Systemic properties of ensembles of metabolic networks: Application of graphical and statistical methods to simple unbranched pathways

Bioinformatics

Volumn 16, Issue 6, 2000, Pages 534-547

  Alves, Rui ^a,b,c   Savageau, Michael A ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b INSTITUTO DE INVESTIGAÇÃO CIENTÍFICA BENTO DA ROCHA CABRAL   (Portugal)

^c INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOCHEMISTRY; BIOSYNTHESIS; CLASSIFICATION; COMPUTER GRAPHICS; CONTROLLED STUDY; MATHEMATICAL MODEL; METABOLISM; NEGATIVE FEEDBACK; NONLINEAR SYSTEM; PRIORITY JOURNAL; STATISTICAL ANALYSIS; STATISTICAL CONCEPTS; STRUCTURE ANALYSIS;

EID: 0033828273     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/16.6.534     Document Type: Article

References (54)

1. Systems analysis of the tricarboxylic acid cycle in Dictyostelium discoideum. II. Control analysis
2. Comparing systemic properties of ensembles of biological networks by graphical and statistical methods
3. Lipid peroxidation in mitochondrial inner membranes 1. An integrative kinetic model
4. Limitation of metabolite concentrations and the conservation of solvent capacity in the living cell
5. Median attractor and transients in random Boolean nets
6. Role of feedback inhibition in stabilizing the classical operon
7. Implementing Sobol quasirandom sequence generator
8. Exploring the new world of the genome with DNA microarrays
9. A top-down approach to the determination of control coefficients in metabolic control theory
10. Structure identifiability of the parameters of a non linear batch reactor model
11. The transcriptional program of sporulation in budding yeast
12. Properties and metabolism of the aqueous cytoplasm and its boundaries
13. Mathematical models of purine metabolism in man
14. Exploring the metabolic and genetic control of gene expression on a genomic scale
15. How do biological systems discriminate among physically similar ions?
16. Lateral position and interaural discrimination-data and black box model
17. Applied statistics: Analysis of variance and regression
18. Cluster analysis and display of genome-wide expression patterns
19. Cut set analysis of compartmental-models with applications to experimental design
20. A continuous time inverse operator for groundwater and contaminant transport modeling-model identifiability
21. Classification of biological networks by their qualitative dynamics
22. Subunit structure of regulator proteins influences the design of gene circuitry: Analysis of perfectly coupled and completely uncoupled circuits
23. Cell behaviour as a dynamic attractor in the intracellular signalling system
24. Generalized differential specific rate equation for microbial growth
25. Metabolic stability and epigenesis in randomly connected nets
26. Homeostasis and differentiation in random genetic control networks
27. The Origins of Order: Self-Organization and Selection in Evolution
28. Modulation by molecular interactions
29. Qualitative analysis of S-systems: Hopf bifurcations
30. Robust observability for a class of time-varying discrete-time uncertain systems
31. Binding of citrate synthase and malate-dehydrogenase to mitochondrial inner membranes-tissue distribution and metabolic effects
32. Model assessment and refinement using strategies from biochemical systems theory: Application to metabolism in human red blood cells
33. Metabolic consequences of enzyme interactions
34. Experimental application of the top-down control analysis to metabolic systems
35. Synergism analysis of biochemical systems. I. Conceptual framework
36. Synergism analysis of biochemical systems. II. Deviations from multiplicativity
37. Biochemical systems analysis II. The steady state solutions for an n-pool system using a power-law approximation
38. Concepts relating the behavior of biochemical systems to their underlying molecular properties
39. The behavior of intact biochemical control systems
40. Optimal design of feedback control by inhibition: Dynamical considerations
41. A critique of the enzymologist's test tube
42. A kinetic formalism for integrative molecular biology: Manifestation in biochemical systems theory and use in elucidating design principles for gene circuits
43. The tricarboxylic-acid cycle in Dictyostelium discoideum: Systemic effects of including protein turnover in the current model
44. The gene expression matrix: Towards the extraction of genetic network architectures
45. Strategies for representing metabolic pathways within biochemical systems theory: Reversible pathways
46. Metabolic pathway characterization from transient-response data obtained in situ. Parameter estimation in S-system models
47. Complexes of sequential metabolic enzymes
48. Analysis of gene expression data using self-organizing maps
49. Power-law approach to modeling biological systems II. Application to ethanol production
50. Accuracy of alternative representations for integrated biochemical systems
51. Design of practically stable n-dimensional feedback systems: A state-space approach
52. Role of regulatory features of the trp operon of Escherichia coli in mediating a response to a nutritional shift