Hierarchical thinking in network biology: The unbiased modularization of biochemical networks

Trends in Biochemical Sciences

Volumn 29, Issue 12, 2004, Pages 641-647

  Papin, Jason A ^a   Reed, Jennifer L ^a   Palsson, Bernhard O ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CALCULATION; CHEMICAL REACTION; PRIORITY JOURNAL; REVIEW; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS;

ANIMALS; BIOCHEMISTRY; COMPUTATIONAL BIOLOGY; HUMANS; METABOLISM; MODELS, BIOLOGICAL; PROTEINS; SIGNAL TRANSDUCTION;

EID: 8544223537     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibs.2004.10.001     Document Type: Review

References (39)

1. L.H. Hartwell From molecular to modular cell biology Nature 402 1999 C47 C52
2. E. Ravasz Hierarchical organization of modularity in metabolic networks Science 297 2002 1551 1555
3. A.W. Rives, and T. Galitski Modular organization of cellular networks Proc. Natl. Acad. Sci. U. S. A. 100 2003 1128 1133
4. D.M. Wolf, and A.P. Arkin Motifs, modules and games in bacteria Curr. Opin. Microbiol. 6 2003 125 134
5. E. Yeger-Lotem Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction Proc. Natl. Acad. Sci. U. S. A. 101 2004 5934 5939
6. M. Ginkel Modular modeling of cellular systems with ProMoT/Diva BioInformatics 19 2003 1169 1176
7. S. Schuster Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae BioInformatics 18 2002 351 361
8. A. Hoffmann The IκB-NF-κB signaling module: temporal control and selective gene activation Science 298 2002 1241 1245
9. G. Michal Biochemical Pathways: an Atlas of Biochemistry and Molecular Biology 1999 Wiley
10. P.C. Lucas NF-κB signaling in lymphocytes: a new cast of characters J. Cell Sci. 117 2004 31 39
11. N.D. Price Genome-scale microbial in silico models: the constraints-based approach Trends Biotechnol. 21 2003 162 169
12. M.W. Covert Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? Biotechnol. Bioeng. 84 2003 763 772
13. M. Schena Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 270 1995 467 470
14. A.P. Burgard Flux coupling analysis of genome-scale metabolic network reconstructions Genome Res. 14 2004 301 312
15. N.D. Price Uniform sampling of steady state flux spaces: means to design experiments and to interpret enzymopathies Biophys. J. 87 2004 2172 2186
16. S. Schuster Use of network analysis of metabolic systems in bioengineering Bioprocess Biosystems Eng. 24 2002 363 372
17. J.A. Papin Extreme pathway lengths and reaction participation in genome-scale metabolic networks Genome Res. 12 2002 1889 1900
18. C.H. Schilling, and B.O. Palsson Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis J. Theor. Biol. 203 2000 249 283
19. T. Pfeiffer METATOOL: for studying metabolic networks BioInformatics 15 1999 251 257
20. J.A. Papin Metabolic pathways in the post-genome era Trends Biochem. Sci. 28 2003 250 258
21. J.L. Reed, and B.O. Palsson Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states Genome Res. 14 2004 1797 1805
22. M.W. Covert Integrating high-throughput and computational data elucidates bacterial networks Nature 429 2004 92 96
23. F.D. Smith, and J.D. Scott Signaling complexes: junctions on the intracellular information super highway Curr. Biol. 12 2002 R32 R40
24. W.S. Hlavacek The complexity of complexes in signal transduction Biotechnol. Bioeng. 84 2003 783 794
25. M. Raman, and M.H. Cobb MAP kinase modules: many roads home Curr. Biol. 13 2003 R886 R888
26. J.A. Papin, and B.O. Palsson The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis Biophys. J. 87 2004 37 46
27. J.G. Reich, and E. Selkov Energy Metabolism of the Cell: a Theoretical Treatise 1981 Academic Press
28. I. Famili, and B.O. Palsson The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools Biophys. J. 85 2003 16 26
29. S. Schuster, and T. Hofer Determining all extreme semi-positive conservation relations in chemical-reaction systems - a test criterion for conservativity J. Chem. Soc. Faraday Trans. 87 1991 2561 2566
30. S. Schuster, and R. Heinrich Minimization of intermediate concentrations as a suggested optimality principle for biochemical networks. 1. theoretical-analysis J. Math. Biol. 29 1991 425 442
31. B.O. Palsson Reducing complexity in metabolic networks: making metabolic meshes manageable Fed. Proc. 46 1987 2485 2489
32. K.J. Kauffman Description and analysis of metabolic connectivity and dynamics in the human red blood cell Biophys. J. 83 2002 646 662
33. A. Arkin A test case of correlation metric construction of a reaction pathway from measurements Science 277 1997 1275 1279
34. N.C. Duarte Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model Genome Res. 14 2004 1298 1309
35. J.D. Han Evidence for dynamically organized modularity in the yeast protein-protein interaction network Nature 430 2004 88 93
36. J. Hasty Engineered gene circuits Nature 420 2002 224 230
37. F.J. Isaacs Prediction and measurement of an autoregulatory genetic module Proc. Natl. Acad. Sci. U. S. A. 100 2003 7714 7719
38. E. Almaas Global organization of metabolic fluxes in the bacterium Escherichia coli Nature 427 2004 839 843
39. B. Palsson In silico biology through 'omics' Nat. Biotechnol. 20 2002 649 650