|
Abadir, M.S., Ferguson, J., Kirkland, T.E. 1988. Logic design
verification via test generation. IEEE
Transactions on Computer-Aided Design, 7(1),
138-148.
Akutsu, T., Kuhara, S., Maruyama, O., and Miyano, S. 1998. A system for
identifying genetic networks in gene expression patterns produced by gene
disruptions and overexpressions. Genome Inform. Ser. Workshop 9:151-160.
Blom, J., De Mattos, M.J. & Grivell, L.A. 2000.
Redirection of the respiro-fermentative flux distribution in Saccharomyces
cerevisiae by overexpression of the transcription factor Hap4p. Appl Environ
Microbiol 66, 1970-3.
Deane, C.M., Salwinski, L., Xenarios, I. & Eisenberg, D. 2002.
Protein interactions: two methods for assessment of the reliability of high
throughput observations. Mol Cell Proteomics 1, 349-56.
De Jong, H. 2002. Modeling
and simulation of genetic regulatory systems: a literature review. Journal of Computational Biology, 9(1), 67-103.
Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. 1998.
Cluster analysis and display of genome-wide expression patterns. Proc Natl
Acad Sci U S A 95, 14863-8.
Fedorov, F.F.
1972. Theory of optimal experimental design,
Academic Press, New York.
Furuchi, T. Ishikawa, H., Miura, N., Ishizuka, M., Kajiya, K., Kuge,
S., Naganuma, A. 2001. Two nuclear proteins, Cin5 and Ydr259c, confer
resistance to cisplatin in Saccharomyces cerevisiae. Mol Pharmacol 59, 470-4.
Hood, L.E., Hunkapiller, M.W., Smith, L.M. 1987. Automated DNA
sequencing and analysis of the human genome. Genomics 1(3), 201-212.
Hughes, T.R., Marton, M., Jones, A., Roberts, C., Stoughton, R.,
Armour, C., Bennett, H., Coffey, E., Dai, H., He, Y. et al. 2000. Functional
discovery via a compendium of expression profiles. Cell 102, 109-26.
Ideker, T., Thorsson, V., and Karp, R. M. 2000a. Discovery of regulatory
interactions through perturbation: inference and experimental design. Proceedings of the Pacific Symposium
on Biocomputing.
Ideker, T., Thorsson, V., Siegel, A. & Hood, L. 2000b. Testing for
differentially-expressed genes by maximum likelihood analysis of microarray
data. Journal of Computational Biology 7,
805-817 (2000).
Ideker, T., Thorsson, V., Ranish, J., Christmas, R., Buhler, J., Eng,
J., Bungarner, R., Goodlett, D., Aebersold, R., Hood, L.E. 2001. Integrated
genomic and proteomic analysis of a systematically perturbed metabolic network.
Science 292, 929-934.
Ideker, T., Ozier, O., Schwikowski, B. & Siegel, A.F. 2002.
Discovering regulatory and signalling circuits in molecular interaction
networks. Bioinformatics 18 Suppl 1,
S233-40.
King, R.D., Whelan, K., Jones, F., Reiser, P., Bryant, C., Muggleton,
S., Kell, D., Oliver, S. 2004. Functional genomic hypothesis generation and
experimentation by a robot scientist. Nature 427, 247-52.
Knight, S.A., Tamai, K.T., Kosman, D.J. & Thiele, D.J. 1994. Identification
and analysis of a Saccharomyces cerevisiae copper homeostasis gene encoding a
homeodomain protein. Mol Cell Biol 14,
7792-804.
Kschischang, F., Frey, B. & Loeliger, H. 2001. Factor graphs and
the sum-product algorithm. IEEE Transactions on Information Theory 47, 498-519.
Lee, T.I., Rinaldi, N., Robert, F., Odom, D., Bar-Joseph, Z., Gerber,
G., Hannett, N., Harbison, C., Thimpson, C., Simon, I. et al. 2002.
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804.
Lew, D.J., Weinert, T. & Pringle, J.R. 1997. Cell cycle control in
Saccharomyces cerevisiae. in The Molecular and Cellular Biology of the Yeast
Saccharomyces: Cell Cycle and Cell Biology
(eds. Pringle, J.R., Broach, J.R. & Jones, E.W.) 607-695 (Cold Spring Harbor
Laboratory Press, Cold Spring Harbor).
Lockhart, D., Winzeler, E. 2000. Genomics, gene expression and DNA
arrays. Nature 405, 827-836.
Natarajan, K. Meyer, M., Jackson, B., Slade, D., Roberts,
C., Hinnebusch, A., Marton, M. 2001. Transcriptional profiling shows that Gcn4p
is a master regulator of gene expression during amino acid starvation in yeast.
Mol Cell Biol 21, 4347-68.
Popper, K. 1959. The logic of scientific discovery, Basic Books Inc.
Raiffa, H., Shlaifer, R. 1962. Applied statistical decision theory. MIT
Press, Cambridge.
Rea, C., Settle, M.A. 1996. An automated test approach for US Air Force
fighter engines. IEEE Aerospace
and Electronic Systems Magazine 11(3),
24-28.
Segal, E., Shapira, M., Regev, A., PeĠer, D., Botstein, D., Koller, D.
2003. Module networks: identifying regulatory modules and their
condition-specific regulators from gene expression data. Nat Genet 34, 166-76.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT,
Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: a software environment for integrated
models of biomolecular interaction networks. Genome Res 11,
2498-2504.
Smith, A., Ward, M.P. & Garrett, S. 1998. Yeast PKA
represses Msn2p/Msn4p-dependent gene expression to regulate growth, stress
response and glycogen accumulation. EMBO J
17, 3556-64.
Tong, S., Koller, D. 2000. Active learning for parameter estimation in
Bayesian networks. In The
Proceedings of the13th conference on Neural Information Processing, 647-563.
Uetz, P., Giot, L., Cagney, G., Mansfield, T., Judson, R., Knight, J.,
Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P. et al. 2000. A
comprehensive analysis of protein-protein interactions in Saccharomyces
cerevisiae. Nature 403,
623-7.
Wagner, A. 2001. How to reconstruct a large genetic network from n gene
perturbations in fewer than n(2) easy steps. Bioinformatics 17(12): 1183-97.
Ward, M.P., Gimeno, C.J., Fink, G.R. & Garrett, S. 1995. SOK2 May
Regulate Cyclic AMP-Dependent Protein Kinase-Stimulated Growth and Pseudohyphal
Development by Repressing Transcription. Molecular and Cellular Biology 15, 6854-6863.
Winzeler, E.A., Shoemaker, D., Astromoff, A., Liang, H., Anderson, K.,
Andre, B., Bangham, R., Benito, R., Boeke, J., Bussey, H. et al. 1999.
Functional characterization of the S. cerevisiae genome by gene deletion and
parallel analysis. Science 285,
901-6.
Workman, C. Jensen, L.J., Jarmer, H., Berka, R., Gautier, L., Nielser,
H.B., Saxild, H.H., Nielsen, C., Brunak, S., Knudsen, S. 2002. A new non-linear
normalization method for reducing variability in DNA microarray experiments. Genome
Biol 3, research0048.
Yeang, C.H., Ideker, T., Jaakkola, T. 2004. Physical network models. Journal of Computational Biology 11(2-3), 243-262.
Web
Site References
http://www.cytoscape.org;
Cytoscape Network Modeling Software
http://mips.gsf.de;
Munich Information Center for Protein Sequences
http://www.proteome.com;
Proteome BioKnowledge Library
|
