Stochastic delay models for molecular clocks and somite formation

Burrage, Kevin, Burrage, Pamela, Leier, Andre and Marquez-Lago, Tatiana T. (2008). Stochastic delay models for molecular clocks and somite formation. In: Derek Abbott, Tomaso Aste, Murray Batchelor, Robert Dewar, Tiziana Di Matteo and Tony Guttmann, Complex Systems II. Complex Systems II, Canberra, ACT Australia, (). 5 - 7 December 2007. doi:10.1117/12.776148

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Author Burrage, Kevin
Burrage, Pamela
Leier, Andre
Marquez-Lago, Tatiana T.
Title of paper Stochastic delay models for molecular clocks and somite formation
Conference name Complex Systems II
Conference location Canberra, ACT Australia
Conference dates 5 - 7 December 2007
Proceedings title Complex Systems II   Check publisher's open access policy
Journal name Proceedings of SPIE - International Society for Optical Engineering   Check publisher's open access policy
Place of Publication Bellingham, WA United States
Publisher S P I E - International Society for Optical Engineering
Publication Year 2008
Year available 2008
Sub-type Fully published paper
DOI 10.1117/12.776148
Open Access Status File (Publisher version)
ISBN 9780819469731
ISSN 0277-786X
Editor Derek Abbott
Tomaso Aste
Murray Batchelor
Robert Dewar
Tiziana Di Matteo
Tony Guttmann
Volume 6802
Total pages 11
Collection year 2009
Language eng
Formatted Abstract/Summary
Delays are an important feature in temporal models of genetic regulation due to slow biochemical processes such as transcription and translation. In this paper we show how to model intrinsic noise effects in a delayed setting by either using a delay stochastic simulation algorithm (DSSA) or, for larger and more complex systems, a generalized Binomial tau-leap method (Bt-DSSA). As a particular application we apply these ideas to modeling somite segmentation in zebrafish across a number of cells in which two linked oscillatory genes her1 and her7 are synchronized via Notch signaling between the cells. 
Subjects 2208 Electrical and Electronic Engineering
3104 Condensed Matter Physics
Keyword Binomial r leap algorithm
Coupled regulatory systems
Delay stochastic simulation algorithm
Multicellular environment
Multiscale modeling
Q-Index Code E1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Conference Paper
Collection: Institute for Molecular Bioscience - Publications
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