Modeling systems biology for research and target prioritization

Pharmacogenomics

Volumn 3, Issue 6, 2002, Pages 739-743

  Forst, Christian V ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIDIABETIC AGENT; APOLIPOPROTEIN E3; DRUG; GENE PRODUCT; GLUCOSE; GUANINE NUCLEOTIDE BINDING PROTEIN; PARATHYROID HORMONE; PARATHYROID HORMONE RECEPTOR; SEX PHEROMONE;

ANIMAL CELL; BAYES THEOREM; BIOLOGY; BLOOD CLOTTING; BONE GROWTH; BONE REMODELING; COMPUTER ANALYSIS; COMPUTER MODEL; COMPUTER SIMULATION; CONFERENCE PAPER; DIABETES MELLITUS; DISEASE COURSE; DRUG RESEARCH; DRUG TARGETING; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE SEQUENCE; GENETIC ANALYSIS; HUMAN; HUMAN CELL; MASS SPECTROMETRY; MATHEMATICAL ANALYSIS; MATING; MAXIMUM LIKELIHOOD METHOD; MOLECULAR INTERACTION; MOUSE; MULTIPLE SCLEROSIS; NONHUMAN; OSTEOPOROSIS; PREDICTION; PROBABILITY; PROTEIN DNA INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; SIGNAL TRANSDUCTION; TREATMENT OUTCOME; TWO HYBRID SYSTEM; YEAST;

ANIMALS; CLINICAL TRIALS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DRUG DELIVERY SYSTEMS; HUMANS; MODELS, BIOLOGICAL;

ANIMALIA;

EID: 0036847987     PISSN: 14622416     EISSN: None     Source Type: Journal    
DOI: 10.1517/14622416.3.6.739     Document Type: Conference Paper

References (24)

1. Foundations of Systems Biology. Kitano H (Ed.), The MIT Press, Cambridge, MA, USA (2001).
2. Ideker T, Thorsson V, Ranish JA et al.: Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934 (2001).
3. Schwikowski B, Uetz P, Fields S: A network of protein-protein interaction in yeast. Nature Biotech. 18, 1257-1261 (2000).
4. Ideker T, Ozier O, Schwikowski B, Siegel AF: Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18, S233-S240 (2002).
5. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási A-L: The large-scale organization of metabolic networks. Nature 407, 651-654 (2000).
6. Watts DJ, Strogatz SH: Collective dynamics of 'small-world' networks. Nature 393, 440-442 (1998).
7. Jeong H, Mason SP, Barabasi AL, Oltvai ZN: Lethality and centrality in protein networks. Nature 411, 41-42 (2001).
8. Forst CV, Schulten K: Evolution of metabolisms: a new method for the comparison of metabolic pathway using genomics information. J. Comput. Biol. 64, 343-360 (1999).
9. Forst CV, Schulten K: Phylogenetic analysis of metabolic pathways. J. Mol. Evol. 52, 471-489 (2001).
10. Forst CV: Network genomics - a novel approach for the analysis of biological systems in the postgenomic era. Mol. Biol. Rep. In Press (2002).
11. Kohn KW: Molecular interaction map of the mammalian cell cycle control and dna repair system. Mol. Biol. Cell. 10, 2703-2734 (1999).
12. Kohn KW: Molecular interaction maps as information organizes and simulation guides. Chaos 11, 84-97 (2001).
13. Maimon R, Browning S: Diagrammatic notation and computational structure of gene networks. Proceedings of the Second International Conference on Systems Biology 311-317 (2001).
14. Fox JJ, Hill CC: From topology to dynamics on biochemical networks. Chaos 11, 809-815 (2001).
15. Kleinstein SH, Singh JP: Towards quantitative simulation of germinal center dynamics: biological and modeling insights from experimental validation. J. Theor. Biol. 211, 253-275 (2001).
16. Schilling CH, Edwards JS, Palsson BO: Toward metabolic phenomics: analysis of genomic data using flux balances. Biotech. Progress 15, 288-295 (1999).
17. Edwards JS, Ibarra RU, Palsson BO: In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nature Biotech. 19, 125-130 (2001).
18. Schaff J, Loew LM: The virtual cell. Pacific Symposium on Biocomputing 4, 228-239 (1999)
19. Smith AE, Slepchenko BM, Schaff JC, Loew LM, Macara IG: Systems analysis of RNA transport. Science 295, 488-491 (2002).
20. Fink CC, Slepchenko B, Moraru II, Watras J, Schaff JC, Loew LM: An image-based model of calcium waves in differentiated neuroblastoma cells. Biophys. J. 79, 163-183 (2000).
21. Terasaki M, Campagnola P, Rolls MM et al.: A new model for nuclear envelope breakdown. Mol. Biol. Cell 12, 503-510 (2001).
22. Mannella CA, Pfeiffer DR, Bradshaw PC et al.: Topology of the mitochondrial inner membrane: dynamics and bioenergetic implications. IUBMB Life 52, 93-100 (2001).
23. Carson JH, Krueger WH, Slepchenko BM, Cui H: RNA trafficking in the virtual cell. Mol. Biol. Cell. 11, 157A-157A (2000).
24. Covert MW, Schilling CH, Famili I et al.: Metabolic modeling of microbial strains in silico. Trends Biol. Sci. 26, 179-186 (2001).