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Publications

Books

Genomic and Molecular Neuro-Oncology. Zhang W and Fuller GN, Jones and Bartlett Publishers, 2003.

Microarray Quality Control. Zhang W, Shmulevich I, Astola J. Wiley, 2004.

Genomic and Molecular Neuro-Oncology. Zhang W and Fuller GN, eds. Translated into Chinese by Pu P et al. Tianjin Science and Technology Translation Publishing Company, 2005.

Computational and Statistical Approaches to Genomics. Second Edition. Zhang W and Shmulevich I. Springer, 2006.

Publications

Kobayashi T, Yamaguchi M, Kim S, Morikawa J, Ogawa S, Ueno S, Suh E, Dougherty E, Shmulevich I, Shiku H, Zhang W. Microarray reveals differences in both tumor and vascular specific gene expression in de novo CD5+ and CD5- diffuse large B-cell lymphomas. Cancer Res. 63:60-66, 2003.

Wang H, Wang H, Shen W, Huang H, Hu L, Ramdas L, Zhou Y, Liao WSL, Fuller GN, Zhang W. Insulin-like Growth Factor Binding Protein 2 Enhances Glioblastoma Invasion via Activation of Invasion Enhancing Genes. Cancer Res. 63:4315-4321, 2003.

Zhang W, Ramdas L, Shen WP, Song WS, Hu L, Hamilton SR. Apoptotic Response to 5-Fluorouracil Treatment is Mediated by Reduced Polyamines, Non-Autocrine Fas Ligand and Induced Tumor Necrosis Factor Receptor 2. Cancer Biol Ther. 2(5):572-8, 2003.

Hao X, Sun B, Hu L, Ladhdesmaki H, Dunmire V, Feng Y, Zhang SW, Wang H, Wu C, Wang H, Fuller GN, Symmans WF, Shmulevich I, Zhang W. Distinctive gene and protein expression between primary breast cancers and their lymph node metastases revealed by combined cDNA microarray and tissue microarray. Cancer Published on line in Feb 2004. 100:1110-22, 2004.

Song SW, Fuller GN, Khan A, Kong S, Shen W, Taylor E, Ramdas L, Lang F, Zhang W. IIp45, a novel IGFBP-2 binding protein, inhibits glioma cell invasion. Proc Natl Acad Sci USA (Track II) 100:13970-75, 2003.

Shmulevich I, Gluhovsky I, Hashimoto RF, Dougherty ER, Zhang W. Steady-state analysis of genetic regulatory networks modeled by probabilistic Boolean networks. Comparative and Functional Genomics 4:601-608, 2003

Hashimoto RF, Kim S, Shmulevich I, Zhang W, Bittner ML, Dougherty ER. A directed-graph algorithm to grow genetic regulatory subnetworks from seed genes based on strength of connection. Bioinformatics 20:1241-7, 2004.

Raza SM, Fuller GR, Rhee CH, Huang S, Hess KR, Zhang W and Sawaya R. Identification of necrosis-associated genes in glioblastoma by cDNA microarray analysis. Clin Cancer Res 10:212-221, 2004.

Ramdas L, Cogdell DE, Jia YJ, Taylor E, Dunmire V, Hu L, Hamilton SR and Zhang W. Optimization of Signal Intensities for Low Expressing Genes on Oligonucleotide Microarrays. BMC Genomics 5:35, 2004.

Mircean C, Shmulevich I, Cogdell D, Choi W, Jia Y, Tabus I, Hamilton SR, Zhang W. Robust estimation of protein expression ratios with lysate microarray technology. Bioinformatics 21(9):1935-42.

Symmans WF, Fiterman DJ, S K Anderson, M Ayers, R Rouzier, V Dunmire, J Stec, V Valero, N Sneige, C Albarracin, Y Wu, J S Ross, P Wagner, R L Theriault, B Arun, H Kuerer, K R Hess, W Zhang, G N Hortobagyi, L Pusztai. A single-gene biomarker identifies breast cancers associated with immature cell type and short duration of prior breastfeeding. Endocrine Related Cancer 12: 1059-1069, 2005.

Chen LL, Trent JC, Wu EF, Fuller GN, Ramdas L, Zhang W, Raymond AK, Prieto VG, Oyedeji CO, Hunt KK, Pollock RE, Feig BW, Hayes K, Choi H, Macapinlac HA, Hittleman W, Velasco MA, Patel S, Burgess MA, Benjamin RS, Frazier ML. A missense mutation in KIT kinase domain I correlates with imatinib resistance in gastrointestinal stromal tumors. Cancer Res 64:5913-5919, 2004.

Choi W, Gerner E, Ramdas L., Dupart J, Carew J., Huang P, Zhang W, Hamilton SR. Combination of 5-fluouracil with diethylnorspermine markedly activates SSAT expression, depletes polyamines and synergistically induces apoptosis in colon cancer cells. J. Biol Chem. 280(5):3295-304, 2005.

Song SW, Fuller GN, Zheng H, Zhang W. Inactivation of the invasion inhibitory protein gene IIp45 in gliomas by alternative splicing. Cancer Res. 65:3562-7, 2005.

Kim J-H, Tuziak T, Hu L, Gold D, Wang Z, Bondaruk J, Fuller GN, Dinney C, Grossman HB, Baggerly K, Zhang W, Czerniak B. Alterations in Transcription Clusters of Key Cellular Functions Underlie Development of Bladder Cancer from in situ Preneoplastic Conditions along Papillary and Non-papillary Pathways. Lab Investigation. 85:532-49, 2005.

Lahdesmaki H, Shmulevich I, Dunmire V, Zhang W. In silico microdissection of microarray data from mixed cell populations. BMC Bioinformatics. 6(1):54, 2005.

Hu J, Kapoor M, Zhang W, Hamilton SR, Coombes K. Analysis of dose-response effects on gene expression data with comparison of microarray platforms. Bioinformatics 1;21(17):3524-9, 2005.

Tabus I, Hategan A, Mircean C, Rissanen J, Shmulevich I, Zhang W, Astola J. Nonlinear modeling of protein expression in protein arrays. IEEE Transactions on Signal Processing. 54:2394-2407, 2006.

McDonald JM, Dunlap S, Cogdell D, Dumnire V, Wei Q, Starzinski-Powitz A, Sawaya R, Bruner J, Fuller GN, Aldape K, Zhang W. Shrew 1 gene, commonly deleted on chromosome 1p36 in oligodendrogliomas, functions to inhibit cell adhesion. Cancer Bio and Therapy. 5(3):300-4, 2006. Cover art of the March issue.

Jiang R, Mircean C, Shmulevich I, Cogdell D, Jia Y, Aldape K, Sawaya R, Bruner J, Fuller GN, Zhang W. Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays. Proteomics 6:2964-2971, 2006. (featured on the cover of April issue).

Choi W, Proctor L, Xia Q, Feng Y, Gerner EW, Chiao PJ, Hamilton SR, Zhang W. Inactivation of IkB contributes to transcriptional activation of spermidine/spermine N(1)-acetyltransferase. Mol Carcinogenesis. 45(9):685-93, 2006.

Wang G, Hu L, Fuller GN, Zhang W. An interaction between insulin-like growth factor binding protein 2 and integrin a5 is essential for IGFBP2-induced cell mobility J. Biol. Chem. 281(20):14085-91. 2006.

Trent JC, Ramdas L, Dupart JJ, Hunt K, Oyedeji C, Taylor EE, Hu L, Chen LL, Benjamin RS, Pollock R, Zhang W. Imatinib Mesylate Induces Expression of Insulin-like Growth Factor Binding Protein 3 in Gastrointestinal Stromal Tumor. Cancer (in press).


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