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ICBP-Related Publications, 2005-present
2007
Deisboeck TS, Wang Z. Cancer dissemination: A consequence of limited carrying capacity? Med Hypotheses 2007; 69(1): 173-177.
Dressman, H. K., Chan, G., Zhai, J., Bild, A., Cragun, J., Sayer, R., Clarke, J., Whitaker, R., Gray, J., Marks, J., Ginsburg, G., Potti, A., West, Berchuck, A., Nevins, J.R., and Lancaster, J. M. (2007). A genomic strategy to personalized treatment of patients with advanced-stage ovarian cancer. J. Clin. Oncol. 25, 517-525.
Ebert MS, Neilson JR, and Sharp PA (2007). MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods, epub ahead of print.
Gerlee P, Anderson AR. An evolutionary hybrid cellular automaton model of solid tumour growth. J Theor Biol. 2007 Feb 12; [Epub ahead of print].
Gerlee and Anderson. Stability Analysis of a Hybrid Cellular Automaton Model of Cell Colony Growth. Physical Review E. 2007;75.
Huang PH, Mukasa A, Bonavia R, Flynn RA, Brewer ZE, Cavenee WK, Furnari FB, and White FM (2007). Quantitative analysis of EGFR vIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma. Proc Natl Acad Sci USA 104, 12867-72.
Kharait S, Hautaniemi S, Wu S, Iwabu A, Lauffenburger DA, and Wells A (2007). Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility. BMC Syst Biol 1, 9.
Kinsella TJ, Kinsella MT, Hong S, Johnson JP, Burback B, Tosca PJ.Toxicology and pharmacokinetic study of orally administered 5-iodo-2-pyrimidinone-2'deoxyribose (IPdR) x 28 days in Fischer-344 rats: impact on the initial clinical phase I trial design of IPdR-mediated radiosensitization. Cancer Chemother Pharmacol. 2007 Jun 12; [Epub ahead of print]
Kong, L.-J., Chang, J., and Nevins, J. R. (2007). Compensation and specificity of function within the E2F family. Oncogene 26, 321-327.
Kumar N, Wolf-Yadlin A, White FM, and Lauffenburger DA (2007). Modeling HER2 Effects on Cell Behavior from Mass Spectrometry Phosphotyrosine Data. PLoS Comput Biol 3, e4.
Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jorgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB, and Pawson T (2007). Systematic discovery of in vivo phosphorylation networks. Cell 129, 1415-26.
Reinhardt HC, Aslanian AS, Lees JA, and Yaffe MB (2007). p53-deficient cells rely on ATM- and ATR-mediated checkpoint signaling through the p38MAPK/MK2 pathway for survival after DNA damage. Cancer Cell 11, 175-189.
Saif MW, Berk G, Cheng YC, Kinsella TJ. IPdR: a novel oral radiosensitizer. Expert Opin Investig Drugs. 2007 Sep;16(9):1415-24.
Thomas M, Lu JJ, Zhang C. Chen J, and Klibanov AM (2007). Identification of novel superior polycationic vectors for gene delivery by high-throughput synthesis and screening of a combinatorial library. Pharm Res 24, 1564-71.
Yamane K, Schupp JE, Kinsella TJ.BRCA1 activates a G2-M cell cycle checkpoint following 6-thioguanine-induced DNA mismatch damage. Cancer Res. 2007 Jul 1;67(13):6286-92.
Wille L, Kemp ML, Sandy P, Lewis CL, and Lauffenburger DA (2007). Epi-allelic Erk1 and Erk2 knockdown series for quantitative analysis of T cell Erk regulation and IL-2 production. Mol Immunol 44, 3085-91.
Zeng X, Kinsella TJ.A novel role for DNA mismatch repair and the autophagic processing of chemotherapy drugs in human tumor cells. Autophagy. 2007 Jul-Aug;3(4):368-70. Epub 2007 Jul 29.
Zhang L, Athale CA, Deisboeck TS. Development of a three-dimensional multiscale agent-based tumor model: simulating gene-protein interaction profiles, cell phenotypes multicellular patterns in brain cancer. J Theor Biol.2007; 244(1): 96-107.
2006
Anderson, S. (and?) A Novel “Sandwhich” Assay for Quantifying Chemo-Regulated Cell Migration Within 3-Dimensional Matrices: Wound healing cytokines exhibit distinct motogenic activities compared to the transmembrane assay, (2006). Cell Motility and the Cytoskeleton, Accepted.
Anderson, S. (and?) Mathematical modelling of the influence of blood rheological properties upon adaptive tumour-induced angiogenesis, (2006). Math. Comput. Modell., Accepted.
Anderson, S. (and?) Computational methods and results for structured multiscale models of tumor invasion, (2006). Multiscale. Model. Simul., 5: 1-20.
Athale C.A., and Deisboeck T.S. The effects of EGF-receptor density on multiscale tumor growth patterns.J. theor. Biol. 238(4): 771-779, 2006.
Bild, A., Potti, A., and Nevins, J. R. (2006). Focusing on pathways to address complex biological and clinical phenotypes. Nat. Rev. Cancer 6, 735-741.
Chang, J. T. and Nevins, J. R. (2006). GATHER – a systems approach to interpreting genomic signatures. Bioinformatics 22, 2926-2933.Cheng, A.S., Jin, V.X., Fan, M., Smith, L.T., Liyanarachchi, S., Yan, P.S., Leu, Y.W., Chan, M.W., Plass, C., Nephew, K.P. et al. Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters. Mol Cell, 21, 393-404, 2006.
Deisboeck TS, Guiot C, Delsanto PP, Pugno N. Does cancer growth depend on surface extension? Med Hypotheses 2006; 67 (6):1338-1341.
Gardino AK, Smerdon S J, and Yaffe MB (2006). Structural determinants of 14-3-3 binding specificities and regulation of subcellular localization of 14-3-3-ligand complexes: a comparison of the X-ray crystal structures of all human 14-3-3 isoforms. Semin Cancer Biol 16, 173-182.
Hallstrom, T. C. and Nevins, J. R. (2006). Jab1 is a specificity factor for E2F1-induced apoptosis. Genes & Dev. 20, 613-623.
J. Lucas, C. Carvalho, Q. Wang, A. Bild, J.R. Nevins and M. West (2006) Sparse statistical modelling in gene expression genomics
http://ftp.stat.duke.edu/WorkingPapers/05-14.html
In: Bayesian Inference for Gene Expression and Proteomics, (eds. K.A. Do, P. Mueller and M. Vannucci), Cambridge University Press, pp155-176.
(The related comprehensive software package BFRM is also available under the Software link)
Janes KA and Yaffe MB (2006). Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Biol 7, 820-828.
Kumar N, Zaman MH, Kim HD, and Lauffenburger DA (2006). A high-throughput migration assay reveals HER2-mediated cell migration arising from increased directional persistence. Biophys J 91, L32-34.
Mansury Y., Diggory M., and Deisboeck T.S.: Evolutionary game theory in an agent-based brain tumor model: exploring the ‘Genotype-phenotype’ link. J. theor. Biol. 238 (1): 146-156, 2006.Potti, A., Mukherjee, S., Prince, R., Dressman, H. K., Bild, A., Koontz, J., Kratzke, R., Watson, M., Kelley, M., Ginsburg, G., Harpole, D., and Nevins, J. R. (2006). A genomic strategy to refine prognosis in non-small cell lung carcinoma. N. Engl. J. Med. 355, 570-580.
Potti, A., Dressman, H. K., Bild, A., Riedel, R. F., Chan, G., Sayer, R., Cragun, J., Cottrill, H., Gray, J., Marks, J., Kelley, M., Berchuck, A., Petersen, R., Harpole, D., Ginsburg, G. S., Febbo, P., Lancaster, J. M., and Nevins, J. R. (2006). A genomic strategy to guide the use of chemotherapeutic drugs in solid tumors. Nat. Med. 12, 1294-1300.
Seo Y, Yan T, Schupp JE, Yamane K, Radivoyevitch T, Kinsella TJ.The interaction between two radiosensitizers: 5-iododeoxyuridine and caffeine.
Cancer Res. 2006 Jan 1;66(1):490-8.
Turner DP, Cortellino S, Schupp JE, Caretti E, Loh T, Kinsella TJ, Bellacosa A.The DNA N-glycosylase MED1 exhibits preference for halogenated pyrimidines and is involved in the cytotoxicity of 5-iododeoxyuridine. Cancer Res. 2006 Aug 1;66(15):7686-93.
2005
A.H. Bild, G. Yao, J.T. Chang, Q. Wang, A. Potti, D. Chasse, M. Joshi, D. Harpole, J.M. Lancaster, A. Berchuck, J.A. Olson, J.R. Marks, H.K. Dressman, M. West and J.R. Nevins (2005) Oncogenic pathway signatures in human cancers as a guide to targeted therapies
http://www.nature.com/nature/journal/v439/n7074/abs/nature04296.html
Nature, 439, 352-357.
Anderson, S. (and?) Modelling the spatio-temporal dynamics of multi-species host-parasitoid interactions: heterogeneous patterns and ecological implications, (2006). J. Thoe. Biol., Accepted.
Anderson, S. (and?) Mathematical Modelling of Dynamic Adaptive Tumour-Induced Angiogenesis: Clinical Implications and Therapeutic Targeting Strategies, (2006). J. Theo. Biol, Accepted.
Anderson, S. (and?) Mathematical Modelling of Radiotherapy Strategies for Early Breast Cancer, (2005). J. Theo. Biol., Accepted.
Anderson, S. (and?) Mathematical modeling of cancer: the future of prognosis and treatment, (2005). Clin Chim Acta, 357: 173-179
Anderson, S. (and?) An Individual Based Model of Rippling Movement in a Myxobacteria Population, (2005). J. Theo. Biol., 234: 341-349.
Anderson, S. (and?) Mathematical modelling of flow in 2D and 3D vascular networks: Applications to anti-angiogenic and chemotherapeutic drug strategies, (2005). Math. Comput. Modell., 41: 1137-1156.
Anderson, S. (and?) A Hybrid Mathematical Model of Solid Tumour Invasion: The Importance of Cell Adhesion, (2005). IMA Math. App. Med. Biol., 22: 163-186.
(The related cell line gene expression data sets are available under the Data link The related software tools (binary regression prediction) are available under the Software link)
B. Parvin, Q. Yang, G. Fontenay, and M.H. Barcellos-Hoff, "Integrated Imaging Informatics--Computational
Systems Biology," Edited, Elsevier, 2005
http://www.elsevier.com/wps/find/bookdescription.cws_home/707460/description
Hu. H, Yan. X, Huang. Y, Han. J and Zhou X.J. (2005) Mining coherent dense sub-graphs across massive biological networks for functional discovery
http://www.cmb.usc.edu/people/xjzhou/CODENSE.pdf
Bioinformatics (ISMB 2005), 21, i213-i221.
(The related software tools CODENSE and iARRAY ANALYZER are at the Software link)
Jin, V.X., Sun, H., Pohar, T.T., Liyanarachchi, S., Palaniswamy, S.K., Huang, T.H. and Davuluri, R.V. ERTargetDB: an integral information resource of transcription regulation of estrogen receptor target genes. J Mol Endocrinol, 35, 225-230, 2005.
Li L, Shi H, Yiannoutsos C, Huang Tim and Nephew K. Epigenetic hypothesis tests for methylation and acetylation in a triple microarray system. J Computational Biol 12, 370-390, 2005.
M. DeLong, G. Yao, Q. Wang, A. Dobra, E.P. Black, J.T.Chang, A. Bild, M. West, J.R. Nevins and H. Dressman (2005) DIG - A system for gene annotation and functional discover
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/13/2957
Bioinformatics, 21, 2957 - 2959.
(The related software/DIG system is available under the DICBP Sharing link)
Palaniswamy, S.K., Jin, V.X., Sun, H. and Davuluri, R.V. OMGProm: a database of orthologous mammalian gene promoters. Bioinformatics, 21, 835-836, 2005.
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