Genome-Scale Models of Metabolic and Regulatory Networks - Systems Biology: Networks, Models, and Applications - page 256

and H. V. Westerhoff (Eds.), Metabolic Engineering in the Post-Genomic Era
(pp. 209-36). Horizon Bioscience, Norwich, U.K., 2004.

8. Price, N. D., et al. Genome-scale microbial in silico models: the constraints-

based approach . Trends in Biotechnology , 21(4):162-9, 2003.

9. Herrgård, M. J., M. W. Covert and B.O. Palsson. Reconstruction of micro-

bial transcriptional regulatory networks . Current Opinion in Biotechnology ,
15(1):70-7, 2004.

10. Michal, G. Biochemical Pathways: An Atlas of Biochemistry and Molecular

Biology . Wiley-Spektrum, New York, 1999.

11. Osterman, A. and R. Overbeek. Missing genes in metabolic pathways: a

comparative genomics approach . Current Opinion in Chemical Biology , 7(2):
238-51, 2003.

12. Kanehisa, M., et al. The KEGG resource for deciphering the genome .

Nucleic Acids Research , 32 (Database issue):D277-80, 2004.

13. Keseler, I. M., et al. EcoCyc: a comprehensive database resource for

Escherichia coli. Nucleic Acids Research , 33 (Database Issue):D334-7, 2005.

14. Reed, J. L., et al. An expanded genome-scale model of Escherichia coli K-12

( i JR904 GSM/GPR) . Genome Biology , 4(9):R54.1-12, 2003.

15. Neidhardt, F. C. Escherichia coli and Salmonella : Cellular and Molecular Biology .

ASM Press, Washington, D.C., 1996.

16. Strathern, J. N., E. W. Jones and J.R. Broach. The Molecular Biology of the

Yeast Saccharomyces: Metabolism and Gene Expression . Cold Spring Harbor
Laboratory, Cold Spring Harbor, N.Y., 1982.

17. Huh, W. K., et al. Global analysis of protein localization in budding yeast .

Nature , 425(6959):686-91, 2003.

18. Prokisch, H., et al. Integrative analysis of the mitochondrial proteome in

yeast . PLoS Biology , 2(6):e160, 2004.

19. Duarte, N. C., M. J. Herrgård and B. Palsson. Reconstruction and validation

of Saccharomyces cerevisiae i ND750, a fully compartmentalized genome-
scale metabolic model . Genome Research , 14(7):1298-309, 2004.

20. Schilling, C. H. and B. O. Palsson. Assessment of the metabolic capabilities

of Haemophilus influenzae Rd through a genome-scale pathway analysis .
Journal of Theoretical Biology , 203(3):249-83, 2000.

21. Schilling, C. H., et al. Genome-scale metabolic model of Helicobacter pylori

26695 . Journal of Bacteriology , 184(16):4582-93, 2002.

22. Becker, S. A. and B. O. Palsson. Genome-scale reconstruction of the

metabolic network in Staphylococcus aureus N315: an initial draft to the
two-dimensional annotation . BMC Microbiology , 5(1):8, 2005.

23. Forster, J., et al. Genome-scale reconstruction of the Saccharomyces cerevisiae

metabolic network . Genome Research , 13(2):244-53, 2003.

24. Vo, T. D., H. J. Greenberg and B.O. Palsson. Reconstruction and functional

characterization of the human mitochondrial metabolic network based
on proteomic and biochemical data .

Journal of Biological Chemistry ,

279(38):39532-40, 2004.

25. Edwards, J. S. and B. O. Palsson. The Escherichia coli MG1655 in silico

metabolic genotype: its definition, characteristics, and capabilities .
Proceedings of the National Academy of Sciences USA , 97(10):5528-33, 2000.

26. Sainz, J., et al. Modeling of yeast metabolism and process dynamics in

batch fermentation . Biotechnology and Bioengineering , 81(7):818-28, 2003.