lieselotte ;

Cerulus, Bram ;

Perez-Samper, Gemma ;

Voordeckers, Karin ;

Van Brussel, Thomas ;

Thienpont, Bernard ;

Lambrechts, Diether ;

Verstrepen, Kevin J. .

ELIFE, 2020, 9 :1-22

[27] Yeast Network and Report of New Stochastic-Credibility Cell Cycle Models [J].

Chis, Oana ;

Dumitru, Opris ;

Concu, Riccardo ;

Shen, Bairong .

CURRENT BIOINFORMATICS, 2011, 6 (01) :35-43

[28] Mechanochemical modeling of morphogenesis in cell polarization for budding yeast [J].

Xie, Jun ;

Lo, Wing-Cheong .

APPLIED MATHEMATICAL MODELLING, 2024, 131 :615-649

[29] Timing Robustness in the Budding and Fission Yeast Cell Cycles [J].

Mangla, Karan ;

Dill, David L. ;

Horowitz, Mark A. .

PLOS ONE, 2010, 5 (02)

[30] Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle [J].

Herajy, Mostafa ;

Schwarick, Martin ;

Heiner, Monika .

TRANSACTIONS ON PETRI NETS AND OTHER MODELS OF CONCURRENCY VIII, 2013, 8100 :123-141

← 1 2 3 4 5 →