M. Krishna and H. Narang, The complexity of mitogen-activated protein kinases (MAPKs) made simple, Cellular and Molecular Life Sciences, vol.65, pp.3525-3544, 2008.

M. R. Junttila, S. Li, and J. Westermarck, Phosphatase-mediated crosstalk between MAPK signaling pathways in the regulation of cell survival, The FASEB Journal, vol.22, pp.954-965, 2007.

Y. H. Shen, Cross-talk between JNK/SAPK and ERK/MAPK Pathways: sustained activation of JNK blocks ERK activation by mitogenic factors, Journal of Biological Chemistry, vol.278, pp.26715-26721, 2003.

E. Zehorai, Z. Yao, A. Plotnikov, and R. Seger, The subcellular localization of MEK and ERK-A novel nuclear translocation signal (NTS) paves a way to the nucleus, Molecular and Cellular Endocrinology, vol.314, pp.213-220, 2010.

D. M. Owens and S. M. Keyse, Differential regulation of MAP kinase signalling by dual-specificity protein phosphatases, Oncogene, vol.26, pp.3203-3213, 2007.

D. K. Morrison and R. J. Davis, Regulation of MAP kinase signaling modules by scaffold proteins in mammals, Annual Review of Cell and Developmental Biology, vol.19, pp.91-118, 2003.

J. M. Kyriakis and J. Avruch, Mammalian mitogen-activated protein kinase signal transduction pathways activated by stress and inflammation, Physiological reviews, vol.81, pp.807-869, 2001.

P. P. Roux and J. Blenis, ERK and p38 MAPK-activated protein kinases: a family of protein kinases with diverse biological functions, Microbiology and molecular biology reviews, vol.68, pp.320-344, 2004.

W. Kolch, M. Calder, and D. Gilbert, When kinases meet mathematics: the systems biology of MAPK signalling, FEBS Letters, vol.579, pp.1891-1895, 2005.

A. Plotnikov, E. Zehorai, S. Procaccia, and R. Seger, The MAPK cascades: Signaling components, nuclear roles and mechanisms of nuclear translocation, Biochimica et Biophysica Acta (BBA) -Molecular Cell Research, vol.1813, pp.1619-1633, 2011.

A. S. Dhillon, S. Hagan, O. Rath, and W. Kolch, MAP kinase signalling pathways in cancer, Oncogene, vol.26, pp.3279-3290, 2007.

E. F. Wagner and Á. Nebreda, Signal integration by JNK and p38 MAPK pathways in cancer development, Nature Reviews Cancer, vol.9, pp.537-549, 2009.

E. Halilovic and D. B. Solit, Therapeutic strategies for inhibiting oncogenic BRAF signaling, Current Opinion in Pharmacology, vol.8, pp.419-426, 2008.

L. Santarpia, S. M. Lippman, and A. K. El-naggar, Targeting the MAPK-RAS-RAF signaling pathway in cancer therapy, Expert Opinion on Therapeutic Targets, vol.16, pp.103-119, 2012.

I. Zachos, P. A. Konstantinopoulos, V. Tzortzis, S. Gravas, and A. Karatzas, Systemic therapy of metastatic bladder cancer in the molecular era: current status and future promise, Expert Opinion on Investigational Drugs, vol.19, pp.875-887, 2010.

H. Yong, M. Koh, and A. Moon, The p38 MAPK inhibitors for the treatment of inflammatory diseases and cancer, Expert Opinion on Investigational Drugs, vol.18, pp.1893-1905, 2009.

R. J. Sullivan and M. B. Atkins, Molecular targeted therapy for patients with melanoma: the promise of MAPK pathway inhibition and beyond, Expert Opinion on Investigational Drugs, vol.19, pp.1205-1216, 2010.

A. Young, J. Lyons, A. L. Miller, V. T. Phan, and I. R. Alarcón, Chapter 1 Ras Signaling and Therapies. Advances in Cancer Research, vol.102, pp.1-17, 2009.

P. I. Poulikakos and D. B. Solit, Resistance to MEK inhibitors: should we cotarget upstream?, Science Signalling, vol.4, p.16, 2011.

K. K. Haagenson and G. S. Wu, The role of MAP kinases and MAP kinase phosphatase-1 in resistance to breast cancer treatment, Cancer and Metastasis Reviews, vol.29, pp.143-149, 2010.

M. S. Chapman and J. N. Miner, Novel mitogen-activated protein kinase kinase inhibitors, Expert Opinion on Investigational Drugs, vol.20, pp.209-220, 2011.

M. Cakir and A. B. Grossman, Targeting MAPK (Ras/ERK) and PI3K/Akt pathways in pituitary tumorigenesis, Expert Opinion on Therapeutic Targets, vol.13, pp.1121-1134, 2009.

C. Montagut and J. Settleman, Targeting the RAF-MEK-ERK pathway in cancer therapy, Cancer Letters, vol.283, pp.125-134, 2009.

G. S. Inamdar, S. V. Madhunapantula, and G. P. Robertson, Targeting the MAPK pathway in melanoma: Why some approaches succeed and other fail, Biochemical Pharmacology, vol.80, pp.624-637, 2010.

R. J. Orton, O. E. Sturm, V. Vyshemirsky, M. Calder, and D. R. Gilbert, Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway, Biochemical Journal, vol.392, p.249, 2005.

C. Y. Huang and J. E. Ferrell, Ultrasensitivity in the mitogen-activated protein kinase cascade, Proceedings of the National Academy of Sciences, vol.93, pp.10078-10083, 1996.

B. N. Kholodenko, Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades, European Journal of Biochemistry, vol.267, pp.1583-1588, 2001.

A. Levchenko, J. Bruck, and P. W. Sternberg, Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties, Proceedings of the National Academy of Sciences, vol.97, pp.5818-5823, 2000.

N. I. Markevich, Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades, The Journal of Cell Biology, vol.164, pp.353-359, 2004.

S. Legewie, B. Schoeberl, N. Blüthgen, and H. Herzel, Competing Docking Interactions can Bring About Bistability in the MAPK Cascade, Biophysical Journal, vol.93, pp.2279-2288, 2007.

P. Smolen, D. A. Baxter, and J. H. Byrne, Bistable MAP kinase activity: a plausible mechanism contributing to maintenance of late long-term potentiation, AJP: Cell Physiology, vol.294, pp.503-515, 2007.

O. E. Sturm, R. Orton, J. Grindlay, M. Birtwistle, and V. Vyshemirsky, The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier, Science Signalling, vol.3, p.90, 2010.

F. A. Brightman and D. A. Fell, Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells, FEBS letters, vol.482, pp.169-174, 2000.

B. Schoeberl, C. Eichler-jonsson, E. D. Gilles, and G. Muller, Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors, Nature biotechnology, vol.20, pp.370-375, 2002.

M. Hatakeyama, S. Kimura, T. Naka, T. Kawasaki, and N. Yumoto, A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling, Biochemical Journal, vol.373, p.451, 2003.

J. J. Hornberg, B. Binder, F. J. Bruggeman, B. Schoeberl, and R. Heinrich, Control of MAPK signalling: from complexity to what really matters, Oncogene, vol.24, pp.5533-5542, 2005.

S. Sasagawa, Y. Ozaki, K. Fujita, and S. Kuroda, Prediction and validation of the distinct dynamics of transient and sustained ERK activation, Nature Cell Biology, vol.7, pp.365-373, 2005.

R. J. Orton, M. E. Adriaens, A. Gormand, O. E. Sturm, and W. Kolch, Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway, BMC Systems Biology, vol.3, p.100, 2009.

W. W. Chen, B. Schoeberl, P. J. Jasper, M. Niepel, and U. B. Nielsen, Inputoutput behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data, Molecular Systems Biology, vol.5, p.239, 2009.

N. Bagheri, M. Shiina, D. A. Lauffenburger, and W. M. Korn, Dynamical Systems Model for Combinatorial Cancer Therapy Enhances Oncolytic Adenovirus Efficacy by MEK-Inhibition, PLoS Computational Biology, vol.7, p.1001085, 2011.

T. Handorf and E. Klipp, Modeling mechanistic biological networks: An advanced Boolean approach, Bioinformatics, vol.28, pp.557-563, 2011.

A. R. Finch, C. J. Caunt, R. M. Perrett, K. Tsaneva-atanasova, and C. A. Mcardle, Dual specificity phosphatases 10 and 16 are positive regulators of EGFstimulated ERK activity: Indirect regulation of ERK signals by JNK/p38 selective MAPK phosphatases, Cellular Signalling, vol.24, pp.1002-1011, 2012.

R. Samaga, J. Saez-rodriguez, L. G. Alexopoulos, P. K. Sorger, and S. Klamt, The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of HighThroughput Data, PLoS Computational Biology, vol.5, p.1000438, 2009.

K. Oda, Y. Matsuoka, A. Funahashi, and H. Kitano, A comprehensive pathway map of epidermal growth factor receptor signaling, Molecular Systems Biology, vol.1, pp.1-17, 2005.

R. Poltz and M. Naumann, Dynamics of p53 and NF-kappaB regulation in response to DNA damage and identification of target proteins suitable for therapeutic intervention, BMC Systems Biology, vol.6, p.125, 2012.

D. Hanahan and R. A. Weinberg, The hallmarks of cancer. Cell, vol.100, pp.57-70, 2000.

J. R. Ho, E. Chapeaublanc, L. Kirkwood, R. Nicolle, and S. Benhamou, Deregulation of Rab and Rab Effector Genes in Bladder Cancer, PLoS One, vol.7, p.39469, 2012.

C. Billerey, D. Chopin, M. H. Aubriot-lorton, D. Ricol, and S. De-medina, Frequent FGFR3 mutations in papillary non-invasive bladder (pTa) tumors, The American journal of pathology, vol.158, 1955.

S. V. Williams, C. D. Hurst, and M. A. Knowles, Oncogenic FGFR3 gene fusions in bladder cancer, Human Molecular Genetics, vol.22, issue.4, pp.795-803, 2012.

A. P. Mitra and R. J. Cote, Molecular Pathogenesis and Diagnostics of Bladder Cancer, Annual Review of Pathology: Mechanisms of Disease, vol.4, pp.251-285, 2009.

A. P. Mitra, R. H. Datar, and R. J. Cote, Molecular Pathways in Invasive Bladder Cancer: New Insights Into Mechanisms, Progression, and Target Identification, Journal of Clinical Oncology, vol.24, pp.5552-5564, 2006.

F. Zindy, C. M. Eischen, D. H. Randle, T. Kamijo, and J. L. Cleveland, Myc signaling via the ARF tumor suppressor regulates p53-dependent apoptosis and immortalization, Genes Dev, vol.12, pp.2424-2433, 1998.

A. Funahashi, M. Morohashi, H. Kitano, and N. Tanimura, CellDesigner: a process diagram editor for gene-regulatory and biochemical networks, BIOSILICO, vol.1, pp.159-162, 2003.

H. Kitano, A. Funahashi, Y. Matsuoka, and K. Oda, Using process diagrams for the graphical representation of biological networks, Nature Biotechnology, vol.23, pp.961-966, 2005.

A. Funahashi, Y. Matsuoka, A. Jouraku, M. Morohashi, and N. Kikuchi, CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks, Proceedings of the IEEE, vol.96, pp.1254-1265, 2008.

A. Naldi, D. Berenguier, A. Fauré, F. Lopez, and D. Thieffry, Logical modelling of regulatory networks with GINsim 2.3, Biosystems, vol.97, pp.134-139, 2009.

C. Chaouiya, A. Naldi, and D. Thieffry, Logical Modelling of Gene Regulatory Networks with GINsim, Methods in Molecular Biology, vol.804, pp.463-479, 2012.

R. Thomas, Regulatory networks seen as asynchronous automata: A logical description, Journal of Theoretical Biology, vol.153, pp.80350-80359, 1991.

R. Thomas, D. Thieffry, and M. Kaufman, Dynamical behaviour of biological regulatory networks-I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state, Bulletin of Mathematical Biology, vol.57, pp.247-276, 1995.

C. Chaouiya, R. E. Mossé, B. Thieffry, and D. , Qualitative analysis of regulatory graphs: a computational tool based on a discrete formal framework, pp.830-832, 2003.

A. Faure, A. Naldi, C. Chaouiya, and D. Thieffry, Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle, Bioinformatics, vol.22, pp.124-131, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00310984

A. Naldi, D. Thieffry, and C. Chaouiya, Decision diagrams for the representation and analysis of logical models of genetic networks. Computational Methods in Systems Biology, pp.233-247, 2007.

A. Naldi, R. E. Thieffry, D. Chaouiya, and C. , Dynamically consistent reduction of logical regulatory graphs, Theoretical Computer Science, vol.412, pp.2207-2218, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01284743

D. Bérenguier, C. Chaouiya, P. T. Monteiro, A. Naldi, and E. Remy, Dynamical modeling and analysis of large cellular regulatory networks, Chaos, vol.23, p.25114, 2013.

R. Thomas, On the relation between the logical structure of systems and their ability to generate multiple steady states or sustained oscillations, Springer Series in Synergetics, vol.9, pp.180-193, 1981.

É. Remy, P. Ruet, and D. Thieffry, Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework, Advances in Applied Mathematics, vol.41, pp.335-350, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00692086

D. Thieffry, Dynamical roles of biological regulatory circuits, Briefings in Bioinformatics, vol.8, pp.220-225, 2007.

R. A. Weinberg, The Biology of cancer, 2007.

M. Takekawa, Y. Kubota, T. Nakamura, and K. Ichikawa, Regulation of stressactivated MAP kinase pathways during cell fate decisions, Nagoya journal of medical science, vol.73, pp.1-14, 2011.

C. Heldin, M. Landström, and A. Moustakas, Mechanism of TGF-b signaling to growth arrest, apoptosis, and epithelial-mesenchymal transition, Current Opinion in Cell Biology, vol.21, pp.166-176, 2009.

M. Tanaka, D. Koul, M. A. Davies, M. Liebert, and P. A. Steck, MMAC1/ PTEN inhibits cell growth and induces chemosensitivity to doxorubicin in human bladder cancer cells, Oncogene, vol.19, pp.5406-5412, 2000.

R. C. Sears, Signaling Networks That Link Cell Proliferation and Cell Fate, Journal of Biological Chemistry, vol.277, 2002.

W. A. Schulz, Understanding urothelial carcinoma through cancer pathways, International Journal of Cancer, vol.119, pp.1513-1518, 2006.

J. Y. Cho, Defective lysosomal targeting of activated fibroblast growth factor receptor 3 in achondroplasia, Proceedings of the National Academy of Sciences, vol.101, pp.609-614, 2004.

J. Schlessinger, Common and Distinct Elements in Cellular Signaling via EGF and FGF Receptors, Science, vol.306, pp.1506-1507, 2004.

C. Cochet, G. N. Gill, J. Meisenhelder, J. A. Cooper, and T. Hunter, C-kinase phosphorylates the epidermal growth factor receptor and reduces its epidermal growth factor-stimulated tyrosine protein kinase activity, Journal of Biological Chemistry, vol.259, pp.2553-2558, 1984.

L. Li, S. F. Chen, and Y. Liu, MAP kinase phosphatase-1, a critical negative regulator of the innate immune response, International journal of clinical and experimental medicine, vol.2, p.48, 2009.

L. Calzone, L. Tournier, S. Fourquet, D. Thieffry, and B. Zhivotovsky, Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement, PLoS Computational Biology, vol.6, p.1000702, 2010.
URL : https://hal.archives-ouvertes.fr/inserm-00704979

S. Foldynova-trantirkova, W. R. Wilcox, and P. Krejci, Sixteen years and counting: The current understanding of fibroblast growth factor receptor 3 (FGFR3) signaling in skeletal dysplasias, Human Mutation, vol.33, pp.29-41, 2012.

R. Priore, L. Dailey, and C. Basilico, Downregulation of Akt activity contributes to the growth arrest induced by FGF in chondrocytes, J Cell Physiol, vol.207, pp.800-808, 2006.

G. Stoll, E. Viara, E. Barillot, and L. Calzone, Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm, BMC Systems Biology, vol.6, p.116, 2012.
URL : https://hal.archives-ouvertes.fr/inserm-00762304

K. Roovers and R. K. Assoian, Integrating the MAP kinase signal into the G 1 phase cell cycle machinery, Bioessays, vol.22, pp.818-826, 2000.

M. L. Blinov, J. R. Faeder, B. Goldstein, and W. S. Hlavacek, A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity, Biosystems, vol.83, pp.136-151, 2006.

J. Feret, V. Danos, J. Krivine, R. Harmer, and W. Fontana, Internal coarsegraining of molecular systems, Proceedings of the National Academy of Sciences of the United States of America, vol.106, pp.6453-6458, 2009.
URL : https://hal.archives-ouvertes.fr/inria-00528330

F. Fages and S. Soliman, From reaction models to influence graphs and back: a theorem, Formal Methods in Systems Biology, vol.5054, pp.90-102, 2008.
URL : https://hal.archives-ouvertes.fr/inria-00419921

S. Sharp and P. Workman, Inhibitors of the HSP90 Molecular Chaperone: Current Status. Advances in Cancer Research, vol.95, pp.323-348, 2006.

J. P. Stein, D. A. Ginsberg, G. D. Grossfeld, S. J. Chatterjee, and D. Esrig, Effect of p21WAF1/CIP1 expression on tumor progression in bladder cancer, Journal of the National Cancer Institute, vol.90, pp.1072-1079, 1998.

N. J. Kennedy and R. J. Davis, Role of JNK in tumor development, Cell Cycle, vol.2, pp.199-201, 2003.

H. Schramek, MAP kinases: from intracellular signals to physiology and disease, Physiology, vol.17, pp.62-67, 2002.