Source Bohringer-Mannheim

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Source Bohringer-Mannheim
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The History of Biological Networks
Structures Strings, Physical
Structures,. Networks Objects with
relationships or discrete transformation Pattern
and Form Dynamics
The Fundamental Problem To use observations
expression levels enzyme
concentrations metabolite
concentrations . To infer
underlying network, its structure, dynamics,
evolution, function and interactions
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The Origins of Metabolic Research
1840s - the first edge!! Justus von Liebig
(1803-73) in the 1840s studied the conversion of
malic acid to fumaric acid.
1860s - Pasteur studies fermentation
1890s - Fischer structure and conversion of sugars
1897 - Edvard Buchner showed that fermentation
could occur in cell free extracts
Hans Buchner (1850-1902)

Eduard Buchner 1860-1917 NP 1907
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1926 Kluyver Donker's "unity of biochemistry"
principle
1930-40s Krebs characterizes citric acid cycle
1945 Norman H. Horowitz First Model of
Metabolic Evolution.
1930-40s Calvin characterizes carbon path in
photosynthesis
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1961 The Operon model of Gene Regulation
1964 Goodwin First mathematical analysis of
Operon model of Gene
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1969- exploration of the dynamics of Boolean
Networks
Remade from Somogyi Sniegoski,96. F2
1969- Biochemical Systems Theory
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1973-4.. First articles on MCA - metabolic
control analysis
Two classes of theorems Control Summation
Connectivity
1995Arkin, McAdams, Ross Stochastic Models of
Gene Regulation
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1995-2005

• Kinetic Model Fitting Westerhoff
• The phenotype of a network (Omholt, Plathe, )
• Network Comparison Labeling of edges/nodes
  (homology)
• Spatial Information
• Network inference
• Designed/Evolved Network
• Modularity
• Robustness
• Evolvability
• Integration of Networks
• Designed Networks.

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Biological sub-cellular Networks

• Signal Transduction Networks
• Protein Interaction Networks
• Alternative Splicing Graph

Biological cellular and supra-cellular Networks
Non-biological Networks

• Social Networks
• The Internet
• Collaboration Networks
• Semantic Networks
• Publications and references

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Todays Schedule
1.00pm         Jotun HeinIntroduction and
Biology of Networks 1.20pm         Chris Holmes
Inference of Networks 1.35pm         Andrea
Rocco Modelling structure and function in
complex networks 1.50pm Gesine Reinert
Statistics for small-world networks 2.10pm
Michael Stumpf Comparative Biology of
Networks 2.25-2.45pm
mini-BREAK 2.45pm         Imre VastrikThe
Reactome 3.15 pm Hector KeunMetabonomics
and modeling metabolic networks. 3.45-4.15pm
maxi-BREAK 4.15 pm
Philip Bang Machine Learning for Systems
Biology 4.45pm        Gail PrestonEvolutionary
Modelling of Nitrogen Metabolism in
Pseudomonas 5.055.20pm Neil JohnsonComplex
Agent-Based Dynamical Networks