The Integrative Cancer Biology Program. [http://icbp.nci.nih.gov/]

Jackson RC: Kinetic simulation of anticancer drug interactions. Int J Biomed Comput. 1980, 11 (3): 197-224. 10.1016/0020-7101(80)90045-8.

Article
CAS
PubMed
Google Scholar

Morrison PF, Allegra CJ: Folate cycle kinetics in human breast cancer cells. JBiolChem. 1989, 264 (18): 10552-10566.

CAS
Google Scholar

Novak B, Tyson JJ: A model for restriction point control of the mammalian cell cycle. J Theor Biol. 2004, 230 (4): 563-579. 10.1016/j.jtbi.2004.04.039.

Article
CAS
PubMed
Google Scholar

Ciliberto A, Novak B, Tyson JJ: Steady states and oscillations in the p53/Mdm2 network. Cell Cycle. 2005, 4 (3): 488-493.

Article
CAS
PubMed
Google Scholar

Ma L, Wagner J, Rice JJ, Hu W, Levine AJ, Stolovitzky GA: A plausible model for the digital response of p53 to DNA damage. Proc Natl Acad Sci U S A. 2005, 102 (40): 14266-14271. 10.1073/pnas.0501352102.

Article
CAS
PubMed
PubMed Central
Google Scholar

Lipniacki T, Paszek P, Brasier AR, Luxon B, Kimmel M: Mathematical model of NF-kappaB regulatory module. J Theor Biol. 2004, 228 (2): 195-215. 10.1016/j.jtbi.2004.01.001.

Article
CAS
PubMed
Google Scholar

Sha W, Moore J, Chen K, Lassaletta AD, Yi CS, Tyson JJ, Sible JC: Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proc Natl Acad Sci U S A. 2003, 100 (3): 975-980. 10.1073/pnas.0235349100.

Article
CAS
PubMed
Google Scholar

Hahnfeldt P, Panigrahy D, Folkman J, Hlatky L: Tumor development under angiogenic signaling: a dynamical theory of tumor growth, treatment response, and postvascular dormancy. Cancer Res. 1999, 59 (19): 4770-4775.

CAS
PubMed
Google Scholar

Hirsch MW, Smale S: Differential equations, dynamical systems, and linear algebra. 1974, New York: Academic Press

Google Scholar

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003, 19 (4): 524-531. 10.1093/bioinformatics/btg015.

Article
CAS
PubMed
Google Scholar

Systems Biology Markup Language. [http://sbml.org]

Ihaka R, Gentleman R: R:a language for data analysis and graphics. Journal of Computational and graphical statistics. 1996, 5: 299-314. 10.2307/1390807.

Google Scholar

MATLAB: version 7.0. Mathworks Inc., Natick, MA. 2004, 7.0

Tong FK, Chow S, Hedley D: Pharmacodynamic monitoring of BAY 43-9006 (Sorafenib) in phase I clinical trials involving solid tumor and AML/MDS patients, using flow cytometry to monitor activation of the ERK pathway in peripheral blood cells. Cytometry B Clin Cytom. 2006

Google Scholar

Yau CY, Wheeler JJ, Sutton KL, Hedley DW: Inhibition of integrin-linked kinase by a selective small molecule inhibitor, QLT0254, inhibits the PI3K/PKB/mTOR, Stat3, and FKHR pathways and tumor growth, and enhances gemcitabine-induced apoptosis in human orthotopic primary pancreatic cancer xenografts. Cancer Res. 2005, 65 (4): 1497-1504. 10.1158/0008-5472.CAN-04-2940.

Article
CAS
PubMed
Google Scholar

Jacobberger JW, Sramkoski RM, Frisa PS, Ye PP, Gottlieb MA, Hedley DW, Shankey TV, Smith BL, Paniagua M, Goolsby CL: Immunoreactivity of Stat5 phosphorylated on tyrosine as a cell-based measure of Bcr/Abl kinase activity. Cytometry A. 2003, 54 (2): 75-88. 10.1002/cyto.a.10063.

Article
PubMed
Google Scholar

Chow S, Patel H, Hedley DW: Measurement of MAP kinase activation by flow cytometry using phospho-specific antibodies to MEK and ERK: potential for pharmacodynamic monitoring of signal transduction inhibitors. Cytometry. 2001, 46 (2): 72-78. 10.1002/cyto.1067.

Article
CAS
PubMed
Google Scholar

Danna EA, Nolan GP: Transcending the biomarker mindset: deciphering disease mechanisms at the single cell level. Curr Opin Chem Biol. 2006, 10 (1): 20-27. 10.1016/j.cbpa.2005.12.021.

Article
CAS
PubMed
Google Scholar

Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP: Causal protein-signaling networks derived from multiparameter single-cell data. Science. 2005, 308 (5721): 523-529. 10.1126/science.1105809.

Article
CAS
PubMed
Google Scholar

Irish JM, Hovland R, Krutzik PO, Perez OD, Bruserud O, Gjertsen BT, Nolan GP: Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell. 2004, 118 (2): 217-228. 10.1016/j.cell.2004.06.028.

Article
CAS
PubMed
Google Scholar

Krutzik PO, Irish JM, Nolan GP, Perez OD: Analysis of protein phosphorylation and cellular signaling events by flow cytometry: techniques and clinical applications. Clin Immunol. 2004, 110 (3): 206-221. 10.1016/j.clim.2003.11.009.

Article
CAS
PubMed
Google Scholar

Preston DL, Kusumi S, Tomonaga M, Izumi S, Ron E, Kuramoto A, Kamada N, Dohy H, Matsuo T, Matsui T: Cancer incidence in atomic bomb survivors. Part III. Leukemia, lymphoma and multiple myeloma, 1950–1987. RadiatRes. 1994, 137 (2 Suppl): S68-S97.

CAS
Google Scholar

Inskip PD, Kleinerman RA, Stovall M, Cookfair DL, Hadjimichael O, Moloney WC, Monson RR, Thompson WD, Wactawski-Wende J, Wagoner JK: Leukemia, lymphoma, and multiple myeloma after pelvic radiotherapy for benign disease. RadiatRes. 1993, 135 (1): 108-124.

CAS
Google Scholar

Boice JD, Blettner M, Kleinerman RA, Stovall M, Moloney WC, Engholm G, Austin DF, Bosch A, Cookfair DL, Krementz ET: Radiation dose and leukemia risk in patients treated for cancer of the cervix. JNatlCancer Inst. 1987, 79 (6): 1295-1311.

Google Scholar

Thompson DE, Mabuchi K, Ron E, Soda M, Tokunaga M, Ochikubo S, Sugimoto S, Ikeda T, Terasaki M, Izumi S: Cancer incidence in atomic bomb survivors. Part II: Solid tumors, 1958–1987. Radiat Res. 1994, 137 (2 Suppl): S17-67.

Article
CAS
PubMed
Google Scholar

Kailath T: Linear Systems. 1980, Englewood Cliffs, NJ: Prentice-Hall

Google Scholar

Isidori A: Nonlinear Control Systems. 1995, Springer-Verlag, 3rd

Chapter
Google Scholar

Athans M, Falb PL: Optimal control; an introduction to the theory and its applications. 1966, New York,: McGraw-Hill

Google Scholar

Bryson AE, Ho YC: Applied Optimal Control. 1975, New York: Hemisphere Publishing Corporation

Google Scholar

Swan GW: Role of optimal control theory in cancer chemotherapy. Math Biosci. 1990, 101 (2): 237-284. 10.1016/0025-5564(90)90021-P.

Article
CAS
PubMed
Google Scholar

Martin R, Teo KL: Optimal control of drug administration in cancer chemotherapy. 1994, River Edge, N.J.: World Scientific

Google Scholar

SBMLR. [http://epbi-radivot.cwru.edu/SBMLR/]

Radivoyevitch T: A two-way interface between limited Systems Biology Markup Language and R. BMC Bioinformatics. 2004, 5 (1): 190-10.1186/1471-2105-5-190.

Article
PubMed
PubMed Central
Google Scholar

Radivoyevitch Lab. [http://epbi-radivot.cwru.edu/]

Yeoh EJ, Ross ME, Shurtleff SA, Williams WK, Patel D, Mahfouz R, Behm FG, Raimondi SC, Relling MV, Patel A, Cheng C, Campana D, Wilkins D, Zhou X, Li J, Liu H, Pui CH, Evans WE, Naeve C, Wong L, Downing JR: Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell. 2002, 1 (2): 133-143. 10.1016/S1535-6108(02)00032-6.

Article
CAS
PubMed
Google Scholar

Radivoyevitch T: Folate system correlations in DNA microarray data. BMC Cancer. 2005, 5: 95-10.1186/1471-2407-5-95.

Article
PubMed
PubMed Central
Google Scholar

ICB approaches to therapeutic gain. [http://epbi-radivot.cwru.edu/ICBtherap/]

Erikson RL, Szybalski W: Molecular Radiobiology of Human Cell Lines. V. Comparative Radiosensitizing Properties of 5-Halodeoxycytidines and 5-Halodeoxyuridines. Radiat Res. 1963, 20: 252-262.

Article
CAS
PubMed
Google Scholar

Djordjevic B, Szybalski W: Genetics of human cell lines. III. Incorporation of 5-bromo- and 5-iododeoxyuridine into the deoxyribonucleic acid of human cells and its effect on radiation sensitivity. J Exp Med. 1960, 112: 509-531. 10.1084/jem.112.3.509.

Article
CAS
PubMed
PubMed Central
Google Scholar

Fornace AJ, Dobson PP, Kinsella TJ: Enhancement of radiation damage in cellular DNA following unifilar substitution with iododeoxyuridine. Int J Radiat Oncol Biol Phys. 1990, 18 (4): 873-878.

Article
CAS
PubMed
Google Scholar

Kinsella TJ, Dobson PP, Mitchell JB, Fornace AJ: Enhancement of X ray induced DNA damage by pre-treatment with halogenated pyrimidine analogs. Int J Radiat Oncol Biol Phys. 1987, 13 (5): 733-739.

Article
CAS
PubMed
Google Scholar

Berry SE, Davis TW, Schupp JE, Hwang HS, de Wind N, Kinsella TJ: Selective radiosensitization of drug-resistant MutS homologue-2 (MSH2) mismatch repair-deficient cells by halogenated thymidine (dThd) analogues: Msh2 mediates dThd analogue DNA levels and the differential cytotoxicity and cell cycle effects of the dThd analogues and 6-thioguanine. Cancer Res. 2000, 60 (20): 5773-5780.

CAS
PubMed
Google Scholar

Berry SE, Garces C, Hwang HS, Kunugi K, Meyers M, Davis TW, Boothman DA, Kinsella TJ: The mismatch repair protein, hMLH1, mediates 5-substituted halogenated thymidine analogue cytotoxicity, DNA incorporation, and radiosensitization in human colon cancer cells. Cancer Res. 1999, 59 (8): 1840-1845.

CAS
PubMed
Google Scholar

Look AT: Oncogenic transcription factors in the human acute leukemias. Science. 1997, 278 (5340): 1059-1064. 10.1126/science.278.5340.1059.

Article
CAS
PubMed
Google Scholar

Pui CH, Evans WE: Acute lymphoblastic leukemia. N Engl J Med. 1998, 339 (9): 605-615. 10.1056/NEJM199808273390907.

Article
CAS
PubMed
Google Scholar

Shih C, Habeck LL, Mendelsohn LG, Chen VJ, Schultz RM: Multiple folate enzyme inhibition: mechanism of a novel pyrrolopyrimidine-based antifolate LY231514 (MTA). Adv Enzyme Regul. 1998, 38: 135-152. 10.1016/S0065-2571(97)00017-4.

Article
CAS
PubMed
Google Scholar

McGahon A, Bissonnette R, Schmitt M, Cotter KM, Green DR, Cotter TG: BCR-ABL maintains resistance of chronic myelogenous leukemia cells to apoptotic cell death. Blood. 1994, 83 (5): 1179-1187.

CAS
PubMed
Google Scholar

Taverna P, Hwang HS, Schupp JE, Radivoyevitch T, Session NN, Reddy G, Zarling DA, Kinsella TJ: Inhibition of base excision repair potentiates iododeoxyuridine-induced cytotoxicity and radiosensitization. Cancer Res. 2003, 63 (4): 838-846.

CAS
PubMed
Google Scholar

Wright G, Tan B, Rosenwald A, Hurt EH, Wiestner A, Staudt LM: A gene expression-based method to diagnose clinically distinct subgroups of diffuse large B cell lymphoma. Proc Natl Acad Sci U S A. 2003, 100 (17): 9991-9996. 10.1073/pnas.1732008100.

Article
CAS
PubMed
PubMed Central
Google Scholar

Rosenwald A, Wright G, Chan WC, Connors JM, Campo E, Fisher RI, Gascoyne RD, Muller-Hermelink HK, Smeland EB, Giltnane JM, Hurt EM, Zhao H, Averett L, Yang L, Wilson WH, Jaffe ES, Simon R, Klausner RD, Powell J, Duffey PL, Longo DL, Greiner TC, Weisenburger DD, Sanger WG, Dave BJ, Lynch JC, Vose J, Armitage JO, Montserrat E, Lopez-Guillermo A, Grogan TM, Miller TP, LeBlanc M, Ott G, Kvaloy S, Delabie J, Holte H, Krajci P, Stokke T, Staudt LM: The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med. 2002, 346 (25): 1937-1947. 10.1056/NEJMoa012914.

Article
PubMed
Google Scholar

Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Staudt LM: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000, 403 (6769): 503-511. 10.1038/35000501.

Article
CAS
PubMed
Google Scholar

Lossos IS, Czerwinski DK, Alizadeh AA, Wechser MA, Tibshirani R, Botstein D, Levy R: Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N Engl J Med. 2004, 350 (18): 1828-1837. 10.1056/NEJMoa032520.

Article
CAS
PubMed
Google Scholar

Michor F, Hughes TP, Iwasa Y, Branford S, Shah NP, Sawyers CL, Nowak MA: Dynamics of chronic myeloid leukaemia. Nature. 2005, 435 (7046): 1267-1270. 10.1038/nature03669.

Article
CAS
PubMed
Google Scholar