Henrik Mannerstrom, Olli Yli-Harja, Andre S Ribeiro
{"title":"Inference of kinetic parameters of delayed stochastic models of gene expression using a markov chain approximation.","authors":"Henrik Mannerstrom, Olli Yli-Harja, Andre S Ribeiro","doi":"10.1155/2011/572876","DOIUrl":null,"url":null,"abstract":"We propose a Markov chain approximation of the delayed stochastic simulation algorithm to infer properties of the mechanisms in prokaryote transcription from the dynamics of RNA levels. We model transcription using the delayed stochastic modelling strategy and realistic parameter values for rate of transcription initiation and RNA degradation. From the model, we generate time series of RNA levels at the single molecule level, from which we use the method to infer the duration of the promoter open complex formation. This is found to be possible even when adding external Gaussian noise to the RNA levels.","PeriodicalId":72957,"journal":{"name":"EURASIP journal on bioinformatics & systems biology","volume":"2011 ","pages":"572876"},"PeriodicalIF":0.0000,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2011/572876","citationCount":"6","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"EURASIP journal on bioinformatics & systems biology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1155/2011/572876","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2010/12/29 0:00:00","PubModel":"Epub","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 6
Abstract
We propose a Markov chain approximation of the delayed stochastic simulation algorithm to infer properties of the mechanisms in prokaryote transcription from the dynamics of RNA levels. We model transcription using the delayed stochastic modelling strategy and realistic parameter values for rate of transcription initiation and RNA degradation. From the model, we generate time series of RNA levels at the single molecule level, from which we use the method to infer the duration of the promoter open complex formation. This is found to be possible even when adding external Gaussian noise to the RNA levels.