Discrete dynamic network modeling of oncogenic signaling: Mechanistic insights for personalized treatment of cancer
Tài liệu tham khảo
Prasad, 2016, Precision oncology: origins, optimism, and potential, Lancet Oncol, 17, e81, 10.1016/S1470-2045(15)00620-8
Letai, 2017, Functional precision cancer medicine—moving beyond pure genomics, Nat Med, 23, 1028, 10.1038/nm.4389
Lynch, 2004, Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib, N Engl J Med, 350, 2129, 10.1056/NEJMoa040938
Maemondo, 2010, Gefitinib or chemotherapy for non-small-cell lung cancer with mutated EGFR, N Engl J Med, 362, 2380, 10.1056/NEJMoa0909530
Mayekar, 2017, Current landscape of targeted therapy in lung cancer, Clin Pharmacol Ther, 102, 757, 10.1002/cpt.810
Ntaios, 2013, CHADS2, CHA2S2DS2-VASc, and long-term stroke outcome in patients without atrial fibrillation, Neurology, 80, 1009, 10.1212/WNL.0b013e318287281b
Udyavar, 2017, Novel hybrid phenotype revealed in small cell lung cancer by a transcription factor network model that can explain tumor heterogeneity, Cancer Res, 77, 1063, 10.1158/0008-5472.CAN-16-1467
Módos, 2017, Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies, NPJ Syst Biol Appl, 3, 2, 10.1038/s41540-017-0003-6
Li, 2017, The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies, Nat Commun, 8, 14356, 10.1038/ncomms14356
Tyson, 2003, Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell, Curr Opin Cell Biol, 15, 221, 10.1016/S0955-0674(03)00017-6
Alon, 2006
Tyson, 2011, Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells, Nat Rev Cancer, 11, 523, 10.1038/nrc3081
Iyengar, 2012, Merging systems biology with pharmacodynamics, Sci Transl Med, 4, 10.1126/scitranslmed.3003563
Lu, 2013, MicroRNA-based regulation of epithelial-hybrid-mesenchymal fate determination, Proc Natl Acad Sci USA, 110, 18144, 10.1073/pnas.1318192110
Zhang, 2014, TGF-β-induced epithelial-to-mesenchymal transition proceeds through stepwise activation of multiple feedback loops, Sci Signal, 7, 10.1126/scisignal.2005304
Steinway, 2016, Discrete dynamic modeling: a network approach for systems pharmacology, AAPS Adv Pharm Sci Series, 81, 10.1007/978-3-319-44534-2_5
Morris, 2010, Logic-based models for the analysis of cell signaling networks, Biochemistry, 49, 3216, 10.1021/bi902202q
Abou-Jaoudé, 2016, Logical modeling and dynamical analysis of cellular networks, Front Genet, 7, 94, 10.3389/fgene.2016.00094
Wynn, 2012, Logic-based models in systems biology: a predictive and parameter-free network analysis method, Integr Biol, 4, 1323, 10.1039/c2ib20193c
Wang, 2012, Boolean modeling in systems biology: an overview of methodology and applications, Phys Biol, 9, 055001, 10.1088/1478-3975/9/5/055001
Mendoza, 1999, Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis, Bioinformatics, 15, 593, 10.1093/bioinformatics/15.7.593
Espinosa-Soto, 2004, A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles, Plant Cell, 16, 2923, 10.1105/tpc.104.021725
Naldi, 2010, Diversity and plasticity of Th cell types predicted from regulatory network modelling, PLoS Comput Biol, 6, e1000912, 10.1371/journal.pcbi.1000912
Li, 2004, The yeast cell-cycle network is robustly designed, Proc Natl Acad Sci USA, 101, 4781, 10.1073/pnas.0305937101
Huang, 2000, Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks, Exp Cell Res, 261, 91, 10.1006/excr.2000.5044
Li, 2006, Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling, PLoS Biol, 4, e312, 10.1371/journal.pbio.0040312
Saez-Rodriguez, 2007, A logical model provides Insights into T Cell receptor signaling, PLoS Comput Biol, 3, e163, 10.1371/journal.pcbi.0030163
Penuel, 1999, Transformation by v-Src: Ras-MAPK and PI3K-mTOR mediate parallel pathways, Mol Biol Cell, 10, 1693, 10.1091/mbc.10.6.1693
Campbell, 2011, Network analysis reveals cross-links of the immune pathways activated by bacteria and allergen, Phys Rev E Stat Nonlin Soft Matter Phys., 84, 031929, 10.1103/PhysRevE.84.031929
Ikushima, 2010, Cellular context-dependent “colors” of transforming growth factor-beta signaling, Cancer Sci., 101, 306, 10.1111/j.1349-7006.2009.01441.x
Zañudo, 2015, Cell fate reprogramming by control of intracellular network dynamics, PLoS Comput Biol, 11, e1004193, 10.1371/journal.pcbi.1004193
Zañudo, 2017, Structure-based control of complex networks with nonlinear dynamics, Proc Natl Acad Sci USA, 114, 7234, 10.1073/pnas.1617387114
Zhang, 2008, Network model of survival signaling in large granular lymphocyte leukemia, Proc Natl Acad Sci USA, 105, 16308, 10.1073/pnas.0806447105
Grieco, 2013, Integrative modelling of the influence of MAPK network on cancer cell fate decision, PLoS Comput Biol, 9, e1003286, 10.1371/journal.pcbi.1003286
Steinway, 2014, Network modeling of TGFβ signaling in hepatocellular carcinoma epithelial-to-mesenchymal transition reveals joint sonic hedgehog and Wnt pathway activation, Cancer Res, 74, 5963, 10.1158/0008-5472.CAN-14-0225
Cohen, 2015, Mathematical modelling of molecular pathways enabling tumour cell invasion and migration, PLoS Comput Biol, 11, e1004571, 10.1371/journal.pcbi.1004571
Chudasama, 2015, Logic-based and cellular pharmacodynamic modeling of Bortezomib responses in U266 human myeloma cells, J Pharmacol Exp Ther, 354, 448, 10.1124/jpet.115.224766
Saez-Rodriguez, 2009, Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction, Mol Syst Biol, 5, 331, 10.1038/msb.2009.87
Khan, 2017, Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures, Nat Commun, 8, 198, 10.1038/s41467-017-00268-2
Steinway, 2015, Combinatorial interventions inhibit TGFβ-driven epithelial-to-mesenchymal transition and support hybrid cellular phenotypes, NPJ Syst Biol Appl, 1, 10.1038/npjsba.2015.14
Jolly, 2017, Computational systems biology of epithelial-hybrid-mesenchymal transitions, Curr Opin Syst Biol, 3, 1, 10.1016/j.coisb.2017.02.004
Komarova, 2013
Wagle, 2011, Dissecting therapeutic resistance to RAF inhibition in melanoma by tumor genomic profiling, J Clin Oncol, 29, 3085, 10.1200/JCO.2010.33.2312
Garraway, 2012, Circumventing cancer drug resistance in the era of personalized medicine, Cancer Discov, 2, 214, 10.1158/2159-8290.CD-12-0012
Malod-Dognin, 2018, Precision medicine ― A promising, yet challenging road lies ahead, Current Opinion in Systems Biology, 7, 1, 10.1016/j.coisb.2017.10.003
Kristensen, 2014, Principles and methods of integrative genomic analyses in cancer, Nat Rev Cancer, 14, 299, 10.1038/nrc3721