Literature DB >> 25170733

Construction of an effective landscape for multistate genetic switches.

Mingyang Lu1, José Onuchic1, Eshel Ben-Jacob2.   

Abstract

Multistate genetic switches play a crucial role during embryonic development and tumorigenesis. An archetypical example is the three-way switch regulating epithelial-hybrid-mesenchymal transitions. We devise a special WKB-based approach to investigate white Gaussian and shot noise effects on three-way switches, and construct an effective landscape in good quantitative agreement with stochastic simulations. This approach allows efficient analytical or numerical calculation of the landscape contours, the optimal path, and the state relative stability for general multicomponent multistate switches.

Mesh:

Year:  2014        PMID: 25170733     DOI: 10.1103/PhysRevLett.113.078102

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  25 in total

1.  DNA-Binding Kinetics Determines the Mechanism of Noise-Induced Switching in Gene Networks.

Authors:  Margaret J Tse; Brian K Chu; Mahua Roy; Elizabeth L Read
Journal:  Biophys J       Date:  2015-10-20       Impact factor: 4.033

2.  Dichotomous noise models of gene switches.

Authors:  Davit A Potoyan; Peter G Wolynes
Journal:  J Chem Phys       Date:  2015-11-21       Impact factor: 3.488

3.  Effects of DNA replication on mRNA noise.

Authors:  Joseph R Peterson; John A Cole; Jingyi Fei; Taekjip Ha; Zaida A Luthey-Schulten
Journal:  Proc Natl Acad Sci U S A       Date:  2015-12-15       Impact factor: 11.205

4.  Careful accounting of extrinsic noise in protein expression reveals correlations among its sources.

Authors:  John A Cole; Zaida Luthey-Schulten
Journal:  Phys Rev E       Date:  2017-06-27       Impact factor: 2.529

5.  Automatic error control during forward flux sampling of rare events in master equation models.

Authors:  Max C Klein; Elijah Roberts
Journal:  J Chem Phys       Date:  2020-01-21       Impact factor: 3.488

6.  Landscape and kinetic path quantify critical transitions in epithelial-mesenchymal transition.

Authors:  Jintong Lang; Qing Nie; Chunhe Li
Journal:  Biophys J       Date:  2021-09-02       Impact factor: 3.699

7.  Modeling putative therapeutic implications of exosome exchange between tumor and immune cells.

Authors:  Mingyang Lu; Bin Huang; Samir M Hanash; José N Onuchic; Eshel Ben-Jacob
Journal:  Proc Natl Acad Sci U S A       Date:  2014-09-22       Impact factor: 11.205

8.  Trajectory-based energy landscapes of gene regulatory networks.

Authors:  Harish Venkatachalapathy; Samira M Azarin; Casim A Sarkar
Journal:  Biophys J       Date:  2021-01-14       Impact factor: 4.033

9.  Modeling the Transitions between Collective and Solitary Migration Phenotypes in Cancer Metastasis.

Authors:  Bin Huang; Mohit Kumar Jolly; Mingyang Lu; Ilan Tsarfaty; Eshel Ben-Jacob; Jose' N Onuchic
Journal:  Sci Rep       Date:  2015-12-02       Impact factor: 4.379

10.  Distinguishing cell phenotype using cell epigenotype.

Authors:  Thomas P Wytock; Adilson E Motter
Journal:  Sci Adv       Date:  2020-03-18       Impact factor: 14.957

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