Andersen ME, Krewski D: Toxicity Testing in the 21st Century: Bringing the Vision to Life. Toxicological Sciences. 2009, 107: 324-330.

Article
CAS
PubMed
Google Scholar

Holsapple MP, Afshari CA, Lehman-McKeeman LD: Forum Series: The "Vision" for Toxicity Testing in the 21st Century: Promises and Conundrums. Toxicological Sciences. 2009, 107: 307-308.

Article
CAS
PubMed
Google Scholar

White RH, Cote I, Zeise L, Fox M, Dominici F, Burke TA, White PD, Hattis DB, Samet JM: State-of-the-Science Workshop Report: Issues and Approaches in Low-Dose-Response Extrapolation for Environmental Health Risk Assessment. Environ Health Perspect. 2008, 117:

Google Scholar

De Rosa C, El-Masri H, Pohl H, Cibulas W, Mumtaz M: Implications of Chemical Mixtures in Public Health Practice. Journal of Toxicology and Environmental Health Part B: Critical Reviews. 2004, 7: 339-350. 10.1080/10937400490498075.

Article
CAS
PubMed
Google Scholar

Lawrence JW, Li Y, Chen S, DeLuca JG, Berger JP, Umbenhauer DR, Moller DE, Zhou G: Differential Gene Regulation in Human Versus Rodent Hepatocytes by Peroxisome Proliferator-activated Receptor (PPAR) α. Journal of Biological Chemistry. 2001, 276: 31521-31527. 10.1074/jbc.M103306200

Article
CAS
PubMed
Google Scholar

Cohen SM, Lawson TA: Rodent bladder tumors do not always predict for humans. Cancer Letters. 1995, 93: 9-16. 10.1016/0304-3835(95)03785-U

Article
CAS
PubMed
Google Scholar

Wambaugh J, Shah I: Simulating Microdosimetry in a Virtual Hepatic Lobule. PLoS Comput Biol. 2010, 6: e1000756- 10.1371/journal.pcbi.1000756

Article
PubMed Central
PubMed
Google Scholar

Shah I, Wambaugh J: Virtual Tissues in Toxicology. Journal of Toxicology and Environmental Health Part B: Critical Reviews. 2010, 13: 314-328. 10.1080/10937404.2010.483948.

Article
CAS
Google Scholar

Kauffman S: Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology. 1969, 22: 437-467. 10.1016/0022-5193(69)90015-0

Article
CAS
PubMed
Google Scholar

Zoltan S, Shoudan L: Modeling the normal and neoplastic cell cycle with 'realistic Boolean genetic networks': Their application for understanding carcinogenesis and assessing therapeutic strategies. Book Modeling the normal and neoplastic cell cycle with 'realistic Boolean genetic networks': Their application for understanding carcinogenesis and assessing therapeutic strategies. 1998, City: World Scientific Publishing,

Google Scholar

Shmulevich I, Dougherty ER, Kim S, Zhang W: Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics. 2002, 18: 261-274. 10.1093/bioinformatics/18.2.261

Article
CAS
PubMed
Google Scholar

Sánchez L, Thieffry D: A Logical Analysis of the Drosophila Gap-gene System. Journal of Theoretical Biology. 2001, 211: 115-141. 10.1006/jtbi.2001.2335

Article
PubMed
Google Scholar

Davidich MI, Bornholdt S: Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast. PLoS ONE. 2008, 3: e1672- 10.1371/journal.pone.0001672

Article
PubMed Central
PubMed
Google Scholar

Li F, Long T, Lu Y, Ouyang Q, Tang C: The yeast cell-cycle network is robustly designed. Proceedings of the National Academy of Sciences of the United States of America. 2004, 101: 4781-4786. 10.1073/pnas.0305937101

Article
PubMed Central
CAS
PubMed
Google Scholar

Faure A, Naldi A, Chaouiya C, Thieffry D: Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics. 2006, 22: e124-131. 10.1093/bioinformatics/btl210

Article
CAS
PubMed
Google Scholar

Saez-Rodriguez J, Alexopoulos LG, Epperlein J, Samaga R, Lauffenburger DA, Klamt S, Sorger PK: Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol. 2009, 5:

Google Scholar

Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S: The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data. PLoS Comput Biol. 2009, 5: e1000438- 10.1371/journal.pcbi.1000438

Article
PubMed Central
PubMed
Google Scholar

Wu M, Yang X, Chan C: A Dynamic Analysis of IRS-PKR Signaling in Liver Cells: A Discrete Modeling Approach. PLoS ONE. 2009, 4: e8040- 10.1371/journal.pone.0008040

Article
PubMed Central
PubMed
Google Scholar

Philippi N, Walter D, Schlatter R, Ferreira K, Ederer M, Sawodny O, Timmer J, Borner C, Dandekar T: Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection. BMC Systems Biology. 2009, 3: 97- 10.1186/1752-0509-3-97

Article
PubMed Central
PubMed
Google Scholar

Zhang R, Shah MV, Yang J, Nyland SB, Liu X, Yun JK, Albert R, Loughran TP: Network model of survival signaling in large granular lymphocyte leukemia. Proceedings of the National Academy of Sciences. 2008, 105: 16308-16313. 10.1073/pnas.0806447105.

Article
CAS
Google Scholar

Martin MT, Judson RS, Reif DM, Kavlock RJ, Dix DJ: Profiling Chemicals Based on Chronic Toxicity Results from the U.S. EPA ToxRef Database. Book Profiling Chemicals Based on Chronic Toxicity Results from the US EPA ToxRef Database. 2009, 117: 392-399. City: National Institute of Environmental Health Sciences,

Google Scholar

Chhabra RS, Bucher JR, Wolfe M, Portier C: Toxicity characterization of environmental chemicals by the US National Toxicology Program: an overview. International Journal of Hygiene and Environmental Health. 2003, 206: 437-445. 10.1078/1438-4639-00240

Article
CAS
PubMed
Google Scholar

Hanahan D, Weinberg RA: The Hallmarks of Cancer. Cell. 2000, 100: 57-70. 10.1016/S0092-8674(00)81683-9

Article
CAS
PubMed
Google Scholar

Butterworth BE: Consideration of both genotoxic and nongenotoxic mechanisms in predicting carcinogenic potential. Mutation Research/Reviews in Genetic Toxicology. 1990, 239: 117-132. 10.1016/0165-1110(90)90033-8.

Article
CAS
Google Scholar

Csikász-Nagy A, Battogtokh D, Chen KC, Novák B, Tyson JJ: Analysis of a Generic Model of Eukaryotic Cell-Cycle Regulation. 2006, 90: 4361-4379.

Google Scholar

Lahav G, Rosenfeld N, Sigal A, Geva-Zatorsky N, Levine AJ, Elowitz MB, Alon U: Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat Genet. 2004, 36: 147-150. 10.1038/ng1293

Article
CAS
PubMed
Google Scholar

Batchelor E, Loewer A, Lahav G: The ups and downs of p53: understanding protein dynamics in single cells. Nat Rev Cancer. 2009, 9: 371-377. 10.1038/nrc2604

Article
PubMed Central
CAS
PubMed
Google Scholar

Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW: Single-cell NF-[kgr]B dynamics reveal digital activation and analogue information processing. Nature. 2010, 466: 267-271. 10.1038/nature09145

Article
PubMed Central
CAS
PubMed
Google Scholar

Spencer SL, Gaudet S, Albeck JG, Burke JM, Sorger PK: Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature. 2009, 459: 428-432. 10.1038/nature08012

Article
PubMed Central
CAS
PubMed
Google Scholar

Luke N, Devito M, Portier C, El-Masri H: Employing a Mechanistic Model for the MAPK Pathway to Examine the Impact of Cellular All or None Behavior on Overall Tissue Response. Dose Response. 2010, 8: 347-367. 10.2203/dose-response.09-017.Luke

Article
PubMed Central
CAS
PubMed
Google Scholar

Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, Sigal A, Milo R, Cohen-Saidon C, Liron Y, Kam Z, et al.: Dynamic Proteomics of Individual Cancer Cells in Response to a Drug. Science. 2008, 322: 1511-1516. 10.1126/science.1160165

Article
CAS
PubMed
Google Scholar

Derrida B: Dynamical phase transition in nonsymmetric spin glasses. Journal of Physics A: Mathematical and General. 1987, 20: L721-10.1088/0305-4470/20/11/009.

Article
Google Scholar

Bornholdt S: Boolean network models of cellular regulation: prospects and limitations. Journal of The Royal Society Interface. 2008, 5: S85-S94. 10.1098/rsif.2008.0132.focus.

Article
PubMed Central
CAS
Google Scholar

Robert J, Lefkowitz SKS: IGF-1 Receptor Signaling through betat-Arrestin. Sci Signal. 2005,

Google Scholar

Schlessinger J: Epidermal Growth Factor Receptor Pathway. Book Epidermal Growth Factor Receptor Pathway. 2005, City,

Google Scholar

White MF: Insulin Signaling Pathway. Sci Signal. 2005,

Google Scholar

David V, Goeddel GC: Tumor Necrosis Factor Pathway. Sci Signal. 2005,

Google Scholar

Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research. 2003, 13: 2498-2504. 10.1101/gr.1239303

Article
PubMed Central
CAS
PubMed
Google Scholar

Ayala J, Boustead J, Chapman S, Svitek C, Oeser J, Robey R, O'Brien R: Insulin-mediated activation of activator protein-1 through the mitogen-activated protein kinase pathway stimulates collagenase-1 gene transcription in the MES 13 mesangial cell line. J Mol Endocrinol. 2004, 33: 263-280. 10.1677/jme.0.0330263

Article
CAS
PubMed
Google Scholar

Newman JRS, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS: Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature. 2006, 441: 840-846. 10.1038/nature04785

Article
CAS
PubMed
Google Scholar

Chevalier S, Macdonald N, Roberts R: Induction of DNA replication by peroxisome proliferators is independent of both tumour necrosis factor (alpha) priming and EGF-receptor tyrosine kinase activity. J Cell Sci. 1999, 112: 4785-4791.

CAS
PubMed
Google Scholar

Nadori F, Lardeux B, Rahmani M, Bringuier A, Durand-Schneider A, Bernuau D: Presence of distinct AP-1 dimers in normal and transformed rat hepatocytes under basal conditions and after epidermal growth factor stimulation. Hepatology. 1997, 26: 1477-1483. 10.1002/hep.510260614

Article
CAS
PubMed
Google Scholar

Greil F, Drossel B: Dynamics of Critical Kauffman Networks under Asynchronous Stochastic Update. Physical Review Letters. 2005, 95: 048701-

Article
PubMed
Google Scholar

Klemm K, Bornholdt S: Stable and unstable attractors in Boolean networks. Physical Review E. 2005, 72: 055101-

Article
Google Scholar

Zwolak JW, Tyson JJ, Watson LT: Parameter Estimation for a Mathematical Model of the Cell Cycle in Frog Eggs. Journal of Computational Biology. 2005, 12: 48-63. 10.1089/cmb.2005.12.48

Article
CAS
PubMed
Google Scholar

Zielinski R, Przytycki P, Zheng J, Zhang D, Przytycka T, Capala J: The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis. BMC Systems Biology. 2009, 3: 88- 10.1186/1752-0509-3-88

Article
PubMed Central
PubMed
Google Scholar

Huang Z, Hahn J: Fuzzy modeling of signal transduction networks. Chemical Engineering Science. 2009, 64: 2044-2056. 10.1016/j.ces.2009.01.041.

Article
CAS
Google Scholar

Rotroff D, Beam A, Dix D, Farmer A, Freeman K, Houck K, Judson R, LeCluyse E, Martin M, Reif D, Ferguson S: Xenobiotic-Metabolizing Enzyme and Transporter Gene Expression in Primary Cultures of Human Hepatocytes Modulated by Toxcast Chemicals. Journal of Toxicology and Environmental Health, Part B: Critical Reviews. 2010, 13: 329-346. 10.1080/10937404.2010.483949.

Article
CAS
Google Scholar

Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M: KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Research. 2010, 38: D355-D360. 10.1093/nar/gkp896

Article
PubMed Central
CAS
PubMed
Google Scholar

Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, et al.: Reactome: a knowledgebase of biological pathways. Nucleic Acids Research. 2005, 33: D428-D432.

Article
PubMed Central
CAS
PubMed
Google Scholar

Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH: PID: the Pathway Interaction Database. Nucleic Acids Research. 2009, 37: D674-D679. 10.1093/nar/gkn653

Article
PubMed Central
CAS
PubMed
Google Scholar

Bassingthwaighte J, Liebovitch LS, West BJ: Fractal Physiology. 1994, Oxford University Press, New York,

Book
Google Scholar

Hunt CA, Yan L, Ropella G, Park S, Sheikh-Bahael S: The multiscale in silico liver. Journal of Critical Care. 2007, 22: 348-349. 10.1016/j.jcrc.2007.10.031.

Article
Google Scholar