TY - JOUR AU - Lynch, T. J. AU - Bell, D. W. AU - Sordella, R. AU - Gurubhagavatula, S. AU - Okimoto, R. A. AU - Brannigan, B. W. AU - Harris, P. L. AU - Haserlat, S. M. AU - Supko, J. G. AU - Haluska, F. G. AU - Louis, D. N. AU - Christiani, D. C. AU - Settleman, J. AU - Haber, D. A. PY - 2004 DA - 2004// TI - Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib JO - N Engl J Med VL - 350 UR - https://doi.org/10.1056/NEJMoa040938 DO - 10.1056/NEJMoa040938 ID - Lynch2004 ER - TY - JOUR AU - Martelli, A. M. AU - Tazzari, P. L. AU - Evangelisisti, C. AU - Chiarini, F. AU - Blalock, W. L. AU - Billi, A. M. AU - Manzoli, L. AU - McCubrey, J. A. AU - Cocco, L. PY - 2007 DA - 2007// TI - Targeting the phosphatidylinositol 3-kinase/Akt/mammalian target of rapamycin module for acute myelogenous leukemia therapy: from bench to bedside JO - Curr Med Chem VL - 14 UR - https://doi.org/10.2174/092986707781368423 DO - 10.2174/092986707781368423 ID - Martelli2007 ER - TY - JOUR AU - Pulakat, L. AU - Demarco, V. G. AU - Whaley-Connell, A. AU - Sowers, J. R. PY - 2011 DA - 2011// TI - The impact of overnutrition on insulin metablic signaling in teh heart and the kidney JO - Cardiorenal Med VL - 1 UR - https://doi.org/10.1159/000327140 DO - 10.1159/000327140 ID - Pulakat2011 ER - TY - JOUR AU - Wheeler-Jones, C. P. PY - 2005 DA - 2005// TI - Cell signaling in the cardiovascular system: an overview JO - Heart VL - 91 UR - https://doi.org/10.1136/hrt.2005.072280 DO - 10.1136/hrt.2005.072280 ID - Wheeler-Jones2005 ER - TY - JOUR AU - Kestler, H. A. AU - Wawra, C. AU - Kracher, B. AU - Kuhl, M. PY - 2008 DA - 2008// TI - Network modeling of signal transduction: establishing the global view JO - Bioessays VL - 30 UR - https://doi.org/10.1002/bies.20834 DO - 10.1002/bies.20834 ID - Kestler2008 ER - TY - JOUR AU - Jordan, J. D. AU - Landau, E. M. AU - Iyengar, R. PY - 2000 DA - 2000// TI - Signaling networks: the origins of cellular multitasking JO - Cell VL - 103 UR - https://doi.org/10.1016/S0092-8674(00)00112-4 DO - 10.1016/S0092-8674(00)00112-4 ID - Jordan2000 ER - TY - JOUR AU - Helikar, T. AU - Konvalina, J. AU - Heidel, J. AU - Rogers, J. A. PY - 2008 DA - 2008// TI - Emergent decision-making in biological signal transduction networks JO - PNAS VL - 105 UR - https://doi.org/10.1073/pnas.0705088105 DO - 10.1073/pnas.0705088105 ID - Helikar2008 ER - TY - STD TI - Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, Barillot E, Zinovyev A: Mathematical modelling of cell-fate decision in response to death receptor engagement. PLoS Comput Biol 2010, 6:e1000702. ID - ref8 ER - TY - STD TI - Helikar T, Kochi N, Kowal B, Dimri M, Naramura M, Raja SM, Band V, Band H, Rogers JA: A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells. PLoS One 2013, 8:e61757. ID - ref9 ER - TY - STD TI - Naldi A, Carneiro J, Chaouiya C, Thieffry D: Diversity and plasticity of Th cell types predicted from regulatory network modelling. PLoS Comput Biol 2010, 6:e1000912. ID - ref10 ER - TY - JOUR AU - Rodriguez, A. AU - Sosa, D. AU - Torres, L. AU - Molina, B. AU - Frias, S. AU - Mendoza, L. PY - 2012 DA - 2012// TI - A Boolean network model of the FA/BRCA pathway JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts036 DO - 10.1093/bioinformatics/bts036 ID - Rodriguez2012 ER - TY - STD TI - Saadatpour A, Wang R-S, Liao A, Liu X, Loughran TP, Albert I, Albert R: Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia. PLoS Comput Biol 2011, 7:e1002267. ID - ref12 ER - TY - STD TI - Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S: The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Comput Biol 2009, 5:e1000438. ID - ref13 ER - TY - STD TI - Sridharan S, Layek R, Datta A, Venkatraj J: Boolean modeling and fault diagnosis in oxidative stress response. BMC Genomics 2012, 13(Suppl 6):S4. ID - ref14 ER - TY - STD TI - Tokar T, Turcan Z, Ulicny J: Boolean network-based model of the Bcl-2 family mediated MOMP regulation. Theor Biol Med Modell 2013, 10:40. ID - ref15 ER - TY - BOOK AU - Kauffman, S. A. PY - 1993: DA - 1993:// TI - The origins of order PB - Oxford University Press CY - New York ID - Kauffman1993: ER - TY - STD TI - Klemm K, Bornholdt S: Stable and unstable attractors in Boolean networks. Phys Rev E 2000, 72:055101. ID - ref17 ER - TY - JOUR AU - Raeymaekers, L. PY - 2002 DA - 2002// TI - Dynamics of Boolean networks controlled by biologically meaningful functions JO - J Theor Biol VL - 218 UR - https://doi.org/10.1006/jtbi.2002.3081 DO - 10.1006/jtbi.2002.3081 ID - Raeymaekers2002 ER - TY - JOUR AU - Shmulevich, I. AU - Dougherty, E. R. AU - Kim, S. AU - Zhang, W. PY - 2001 DA - 2001// TI - Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.2.261 DO - 10.1093/bioinformatics/18.2.261 ID - Shmulevich2001 ER - TY - JOUR AU - Shmulevich, I. AU - Dougherty, E. R. AU - Zhang, W. PY - 2002 DA - 2002// TI - Gene perturbation and intervention in probabilistic Boolean networks JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.10.1319 DO - 10.1093/bioinformatics/18.10.1319 ID - Shmulevich2002 ER - TY - JOUR AU - Shmulevich, I. AU - Lähdesmäki, H. AU - Dougherty, E. R. AU - Astola, J. AU - Zhang, W. PY - 2003 DA - 2003// TI - The role of certain Post classes in Boolean network models of genetic networks JO - PNAS VL - 100 UR - https://doi.org/10.1073/pnas.1534782100 DO - 10.1073/pnas.1534782100 ID - Shmulevich2003 ER - TY - JOUR AU - Huepe, C. AU - Aldana-González, M. PY - 2002 DA - 2002// TI - Dynamical phase transition in a neural network model with noise: an exact solution JO - J Stat Phys VL - 108 UR - https://doi.org/10.1023/A:1015777824097 DO - 10.1023/A:1015777824097 ID - Huepe2002 ER - TY - JOUR AU - Derrida, B. AU - Pomeau, Y. PY - 1986 DA - 1986// TI - Random neworks of automata: a simple annealed approximation JO - Europhys Lett VL - 1 UR - https://doi.org/10.1209/0295-5075/1/2/001 DO - 10.1209/0295-5075/1/2/001 ID - Derrida1986 ER - TY - JOUR AU - Kauffman, S. AU - Peterson, C. AU - Samuelsson, B. AU - Troein, C. PY - 2004 DA - 2004// TI - Genetic networks with canalyzing Boolean rules are always stable JO - PNAS VL - 101 UR - https://doi.org/10.1073/pnas.0407783101 DO - 10.1073/pnas.0407783101 ID - Kauffman2004 ER - TY - JOUR AU - Amaral, L. A. N. AU - Diaz-Guilera, A. AU - Moreira, A. A. AU - Goldberger, A. L. AU - Lipsitz, L. A. PY - 2004 DA - 2004// TI - Emergence of complex dynamics in a simple model of signaling networks JO - PNAS VL - 101 UR - https://doi.org/10.1073/pnas.0404843101 DO - 10.1073/pnas.0404843101 ID - Amaral2004 ER - TY - STD TI - Shmulevich I, Kauffman SA: Activities and sensitivities in Boolean network models. Phys Rev Lett 2004, 93(4):048701. ID - ref26 ER - TY - JOUR AU - Kochi, N. AU - Wang, Z. PY - 2014 DA - 2014// TI - An algebraic method and a genetic algorithm to the identification of fuzzy measures based on Choquet integrals JO - J Intell Fuzzy Syst: Appl Eng Technol VL - 26 ID - Kochi2014 ER - TY - JOUR AU - Murofushi, T. AU - Sugeno, M. PY - 1989 DA - 1989// TI - An interpretation of fuzzy measure and the Choquet integralas an integral with respect to a fuzzy measure JO - Fuzzy Sets Syst VL - 29 UR - https://doi.org/10.1016/0165-0114(89)90194-2 DO - 10.1016/0165-0114(89)90194-2 ID - Murofushi1989 ER - TY - JOUR AU - Murofushi, T. AU - Sugeno, M. AU - Machida, M. PY - 1994 DA - 1994// TI - Non-monotonic fuzzy measures and the Choquet integral JO - Fuzzy Sets Syst VL - 64 UR - https://doi.org/10.1016/0165-0114(94)90008-6 DO - 10.1016/0165-0114(94)90008-6 ID - Murofushi1994 ER - TY - BOOK AU - Wang, Z. AU - Klir, G. J. PY - 1992 DA - 1992// TI - Fuzzy Measure Theory PB - Plenum CY - New York UR - https://doi.org/10.1007/978-1-4757-5303-5 DO - 10.1007/978-1-4757-5303-5 ID - Wang1992 ER - TY - BOOK AU - Wang, Z. AU - Yang, R. AU - Leung, K. S. PY - 2010 DA - 2010// TI - Nonlinear Integrals and Their Applications in Data Mining PB - World Scientific CY - Singapore ID - Wang2010 ER - TY - JOUR AU - Kochi, N. AU - Matache, M. T. PY - 2012 DA - 2012// TI - Mean-field boolean network model of a signal transduction network JO - Biosystems VL - 108 UR - https://doi.org/10.1016/j.biosystems.2011.12.001 DO - 10.1016/j.biosystems.2011.12.001 ID - Kochi2012 ER - TY - STD TI - Helikar T, Kowal B, McClenathan S, Bruckner M, Rowley T, Wicks B, Shrestha M, Limbu K, Rogers JA: The cell collective: toward an open and collaborative approach to systems biology. BMC Syst Biol 2012, 6:96. ID - ref33 ER - TY - JOUR AU - Helikar, T. AU - Kowal, B. AU - Rogers, J. A. PY - 2013 DA - 2013// TI - A cell simulator platform: the cell collective JO - Clin Pharmacol Ther VL - 93 UR - https://doi.org/10.1038/clpt.2013.41 DO - 10.1038/clpt.2013.41 ID - Helikar2013 ER - TY - STD TI - Matache MT, Matache V: On the sensitivity to noise of a boolean function. J Math Phys 2009, 50:103512. ID - ref35 ER - TY - JOUR AU - Guénolé, A. AU - Srivas, R. AU - Vreeken, K. AU - Wang, Z. Z. AU - Wang, S. AU - Krogan, N. J. AU - Ideker, T. PY - 2013 DA - 2013// TI - Dissection of DNA damage responses using multiconditional genetic interaction maps JO - Mol Cell VL - 49 UR - https://doi.org/10.1016/j.molcel.2012.11.023 DO - 10.1016/j.molcel.2012.11.023 ID - Guénolé2013 ER - TY - STD TI - Sahin O, Fröhlich H, Löbke C, Korf U, Burmester S, Majety M, Mattern J, Schupp I, Chaouiya C, Thieffry D, Poustka A, Wiemann S, Beissbarth T, Arlt D: Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst Biol 2009, 3:1. doi:10.1186/1752-0509-3-1. ID - ref37 ER - TY - STD TI - Menden MP, Iorio F, Garnett M, McDermott U, Benes CH, Ballester PJ, Saez-Rodriguez J: Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties. PLoS one 2013, 8(4):e61318. ID - ref38 ER - TY - STD TI - Jansen K, Matache MT: Phase transition of Boolean networks with partially nested canalizing functions. Eur Phys J B 2013, 86:316. ID - ref39 ER - TY - JOUR AU - Peixoto, T. P. PY - 2010 DA - 2010// TI - The phase diagram of random Boolean networks with nested canalizing functions JO - Eur Phys J B VL - 78 UR - https://doi.org/10.1140/epjb/e2010-10559-0 DO - 10.1140/epjb/e2010-10559-0 ID - Peixoto2010 ER -