Literature DB >> 19139763

Stochastic modelling for quantitative description of heterogeneous biological systems.

Darren J Wilkinson1.   

Abstract

Two related developments are currently changing traditional approaches to computational systems biology modelling. First, stochastic models are being used increasingly in preference to deterministic models to describe biochemical network dynamics at the single-cell level. Second, sophisticated statistical methods and algorithms are being used to fit both deterministic and stochastic models to time course and other experimental data. Both frameworks are needed to adequately describe observed noise, variability and heterogeneity of biological systems over a range of scales of biological organization.

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Year:  2009        PMID: 19139763     DOI: 10.1038/nrg2509

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  73 in total

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Journal:  Syst Biol (Stevenage)       Date:  2006-07

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Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-25       Impact factor: 11.205

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Authors:  Hong Li; Yang Cao; Linda R Petzold; Daniel T Gillespie
Journal:  Biotechnol Prog       Date:  2007-09-26

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Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-26       Impact factor: 11.205

Review 6.  Unlocking the Mdm2-p53 loop: ubiquitin is the key.

Authors:  Hilary V Clegg; Koji Itahana; Yanping Zhang
Journal:  Cell Cycle       Date:  2007-11-25       Impact factor: 4.534

7.  Modelling the checkpoint response to telomere uncapping in budding yeast.

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Journal:  J R Soc Interface       Date:  2007-02-22       Impact factor: 4.118

Review 8.  Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation.

Authors:  Luis López-Maury; Samuel Marguerat; Jürg Bähler
Journal:  Nat Rev Genet       Date:  2008-08       Impact factor: 53.242

9.  Automated tracking of gene expression in individual cells and cell compartments.

Authors:  Hailin Shen; Glyn Nelson; David E Nelson; Stephnie Kennedy; David G Spiller; Tony Griffiths; Norman Paton; Stephen G Oliver; Michael R H White; Douglas B Kell
Journal:  J R Soc Interface       Date:  2006-12-22       Impact factor: 4.118

10.  Explaining oscillations and variability in the p53-Mdm2 system.

Authors:  Carole J Proctor; Douglas A Gray
Journal:  BMC Syst Biol       Date:  2008-08-18
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  167 in total

1.  Stochastic steady state gain in a gene expression process with mRNA degradation control.

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Journal:  J R Soc Interface       Date:  2012-01-11       Impact factor: 4.118

Review 2.  Systems immunology: a survey of modeling formalisms, applications and simulation tools.

Authors:  Vipin Narang; James Decraene; Shek-Yoon Wong; Bindu S Aiswarya; Andrew R Wasem; Shiang Rong Leong; Alexandre Gouaillard
Journal:  Immunol Res       Date:  2012-09       Impact factor: 2.829

Review 3.  Proteomics and systems biology: current and future applications in the nutritional sciences.

Authors:  J Bernadette Moore; Mark E Weeks
Journal:  Adv Nutr       Date:  2011-06-28       Impact factor: 8.701

Review 4.  Classic and contemporary approaches to modeling biochemical reactions.

Authors:  William W Chen; Mario Niepel; Peter K Sorger
Journal:  Genes Dev       Date:  2010-09-01       Impact factor: 11.361

Review 5.  Phenomics: the next challenge.

Authors:  David Houle; Diddahally R Govindaraju; Stig Omholt
Journal:  Nat Rev Genet       Date:  2010-12       Impact factor: 53.242

6.  Discrete-continuous reaction-diffusion model with mobile point-like sources and sinks.

Authors:  Svyatoslav Kondrat; Olav Zimmermann; Wolfgang Wiechert; Eric von Lieres
Journal:  Eur Phys J E Soft Matter       Date:  2016-01-29       Impact factor: 1.890

Review 7.  Systems biology: perspectives on multiscale modeling in research on endocrine-related cancers.

Authors:  Robert Clarke; John J Tyson; Ming Tan; William T Baumann; Lu Jin; Jianhua Xuan; Yue Wang
Journal:  Endocr Relat Cancer       Date:  2019-06       Impact factor: 5.678

8.  Full-length RNA-seq from single cells using Smart-seq2.

Authors:  Simone Picelli; Omid R Faridani; Asa K Björklund; Gösta Winberg; Sven Sagasser; Rickard Sandberg
Journal:  Nat Protoc       Date:  2014-01-02       Impact factor: 13.491

9.  Model discrimination in dynamic molecular systems: application to parotid de-differentiation network.

Authors:  Jaejik Kim; Jiaxu Li; Srirangapatnam G Venkatesh; Douglas S Darling; Grzegorz A Rempala
Journal:  J Comput Biol       Date:  2013-07       Impact factor: 1.479

10.  Stochastic phenotypic interconversion in tumors can generate heterogeneity.

Authors:  Giuseppina Simone
Journal:  Eur Biophys J       Date:  2016-12-09       Impact factor: 1.733

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