Literature DB >> 23829723

Stochastic processes with distributed delays: chemical Langevin equation and linear-noise approximation.

Tobias Brett1, Tobias Galla.   

Abstract

We develop a systematic approach to the linear-noise approximation for stochastic reaction systems with distributed delays. Unlike most existing work our formalism does not rely on a master equation; instead it is based upon a dynamical generating functional describing the probability measure over all possible paths of the dynamics. We derive general expressions for the chemical Langevin equation for a broad class of non-Markovian systems with distributed delay. Exemplars of a model of gene regulation with delayed autoinhibition and a model of epidemic spread with delayed recovery provide evidence of the applicability of our results.

Mesh:

Year:  2013        PMID: 23829723     DOI: 10.1103/PhysRevLett.110.250601

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


  13 in total

1.  Bayesian inference of distributed time delay in transcriptional and translational regulation.

Authors:  Boseung Choi; Yu-Yu Cheng; Selahattin Cinar; William Ott; Matthew R Bennett; Krešimir Josić; Jae Kyoung Kim
Journal:  Bioinformatics       Date:  2020-01-15       Impact factor: 6.937

2.  Intrinsic noise, Delta-Notch signalling and delayed reactions promote sustained, coherent, synchronized oscillations in the presomitic mesoderm.

Authors:  Joseph W Baron; Tobias Galla
Journal:  J R Soc Interface       Date:  2019-11-27       Impact factor: 4.118

3.  Effects of cell cycle noise on excitable gene circuits.

Authors:  Alan Veliz-Cuba; Chinmaya Gupta; Matthew R Bennett; Krešimir Josić; William Ott
Journal:  Phys Biol       Date:  2016-11-30       Impact factor: 2.583

4.  Modeling delay in genetic networks: from delay birth-death processes to delay stochastic differential equations.

Authors:  Chinmaya Gupta; José Manuel López; Robert Azencott; Matthew R Bennett; Krešimir Josić; William Ott
Journal:  J Chem Phys       Date:  2014-05-28       Impact factor: 3.488

5.  Stochastic modeling of biochemical systems with multistep reactions using state-dependent time delay.

Authors:  Qianqian Wu; Tianhai Tian
Journal:  Sci Rep       Date:  2016-08-24       Impact factor: 4.379

6.  Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes.

Authors:  Nick E Phillips; Cerys Manning; Nancy Papalopulu; Magnus Rattray
Journal:  PLoS Comput Biol       Date:  2017-05-11       Impact factor: 4.475

7.  Stochasticity in the miR-9/Hes1 oscillatory network can account for clonal heterogeneity in the timing of differentiation.

Authors:  Nick E Phillips; Cerys S Manning; Tom Pettini; Veronica Biga; Elli Marinopoulou; Peter Stanley; James Boyd; James Bagnall; Pawel Paszek; David G Spiller; Michael Rh White; Marc Goodfellow; Tobias Galla; Magnus Rattray; Nancy Papalopulu
Journal:  Elife       Date:  2016-10-04       Impact factor: 8.140

8.  Noise Decomposition Principle in a Coherent Feed-Forward Transcriptional Regulatory Loop.

Authors:  Rong Gui; Quan Liu; Yuangen Yao; Haiyou Deng; Chengzhang Ma; Ya Jia; Ming Yi
Journal:  Front Physiol       Date:  2016-11-30       Impact factor: 4.566

9.  Filtering and inference for stochastic oscillators with distributed delays.

Authors:  Silvia Calderazzo; Marco Brancaccio; Bärbel Finkenstädt
Journal:  Bioinformatics       Date:  2019-04-15       Impact factor: 6.937

10.  Frequency spectrum of chemical fluctuation: A probe of reaction mechanism and dynamics.

Authors:  Sanggeun Song; Gil-Suk Yang; Seong Jun Park; Sungguan Hong; Ji-Hyun Kim; Jaeyoung Sung
Journal:  PLoS Comput Biol       Date:  2019-09-16       Impact factor: 4.475

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