Biostatistics & Bioinformatics Shared Resource

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Publications

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2006

Artym VV, Zhang Y, Seillier-Moiseiwitsch F, Yamada KM, Mueller SC. Dynamic interactions of Cortactin and Membrane Type 1 Matrix Metalloproteinase at invadopodia: Defining the stages of invadopodia formation and function. Cancer Research 66:3034-3043, 2006.

Bowden ET, Onikoyi E, Slack R, Myoui A, Yoneda T, Yamada KM, Mueller S. Co-localization of cortactin and phosphotyrosine identifies active invadopodia in human breast cancer cells. Experimental Cell Research 312(8):1240-53,2006.

Collins S, Coppa N, Zhang Y, Collins B, McRae D, Jean W. Cyberknife radiosurgery in the treatment of complex skull base tumors: analysis of treatment planning parameters. Radiation Oncology, 1:46, 2006.

Lazaro AM, Steiner NK, Cao K, Slack R, Chen DS, Xiao Y, Beduhn E, Ng J, Hartzman RJ, Hurley CK. Searching for HLA-DRB1*1206 in volunteer marrow donors in four US population groups. Tissue Antigens 68(5):439-441, 2006.

Mandelblatt J, Kreling B, Figeuriedo M, Feng S. What is the impact of shared decision making on treatment and outcomes for older women with breast cancer? J Clin Oncol 2006 Sep 18 [Epub ahead of print].

Orvisky E, Drake SK, Martin BM, Ressom H, Varghese RS, Saha D, Hortin GL, Loffredo CA, Goldman R. Enrichment of low molecular weight fraction of serum for mass spectrometric analysis of peptides associated with hepatocellular carcinoma. Proteomics 6(9):2895-2902, 2006.

Sarfaty M, Feng S. Choice of screening modality in a colorectal cancer education and screening program for the uninsured. Journal of Cancer Education 21(1):43-49, 2006.

Trock B, Hilakivi-Clarke L, Clarke R. Meta-analysis of soy intake and breast cancer risk. J Natl Cancer Inst 98(7):459-471, 2006.

Wang J, Liang W, Cullen J, Chen MY, Feng S, Yi B, Mandelblatt J, Schwarz M. Influence of culture and cancer worry on colorectal cancer screening among older Chinese-American women. Ethnicity and Disease, 16(2):401-411, 2006.

Zhu Y, Singh B, Hewitt S, Liu A, Gomez B, Wang A, Clarke R. Expression patterns among proteins associated with endocrine responsiveness in breast cancer: Interferon regulatory factor-1, human X-box binding protein-1, nuclear factor kappa B, nucleophosmin, estrogen receptor-alpha, and progesterone receptor. International Journal of Oncology 28(1):67-76, 2006.

Zhu Y, Wang A, Liu MC, Zwart A, Lee RY, Gallagher A, Wang Y, Miller WR, Dixon JM, Clarke R. Estrogen receptor alpha (ER) positive breast tumors and breast cancer cell lines share similarities in their transcriptome data structures. International Journal of Oncology 29: 1581-1589, 2006.

Di Giovanni S, Knights CD, Rao M, Yakovlev A, Beers J, Catania J, Avantaggiati ML, Faden AI. The tumor suppressor protein p53 is required for neurite outgrowth and axon regeneration. EMBO J 25:4084-4096, 2006.

Knights CD, Catania J, Di Giovanni S, Muratoglu S, Perez R, Swartzbeck A, Quong AA, Zhang X, Beerman T, Pestell RG, Avantaggiati ML. Distinct p53 acetylation cassettes differentially influence gene-expression patterns and cell fate. J Cell Biol 173(4):533-544, 2006.

Chu H, Nie L, Cole SR. Sample size and statistical power assessing intervention effects in the context of mixture distributions with detection limits. Statistics in Medicine 15(25):2647-5, 2006.

Chu H, Nie L. A note on comparing exposure data to a regulatory limit in the presence of unexposed and a limit of detection. Biomedical Journal 47(6):880-88, 2006.

Nie L, Wu G, Zhang W. Correlation between mrna and protein abundance in Desulfovibrio vulgaris: A multiple regression to identify sources of variations. Biochemical and Biophysical Research Communications 339:603-610, 2006.

Nie L, Yang M. Strong consistency of MLE in nonlinear mixed-effects models with large cluster size. Sankhya 67(4):736-763, 2006.

Nie L, Chu H, Cole S. A general approach for sample size and statistical power calculation using a mixture model in the presence of detection limits, Contemporary Clinical Trials 27(5):483-491, 2006.

Potra FA, Liu X, Seillier-Moiseiwitsch F, Roy A, Hang Y, Marten MR, Raman B, Whisnant C. Protein image alignment via piecewise affine transformations, Journal of Computational Biology 13:614-630, 2006.

Nie L, Wu G, Brockman FJ, Zhang W. Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: Zero-inflated Poisson regression models to predict abundance for undetected proteins. Bioinformatics 22(13):1641-7, 2006.

Nie L, Wu G, Zhang W. Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis. Genetics 174(4):2229-2243,2006.

Wu G, Nie L, Zhang W. Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence. Antonie Van Leeuwenhoek 89(1):135-146, 2006.

Zhang W, Culley DE, Nie L, Brockman FJ. DNA microarray analysis of anaerobic Methanosarcina barkeri reveals responses to heat shock and air exposure. J Ind Microbiol Biotechnol 33(9):784-790, 2006.

Zhang W, Culley DE, Gritsenko MA, Moore RJ, Nie L, Scholten JC, Petritis K, Strittmatter EF, Camp DG, Smith RD, Brockman FJ. LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris. Biochem Biophys Res Commun 349(4):1412-1419, 2006.

Zhang W, Gritsenko MA, Moore RJ, Culley DE, Nie L, Petritis K, Strittmatter EF, Camp DG, Smith RD, Brockman FJ. A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry. Proteomics 6(15):4286-4299, 2006.

Liu H, Hu ZZ, Torii M, Wu C, and Friedman C. Quantitative assessment of dictionary-based protein named entity tagging. Journal of American Medical Informatics Association 13:497-507, 2006.

Xu H, Markatou M, Dimova R, Liu H, and Friedman C. Machine learning and word sense disambiguation in the biomedical domain: Design and evaluation issues. BMC Bioinformatics, online July 5, 2006.

Liu H, Hu ZZ, Wu C. BioThesaurus: a thesaurus of gene and protein names. Bioinformatics 22(1):103-5, 2006.

Ressom H, Zhang Y, Xuan J, Wang Y, Clarke R. Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence. IEEE Symp Compl Intel Bioinf Comput Biol 435-442, 2006.

Ressom H, Zhang Y, Xuan J, Wang Y, Clarke R. Inferring network interactions using recurrent neural networks and swarm intelligence. Conf Proc IEEE Eng Med Biol Soc 1:4241-4244, 2006.

Ressom H, Varghese RS, Orvisky E, Drake SK, Hortin GL, bdel-Hamid M, Loffredo C, Goldman R. Ant colony optimization for biomarker identification from maldi-tof mass spectra. Conf Proc IEEE Eng Med Biol Soc 1:4560-4563, 2006.