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Systems Biology
Dec. 21, 2004
Not just an assembly of genes and proteins. The properties of
a system cannot be fully understood merely by drawing a
diagram of interconnections among biomolecules.
-- static roadmaps
The traffic pattern is a key to understand how a system is working.
-- dynamic networks
Four key properties of systems biology
1. System structure
-- Network of gene interactions
-- Network of biochemical pathways
-- Mechanism of interactions that modulate physical properties of
intracellular/multicellular structure
2. Systems dynamics
-- System behavior over time course
-- Bifurcation analysis that traces time-varying changes in the state of
system in a multidimensional space
3. The control method
-- Mechanism that controls the state of the cell
 to minimize malfunction
 to provide potential therapeutic strategies for treatment of diseases
4. The design method
-- To modify and construct biological systems having
desired properties
devised based on the definite design principles and simulations
instead of blind trial-and-error
Focusing points to formulate systems biology
1. Identification of gene regulatory logic and biochemical network
A) Conventional methods
-- Series of experiments
-- Surveys on literature
B) Systematic methods
-- Database built-up
-- Experiments on the expression profile (microarray analyses)
2. Automatic discovery system
A) Advantage– mainly useful for studying transcriptional regulation
example: microarray-based analysis
B) Deficiency– ambiguous hypotheses may be generated
Idealized process of systems biology research