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| ASSOC | CHR | DATA | DB | DYN | EVOL | EXP | FUN | GI | MET | METHY | MICRO | NS | P2P | DEG | REC | REG | REV | SIG | TRANS |
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2006
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Jensen, Lars J., Jensen, Thomas S., de Lichtenberg, Ulrik, Brunak, S., and Bork, Peer (2006). "Co-evolution of transcriptional and post-translational cell-cycle regulation." Nature.
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Lamb, J., Crawford, E. D., Peck, D., Modell, J. W., Blat, I. C., Wrobel, M. J., Lerner, J., Brunet, J. P., Subramanian, A., Ross, K. N., Reich, M., Hieronymus, H., Wei, G., Armstrong, S. A., Haggarty, S. J., Clemons, P. A., Wei, R., Carr, S. A., Lander, E. S., and Golub, T. R. (2006). "The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.." Science, 313, 1929-1935.
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Chua, G., Morris, Q. D., Sopko, R., Robinson, M. D., Ryan, O., Chan, E. T., Frey, B. J., Andrews, B. J., Boone, C., and Hughes, T. R. (2006). "Identifying transcription factor functions and targets by phenotypic activation.." Proc Natl Acad Sci U S A, 103, 12045-12050.
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Haynes, C., Oldfield, C. J., Ji, F., Klitgord, N., Cusick, M. E., Radivojac, P., Uversky, V. N., Vidal, M., and Iakoucheva, L. M. (2006). "Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes.." PLoS Comput Biol, 2.
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Ptacek, Jason and Snyder, Michael (2006). "Charging it up: global analysis of protein phosphorylation.." Trends Genet(52).
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Deutscher, David, Meilijson, Isaac, Kupiec, Martin, and Ruppin, Eytan (2006). "Multiple knockout analysis of genetic robustness in the yeast metabolic network." Nature Genetics, 38, 993-998.
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. "Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states." PLoS Computational Biology.
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Collins, Sean R., Schuldiner, Maya, Krogan, Nevan J., and Weissman, Jonathan S. (2006). "A strategy for extracting and analyzing large-scale quantitative epistatic interaction data." Genome Biology, 7, R63+.
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Herrgard, Markus J., Fong, Stephen S., and Palsson, Bernhard (2006). "Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles." PLoS Computational Biology, 2, e72+.
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Kafri, Ran, Levy, Melissa, and Pilpel, Yitzhak (2006). "The regulatory utilization of genetic redundancy through responsive backup circuits.." Proc Natl Acad Sci U S A.
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Lehner, Ben, Crombie, Catriona, Tischler, Julia, Fortunato, Angelo, and Fraser, Andrew G. (2006). "Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways." Nature Genetics, 38, 896-903.
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Yu, Haiyuan, Xia, Yu, Trifonov, Valery, and Gerstein, Mark (2006). "Design principles of molecular networks revealed by global comparisons and composite motifs." Genome Biology, 7, R55+.
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Beyer, A., Workman, C., Hollunder, J., Radke, D., Mauller, U., Wilhelm, T., and Ideker, T. (2006). "Integrated assessment and prediction of transcription factor binding.." PLoS Comput Biol, 2.
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Ho, Su-Wen W., Jona, Ghil, Chen, Christina T L T., Johnston, Mark, and Snyder, Michael (2006). "Linking DNA-binding proteins to their recognition sequences by using protein microarrays.." Proc Natl Acad Sci U S A.
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Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C., Myers, Chad L., Parsons, Ainslie, Friesen, Helena, Oughtred, Rose, Tong, Amy, Stark, Chris, Ho, Yuen, Botstein, David, Andrews, Brenda, Boone, Charles, Troyanskya, Olga G., Ideker, Trey, Dolinski, Kara, Batada, Nizar N., and Tyers, Mike (2006). "Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae." Journal of Biology, 5, 11+.
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Balaji, S., Iyer, L. M., Aravind, L., and Babu, M. M. (2006). "Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks.." J Mol Biol, 360, 204-212.
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Tanay, Amos (2006). "Extensive low-affinity transcriptional interactions in the yeast genome.." Genome Res.
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Workman, Christopher T., Mak, Craig H., Mccuine, Scott, Tagne, Jean-Bosco, Agarwal, Maya, Ozier, Owen, Begley, Thomas J., Samson, Leona D., and Ideker, Trey (2006). "A Systems Approach to Mapping DNA Damage Response Pathways." Science, 312, 1054-1059.
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Herrgård, M. J., Lee, B. S., Portnoy, V., and Palsson, B. Ø. (2006). "Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.." Genome Res, 16, 627-635.
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Spirin, Victor, Gelfand, Mikhail S S., Mironov, Andrey A A., and Mirny, Leonid A A. (2006). "A metabolic network in the evolutionary context: Multiscale structure and modularity.." Proc Natl Acad Sci U S A.
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Sharan, Roded and Ideker, Trey (2006). "Modeling cellular machinery through biological network comparison." Nature Biotechnology, 24, 427-433.
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Nguyen, Dat H. and D'Haeseleer, Patrik (2006). "Deciphering principles of transcription regulation in eukaryotic genomes." Mol Syst Biol, 2, msb4100054-E1-msb4100054-E10.
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Jaimovich, A., Elidan, G., Margalit, H., and Friedman, N. (2006). "Towards an integrated protein-protein interaction network: a relational markov network approach.." J Comput Biol, 13, 145-164.
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Scott, J., Ideker, T., Karp, R. M., and Sharan, R. (2006). "Efficient algorithms for detecting signaling pathways in protein interaction networks.." J Comput Biol, 13, 133-144.
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Bhattacharyya, Roby P P., Reményi, Attila, Yeh, Brian J J., and Lim, Wendell A A. (2006). "Domains, Motifs, and Scaffolds: The Role of Modular Interactions in the Evolution and Wiring of Cell Signaling Circuits.." Annu Rev Biochem.
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Krogan, Nevan J., Cagney, Gerard, Yu, Haiyuan, Zhong, Gouqing, Guo, Xinghua, Ignatchenko, Alexandr, Li, Joyce, Pu, Shuye, Datta, Nira, Tikuisis, Aaron P., Punna, Thanuja, Peregrãn-Alvarez, Josã© M., Shales, Michael, Zhang, Xin, Davey, Michael, Robinson, Mark D., Paccanaro, Alberto, Bray, James E., Sheung, Anthony, Beattie, Bryan, Richards, Dawn P., Canadien, Veronica, Lalev, Atanas, Mena, Frank, Wong, Peter, Starostine, Andrei, Canete, Myra M., Vlasblom, James, Wu, Samuel, Orsi, Chris, Collins, Sean R., Chandran, Shamanta, Haw, Robin, Rilstone, Jennifer J., Gandi, Kiran, Thompson, Natalie J., Musso, Gabe, St Onge, Peter, Ghanny, Shaun, Lam, Mandy H. Y., Butland, Gareth, Altaf-Ul, Amin M., Kanaya, Shigehiko, Shilatifard, Ali, O'Shea, Erin, Weissman, Jonathan S., Ingles, James C., Hughes, Timothy R., Parkinson, John, Gerstein, Mark, Wodak, Shoshana J., Emili, Andrew, and Greenblatt, Jack F. (2006). "Global landscape of protein complexes in the yeast Saccharomyces cerevisiae." Nature.
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Borneman, A. R., Leigh-Bell, J. A., Yu, H., Bertone, P., Gerstein, M., and Snyder, M. (2006). "Target hub proteins serve as master regulators of development in yeast.." Genes Dev, 20, 435-448.
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He, X. and Zhang, J. (2006). "Transcriptional reprogramming and backup between duplicate genes: is it a genomewide phenomenon?." Genetics, 172, 1363-1367.
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Sopko, R., Huang, D., Preston, N., Chua, G., Papp, B., Kafadar, K., Snyder, M., Oliver, S. G., Cyert, M., Hughes, T. R., Boone, C., and Andrews, B. (2006). "Mapping pathways and phenotypes by systematic gene overexpression.." Mol Cell, 21, 319-330.
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Guo, Xiang, Tatsuoka, Kay, and Liu, Rongxiang (2006). "Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae." Bioinformatics, 22.
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Campillos, Mónica, von Mering, Christian, Jensen, Lars Juhl J., and Bork, Peer (2006). "Identification and analysis of evolutionarily cohesive functional modules in protein networks.." Genome Res.
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Gavin, Anne-Claude, Aloy, Patrick, Grandi, Paola, Krause, Roland, Boesche, Markus, Marzioch, Martina, Rau, Christina, Jensen, Lars J., Bastuck, Sonja, Dümpelfeld, Birgit, Edelmann, Angela, Heurtier, Marie-Anne, Hoffman, Verena, Hoefert, Christian, Klein, Karin, Hudak, Manuela, Michon, Anne-Marie, Schelder, Malgorzata, Schirle, Markus, Remor, Marita, Rudi, Tatjana, Hooper, Sean, Bauer, Andreas, Bouwmeester, Tewis, Casari, Georg, Drewes, Gerard, Neubauer, Gitte, Rick, Jens M., Kuster, Bernhard, Bork, Peer, Russell, Robert B., and Superti-Furga, Giulio (2006). "Proteome survey reveals modularity of the yeast cell machinery." Nature.
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Keshet, Ilana, Schlesinger, Yeshayahu, Farkash, Shlomit, Rand, Eyal, Hecht, Merav, Segal, Eran, Pikarski, Eli, Young, Richard A., Niveleau, Alain, Cedar, Howard, and Simon, Itamar (2006). "Evidence for an instructive mechanism of de novo methylation in cancer cells." Nature Genetics, 38, 149-153.
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Li, D., Li, J., Ouyang, S., Wang, J., Wu, S., Wan, P., Zhu, Y., Xu, X., and He, F. (2006). "Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: large-scale organization and robustness.." Proteomics, 6, 456-461.
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Maciag, Karolina, Altschuler, Steven J., Slack, Michael D., Krogan, Nevan J., Emili, Andrew, Greenblatt, Jack F., Maniatis, Tom, and Wu, Lani F. (2006). "Systems-level analyses identify extensive coupling among gene expression machines." Mol Syst Biol, 2, msb4100045-E1-msb4100045-E14.
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Slonim, Noam, Elemento, Olivier, and Tavazoie, Saeed (2006). "Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks." Mol Syst Biol, 2, msb4100047-E1-msb4100047-E14.
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Pokholok, D.K., Zeitlinger, J., Hannett, N.M., Reynolds, D.B., and Young, R.A. (2006). "Activated Signal Transduction Kinases Frequently Occupy Target Genes." Science's STKE, 313, 533.
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Bandyopadhyay, Sourav, Sharan, Roded, and Ideker, Trey (2006). "Systematic identification of functional orthologs based on protein network comparison." Genome Res., 16(3), 428-435.
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Vitkup, D., Kharchenko, P., and Wagner, A. (2006). "Influence of metabolic network structure and function on enzyme evolution." Genome Biology, 7(5), R39.
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Warner, G. J., Adeleye, Y. A., and Ideker, T. (2006). "Interactome networks: the state of the science.." Genome Biol, 7.
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Blanchette, M., Bataille, A.R., Chen, X., Poitras, C., Laganiere, J., Lefebvre, C., Deblois, G., Giguere, V., Ferretti, V., Bergeron, D., and others (2006). "Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression." Genome Research, 16, 656.
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Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C.A.M., Taylor, M.S., Engström, P.G., Frith, M.C., and others (2006). "Genome-wide analysis of mammalian promoter architecture and evolution." .
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Davidson, E.H. and Erwin, D.H. (2006). "Gene Regulatory Networks and the Evolution of Animal Body Plans." Science, 311, 796.
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Gat-VIks, I., Tanay, A., Raijman, D., and Shamir, Ron (2006). "A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks." Journal of Computational Biology, 13(2), 165.
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Kharchenko, P., Chen, L., Freund, Y., Vitkup, D., and Church, G. M. (2006). "Identifying metabolic enzymes with multiple types of association evidence.." BMC Bioinformatics, 7.
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Newman, J.R.S., Ghaemmaghami, S., Ihmels, J., Breslow, D.K., Noble, M., DeRisi, J.L., and Weissman, J.S. (2006). "Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise." Nature, 441, 840-846.
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Odom, D.T., Dowell, R.D., Jacobsen, E.S., Nekludova, L., Rolfe, P.A., Danford, T.W., Gifford, D.K., Fraenkel, E., Bell, G.I., and Young, R.A. (2006). "Core transcriptional regulatory circuitry in human hepatocytes." Nature.
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Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thastrom, A., Field, Y., Moore, IK, Wang, JP, and Widom, J. (2006). "A genomic code for nucleosome positioning.." Nature.
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Yeang, C.H. and Jaakkola, T. (2006). "Modeling the Combinatorial Functions of Multiple Transcription Factors." JOURNAL OF COMPUTATIONAL BIOLOGY, 13, 463.
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