Optimization in computational systems biology
JR Banga - BMC systems biology, 2008 - Springer
Optimization aims to make a system or design as effective or functional as possible.
Mathematical optimization methods are widely used in engineering, economics and science …
Mathematical optimization methods are widely used in engineering, economics and science …
Time optimal entrainment control for circadian rhythm
The circadian rhythm functions as a master clock that regulates many physiological
processes in humans including sleep, metabolism, hormone secretion, and neurobehavioral …
processes in humans including sleep, metabolism, hormone secretion, and neurobehavioral …
In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks
We describe an innovative experimental and computational approach to control the
expression of a protein in a population of yeast cells. We designed a simple control …
expression of a protein in a population of yeast cells. We designed a simple control …
Biological switches and clocks
To introduce this special issue on biological switches and clocks, we review the historical
development of mathematical models of bistability and oscillations in chemical reaction …
development of mathematical models of bistability and oscillations in chemical reaction …
Circadian phase resetting via single and multiple control targets
Circadian entrainment is necessary for rhythmic physiological functions to be appropriately
timed over the 24-hour day. Disruption of circadian rhythms has been associated with sleep …
timed over the 24-hour day. Disruption of circadian rhythms has been associated with sleep …
Pharmaceutical-based entrainment of circadian phase via nonlinear model predictive control
The widespread adoption of closed-loop control in systems biology has resulted from
improvements in sensors, computing, actuation, and the discovery of alternative sites of …
improvements in sensors, computing, actuation, and the discovery of alternative sites of …
Synchrony and entrainment properties of robust circadian oscillators
Systems theoretic tools (ie mathematical modelling, control, and feedback design) advance
the understanding of robust performance in complex biological networks. We highlight …
the understanding of robust performance in complex biological networks. We highlight …
Light-based circadian rhythm control: Entrainment and optimization
Light is a strong synchronizer for circadian rhythm—the 24-h biological oscillation in plants,
insects, and mammals. This paper considers the circadian entrainment problem for a …
insects, and mammals. This paper considers the circadian entrainment problem for a …
Multiscale complexity in the mammalian circadian clock
YR Yamada, DB Forger - Current opinion in genetics & development, 2010 - Elsevier
The field of systems biology studies how the interactions among individual components (eg
genes and proteins) yield interesting and complex behavior. The circadian (daily) …
genes and proteins) yield interesting and complex behavior. The circadian (daily) …
Controlling the phase of an oscillator: a phase response curve approach
The paper discusses elementary control strategies to control the phase of an oscillator. Both
feedforward and feedback (P and PI) control laws are designed based on the phase …
feedforward and feedback (P and PI) control laws are designed based on the phase …