Identification of potential targets in biological signalling systems through network perturbation analysis

Abdi, 2008, Fault diagnosis engineering of digital circuits can identify vulnerable molecules in complex cellular pathways, Sci. Signal., 1, 10.1126/scisignal.2000008 Albert, 2000, Error and attack tolerance of complex networks, Nature, 406, 378, 10.1038/35019019 Bar-Even, 2006, Noise in protein expression scales with natural protein abundance, Nat. Genet., 38, 636, 10.1038/ng1807 Bushnell, 2000 Chaves, 2005, Robustness and fragility of Boolean models for genetic regulatory networks, J. Theor. Biol., 235, 431, 10.1016/j.jtbi.2005.01.023 Chuang, 2007, Network-based classification of breast cancer metastasis, Mol. Syst. Biol., 3, 140, 10.1038/msb4100180 Dartnell, 2005, Robustness of the p53 network and biological hackers, FEBS Lett., 579, 3037, 10.1016/j.febslet.2005.03.101 Ernens, 2006, Adenosine inhibits matrix metalloproteinase-9 secretion by neutrophils: implication of A2a receptor and cAMP/PKA/Ca2+ pathway, Circ Res., 99, 590, 10.1161/01.RES.0000241428.82502.d4 Esmaeili, 2009, A multi-objective differential evolutionary approach toward more stable gene regulatory networks, BioSystems, 98, 127, 10.1016/j.biosystems.2009.09.002 Fredholm, 2007, Adenosine, an endogenous distress signal, modulates tissue damage and repair, Cell Death Differ., 14, 1315, 10.1038/sj.cdd.4402132 Friedel, 2007, Influence of degree correlations on network structure and stability in protein–protein interaction networks, BMC Bioinform., 8, 297, 10.1186/1471-2105-8-297 Han, 2004, Evidence for dynamically organized modularity in the yeast protein–protein interaction network, Nature, 430, 88, 10.1038/nature02555 Headrick, 2003, Acute adenosinergic cardioprotection in ischemic-reperfused hearts, Am. J. Physiol. Heart Circ. Physiol., 285, H1797, 10.1152/ajpheart.00407.2003 Helikar, 2008, Emergent decision-making in biological signal transduction networks, Proc. Natl. Acad. Sci. U.S.A., 105, 1913, 10.1073/pnas.0705088105 Jacobson, 2006, Adenosine receptors as therapeutic targets, Nat. Rev. Drug Discov., 5, 247, 10.1038/nrd1983 Janes, 2003, A high-throughput quantitative multiplex kinase assay for monitoring information flow in signaling networks: application to sepsis–apoptosis, Mol. Cell. Proteomics, 2, 463, 10.1074/mcp.M300045-MCP200 Janes, 2006, The response of human epithelial cells to TNF involves an inducible autocrine cascade, Cell, 124, 1225, 10.1016/j.cell.2006.01.041 Jin, 2009, Guest editorial: special section on evolving gene regulatory networks, BioSystems, 98, vi, 10.1016/S0303-2647(09)00181-6 Kauffman, 1969, Metabolic stability and epigenesis in randomly constructed genetic nets, J. Theor. Biol., 22, 437, 10.1016/0022-5193(69)90015-0 KEGG, 2009, Calcium signaling pathway Kitano, 2007, A robustness-based approach to systems-oriented drug design, Nat. Rev. Drug Discov., 6, 202, 10.1038/nrd2195 Klamt, 2006, A methodology for the structural and functional analysis of signaling and regulatory networks, BMC Bioinform., 7, 56, 10.1186/1471-2105-7-56 Mani, 2008, A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas, Mol. Syst. Biol., 4, 16, 10.1038/msb.2008.2 Saez-Rodriguez, 2007, A logical model provides insights into T cell receptor signaling, PLoS Comput. Biol., 3, e163, 10.1371/journal.pcbi.0030163 Samaga, 2009, The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data, PLoS Comput. Biol., 5, e1000438, 10.1371/journal.pcbi.1000438 Schulte, 2003, Signalling from adenosine receptors to mitogen-activated protein kinases, Cell Signal., 15, 813, 10.1016/S0898-6568(03)00058-5 Sitkovsky, 2004, Physiological control of immune response and inflammatory tissue damage by hypoxia-inducible factors and adenosine A2A receptors, Annu. Rev. Immunol., 22, 657, 10.1146/annurev.immunol.22.012703.104731 Stelling, 2004, Robustness of cellular functions, Cell, 118, 675, 10.1016/j.cell.2004.09.008 Wagner, 2008, Playing hide and seek with adenosine receptors, Clin. Transl. Sci., 1, 133, 10.1111/j.1752-8062.2008.00022.x Wilkins, 2008, Sticking together? Falling apart? Exploring the dynamics of the interactome, Trends Biochem. Sci., 33, 195, 10.1016/j.tibs.2008.03.001 Zotenko, 2008, Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality, PLoS Comput. Biol., 4, e1000140, 10.1371/journal.pcbi.1000140