NDLI: Adaptive coarse-graining for transient and quasi-equilibrium analyses of stochastic gene regulation

Content Provider	IEEE Xplore Digital Library
Author	Tapia, J.J. Faeder, J.R. Munsky, B.
Copyright Year	2012
Description	Author affiliation: Department of Computational and Systems Biology. University of Pittsburgh, PA 15260, USA (Faeder, J.R.) \|\| Department of Computational and Systems Biology, University of Pittsburgh, PA 15260, USA (Tapia, J.J.) \|\| Information Sciences Group, The Center For Nonlinear Studies, Los Alamos National Laboratory, NM 87545, USA (Munsky, B.)
Abstract	Intracellular populations of genes, RNA and proteins are often described by continuous-time, discrete-state Markov processes, whose time-varying probability distributions evolve according to the large or infinite dimensional linear ordinary differential equation known as the chemical master equation (CME). Numerical integration and stochastic simulation of the CME are often impossible or time consuming. We introduce new methods to project the full CME onto a lower dimensional space, while retaining the transient and equilibrium statistics of the original process. First, we investigate three complementary sets of coarse-graining rules: (i) The previously described finite state projection approach; (ii) A modification of existing coarse-graining approaches to reduce the system dimension while capturing the processes equilibrium distribution; and (iii) New time-scale correction terms to recapture transient dynamics of the original system. Next, we explore different iterative algorithms that automatically adapt the projection resolution to improve accuracy and efficiency of the CME solution. We test these projection and refinement strategies on several gene regulatory processes, and we comment on the efficiency and accuracy of the coarse-graining rules and refinement strategies.
Starting Page	5361
Ending Page	5366
File Size	743857
Page Count	6
File Format	PDF
ISBN	9781467320658
ISSN	07431546
e-ISBN	9781467320665
e-ISBN	9781467320641
DOI	10.1109/CDC.2012.6425828
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-12-10
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Interpolation Sociology Statistics Markov processes Chemicals
Content Type	Text
Resource Type	Article
Subject	Control and Optimization Control and Systems Engineering Modeling and Simulation

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
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7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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