Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA

Federica Ciocchetta; Jane Hillston; Martin Kos; David Tollervey

doi:10.1016/j.tcs.2008.07.012

Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA

Federica Ciocchetta, Jane Hillston, Martin Kos, David Tollervey

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

Abstract

In this paper we present a quantified model of the synthesis of pre-rRNAs in yeast. The chemical kinetics simulation software Dizzy has been used as both the modelling and simulation framework of our study. The simulations have been used to investigate the mechanism of co-transcriptional cleavage which can occur during the synthesis of pre-rRNAs.

Throughout the paper we emphasise the strong role of experimental data both in shaping the model and in guiding the analysis which is carried out. Parameter estimation procedures have been used to fit the model to the data and we discuss the validation of the model against the available experimental data. Simulation based on Gillespie’s algorithm is considered to be the reference method for our analysis and a comparison with other simulators is reported. Finally, we define an extended model, that relaxes one of the assumptions of the initial model.

Original language	English
Pages (from-to)	41-54
Number of pages	14
Journal	Theoretical Computer Science
Volume	408
Issue number	1
DOIs	https://doi.org/10.1016/j.tcs.2008.07.012
Publication status	Published - 2008

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10.1016/j.tcs.2008.07.012

http://www.sciencedirect.com/science/article/pii/S0304397508005045

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title = "Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA",

abstract = "In this paper we present a quantified model of the synthesis of pre-rRNAs in yeast. The chemical kinetics simulation software Dizzy has been used as both the modelling and simulation framework of our study. The simulations have been used to investigate the mechanism of co-transcriptional cleavage which can occur during the synthesis of pre-rRNAs.Throughout the paper we emphasise the strong role of experimental data both in shaping the model and in guiding the analysis which is carried out. Parameter estimation procedures have been used to fit the model to the data and we discuss the validation of the model against the available experimental data. Simulation based on Gillespie{\textquoteright}s algorithm is considered to be the reference method for our analysis and a comparison with other simulators is reported. Finally, we define an extended model, that relaxes one of the assumptions of the initial model.",

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T1 - Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA

AU - Ciocchetta, Federica

AU - Hillston, Jane

AU - Kos, Martin

AU - Tollervey, David

PY - 2008

Y1 - 2008

N2 - In this paper we present a quantified model of the synthesis of pre-rRNAs in yeast. The chemical kinetics simulation software Dizzy has been used as both the modelling and simulation framework of our study. The simulations have been used to investigate the mechanism of co-transcriptional cleavage which can occur during the synthesis of pre-rRNAs.Throughout the paper we emphasise the strong role of experimental data both in shaping the model and in guiding the analysis which is carried out. Parameter estimation procedures have been used to fit the model to the data and we discuss the validation of the model against the available experimental data. Simulation based on Gillespie’s algorithm is considered to be the reference method for our analysis and a comparison with other simulators is reported. Finally, we define an extended model, that relaxes one of the assumptions of the initial model.

AB - In this paper we present a quantified model of the synthesis of pre-rRNAs in yeast. The chemical kinetics simulation software Dizzy has been used as both the modelling and simulation framework of our study. The simulations have been used to investigate the mechanism of co-transcriptional cleavage which can occur during the synthesis of pre-rRNAs.Throughout the paper we emphasise the strong role of experimental data both in shaping the model and in guiding the analysis which is carried out. Parameter estimation procedures have been used to fit the model to the data and we discuss the validation of the model against the available experimental data. Simulation based on Gillespie’s algorithm is considered to be the reference method for our analysis and a comparison with other simulators is reported. Finally, we define an extended model, that relaxes one of the assumptions of the initial model.

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DO - 10.1016/j.tcs.2008.07.012

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VL - 408

SP - 41

EP - 54

JO - Theoretical Computer Science

JF - Theoretical Computer Science

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ER -

Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA

Abstract

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SynthSys; formerly CSBE: Centre for Systems Biology at Edinburgh

CODA: Process Algebra Approaches to Collective Dynamics.

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Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA

Abstract

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Projects

SynthSys; formerly CSBE: Centre for Systems Biology at Edinburgh

CODA: Process Algebra Approaches to Collective Dynamics.

Cite this