Source BohringerMannheim The History of Biological Networks Structures

Source Bohringer-Mannheim

The History of Biological Networks Structures Strings, Physical Structures, …. Networks: Objects with relationships or discrete transformation Pattern and Form Dynamics The Fundamental Problem: I To use observations: S I expression levels I enzyme concentrations I metabolite concentrations ……. To infer underlying network, its structure, dynamics, evolution, function and interactions 2 1 4 3 P

The Origins of Metabolic Research Louis Pasteur 1822 -95 1840 s - the first edge!! Justus von Liebig (1803 -73) in the 1840 s studied the conversion of malic acid to fumaric acid. 1860 s - Pasteur studies fermentation + Eduard Buchner 1860 -1917 NP 1907 fermentation could occur in cell free extracts Hans Buchner (1850 -1902) 1897 - Edvard Buchner showed that Emil Hermann Fischer 1852 -1919 NP 1902 1890 s - Fischer structure and conversion of sugars

1910 s-20 s - Michaelis, Menten (1913) - Briggs, Haldane (1925) studies rate laws for simple enzymatic reaction (simplified). S E P 1926 Kluyver & Donker's "unity of biochemistry" principle Hans Adolf Krebs 1900 -1981 NP 1953 1930 -40 s Krebs characterizes citric acid cycle 1945 Norman H. Horowitz First Model of Metabolic Evolution. Melvin Calvin 1911 -97 NP 61 1930 -40 s Calvin characterizes carbon path in photosynthesis

1961 The Operon model of Gene Regulation Jacques Monod François Jacob 1920 - 1910 -76 NP 1965 m. RNA Factor A m. RNA promoter A B Factor B 1964 Goodwin First mathematical analysis of Operon model of Gene protein NP 1965 m. RNA Gene

1969 - exploration of the dynamics of Boolean Networks Stuart Kauffman Time 1 Factor A Time 3 Time T Gene 1 m. RNA Time 2 Factor B Factor C Remade from Somogyi & Sniegoski, 96. F 2 1969 - Biochemical Systems Theory Gene 2 Gene 3 Gene 4 Gene n Michael Savageau X 0' = 0 X 0 g 00 X 1 g 01 - 0 X 0 h 00 X 1 h 01 X 1' = 1 X 0 g 10 X 1 g 11 - 1 X 0 h 10 X 1 h 11 X 1

E, n P 1 S 1 P 2 1995: Arkin, Mc. Adams, Ross: Stochastic Models of Gene Regulation protein promoter m. RNA Gene Reinhart Heinrich From Fell Two classes of theorems Control Summation Connectivity Henrik Kacser 1918 -95 1973 -4. . : First articles on MCA - metabolic control analysis

1995 -2005 Metabolic Pathways, Flux Analysis and Genome Annotation Palsson Schilling Fell Schuster I 2 S I 1 I 4 I 3 • 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. P

Biological sub-cellular Networks • Signal Transduction Networks • Protein Interaction Networks • Alternative Splicing Graph Biological cellular and supra-cellular Networks Cellular Above the Cell • Neural Networks • Immunological Networks • Disease Networks • Genealogical Networks Non-biological Networks • Social Networks • The Internet • Collaboration Networks • Semantic Networks • Publications and references

Today’s Schedule 1. 00 pm Jotun Hein: Introduction and Biology of Networks 1. 20 pm Chris Holmes: Inference of Networks 1. 35 pm Andrea Rocco: Modelling structure and function in complex networks 1. 50 pm Gesine Reinert: Statistics for small-world networks 2. 10 pm Michael Stumpf: Comparative Biology of Networks 2. 25 -2. 45 pm mini-BREAK 2. 45 pm Imre Vastrik: The Reactome 3. 15 pm Hector Keun: Metabonomics and modeling metabolic networks. 3. 45 -4. 15 pm maxi-BREAK 4. 15 pm Philip Bang: Machine Learning for Systems Biology 4. 45 pm Gail Preston: Evolutionary Modelling of Nitrogen Metabolism in Pseudomonas 5. 05– 5. 20 pm Neil Johnson: Complex Agent-Based Dynamical Networks