The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks
暂无分享,去创建一个
Luay Nakhleh | Melissa Muller | Prahlad T. Ram | Derek A. Ruths | Jen-Te Tseng | P. Ram | L. Nakhleh | M. Muller | Jen-Te Tseng
[1] David A Foster,et al. Alternative phospholipase D/mTOR survival signal in human breast cancer cells , 2005, Oncogene.
[2] Luay Nakhleh,et al. Hypothesis Generation in Signaling Networks , 2006, J. Comput. Biol..
[3] M. Campbell,et al. PANTHER: a library of protein families and subfamilies indexed by function. , 2003, Genome research.
[4] Shankar Subramaniam,et al. Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[5] Ravi Iyengar,et al. Computational approaches for modeling regulatory cellular networks. , 2004, Trends in cell biology.
[6] Chi-Ying F. Huang,et al. Ultrasensitivity in the mitogen-activated protein kinase cascade. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[7] Jason A. Papin,et al. The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. , 2004, Biophysical journal.
[8] J E Ferrell,et al. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. , 1998, Science.
[9] Kun-Liang Guan,et al. Dysregulation of the TSC-mTOR pathway in human disease , 2004, Nature Genetics.
[10] Prahlad T. Ram,et al. Formation of Regulatory Patterns During Signal Propagation in a Mammalian Cellular Network , 2005, Science.
[11] Prahlad T. Ram,et al. MAP Kinase Phosphatase As a Locus of Flexibility in a Mitogen-Activated Protein Kinase Signaling Network , 2002, Science.
[12] Richard Banks,et al. Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach , 2007, Bioinform..
[13] D. Sabatini,et al. Growing roles for the mTOR pathway. , 2005, Current opinion in cell biology.
[14] W. S. Hlavacek,et al. A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. , 2006, Bio Systems.
[15] Carolyn L. Talcott,et al. Pathway Logic: Executable Models of Biological Networks , 2004, WRLA.
[16] C. Helms,et al. Identification of Sonic hedgehog as a candidate gene responsible for holoprosencephaly , 1996, Nature Genetics.
[17] Monika Heiner,et al. Application of Petri net based analysis techniques to signal transduction pathways , 2006, BMC Bioinformatics.
[18] J. Bailey. Complex biology with no parameters , 2001, Nature Biotechnology.
[19] Stefan Bornholdt,et al. Topology of biological networks and reliability of information processing , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[20] D. Feldman,et al. Mechanisms of Disease: β-adrenergic receptors—alterations in signal transduction and pharmacogenomics in heart failure , 2005, Nature Clinical Practice Cardiovascular Medicine.
[21] Hiroyuki Ogata,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..
[22] R. Albert,et al. Predicting Essential Components of Signal Transduction Networks: A Dynamic Model of Guard Cell Abscisic Acid Signaling , 2006, PLoS biology.
[23] Hugh D. Spence,et al. Minimum information requested in the annotation of biochemical models (MIRIAM) , 2005, Nature Biotechnology.
[24] H. D. Jong,et al. Qualitative simulation of the initiation of sporulation in Bacillus subtilis , 2004, Bulletin of mathematical biology.
[25] D. Bray. Protein molecules as computational elements in living cells , 1995, Nature.
[26] Pierre N. Robillard,et al. Modeling and Simulation of Molecular Biology Systems Using Petri Nets: Modeling Goals of Various Approaches , 2004, J. Bioinform. Comput. Biol..
[27] D. Kwiatkowski,et al. Tuberous sclerosis: a GAP at the crossroads of multiple signaling pathways. , 2005, Human molecular genetics.
[28] P. Cluzel,et al. A natural class of robust networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[29] Jason A. Papin,et al. Metabolic pathways in the post-genome era. , 2003, Trends in biochemical sciences.
[30] S. Kauffman,et al. Genetic networks with canalyzing Boolean rules are always stable. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[31] T. S. P. S.,et al. GROWTH , 1924, Nature.
[32] Hiroshi Matsuno,et al. Structural Modeling and Analysis of Signaling Pathways Based on Petri Nets , 2006, J. Bioinform. Comput. Biol..
[33] Paul Tempst,et al. Phosphorylation and Functional Inactivation of TSC2 by Erk Implications for Tuberous Sclerosisand Cancer Pathogenesis , 2005, Cell.
[34] Jason A. Papin,et al. Reconstruction of cellular signalling networks and analysis of their properties , 2005, Nature Reviews Molecular Cell Biology.
[35] B. Palsson,et al. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. , 2000, Journal of theoretical biology.
[36] Ming You,et al. TSC2 Integrates Wnt and Energy Signals via a Coordinated Phosphorylation by AMPK and GSK3 to Regulate Cell Growth , 2006, Cell.
[37] R. Iyengar,et al. Modeling cell signaling networks. , 2004, Biology of the cell.
[38] D. Hanahan,et al. The Hallmarks of Cancer , 2000, Cell.
[39] Atsushi Doi,et al. Biopathways representation and simulation on hybrid functional Petri net , 2003, Silico Biol..
[40] Lewis C Cantley,et al. Feedback inhibition of Akt signaling limits the growth of tumors lacking Tsc2. , 2005, Genes & development.
[41] Gordon B Mills,et al. mTOR inhibition induces upstream receptor tyrosine kinase signaling and activates Akt. , 2006, Cancer research.
[42] Hassane Alla,et al. Discrete, continuous, and hybrid Petri Nets , 2004 .
[43] Thomas A. Henzinger,et al. Qualitative networks: a symbolic approach to analyze biological signaling networks , 2007, BMC Systems Biology.
[44] Gordon B. Mills,et al. The energy sensing LKB1–AMPK pathway regulates p27kip1 phosphorylation mediating the decision to enter autophagy or apoptosis , 2007, Nature Cell Biology.
[45] Wen-Lin Kuo,et al. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. , 2006, Cancer cell.
[46] Madhukar S. Dasika,et al. A computational framework for the topological analysis and targeted disruption of signal transduction networks. , 2006, Biophysical journal.
[47] Madalena Chaves,et al. Robustness and fragility of Boolean models for genetic regulatory networks. , 2005, Journal of theoretical biology.
[48] R. Iyengar,et al. Signaling Networks The Origins of Cellular Multitasking , 2000, Cell.
[49] Timothy Cash,et al. Regulation of B-Raf Kinase Activity by Tuberin and Rheb Is Mammalian Target of Rapamycin (mTOR)-independent* , 2004, Journal of Biological Chemistry.
[50] Christopher Tudan,et al. The Rb-family protein p107 inhibits translation by a PDK1-dependent mechanism , 2002, Oncogene.
[51] Erwin P. Gianchandani,et al. Systems analyses characterize integrated functions of biochemical networks. , 2006, Trends in biochemical sciences.
[52] A. Hoffmann,et al. The I (cid:1) B –NF-(cid:1) B Signaling Module: Temporal Control and Selective Gene Activation , 2022 .
[53] Vittorio Rosato,et al. Parameter estimate of signal transduction pathways , 2006, BMC Neuroscience.
[54] Claudine Chaouiya,et al. Petri net modelling of biological networks , 2007, Briefings Bioinform..
[55] Gordon B Mills,et al. Network topology determines dynamics of the mammalian MAPK1,2 signaling network: bifan motif regulation of C‐Raf and B‐Raf isoforms by FGFR and MC1R , 2008, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[56] L. Glass,et al. The logical analysis of continuous, non-linear biochemical control networks. , 1973, Journal of theoretical biology.
[57] T. Hunter,et al. Signaling—2000 and Beyond , 2000, Cell.
[58] J. Avruch,et al. Insulin and amino-acid regulation of mTOR signaling and kinase activity through the Rheb GTPase , 2006, Oncogene.