TY - JOUR AU - Karamouzis, M. V. AU - Papavassiliou, A. G. PY - 2014 DA - 2014// TI - Tackling the cancer signal transduction “labyrinth”: A combinatorial use of biochemical tools with mathematical models will enhance the identification of optimal targets for each molecular defect JO - Cancer VL - 120 UR - https://doi.org/10.1002/cncr.28424 DO - 10.1002/cncr.28424 ID - Karamouzis2014 ER - TY - JOUR AU - Tabchy, A. AU - Ma, C. X. AU - Bose, R. AU - Ellis, M. J. PY - 2013 DA - 2013// TI - Incorporating genomics into breast cancer clinical trials and care JO - Clin Cancer Res VL - 19 UR - https://doi.org/10.1158/1078-0432.CCR-13-0837 DO - 10.1158/1078-0432.CCR-13-0837 ID - Tabchy2013 ER - TY - JOUR AU - Werner, H. M. J. AU - Mills, G. B. AU - Ram, P. T. PY - 2014 DA - 2014// TI - Cancer systems biology: a peek into the future of patient care? JO - Nat Rev Clin Oncol VL - 11 UR - https://doi.org/10.1038/nrclinonc.2014.6 DO - 10.1038/nrclinonc.2014.6 ID - Werner2014 ER - TY - JOUR AU - Gonzalez-Angulo, A. M. AU - Hennessy, B. T. J. AU - Mills, G. B. PY - 2010 DA - 2010// TI - Future of personalized medicine in oncology: A systems biology approach JO - J Clin Oncol Off J Am Soc Clin Oncol VL - 28 UR - https://doi.org/10.1200/JCO.2009.27.0777 DO - 10.1200/JCO.2009.27.0777 ID - Gonzalez-Angulo2010 ER - TY - STD TI - Wang E. Cancer systems biology. CRC Press. 2010. ID - ref5 ER - TY - JOUR AU - Janku, F. AU - Wheler, J. J. AU - Westin, S. N. AU - Moulder, S. L. AU - Naing, A. AU - Tsimberidou, A. M. PY - 2012 DA - 2012// TI - Pi3k/akt/mtor inhibitors in patients with breast and gynecologic malignancies harboring pik3ca mutations JO - J Clin Oncol Off J Am Soc Clin Oncol VL - 30 UR - https://doi.org/10.1200/JCO.2011.36.1196 DO - 10.1200/JCO.2011.36.1196 ID - Janku2012 ER - TY - JOUR PY - 2012 DA - 2012// TI - Comprehensive molecular characterization of human colon and rectal cancer JO - Nature VL - 487 UR - https://doi.org/10.1038/nature11252 DO - 10.1038/nature11252 ID - ref7 ER - TY - JOUR PY - 2013 DA - 2013// TI - Comprehensive molecular characterization of clear cell renal cell carcinoma JO - Nature VL - 499 UR - https://doi.org/10.1038/nature12222 DO - 10.1038/nature12222 ID - ref8 ER - TY - JOUR AU - Kitano, H. PY - 2007 DA - 2007// TI - A robustness-based approach to systems-oriented drug design JO - Nat Rev Drug Discov VL - 6 UR - https://doi.org/10.1038/nrd2195 DO - 10.1038/nrd2195 ID - Kitano2007 ER - TY - JOUR AU - Sikkema, A. H. AU - den Dunnen, W. F. A. AU - Diks, S. H. AU - Peppelenbosch, M. P. AU - de Bont, E. S. J. M. PY - 2012 DA - 2012// TI - Optimizing targeted cancer therapy: Towards clinical application of systems biology approaches JO - Crit Rev Oncol Hematol VL - 82 UR - https://doi.org/10.1016/j.critrevonc.2011.05.002 DO - 10.1016/j.critrevonc.2011.05.002 ID - Sikkema2012 ER - TY - JOUR AU - Albeck, J. G. AU - Mills, G. B. AU - Brugge, J. S. PY - 2013 DA - 2013// TI - Frequency-modulated pulses of erk activity transmit quantitative proliferation signals JO - Mol Cell VL - 49 UR - https://doi.org/10.1016/j.molcel.2012.11.002 DO - 10.1016/j.molcel.2012.11.002 ID - Albeck2013 ER - TY - JOUR AU - Basu, A. AU - Bodycombe, N. E. AU - Cheah, J. H. AU - Price, E. V. AU - Liu, K. AU - Schaefer, G. I. PY - 2013 DA - 2013// TI - An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules JO - Cell VL - 154 UR - https://doi.org/10.1016/j.cell.2013.08.003 DO - 10.1016/j.cell.2013.08.003 ID - Basu2013 ER - TY - JOUR AU - Andrianantoandro, E. AU - Basu, S. AU - Karig, D. K. AU - Weiss, R. PY - 2006 DA - 2006// TI - Synthetic biology: new engineering rules for an emerging discipline JO - Mol Syst Biol VL - 2 UR - https://doi.org/10.1038/msb4100073 DO - 10.1038/msb4100073 ID - Andrianantoandro2006 ER - TY - JOUR AU - Khalil, A. S. AU - Collins, J. J. PY - 2010 DA - 2010// TI - Synthetic biology: applications come of age JO - Nat Rev Genet VL - 11 UR - https://doi.org/10.1038/nrg2775 DO - 10.1038/nrg2775 ID - Khalil2010 ER - TY - JOUR AU - Gardner, T. S. AU - Cantor, C. R. AU - Collins, J. J. PY - 2000 DA - 2000// TI - Construction of a genetic toggle switch in escherichia coli JO - Nature VL - 403 UR - https://doi.org/10.1038/35002131 DO - 10.1038/35002131 ID - Gardner2000 ER - TY - JOUR AU - Elowitz, M. AU - Leibler, S. PY - 2000 DA - 2000// TI - A synthetic oscillatory network of transcriptional regulators JO - Nature VL - 403 UR - https://doi.org/10.1038/35002125 DO - 10.1038/35002125 ID - Elowitz2000 ER - TY - JOUR AU - Basu, S. AU - Mehreja, R. AU - Thiberge, S. AU - Chen, M. T. AU - Weiss, R. PY - 2004 DA - 2004// TI - Spatiotemporal control of gene expression with pulse-generating networks JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0307571101 DO - 10.1073/pnas.0307571101 ID - Basu2004 ER - TY - JOUR AU - Lillacci, G. AU - Khammash, M. PY - 2010 DA - 2010// TI - Parameter estimation and model selection in computational biology JO - PLoS Comput Biol VL - 6 UR - https://doi.org/10.1371/journal.pcbi.1000696 DO - 10.1371/journal.pcbi.1000696 ID - Lillacci2010 ER - TY - JOUR AU - Oguz, C. AU - Laomettachit, T. AU - Chen, K. AU - Watson, L. AU - Baumann, W. AU - Tyson, J. PY - 2013 DA - 2013// TI - Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model JO - BMC Syst Biol VL - 7 UR - https://doi.org/10.1186/1752-0509-7-53 DO - 10.1186/1752-0509-7-53 ID - Oguz2013 ER - TY - JOUR AU - Bianconi, F. AU - Baldelli, E. AU - Ludovini, V. AU - Crinò, L. AU - Valigi, P. PY - 2012 DA - 2012// TI - Computational model of EGFR and IGF1R pathways in lung cancer: A systems biology approach for translational oncology JO - Biotechnol Adv VL - 30 UR - https://doi.org/10.1016/j.biotechadv.2011.05.010 DO - 10.1016/j.biotechadv.2011.05.010 ID - Bianconi2012 ER - TY - JOUR AU - Rodriguez-Fernandez, M. AU - Banga, J. R. AU - Doyle III, F. J. PY - 2012 DA - 2012// TI - Novel global sensitivity analysis methodology accounting for the crucial role of the distribution of input parameters: application to systems biology models JO - Int J Robust Nonlinear Control VL - 22 UR - https://doi.org/10.1002/rnc.2797 DO - 10.1002/rnc.2797 ID - Rodriguez-Fernandez2012 ER - TY - JOUR AU - Tarantola, S. AU - Becker, W. AU - Zeitz, D. PY - 2012 DA - 2012// TI - A comparison of two sampling methods for global sensitivity analysis JO - Comput Phys Commun VL - 183 UR - https://doi.org/10.1016/j.cpc.2011.12.015 DO - 10.1016/j.cpc.2011.12.015 ID - Tarantola2012 ER - TY - JOUR AU - Lebedeva, G. AU - Sorokin, A. AU - Faratian, D. AU - Mullen, P. AU - Goltsov, A. AU - Langdon, S. P. PY - 2012 DA - 2012// TI - Model-based global sensitivity analysis as applied to identification of anti-cancer drug targets and biomarkers of drug resistance in the erbb2/3 network JO - Eur J Pharm Sci VL - 46 UR - https://doi.org/10.1016/j.ejps.2011.10.026 DO - 10.1016/j.ejps.2011.10.026 ID - Lebedeva2012 ER - TY - JOUR AU - Von Dassow, G. AU - Meir, E. AU - Munro, E. M. AU - Odell, G. M. PY - 2000 DA - 2000// TI - The segment polarity network is a robust developmental module JO - Nature VL - 406 UR - https://doi.org/10.1038/35018085 DO - 10.1038/35018085 ID - Von Dassow2000 ER - TY - JOUR AU - Dayarian, A. AU - Chaves, M. AU - Sontag, E. D. AU - Sengupta, A. M. PY - 2009 DA - 2009// TI - Shape, size, and robustness: Feasible regions in the parameter space of biochemical networks JO - PLoS Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000256 DO - 10.1371/journal.pcbi.1000256 ID - Dayarian2009 ER - TY - JOUR AU - Chaves, M. AU - Sengupta, A. AU - Sontag, E. PY - 2009 DA - 2009// TI - Geometry and topology of parameter space: investigating measures of robustness in regulatory networks JO - J Math Biol VL - 59 UR - https://doi.org/10.1007/s00285-008-0230-y DO - 10.1007/s00285-008-0230-y ID - Chaves2009 ER - TY - JOUR AU - Rizk, A. AU - Batt, G. AU - Fages, F. AU - Soliman, S. PY - 2009 DA - 2009// TI - A general computational method for robustness analysis with applications to synthetic gene networks JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp200 DO - 10.1093/bioinformatics/btp200 ID - Rizk2009 ER - TY - JOUR AU - Kwon, Y. K. AU - Cho, K. H. PY - 2008 DA - 2008// TI - Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics JO - Bioinformatics (Oxford, England) VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn060 DO - 10.1093/bioinformatics/btn060 ID - Kwon2008 ER - TY - JOUR AU - Morohashi, M. AU - Winn, A. E. AU - Borisuk, M. T. AU - Bolouri, H. AU - Doyle, J. AU - Kitano, H. PY - 2002 DA - 2002// TI - Robustness as a measure of plausibility in models of biochemical networks JO - J Theor Biol VL - 216 UR - https://doi.org/10.1006/jtbi.2002.2537 DO - 10.1006/jtbi.2002.2537 ID - Morohashi2002 ER - TY - JOUR AU - Hafner, M. AU - Koeppl, H. AU - Hasler, M. AU - Wagner, A. PY - 2009 DA - 2009// TI - ‘glocal’ robustness analysis and model discrimination for circadian oscillators JO - PLoS Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000534 DO - 10.1371/journal.pcbi.1000534 ID - Hafner2009 ER - TY - JOUR AU - Ceska, M. AU - Safránek, D. AU - Dražan, S. AU - Brim, L. PY - 2014 DA - 2014// TI - Robustness analysis of stochastic biochemical systems JO - PloS one VL - 9 UR - https://doi.org/10.1371/journal.pone.0094553 DO - 10.1371/journal.pone.0094553 ID - Ceska2014 ER - TY - JOUR AU - Salerno, L. AU - Cosentino, C. AU - Merola, A. AU - Bates, D. G. AU - Amato, F. PY - 2013 DA - 2013// TI - Validation of a model of the GAL regulatory system via robustness analysis of its bistability characteristics JO - BMC Syst Biol VL - 7 UR - https://doi.org/10.1186/1752-0509-7-39 DO - 10.1186/1752-0509-7-39 ID - Salerno2013 ER - TY - JOUR AU - Cedersund, G. PY - 2012 DA - 2012// TI - Conclusions via unique predictions obtained despite unidentifiability: new definitions and a general method JO - FEBS J VL - 279 UR - https://doi.org/10.1111/j.1742-4658.2012.08725.x DO - 10.1111/j.1742-4658.2012.08725.x ID - Cedersund2012 ER - TY - JOUR AU - Bianconi, F. AU - Baldelli, E. AU - Ludovini, V. AU - Crinò, L. AU - Perruccio, K. AU - Valigi, P. PY - 2013 DA - 2013// TI - Robustness of complex feedback systems: application to oncological biochemical network JO - Int J Confl Manag VL - 86 ID - Bianconi2013 ER - TY - JOUR AU - Mathew, S. AU - Bartels, J. AU - Banerjee, I. AU - Vodovotz, Y. PY - 2014 DA - 2014// TI - Global sensitivity analysis of a mathematical model of acute inflammation identifies nonlinear dependence of cumulative tissue damage on host interleukin-6 responses JO - J Theor Biol VL - 358 UR - https://doi.org/10.1016/j.jtbi.2014.05.036 DO - 10.1016/j.jtbi.2014.05.036 ID - Mathew2014 ER - TY - JOUR AU - Kitano, H. PY - 2007 DA - 2007// TI - Towards a theory of biological robustness JO - Mol Syst Biol VL - 3 ID - Kitano2007 ER - TY - JOUR AU - Huang, C. Y. AU - Huang, C. H. AU - Chang, P. M. -. H. AU - Wu, M. Y. AU - Ng, K. L. PY - 2014 DA - 2014// TI - In silico identification of potential targets and drugs for non-small cell lung cancer JO - IET Syst Biol VL - 8 UR - https://doi.org/10.1049/iet-syb.2013.0035 DO - 10.1049/iet-syb.2013.0035 ID - Huang2014 ER - TY - JOUR AU - Sheather, S. J. PY - 2004 DA - 2004// TI - Density estimation JO - Stat Sci VL - 19 UR - https://doi.org/10.1214/088342304000000297 DO - 10.1214/088342304000000297 ID - Sheather2004 ER - TY - JOUR AU - Borgonovo, E. AU - Tarantola, S. AU - Plischke, E. AU - Morris, M. D. PY - 2013 DA - 2013// TI - Transformations and invariance in the sensitivity analysis of computer experiments JO - J R Stat Soc Ser B Stat Methodol VL - 76 UR - https://doi.org/10.1111/rssb.12052 DO - 10.1111/rssb.12052 ID - Borgonovo2013 ER - TY - JOUR AU - Hwang, J. N. AU - Lay, S. R. AU - Lippman, A. PY - 1994 DA - 1994// TI - Nonparametric multivariate density estimation: a comparative study JO - IEEE Trans Signal Process VL - 42 UR - https://doi.org/10.1109/78.324744 DO - 10.1109/78.324744 ID - Hwang1994 ER - TY - JOUR AU - Borgonovo, E. PY - 2007 DA - 2007// TI - A new uncertainty importance measure JO - Reliab Eng Syst Saf VL - 92 UR - https://doi.org/10.1016/j.ress.2006.04.015 DO - 10.1016/j.ress.2006.04.015 ID - Borgonovo2007 ER - TY - JOUR AU - Alon, U. PY - 2007 DA - 2007// TI - Network motifs: theory and experimental approaches JO - Nat Rev Genet VL - 8 UR - https://doi.org/10.1038/nrg2102 DO - 10.1038/nrg2102 ID - Alon2007 ER - TY - STD TI - Szallasi Z, Stelling J, Periwal V. System modeling in cellular biology. from concepts to nuts and bolts. 2006. ID - ref43 ER - TY - JOUR AU - Ludovini, V. AU - Bellezza, G. AU - Pistola, L. AU - Bianconi, F. AU - Carlo, L. D. AU - Sidoni, A. PY - 2009 DA - 2009// TI - High coexpression of both insulin-like growth factor receptor-1 (igfr-1) and epidermal growth factor receptor (egfr) is associated with shorter disease-free survival in resected non-small-cell lung cancer patients JO - Ann Oncol. 2009 May VL - 20(5) ID - Ludovini2009 ER - TY - JOUR AU - Falconi, A. AU - Lopes, G. AU - Parker, J. L. PY - 2014 DA - 2014// TI - Biomarkers and receptor targeted therapies reduce clinical trial risk in non–small-cell lung cancer JO - J Thorac Oncol VL - 9 UR - https://doi.org/10.1097/JTO.0000000000000075 DO - 10.1097/JTO.0000000000000075 ID - Falconi2014 ER - TY - STD TI - Bianconi F, Chelliah V. BIOMD0000000427 - Bianconi2012 - EGFR and IGF1R Pathway in Lung Cancer. http://www.ebi.ac.uk/biomodels-main/BIOMD0000000427. UR - http://www.ebi.ac.uk/biomodels-main/BIOMD0000000427 ID - ref46 ER - TY - STD TI - Bianconi F, Lillacci G, Valigi P. Dynamic modeling and parameter identification for biological networks: application to the dna damage and repair processes. 2010:478–510. ID - ref47 ER - TY - STD TI - Bianconi F, Baldelli E, Valigi P. An approach to the conditional robustness problem for biochemical networks. In: American Control Conference (ACC), 2014: 2014. p. 3417–424. doi:http://dx.doi.org/10.1109/ACC.2014.6859085. UR - http://dx.doi.org/10.1109/ACC.2014.6859085 ID - ref48 ER - TY - JOUR AU - Ahmed, S. AU - Grant, K. G. AU - Edwards, L. E. AU - Rahman, A. AU - Cirit, M. AU - Goshe, M. B. PY - 2014 DA - 2014// TI - Data-driven modeling reconciles kinetics of erk phosphorylation, localization, and activity states. JO - Mol Syst Biol VL - 10 UR - https://doi.org/10.1002/msb.134708 DO - 10.1002/msb.134708 ID - Ahmed2014 ER - TY - JOUR AU - Wu, D. W. AU - Wu, T. C. AU - Wu, J. Y. AU - Cheng, Y. W. AU - Chen, Y. C. AU - Lee, M. C. PY - 2014 DA - 2014// TI - Phosphorylation of paxillin confers cisplatin resistance in non-small cell lung cancer via activating ERK-mediated Bcl-2 expression JO - Oncogene VL - 33 UR - https://doi.org/10.1038/onc.2013.389 DO - 10.1038/onc.2013.389 ID - Wu2014 ER - TY - JOUR AU - Sahin, O. AU - Fröhlich, H. AU - Löbke, C. AU - Korf, U. AU - Burmester, S. AU - Majety, M. PY - 2009 DA - 2009// TI - Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance JO - BMC Syst Biol VL - 3 UR - https://doi.org/10.1186/1752-0509-3-1 DO - 10.1186/1752-0509-3-1 ID - Sahin2009 ER - TY - JOUR AU - Glick, N. PY - 1975 DA - 1975// TI - Measurements of separation among probability densities or random variables JO - Can J Stat VL - 3 UR - https://doi.org/10.2307/3315284 DO - 10.2307/3315284 ID - Glick1975 ER - TY - JOUR AU - Vasan, N. AU - Boyer, J. AU - Herbst, R. S. PY - 2014 DA - 2014// TI - A ras renaissance: Emerging targeted therapies for kras-mutated non-small cell lung cancer. JO - Clin Cancer Res VL - 20 UR - https://doi.org/10.1158/1078-0432.CCR-13-1762 DO - 10.1158/1078-0432.CCR-13-1762 ID - Vasan2014 ER - TY - JOUR AU - Viana, F. A. AU - Venter, G. AU - Balabanov, V. PY - 2010 DA - 2010// TI - An algorithm for fast optimal latin hypercube design of experiments JO - Int J Numer Methods Eng VL - 82 ID - Viana2010 ER -