S. Geenen, P. Taylor, J. Snoep, I. Wilson, J. Kenna et al., Systems biology tools for toxicology, Archives of Toxicology, vol.3, issue.3, pp.1251-1271, 2012.
DOI : 10.1006/mben.2001.0187

URL : https://link.springer.com/content/pdf/10.1007%2Fs00204-012-0857-8.pdf

R. Iyengar, S. Zhao, S. Chung, D. Mager, and J. Gallo, Merging Systems Biology with Pharmacodynamics, Science Translational Medicine, vol.3, issue.8, pp.126-127, 2012.
DOI : 10.1038/nrd1470

URL : http://europepmc.org/articles/pmc3405973?pdf=render

S. Zhao and R. Iyengar, Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action, Annual Review of Pharmacology and Toxicology, vol.52, issue.1, pp.505-521, 2012.
DOI : 10.1146/annurev-pharmtox-010611-134520

F. Bois and . Mcsim, GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models, Bioinformatics, vol.24, issue.17, pp.1453-1454, 2009.
DOI : 10.1093/bioinformatics/btn338

URL : https://hal.archives-ouvertes.fr/ineris-00961935

A. Wilmes, A. Limonciel, L. Aschauer, K. Moenks, C. Bielow et al., Application of integrated transcriptomic, proteomic and metabolomic profiling for the delineation of mechanisms of drug induced cell stress, Journal of Proteomics, vol.79, pp.180-194, 2013.
DOI : 10.1016/j.jprot.2012.11.022

URL : https://hal.archives-ouvertes.fr/ineris-00963456

D. Tedesco and L. Haragsim, Cyclosporine: A Review, Journal of Transplantation, vol.331, issue.9, p.230386, 2012.
DOI : 10.1111/j.1742-7843.2008.00327.x

J. König, F. Müller, and M. Fromm, Transporters and Drug-Drug Interactions: Important Determinants of Drug Disposition and Effects, Pharmacological Reviews, vol.65, issue.3, pp.944-966, 2013.
DOI : 10.1124/pr.113.007518

P. Jennings, C. Koppelstaetter, S. Aydin, T. Abberger, A. Wolf et al., Cyclosporine A induces senescence in renal tubular epithelial cells

, Am J Physiol Renal Physiol, vol.293, pp.831-838, 2007.

W. Bennett, A. Demattos, M. Meyer, T. Andoh, and J. Barry, Chronic cyclosporine nephropathy: The Achilles' heel of immunosuppressive therapy, Kidney International, vol.50, issue.4, pp.1089-1100, 1996.
DOI : 10.1038/ki.1996.415

C. Olbricht, M. Steinker, W. Auch-schwelk, C. Bossaller, J. Haas et al., Effect of cyclosporin on kidney proteolytic enzymes in men and rats, Nephrol Dial Transplant, vol.9, pp.22-26, 1994.

P. Cid, T. , C. Garcia, J. , C. Alvarez et al., Antioxidant nutrients protect against cyclosporine A nephrotoxicity, Toxicology, vol.189, pp.99-111, 2003.

P. Jennings, A. Limonciel, L. Felice, and M. Leonard, An overview of transcriptional regulation in response to toxicological insult, Archives of Toxicology, vol.10, issue.2, pp.49-72, 2013.
DOI : 10.2174/138920009787522151

A. Limonciel, A. Wilmes, L. Aschauer, R. Radford, K. Bloch et al., Oxidative stress induced by potassium bromate exposure results in altered tight junction protein expression in renal proximal tubule cells, Archives of Toxicology, vol.269, issue.1, pp.1741-1751, 2012.
DOI : 10.1016/j.tox.2010.01.002

A. Wilmes, D. Crean, S. Aydin, W. Pfaller, P. Jennings et al., Identification and dissection of the Nrf2 mediated oxidative stress pathway in human renal proximal tubule toxicity, Toxicology in Vitro, vol.25, issue.3, pp.613-622, 2011.
DOI : 10.1016/j.tiv.2010.12.009

D. Crean, F. L. Taylor, C. Rabb, H. Jennings, P. Leonard et al., Glucose reintroduction triggers the activation of Nrf2 during experimental ischemia reperfusion, Molecular and Cellular Biochemistry, vol.56, issue.1-2, pp.231-238, 2012.
DOI : 10.1002/glia.20676

Q. Zhang, J. Pi, C. Woods, and M. Andersen, Phase I to II cross-induction of xenobiotic metabolizing enzymes: A feedforward control mechanism for potential hormetic responses, Toxicology and Applied Pharmacology, vol.237, issue.3, pp.345-356, 2009.
DOI : 10.1016/j.taap.2009.04.005

J. Kaspar, S. Niture, and A. Jaiswal, Nrf2:INrf2 (Keap1) signaling in oxidative stress, Free Radical Biology and Medicine, vol.47, issue.9, pp.1304-1309, 2009.
DOI : 10.1016/j.freeradbiomed.2009.07.035

URL : http://europepmc.org/articles/pmc2763938?pdf=render

N. Villeneuve, A. Lau, and D. Zhang, Regulation of the Nrf2???Keap1 Antioxidant Response by the Ubiquitin Proteasome System: An Insight into Cullin-Ring Ubiquitin Ligases, Antioxidants & Redox Signaling, vol.13, issue.11, pp.1699-1712, 2010.
DOI : 10.1089/ars.2010.3211

T. Nguyen, H. Huang, and C. Pickett, Transcriptional Regulation of the Antioxidant Response Element, Journal of Biological Chemistry, vol.267, issue.20, pp.15466-15473, 2000.
DOI : 10.1074/jbc.274.39.27545

Y. Dai, K. Iwanaga, Y. Lin, M. Hebert, C. Davis et al., In vitro metabolism of cyclosporine A by human kidney CYP3A5, Biochemical Pharmacology, vol.68, issue.9, pp.1889-1902, 2004.
DOI : 10.1016/j.bcp.2004.07.012

F. Bois, Bayesian Inference, Methods Mol Biol, vol.930, pp.597-636, 2013.
DOI : 10.1007/978-1-62703-059-5_25

URL : https://hal.archives-ouvertes.fr/ineris-00969477

S. Greenland, Sensitivity Analysis, Monte Carlo Risk Analysis, and Bayesian Uncertainty Assessment, Risk Analysis, vol.21, issue.4, pp.579-583, 2001.
DOI : 10.1111/0272-4332.214136

A. Gelman and D. Rubin, Inference from Iterative Simulation Using Multiple Sequences, Statistical Science, vol.7, issue.4, pp.457-511, 1992.
DOI : 10.1214/ss/1177011136

URL : https://doi.org/10.1214/ss/1177011136

A. Limonciel, L. Aschauer, A. Wilmes, S. Prajczer, M. Leonard et al., Lactate is an ideal non-invasive marker for evaluating temporal alterations in cell stress and toxicity in repeat dose testing regimes, Toxicology in Vitro, vol.25, issue.8, pp.1855-1862, 2011.
DOI : 10.1016/j.tiv.2011.05.018

X. Jiang and A. Kopp-schneider, Summarizing EC50 estimates from multiple dose-response experiments: A comparison of a meta-analysis strategy to a mixed-effects model approach, Biometrical Journal, vol.213, issue.3, 2014.
DOI : 10.1016/j.toxlet.2012.07.012

R. Team, R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, 2012.

S. Adler, D. Basketter, S. Creton, O. Pelkonen, J. Van-benthem et al., Alternative (non-animal) methods for cosmetics testing: current status and future prospects???2010, Archives of Toxicology, vol.277, issue.6, pp.367-485, 2011.
DOI : 10.1016/j.tox.2010.08.016

URL : https://hal.archives-ouvertes.fr/ineris-00963274

S. Coecke, O. Pelkonen, S. Leite, U. Bernauer, J. Bessems et al., Toxicokinetics as a key to the integrated toxicity risk assessment based primarily on non-animal approaches, Toxicology in Vitro, vol.27, issue.5, pp.1570-1577, 2013.
DOI : 10.1016/j.tiv.2012.06.012

URL : https://hal.archives-ouvertes.fr/ineris-00963488

F. Muller and M. Fromm, Transporter-mediated drug???drug interactions, Pharmacogenomics, vol.48, issue.7, pp.1017-1037, 2011.
DOI : 10.1038/clpt.1984.141

V. Pekovic-vaughan, J. Gibbs, H. Yoshitane, N. Yang, D. Pathiranage et al., The circadian clock regulates rhythmic activation of the NRF2/glutathione-mediated antioxidant defense pathway to modulate pulmonary fibrosis, Genes & Development, vol.28, issue.6, pp.548-560, 2014.
DOI : 10.1101/gad.237081.113

R. Cauduro, C. Costa, F. Lhulier, R. Garcia, R. Cabral et al., Endothelin-1 plasma levels and hypertension in cyclosporine-treated renal transplant patients, Clinical Transplantation, vol.16, issue.4, pp.470-474, 2005.
DOI : 10.1161/01.HYP.34.4.876

J. Campistol, P. Inigo, W. Jimenez, S. Lario, P. Clesca et al., Losartan decreases plasma levels of TGF-??1 in transplant patients with chronic allograft nephropathy, Kidney International, vol.56, issue.2, pp.714-719, 1999.
DOI : 10.1046/j.1523-1755.1999.00597.x

B. Ozdemir, F. Ozdemir, B. Demirhan, and M. Haberal, TGF-beta1 expression in renal allograft rejection and cyclosporine A toxicity, Transplantation, vol.80, pp.1681-1685, 2005.

R. Pichler, N. Franceschini, B. Young, C. Hugo, T. Andoh et al., Pathogenesis of cyclosporine nephropathy: roles of angiotensin II and osteopontin, J Am Soc Nephrol, vol.6, pp.1186-1196, 1995.

P. Justo, C. Lorz, A. Sanz, J. Egido, and A. Ortiz, Intracellular Mechanisms of Cyclosporin A-Induced Tubular Cell Apoptosis, Journal of the American Society of Nephrology, vol.14, issue.12, pp.3072-3080, 2003.
DOI : 10.1097/01.ASN.0000099383.57934.0E

URL : http://jasn.asnjournals.org/content/14/12/3072.full.pdf

W. Zhang, F. Li, and L. Nie, Integrating multiple 'omics' analysis for microbial biology: application and methodologies, Microbiology, vol.8, issue.4, pp.287-301, 2010.
DOI : 10.1002/pmic.200701005

URL : http://mic.microbiologyresearch.org/deliver/fulltext/micro/156/2/287.pdf?itemId=/content/journal/micro/10.1099/mic.0.034793-0&mimeType=pdf&isFastTrackArticle=

G. Cramer, K. Urano, S. Delrot, M. Pezzotti, and K. Shinozaki, Effects of abiotic stress on plants: a systems biology perspective, BMC Plant Biology, vol.11, issue.1, p.163, 2011.
DOI : 10.1093/mp/ssq016

URL : https://bmcplantbiol.biomedcentral.com/track/pdf/10.1186/1471-2229-11-163?site=bmcplantbiol.biomedcentral.com

T. Tan, S. Lim, A. Khan, and S. Ranganathan, A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the "-omics" era, BMC Genomics, vol.10, issue.Suppl 3, p.36, 2009.
DOI : 10.1186/1471-2164-10-S3-S36

N. Quignot and F. Bois, A Computational Model to Predict Rat Ovarian Steroid Secretion from In Vitro Experiments with Endocrine Disruptors, PLoS ONE, vol.86, issue.1, p.53891, 2013.
DOI : 10.1371/journal.pone.0053891.s001

URL : https://hal.archives-ouvertes.fr/ineris-00961794

, Systems biology modeling of omics data: effect of cyclosporine a on the Nrf2 pathway in human renal cells, BMC Systems Biology, vol.8, p.76, 2014.