Computational approaches for modeling regulatory cellular networks

Hartwell, 1999, From molecular to modular cell biology, Nature, 402, C47, 10.1038/35011540 Lum, 2004, The Hedgehog response network: sensors, switches, and routers, Science, 304, 1755, 10.1126/science.1098020 Zhu, 2001, Global analysis of protein activities using proteome chips, Science, 293, 2101, 10.1126/science.1062191 Uetz, 2000, A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae, Nature, 403, 623, 10.1038/35001009 Ho, 2002, Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry, Nature, 415, 180, 10.1038/415180a Giot, 2003, A protein interaction map of Drosophila melanogaster, Science, 302, 1727, 10.1126/science.1090289 Ghaemmaghami, 2003, Global analysis of protein expression in yeast, Nature, 425, 737, 10.1038/nature02046 Huh, 2003, Global analysis of protein localization in budding yeast, Nature, 425, 686, 10.1038/nature02026 Maslov, 2002, Specificity and stability in topology of protein networks, Science, 296, 910, 10.1126/science.1065103 Milo, 2004, Superfamilies of evolved and designed networks, Science, 303, 1538, 10.1126/science.1089167 Strogatz, 2001, Exploring complex networks, Nature, 410, 268, 10.1038/35065725 Stelling, 2002, Metabolic network structure determines key aspects of functionality and regulation, Nature, 420, 190, 10.1038/nature01166 Ferrell, 1998, The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes, Science, 280, 895, 10.1126/science.280.5365.895 Alm, 2003, Biological networks, Curr. Opin. Struct. Biol., 13, 193, 10.1016/S0959-440X(03)00031-9 Jordan, 2000, Signaling networks: the origins of cellular multitasking, Cell, 103, 193, 10.1016/S0092-8674(00)00112-4 Weng, 1999, Complexity in biological signaling systems, Science, 284, 92, 10.1126/science.284.5411.92 Vogelstein, 2000, Surfing the p53 network, Nature, 408, 307, 10.1038/35042675 Haugh, 1997, Physical modulation of intracellular signaling processes by locational regulation, Biophys. J., 72, 2014, 10.1016/S0006-3495(97)78846-5 Lippincott-Schwartz, 2001, Studying protein dynamics in living cells, Nat. Rev. Mol. Cell Biol., 2, 444, 10.1038/35073068 Hirschberg, 2000, Kinetic analysis of intracellular trafficking in single living cells with vesicular stomatitis virus protein G–green fluorescent protein hybrids, Methods Enzymol., 327, 69, 10.1016/S0076-6879(00)27268-6 Hasty, 2001, Designer gene networks: towards fundamental cellular control, Chaos, 11, 207, 10.1063/1.1345702 Arkin, 1998, Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells, Genetics, 149, 1633, 10.1093/genetics/149.4.1633 McAdams, 1997, Stochastic mechanisms in gene expression, Proc. Natl. Acad. Sci. U. S. A., 94, 814, 10.1073/pnas.94.3.814 Ozbudak, 2004, Multistability in the lactose utilization network of Escherichia coli, Nature, 427, 737, 10.1038/nature02298 Fink, 1999, Morphological control of inositol-1,4,5-trisphosphate-dependent signals, J. Cell Biol., 147, 929, 10.1083/jcb.147.5.929 Smith, 2002, Systems analysis of Ran transport, Science, 295, 488, 10.1126/science.1064732 Fink, 2000, An image-based model of calcium waves in differentiated neuroblastoma cells, Biophys. J., 79, 163, 10.1016/S0006-3495(00)76281-3 Dundr, 2002, A kinetic framework for a mammalian RNA polymerase in vivo, Science, 298, 1623, 10.1126/science.1076164 Firth, 2000, Stochastic simulation of cell signaling pathways, 263 Hoffmann, 2002, The IkappaB–NF-kappaB signaling module: temporal control and selective gene activation, Science, 298, 1241, 10.1126/science.1071914 Haugh, 2004, Spatial analysis of 3′ phosphoinositide signaling in living fibroblasts: I. Uniform stimulation model and bounds on dimensionless groups, Biophys. J., 86, 589, 10.1016/S0006-3495(04)74137-5 Schneider, 2004, Spatial analysis of 3′ phosphoinositide signaling in living fibroblasts: II. Parameter estimates for individual cells from experiments, Biophys. J., 86, 599, 10.1016/S0006-3495(04)74138-7 Haugh, 2002, A unified model for signal transduction reactions in cellular membranes, Biophys. J., 82, 591, 10.1016/S0006-3495(02)75424-6 Shvartsman, 2002, Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis, Development, 129, 2577, 10.1242/dev.129.11.2577 Houchmandzadeh, 2002, Establishment of developmental precision and proportions in the early Drosophila embryo, Nature, 415, 798, 10.1038/415798a Resat, 2003, An integrated model of epidermal growth factor receptor trafficking and signal transduction, Biophys. J., 85, 730, 10.1016/S0006-3495(03)74516-0 Franks, 2002, A Monte Carlo model reveals independent signaling at central glutamatergic synapses, Biophys. J., 83, 2333, 10.1016/S0006-3495(02)75248-X Lee, 2003, The immunological synapse balances T cell receptor signaling and degradation, Science, 302, 1218, 10.1126/science.1086507 Bhalla, 1999, Emergent properties of networks of biological signaling pathways, Science, 283, 381, 10.1126/science.283.5400.381 Ferrell, 2002, Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability, Curr. Opin. Cell Biol., 14, 140, 10.1016/S0955-0674(02)00314-9 Bhalla, 2001, Robustness of the bistable behavior of a biological signaling feedback loop, Chaos, 11, 221, 10.1063/1.1350440 Bagowski, 2001, Bistability in the JNK cascade, Curr. Biol., 11, 1176, 10.1016/S0960-9822(01)00330-X Schlessinger, 1992, Growth factor signaling by receptor tyrosine kinases, Neuron, 9, 383, 10.1016/0896-6273(92)90177-F Chiu, 2002, Ras signalling on the endoplasmic reticulum and the Golgi, Nat. Cell Biol., 4, 343, 10.1038/ncb783 Bivona, 2003, Phospholipase Cγ activates Ras on the Golgi apparatus by means of RasGRP1, Nature, 424, 694, 10.1038/nature01806 Ebinu, 1998, RasGRP, a Ras guanyl nucleotide-releasing protein with calcium- and diacylglycerol-binding motifs, Science, 280, 1082, 10.1126/science.280.5366.1082 Cullen, 2002, Integration of calcium and Ras signaling, Nat. Rev. Mol. Cell Biol., 3, 339, 10.1038/nrm808 Brightman, 2000, Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells, FEBS Lett., 482, 169, 10.1016/S0014-5793(00)02037-8 Yamada, 2004, Model analysis of difference between EGF pathway and FGF pathway, Biochem. Biophys. Res. Commun., 314, 1113, 10.1016/j.bbrc.2004.01.009 Schamel, 1996, Signal transduction: specificity of growth factors explained by parallel distributed processing, Med. Hypotheses, 47, 249, 10.1016/S0306-9877(96)90088-2 Traverse, 1994, EGF triggers neuronal differentiation of PC12 cells that overexpress the EGF receptor, Curr. Biol., 4, 694, 10.1016/S0960-9822(00)00154-8 Mark, 1995, Stimulation of neurite outgrowth in PC12 cells by EGF and KCl depolarization: a Ca(2+)-independent phenomenon, J. Cell Biol., 130, 701, 10.1083/jcb.130.3.701 Murphy, 2002, Molecular interpretation of ERK signal duration by immediate early gene products, Nat. Cell Biol., 4, 556, 10.1038/ncb822 Murphy, 2004, A network of immediate early gene products propagates subtle differences in mitogen-activated protein kinase signal amplitude and duration, Mol. Cell. Biol., 24, 144, 10.1128/MCB.24.1.144-153.2004 Okazaki, 1995, The Mos/MAP kinase pathway stabilizes c-Fos by phosphorylation and augments its transforming activity in NIH 3T3 cells, EMBO J., 14, 5048, 10.1002/j.1460-2075.1995.tb00187.x Chen, 1996, Phosphorylation of c-Fos at the C-terminus enhances its transforming activity, Oncogene, 12, 1493 Sun, 1993, MKP-1 (3CH134), an immediate early gene product, is a dual specificity phosphatase that dephosphorylates MAP kinase in vivo, Cell, 75, 487, 10.1016/0092-8674(93)90383-2 Bhalla, 2002, MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network, Science, 297, 1018, 10.1126/science.1068873 Vasudeva, 2004, Adaptive stochastic-deterministic chemical kinetic simulations, Bioinformatics, 20, 78, 10.1093/bioinformatics/btg376 Puchalka, 2004, Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks, Biophys. J., 86, 1357, 10.1016/S0006-3495(04)74207-1 Mogilner, 2003, Force generation by actin polymerization II: the elastic ratchet and tethered filaments, Biophys. J., 84, 1591, 10.1016/S0006-3495(03)74969-8 Peskin, 1993, Cellular motions and thermal fluctuations: the Brownian ratchet, Biophys. J., 65, 316, 10.1016/S0006-3495(93)81035-X Pollard, 2003, Cellular motility driven by assembly and disassembly of actin filaments, Cell, 112, 453, 10.1016/S0092-8674(03)00120-X Weiner, 1999, Spatial control of actin polymerization during neutrophil chemotaxis, Nat. Cell Biol., 1, 75, 10.1038/10042 Welch, 1997, Actin polymerization is induced by Arp2/3 protein complex at the surface of Listeria monocytogenes, Nature, 385, 265, 10.1038/385265a0 Mallavarapu, 1999, Regulated actin cytoskeleton assembly at filopodium tips controls their extension and retraction, J. Cell Biol., 146, 1097, 10.1083/jcb.146.5.1097 Bell, 1978, Models for the specific adhesion of cells to cells, Science, 200, 618, 10.1126/science.347575 Howard, 2001 Theriot, 2000, The polymerization motor, Traffic, 1, 19, 10.1034/j.1600-0854.2000.010104.x Gerbal, 2000, An elastic analysis of Listeria monocytogenes propulsion, Biophys. J., 79, 2259, 10.1016/S0006-3495(00)76473-3 Tsien, 1993, FRET for studying intracellular signalling, Trends Cell Biol., 3, 242, 10.1016/0962-8924(93)90124-J Violin, 2003, A genetically encoded fluorescent reporter reveals oscillatory phosphorylation by protein kinase C, J. Cell Biol., 161, 899, 10.1083/jcb.200302125 Dundr, 2002, Quantitation of GFP-fusion proteins in single living cells, J. Struct. Biol., 140, 92, 10.1016/S1047-8477(02)00521-X Slepchenko, 2003, Quantitative cell biology with the Virtual Cell, Trends Cell Biol., 13, 570, 10.1016/j.tcb.2003.09.002 McAdams, 2003, A bacterial cell-cycle regulatory network operating in time and space, Science, 301, 1874, 10.1126/science.1087694 Maskery, 2004, Growth Cone Pathfinding: a competition between deterministic and stochastic events, BMC Neurosci., 5, 22, 10.1186/1471-2202-5-22 Saucerman, 2003, Modeling beta-adrenergic control of cardiac myocyte contractility in silico, J. Biol. Chem., 278, 47997, 10.1074/jbc.M308362200 Eungdamrong, 2004, Modeling cell signaling networks, Biol. Cell., 96, 355, 10.1016/j.biolcel.2004.03.004 Wolf, 2002, Fifteen minutes of fim: control of type 1 pili expression in E. coli, OMICS, 6, 91, 10.1089/15362310252780852 Rao, 2002, Control, exploitation and tolerance of intracellular noise, Nature, 420, 231, 10.1038/nature01258 Mellman, 2003, Computational cell biology, J. Cell Biol., 161, 463, 10.1083/jcb.200303202