Backward simulation for inferring hidden biomolecular kinetic profiles

Summary: Our backward simulation (BS) is an approach to infer the dynamics of individual components in ordinary differential equation (ODE) models, given the information on relatively downstream components or their sums. Here, we demonstrate the use of BS to infer protein synthesis rates with a give...

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Autores principales:	Junghun Chae, Roktaek Lim, Cheol-Min Ghim, Pan-Jun Kim
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Biophysics Systems biology Computer sciences Science (General) Q1-390
Acceso en línea:	https://doaj.org/article/eb4b63cc2fd143ba8b585f447c15bacc
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spelling	oai:doaj.org-article:eb4b63cc2fd143ba8b585f447c15bacc2021-11-18T04:51:42ZBackward simulation for inferring hidden biomolecular kinetic profiles2666-166710.1016/j.xpro.2021.100958https://doaj.org/article/eb4b63cc2fd143ba8b585f447c15bacc2021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S266616672100664Xhttps://doaj.org/toc/2666-1667Summary: Our backward simulation (BS) is an approach to infer the dynamics of individual components in ordinary differential equation (ODE) models, given the information on relatively downstream components or their sums. Here, we demonstrate the use of BS to infer protein synthesis rates with a given profile of protein concentrations over time in a circadian system. This protocol can also be applied to a wide range of problems with undetermined dynamics at the upstream levels.For complete details on the use and execution of this protocol, please refer to Lim et al. (2021).Junghun ChaeRoktaek LimCheol-Min GhimPan-Jun KimElsevierarticleBiophysicsSystems biologyComputer sciencesScience (General)Q1-390ENSTAR Protocols, Vol 2, Iss 4, Pp 100958- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biophysics Systems biology Computer sciences Science (General) Q1-390
spellingShingle	Biophysics Systems biology Computer sciences Science (General) Q1-390 Junghun Chae Roktaek Lim Cheol-Min Ghim Pan-Jun Kim Backward simulation for inferring hidden biomolecular kinetic profiles
description	Summary: Our backward simulation (BS) is an approach to infer the dynamics of individual components in ordinary differential equation (ODE) models, given the information on relatively downstream components or their sums. Here, we demonstrate the use of BS to infer protein synthesis rates with a given profile of protein concentrations over time in a circadian system. This protocol can also be applied to a wide range of problems with undetermined dynamics at the upstream levels.For complete details on the use and execution of this protocol, please refer to Lim et al. (2021).
format	article
author	Junghun Chae Roktaek Lim Cheol-Min Ghim Pan-Jun Kim
author_facet	Junghun Chae Roktaek Lim Cheol-Min Ghim Pan-Jun Kim
author_sort	Junghun Chae
title	Backward simulation for inferring hidden biomolecular kinetic profiles
title_short	Backward simulation for inferring hidden biomolecular kinetic profiles
title_full	Backward simulation for inferring hidden biomolecular kinetic profiles
title_fullStr	Backward simulation for inferring hidden biomolecular kinetic profiles
title_full_unstemmed	Backward simulation for inferring hidden biomolecular kinetic profiles
title_sort	backward simulation for inferring hidden biomolecular kinetic profiles
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/eb4b63cc2fd143ba8b585f447c15bacc
work_keys_str_mv	AT junghunchae backwardsimulationforinferringhiddenbiomolecularkineticprofiles AT roktaeklim backwardsimulationforinferringhiddenbiomolecularkineticprofiles AT cheolminghim backwardsimulationforinferringhiddenbiomolecularkineticprofiles AT panjunkim backwardsimulationforinferringhiddenbiomolecularkineticprofiles
_version_	1718425009844649984

Backward simulation for inferring hidden biomolecular kinetic profiles

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