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Chua, G., Robinson, M. D., Morris, Q., and Hughes, T. R. (2004). "Transcriptional networks: reverse-engineering gene regulation on a global scale.." Curr Opin Microbiol, 7, 638-646.
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Kelley, B. P., Yuan, B., Lewitter, F., Sharan, R., Stockwell, B. R., and Ideker, T. (2004). "PathBLAST: a tool for alignment of protein interaction networks.." Nucleic Acids Res, 32.
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Beer, M. A. and Tavazoie, S. (2004). "Predicting gene expression from sequence.." Cell, 117, 185-198.
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Gao, F., Foat, B. C., and Bussemaker, H. J. (2004). "Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.." BMC Bioinformatics, 5.
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Burgard, Anthony P., Nikolaev, Evgeni V., Schilling, Christophe H., and Maranas, Costas D. (2004). "Flux Coupling Analysis of Genome-Scale Metabolic Network Reconstructions." Genome Res., 14, 301-312.
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Friedman, N. (2004). "Inferring cellular networks using probabilistic graphical models.." Science, 303, 799-805.
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Pritsker, Moshe, Liu, Yir-Chung, Beer, Michael A., and Tavazoie, Saeed (2004). "Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation." Genome Res., 14, 99-108.
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Haugen, A. C., Kelley, R., Collins, J. B., Tucker, C. J., Deng, C., Afshari, C. A., Brown, J. M., Ideker, T., and Van Houten, B. (2004). "Integrating phenotypic and expression profiles to map arsenic-response networks.." Genome Biol, 5.
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Morley, M., Molony, C.M., Weber, T.M., Devlin, J.L., Ewens, K.G., Spielman, R.S., and Cheung, V.G. (2004). "Genetic analysis of genome-wide variation in human gene expression." Nature, 430, 743-747.
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Wong, S.L., Zhang, L.V., Tong, A.H.Y., Li, Z., Goldberg, D.S., King, O.D., Lesage, G., Vidal, M., Andrews, B., Bussey, H., and others (2004). "Combining biological networks to predict genetic interactions." Proceedings of the National Academy of Sciences, 101(44), 15682-15687.
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Covert, M.W., Knight, E.M., Reed, J.L., Herrgard, M.J., and Palsson, B.O. (2004). "Integrating high-throughput and computational data elucidates bacterial networks." Nature, 429(6987), 92-96.
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Herrgard, MJ, Covert, MW, and Palsson, BO (2004). "Reconstruction of microbial transcriptional regulatory networks.." Curr Opin Biotechnol, 15(1), 70-7.
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Tanay, A. and Shamir, R. (2004). "Multilevel modeling and inference of transcription regulation.." J Comput Biol, 11, 357-375.
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Yeang, C. H., Ideker, T., and Jaakkola, T. (2004). "Physical network models.." J Comput Biol, 11, 243-262.
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Zhu, J., Lum, PY, Lamb, J., GuhaThakurta, D., Edwards, SW, Thieringer, R., Berger, JP, Wu, MS, Thompson, J., Sachs, AB, and others (2004). "An integrative genomics approach to the reconstruction of gene networks in segregating populations." Cytogenetic and Genome Research, 105(2-4), 363-374.
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Scholtens, D. and Gentleman, R. (2004). "Making sense of high-throughput protein-protein interaction data." Statistical Aplications in Genetics and Molecular Biology, 3.
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