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A stochastic model of size control in the budding yeast cell cycle
(2019-06-20)
Background
Cell size is a key characteristic that significantly affects many aspects of cellular physiology. There are specific control mechanisms during cell cycle that maintain the cell size within a range from generation ...
JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations
(Biomed Central Ltd, 2015-12-24)
Background
Most biomolecular reaction modeling tools allow users to build models with a single list of parameter values. However, a common scenario involves different parameterizations of the model to account for the ...
A simple theoretical framework for understanding heterogeneous differentiation of CD4(+) T cells
(Biomed Central Ltd, 2012-06-14)
Background
CD4+ T cells have several subsets of functional phenotypes, which play critical yet diverse roles in the immune system. Pathogen-driven differentiation of these subsets of cells is often heterogeneous in terms ...
Models in biology: lessons from modeling regulation of the eukaryotic cell cycle
(Biomed Central Ltd, 2015-07-01)
In this essay we illustrate some general principles of mathematical modeling in biology by our experiences in studying the molecular regulatory network underlying eukaryotic cell division. We discuss how and why the models ...
Predicting network modules of cell cycle regulators using relative protein abundance statistics
(2017-02-28)
Background
Parameter estimation in systems biology is typically done by enforcing experimental observations through an objective function as the parameter space of a model is explored by numerical simulations. Past studies ...
Cell cycle control and environmental response by second messengers in Caulobacter crescentus
(2020-09-30)
Background
Second messengers, c-di-GMP and (p)ppGpp, are vital regulatory molecules in bacteria, influencing cellular processes such as biofilm formation, transcription, virulence, quorum sensing, and proliferation. While ...
Natural antisense transcript of Period2, Per2AS, regulates the amplitude of the mouse circadian clock
(Cold Spring Harbor Laboratory Press, 2021-05-20)
In mammals, a set of core clock genes form transcription–translation feedback loops to generate circadian oscillations. In mammals, a set of core clock genes form transcription–translation feedback loops to generate circadian ...
A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM
(CELL PRESS, 1999-11)
Many organisms display rhythms of physiology and behavior that are entrained to the 24-h cycle of light and darkness prevailing on Earth. Under constant conditions of illumination and temperature, these internal biological ...
Mathematical model of the cell division cycle of fission yeast
(AIP Publishing, 2001-03)
Much is known about the genes and proteins controlling the cell cycle of fission yeast. Can these molecular components be spun together into a consistent mechanism that accounts for the observed behavior of growth and ...
Minimal Models for Cell-Cycle Control Based on Competitive Inhibition and Multisite Phosphorylations of Cdk Substrates
(CELL PRESS, 2013-03)
The eukaryotic cell cycle is characterized by alternating oscillations in the activities of cyclin-dependent kinase (Cdk) and the anaphase-promoting complex (APC). Successful completion of the cell cycle is dependent on ...