TY - JOUR AU - Janes, K. A. AU - Kelly, J. R. AU - Gaudet, S. AU - Albeck, J. G. AU - Sorger, P. K. AU - Lauffenburger, D. A. PY - 2004 DA - 2004// TI - Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data JO - J Comput Biol VL - 11 UR - https://doi.org/10.1089/cmb.2004.11.544 DO - 10.1089/cmb.2004.11.544 ID - Janes2004 ER - TY - JOUR AU - Janes, K. A. AU - Yaffe, M. B. PY - 2006 DA - 2006// TI - Data-driven modelling of signal-transduction networks JO - Nat Rev Mol Cell Biol VL - 7 UR - https://doi.org/10.1038/nrm2041 DO - 10.1038/nrm2041 ID - Janes2006 ER - TY - JOUR AU - Jaqaman, K. AU - Danuser, G. PY - 2006 DA - 2006// TI - Linking data to models: data regression JO - Nat Rev Mol Cell Biol VL - 7 UR - https://doi.org/10.1038/nrm2030 DO - 10.1038/nrm2030 ID - Jaqaman2006 ER - TY - STD TI - Duren Z, Wang Y. A systematic method to identify modulation of transcriptional regulation via chromatin activity reveals regulatory network during mESC differentiation. Scientific Reports 6. 2016; 22656. doi:10.1038/srep22656. ID - ref4 ER - TY - JOUR AU - Calzone, L. AU - Tournier, L. AU - Fourquet, S. AU - Thieffry, D. AU - Zhivotovsky, B. AU - Barillot, E. AU - Zinovyev, A. PY - 2010 DA - 2010// TI - Mathematical modelling of cell-fate decision in response to death receptor engagement JO - PLoS Comput Biol VL - 6 UR - https://doi.org/10.1371/journal.pcbi.1000702 DO - 10.1371/journal.pcbi.1000702 ID - Calzone2010 ER - TY - JOUR AU - Kauffman, S. A. PY - 1969 DA - 1969// TI - Homeostasis and differentiation in random genetic control networks JO - Nature VL - 224 UR - https://doi.org/10.1038/224177a0 DO - 10.1038/224177a0 ID - Kauffman1969 ER - TY - JOUR AU - Kauffman, S. A. PY - 1969 DA - 1969// TI - Metabolic stability and epigenesis in randomly constructed genetic nets JO - J Theor Biol VL - 22 UR - https://doi.org/10.1016/0022-5193(69)90015-0 DO - 10.1016/0022-5193(69)90015-0 ID - Kauffman1969 ER - TY - JOUR AU - Mitsos, A. AU - Melas, I. N. AU - Siminelakis, P. AU - Chairakaki, A. D. AU - Saez-Rodriguez, J. AU - Alexopoulos, L. G. PY - 2009 DA - 2009// TI - Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data JO - PLoS Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000591 DO - 10.1371/journal.pcbi.1000591 ID - Mitsos2009 ER - TY - JOUR AU - Saez-Rodriguez, J. AU - Simeoni, L. AU - Lindquist, J. A. AU - Hemenway, R. AU - Bommhardt, U. AU - Arndt, B. AU - Haus, U. U. AU - Weismantel, R. AU - Gilles, E. D. AU - Klamt, S. AU - Schraven, B. PY - 2007 DA - 2007// TI - A logical model provides insights into T cell receptor signaling JO - PLoS Comput Biol VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030163 DO - 10.1371/journal.pcbi.0030163 ID - Saez-Rodriguez2007 ER - TY - JOUR AU - Sharan, R. AU - Karp, R. M. PY - 2013 DA - 2013// TI - Reconstructing boolean models of signaling JO - J Comput Biol VL - 20 UR - https://doi.org/10.1089/cmb.2012.0241 DO - 10.1089/cmb.2012.0241 ID - Sharan2013 ER - TY - JOUR AU - Thomas, R. PY - 1973 DA - 1973// TI - Boolean formalization of genetic control circuits JO - J Theor Biol VL - 42 UR - https://doi.org/10.1016/0022-5193(73)90247-6 DO - 10.1016/0022-5193(73)90247-6 ID - Thomas1973 ER - TY - JOUR AU - Aldridge, B. B. AU - Saez-Rodriguez, J. AU - Muhlich, J. L. AU - Sorger, P. K. AU - Lauffenburger, D. A. PY - 2009 DA - 2009// TI - Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling JO - PLoS Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000340 DO - 10.1371/journal.pcbi.1000340 ID - Aldridge2009 ER - TY - JOUR AU - Zhang, F. AU - Chen, H. AU - Zhao, L. N. AU - Liu, H. AU - Przytycka, T. M. AU - Zheng, J. PY - 2016 DA - 2016// TI - Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways JO - BMC Syst Biol. VL - 10 UR - https://doi.org/10.1186/s12918-015-0249-9 DO - 10.1186/s12918-015-0249-9 ID - Zhang2016 ER - TY - JOUR AU - Huang, Z. Y. AU - Hahn, J. PY - 2009 DA - 2009// TI - Fuzzy modeling of signal transduction networks JO - Chem Eng Sci VL - 64 UR - https://doi.org/10.1016/j.ces.2009.01.041 DO - 10.1016/j.ces.2009.01.041 ID - Huang2009 ER - TY - JOUR AU - Morris, M. K. AU - Saez-Rodriguez, J. AU - Clarke, D. C. AU - Sorger, P. K. AU - Lauffenburger, D. A. PY - 2011 DA - 2011// TI - Training signaling pathway maps to biochemical data with constrained fuzzy logic: Quantitative analysis of liver cell responses to inflammatory stimuli JO - PLoS Comput Biol VL - 7 UR - https://doi.org/10.1371/journal.pcbi.1001099 DO - 10.1371/journal.pcbi.1001099 ID - Morris2011 ER - TY - JOUR AU - Zheng, J. AU - Zhang, D. AU - Przytycki, P. F. AU - Zielinski, R. AU - Capala, J. AU - Przytycka, T. M. PY - 2010 DA - 2010// TI - Simboolnet–a cytoscape plugin for dynamic simulation of signaling networks JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp617 DO - 10.1093/bioinformatics/btp617 ID - Zheng2010 ER - TY - JOUR AU - Albeck, J. G. AU - Burke, J. M. AU - Aldridge, B. B. AU - Zhang, M. AU - Lauffenburger, D. A. AU - Sorger, P. K. PY - 2008 DA - 2008// TI - Quantitative analysis of pathways controlling extrinsic apoptosis in single cells JO - Mol Cell VL - 30 UR - https://doi.org/10.1016/j.molcel.2008.02.012 DO - 10.1016/j.molcel.2008.02.012 ID - Albeck2008 ER - TY - JOUR AU - Michaelis, L. AU - Menten, M. L. PY - 1913 DA - 1913// TI - Die kinetik der invertinwirkung JO - Biochem VL - Z ID - Michaelis1913 ER - TY - STD TI - Neumann L, Pforr C, Beaudouin J, Pappa A, Fricker N, Krammer PH, Lavrik IN, Eils R. Dynamics within the CD95 death-inducing signaling complex decide life and death of cells. Mol Syst Biol. 2010; 6(352). doi:10.1038/msb.2010.6. ID - ref19 ER - TY - JOUR AU - Novák, B. AU - Tyson, J. J. PY - 2004 DA - 2004// TI - A model for restriction point control of the mammalian cell cycle JO - J Theor Biol VL - 230 UR - https://doi.org/10.1016/j.jtbi.2004.04.039 DO - 10.1016/j.jtbi.2004.04.039 ID - Novák2004 ER - TY - JOUR AU - Dresch, J. M. AU - Thompson, M. A. AU - Arnosti, D. N. AU - Chiu, C. PY - 2013 DA - 2013// TI - Two-layer mathematical modeling of gene expression: Incorporating DNA-level information and system dynamics JO - SIAM J Appl Math VL - 73 UR - https://doi.org/10.1137/120887588 DO - 10.1137/120887588 ID - Dresch2013 ER - TY - STD TI - Dresch JM, Liu X, Arnosti DN, Ay A. Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects. BMC Syst Biol.2010;4(142). doi:10.1186/1752-0509-4-142. ID - ref22 ER - TY - JOUR AU - He, X. AU - Samee, M. A. H. AU - Blatti, C. AU - Sinha, S. PY - 2010 DA - 2010// TI - Thermodynamics-based models of transcriptional regulation by enhancers: The roles of synergistic activation, cooperative binding and short-range repression JO - PLoS Comput Biol. VL - 6 UR - https://doi.org/10.1371/journal.pcbi.1000935 DO - 10.1371/journal.pcbi.1000935 ID - He2010 ER - TY - JOUR AU - Peng, S. C. AU - Wong, D. S. AU - Tung, K. C. AU - Chen, Y. Y. AU - Chao, C. C. AU - Peng, C. H. AU - Chuang, Y. J. AU - Tang, C. Y. PY - 2010 DA - 2010// TI - Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-kB signaling-induced gene expression responses in inflammation JO - BMC Bioinforma VL - 11 UR - https://doi.org/10.1186/1471-2105-11-308 DO - 10.1186/1471-2105-11-308 ID - Peng2010 ER - TY - JOUR AU - Chang, C. AU - Ding, Z. AU - Hung, Y. S. AU - Fung, P. C. PY - 2008 DA - 2008// TI - Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data JO - Proc Natl Acad Sci USA VL - 24 ID - Chang2008 ER - TY - JOUR AU - Liao, J. C. AU - Boscolo, R. AU - Yang, Y. L. AU - Tran, L. M. AU - Sabatti, C. AU - Roychowdhury, V. P. PY - 2003 DA - 2003// TI - Network component analysis: reconstruction of regulatory signals in biological systems JO - Proc Natl Acad Sci USA VL - 100 UR - https://doi.org/10.1073/pnas.2136632100 DO - 10.1073/pnas.2136632100 ID - Liao2003 ER - TY - JOUR AU - Noor, A. AU - Ahmad, A. AU - Serpedin, E. AU - Nounou, M. AU - Nounou, H. PY - 2013 DA - 2013// TI - ROBNCA: robust network component analysis for recovering transcription factor activities JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt433 DO - 10.1093/bioinformatics/btt433 ID - Noor2013 ER - TY - JOUR AU - Melas, I. N. AU - Mitsos, A. AU - Messinis, D. E. AU - Weiss, T. S. AU - Alexopoulos, L. G. PY - 2011 DA - 2011// TI - Combined logical and data-driven models for linking signalling pathways to cellular response JO - BMC Syst Biol VL - 5 UR - https://doi.org/10.1186/1752-0509-5-107 DO - 10.1186/1752-0509-5-107 ID - Melas2011 ER - TY - JOUR AU - Shannon, P. AU - Markiel, A. AU - Ozier, O. AU - Baliga, N. S. AU - Wang, J. T. AU - Ramage, D. AU - Amin, N. AU - Schwikowski, B. AU - Ideker, T. PY - 2003 DA - 2003// TI - Cytoscape: a software environment for integrated models of biomolecular interaction networks JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1239303 DO - 10.1101/gr.1239303 ID - Shannon2003 ER - TY - JOUR AU - Ay, A. AU - Arnosti, D. N. PY - 2011 DA - 2011// TI - Mathematical modeling of gene expression: a guide for the perplexed biologist JO - Crit Rev Biochem Mol Biol VL - 46 UR - https://doi.org/10.3109/10409238.2011.556597 DO - 10.3109/10409238.2011.556597 ID - Ay2011 ER - TY - JOUR AU - Bakkenist, C. J. AU - Kastan, M. B. PY - 2003 DA - 2003// TI - Dna damage activates ATM through intermolecular autophosphorylation and dimer dissociation JO - Nature VL - 421 UR - https://doi.org/10.1038/nature01368 DO - 10.1038/nature01368 ID - Bakkenist2003 ER - TY - JOUR AU - Norbury, C. J. AU - Zhivotovsky, B. PY - 2004 DA - 2004// TI - DNA damage-induced apoptosis JO - Oncogene VL - 23 UR - https://doi.org/10.1038/sj.onc.1207532 DO - 10.1038/sj.onc.1207532 ID - Norbury2004 ER - TY - JOUR AU - Dhanalakshmi, S. AU - Agarwal, C. AU - Singh, R. P. AU - Agarwal, R. PY - 2005 DA - 2005// TI - Silibinin up-regulates DNA-protein kinase-dependent P53 activation to enhance UVB-induced apoptosis in mouse epithelial JB6 cells JO - J Biol Macromol VL - 280 ID - Dhanalakshmi2005 ER - TY - JOUR AU - Ekins, S. AU - Nikolsky, Y. AU - Bugrim, A. AU - Kirillov, E. AU - Nikolskaya, T. PY - 2007 DA - 2007// TI - Pathway mapping tools for analysis of high content data JO - Methods Mol Biol. VL - 356 ID - Ekins2007 ER - TY - JOUR AU - Glover, K. P. AU - Chen, Z. AU - Markell, L. K. AU - Han, X. PY - 2015 DA - 2015// TI - Synergistic gene expression signature observed in TK6 cells upon co-exposure to UVC-irradiation and protein kinase c-activating tumor promoters JO - PLoS ONE VL - 10 UR - https://doi.org/10.1371/journal.pone.0139850 DO - 10.1371/journal.pone.0139850 ID - Glover2015 ER - TY - JOUR AU - Lee, M. J. AU - Ye, A. S. AU - Gardino, A. K. AU - Heijink, A. M. AU - Sorger, P. K. AU - MacBeath, G. AU - Yaffe, M. B. PY - 2012 DA - 2012// TI - Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks JO - Cell VL - 149 UR - https://doi.org/10.1016/j.cell.2012.03.031 DO - 10.1016/j.cell.2012.03.031 ID - Lee2012 ER -