Biostatistics & Bioinformatics Shared Resource

BBSR Home | Services & Fees | Educational Resources | Publications | Schedule

Publications

2003 2004 2005 2006 2007 2008

2008

Chen J, Higby R, Tian D, Tan D, Johnson MD, Xiao Y, Kellar KJ, Feng S, Shields PG. Toxicological analysis of low-nicotine and nicotine-free cigarettes. Toxicology 249(2-3):194-203, 2008.

Clarke R, Ressom H, Wang A, Xuan J, Liu M, Gehan E, Wang Y. The properties of very high dimensional data spaces: Implications for exploring gene and protein expression data. Nature Reviews Cancer 8:37-49, 2008.

Deeken J, Slack R, Marshall J. Irinotecan and uridine diphosphate glucuronosyltransferase 1A1 pharmacogenetics: To test or not to test, that is the question. Cancer 133(7):1502-1510, 2008.

Fishbein T, Novitskiy G, Mishra L, Matsumoto C, Kaufman S, Goyal S, Shetty K, Johnson L, Lu A, Wang A, Hu F, Kallakury B, Lough D, Zasloff M. Nod 2 expressing bone marrow derived cells appear to regulate epithelial innate immunity of the transplanted human small intestine. Gut 57(3):323-30, 2008.

Graves KD, Huerta E, Cullen J, Kaufman E, Sheppard V, Luta G, Isaacs C, Schwartz MD, Mandelblatt J. Perceived risk of breast cancer among Latinas attending community clinics: Risk comprehension and relationship with mammography adherence. Cancer Causes and Control 19(10):1373-1382, 2008.

Liang W, Wang JH, Chen M, Feng S, Lee MM, Schwartz MD, Pasick RJ, Mandelblatt JS. Developing and validating a measure of Chinese cultural views of health and cancer. Health Education and Behavior 35:361-375, 2008.

O'Neill SC, Luta G, Peshkin BN, Abraham A, Walker L, Tercyak K. Adolescent medical providers' willingness to offer genetic susceptibility testing: Influence of disease, lifestyle and other factors. In press: Journal of Pediatric Psychology, 2008.

Ressom HW, Varghese RS, Goldman L, An Y, Loffredo CA, bdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Drake SK, Goldman R. (2008) Analysis of MALDI-TOF mass spectrometry data for discovery of peptide and glycan biomarkers of hepatocellular carcinoma. Journal of Proteome Research 7(2):603-610, 2008.

Ressom HW, Varghese RS, Zhang Z, Xuan J, Clarke R. Classification algorithms for phenotype prediction in genomics and proteomics. Front. Biosci. 13:691-708, 2008.

Ressom HW, Varghese RS, Goldman L, Loffredo CA, bdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Goldman R. Analysis of MALDI-TOF mass spectrometry data for detection of glycan biomarkers. In: Proceedings of Pacific Symposium in Biocomputing, pp. 216-227, 2008.

Saha DT, Davidson BJ, Wang A, Pollock AJ, Orden RA, Goldman R. Quantification of DNA repair capacity in whole blood of patients with head and neck cancer and healthy donors by comet assay. Mutat Res 650(1):55-62, 2008.

Sheppard VB, Wang J, Yi B, Harrison TM, Feng S, Huerta EE, Mandelblatt J, Latin American Cancer Research Coalition. Are healthcare relationships important for mammography adherence in Latinas? Journal of General Internal Medicine 23(12):2024-30, 2008.

Shetty K, Hussain M, Nei L, KR Reddy, ASF Lok. Prevalence and significance of occult hepatitis B in a liver transplant population with chronic hepatitis C. Liver Transplantation 14: 534- 540, 2008.

Solomon DA, Kim JS, Jenkins S, Ressom H, Huang M, Coppa N, Mabanta L, Bigner D, Yan H, Jean W, Waldman T. Identification of p18 INK4c as a tumor suppressor gene in glioblastoma multiforme. Cancer Research 68(8):2564-2569, 2008.

Solomon DA, Kim JS, Cronin JC, Sibenaller Z, Ryken T, Rosenberg SA, Ressom H, Jean W, Bigner D, Yan H, Samuels Y, Waldman T. Mutational Inactivation of PTPRD in Glioblastoma Multiforme and Malignant Melanoma. Cancer Res 68:10300-10306, 2008.

Song J, Liu H, Ressom H, Tiwari S, Ecelbarger CM: Chronic rosiglitazone therapy normalizes expression of ACE1, SCD1 and other genes in the kidney of obese Zucker rats as determined by microarray analysis. Experimental and Clinical Endocrinology and Diabetes 116(6):315-325, 2008.

Tan D, Goerlitz DS, Dumitrescu R, Seillier-Moiseiwitsch F, Spernak SM, Orden RA, Cheng J, Goldman R, Shield PG. Associations between Cigarette Smoking and Mitochondrial DNA Abnormalities in Buccal Cells. Carcinogenesis 29:1170-1177, 2008.

Tang Y, Kitisin K, Jogunoori W, Li C, Deng CX, Mueller SC, Ressom H, Rashid A, He AR, Mendelson JS, Jessup JM, Shetty K, Zasloff M, Mishra B, Reddy EP, Johnson L, Mishra L. Progenitor/stem cells give rise to liver cancer due to aberrant TGF-beta and IL-6 signaling. Proc Natl Acad Sci U S A 105(7):2445-2450, 2008.

Amundson SA, Do KT, Vinikoor LC, Lee RA, Koch-Paiz CA, Ahn J, Reimers M, Chen Y, Scudiero DA, Weinstein JN, Trent JM, Bittner ML, Meltzer PS, Fornace AJ, Jr. Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen. Cancer Res 68(2):415-424, 2008.

Chen l, Eang C, Shih M, Wang T, Zhang Z, Clarke R, Hoffman E, Wang Y, Xuan J. Biomarker identification by knowledge driven multilevel ICA and motif analysis. Int J Data Mining Bioinformatics,2008.

Gong T, Xuan J, Wang C, Li H, Hoffman E, Clarke R, Wang Y. Gene module identification from microarray data using nonnegative independent component analysis. Gene Reg Sys Biol 1:349-363, 2008.

Xuan J, Wang Y, Hoffman E, Clarke R. Cross phenotype normalization of microarray data. Front Biosci, in press, 2008.

Yu H, Gong X, Luo X, Han W, Hong G, Singh B, Tang CK. Co-expression of EGFRvIII with ErbB-2 enhances tumorigenesis: EGFRvIII mediated constitutively activated and sustained signaling pathways, whereas EGF-induced a transient effect on EGFR-mediated signaling pathways. Cancer Biol Ther 7(11), 2008.

Chu H, Nie L, Zhu M. On estimation of bivariate biomarkers with known detection limits. Environmetrics 19:301-317, 2008.

Ahn C, Seillier-Moiseiwitsch F, Koch GG. Predictive tests for linked changes. Statistics in Medicine 27:4790-4804, 2008.

Bebu I, Mathew T. Comparing the means and variances of a bivariate lognormal distribution. Statistics in Medicine 27:2684-2696, 2008.

Bebu I, Mathew T. Confidence intervals for limited moments and truncated moments in normal and lognormal models. In press: Statistics and Probability Letters, 2008.

Clarke R, Ressom H, Wang A, Xuan J, Liu M, Gehan E, Wang, Y. The properties of very high dimensional data spaces: Implications for exploring gene and protein expression data. Nature Reviews Cancer 8:37-49, 2008.

Last M, Luta G, Orso A, Porter A, Young S. Pooled ANOVA. In press: Computational Statistics and Data Analysis, 52(12): 5215-5228, 2008.

Nie L, Chu H, Korostyshevskiy V. Bias reduction for nonparametric correlation coefficients under the bivariate normal copula assumption with known detection limits. The Canadian Journal of Statistics 36(3):427-442, 2008.

Wang A. A note on checking the Clayton model assumption based on left truncated bivariate data. Statistics and Probability Letters 78:1168-1173, 2008.

Wang A Goodness-of-fit tests for Archimedean copula models. In press: Statistica Sinica, 2008.

Wang A, Oakes D. Some properties of the Kendall distribution in bivariate Archimedean copula models under censoring. Statistics and Probability Letters 78(16):2578-2583, 2008.

Zhang L, Dmitrienko A, Luta G. Sample size calculations in thorough QT studies. Journal of Biopharmaceutical Statistics 18:468-482, 2008.

Arighi C, Liu H, Natale D, Barker W, Drabkin H, Hu ZZ, Blake J, Smith B, Wu C. TGF-beta signaling proteins and the protein ontology. In: Proceedings of Bio-Ontologies 2008, Lord P, Shah N, Sansone S-A, Corckerill M (editors), 2008.

Bebu I, Seilllier-Moiseiwitsch F, Liu H. Analysis of microarray titration experiments. In: Proceedings of BIOCOMP 2008, Arabnia HR (editor), pp. 942-946, 2008.

Hu ZZ, Cohen KB, Hirschman L, Valencia A, Liu H, Wu C. iProLINK: A framework for linking text mining with ontology and systems biology. In: Proceedings of Bioinformatics and Biomedicine (BIBM), Chen X-W, Hu X, Kim S (editors), pp. 467-72, 2008.

Kestler HA, Muller A, Kraus JM, Buchholz M, Gress TM, Liu H, Kane DW, Zeeberg BR, Weinstein JN VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinformatics 9(1):67, 2008.

Koru AG, Zhang D, El Emam K, Liu H. An investigation into the functional form of size-defect relationship for software modules. In press: IEEE Trans. Software Eng., 2008.

Koru AG, El Emam K, Zhang D, Liu H, Mathew D. Theory of relative defect proneness. Empirical Software Engineering, 13 (5): 473-498, 2008.

Liu H, Li X, Yoon V, Clarke R. Annotating breast cancer microarray samples using ontologies. In: Proceedings of American Medical Informatics Association (AMIA), Suermondt J (editor) pp. 414-418, 2008.

Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, Liu H, Weinstein JN. SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. BMC Bioinformatics 9:313, 2008.

Safavi H, Correa N, Xiong W, Roy A, Adali T, Korostyshevskiy V, Whisnant C, Seillier-Moiseiwitsch F. Independent component analysis of 2D electrophoresis gels. Electrophoresis 29:4017-4026, 2008.

Torii M, Hu ZZ, Wu C, Liu H. BioTagger-GM: A biological named entity tagging system. Journal of American Medical Informatics Association, 16(2):247-255, 2008.

Torii M, Liu H. At-least-N voting over biomedical named entity recognition systems. In press: Proceedings of BioLink : Linking Literature, Information and Knowledge for Biology, Toronto, Ontario, 2008.

Torii M, Liu H. Feature subsetting for biomedical document classification. In: Proceedings of the Workshop on Intelligent Data Analysis in BioMedicine and Pharmacology (IDAMAP), Holmes J, Tucker A (editors), pp. 34-38, 2008.

Xu G, Niu Z, Uetz P, Liu, H. Comparison of document classification for protein-protein interaction document retrieval. In: Bioinformatics and Biomedicine Workshops (BHI), Chen X-W, Hu X, Kim S (editors), pp. 83-90, 2008.

Xu G, Yin L, Torii M, Niu Z, Wu C, Hu ZZ, Liu H. Document classification for mining host pathogen protein-protein interactions. In: Proceedings of Bioinformatics and Biomedicine (BIBM) 2008, Chen X-W, Hu X, Kim S (editors), pp. 461-66, 2008.

Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Fundel K, Leaman R, Hakenberg J, Sun C, Liu HH, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, Hirschman L. Overview of BioCreative II gene normalization. Genome Biology 9 Suppl 2:S3, 2008.

Smith L, Tanabe LK, Ando RJ, Kuo CJ, Chung IF, Hsu CN, Lin YS, Klinger R, Friedrich CM, Ganchev K, Torii M, Liu H, Haddow B, Struble CA, Povinelli RJ, Vlachos A, Baumgartner WA Jr, Hunter L, Carpenter B, Tsai RT, Dai HJ, Liu F, Chen Y, Sun C, Katrenko S, Adriaans P, Blaschke C, Torres R, Neves M, Nakov P, Divoli A, Maña-López M, Mata J, Wilbur WJ. Overview of BioCreative II gene mention recognition. Genome Biology 9 Suppl 2:S2, 2008.

Ressom H, Varghese RS, Zhang Z, Xuan J, Clarke R. Classification algorithms for phenotype prediction in genomics and proteomics. Front Biosci 13:691-708, 2008.

Zhang Y, Xuan J, los Reyes BG, Clarke R, Ressom H. Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data. BMC Bioinformatics 9:203, 2008.

Zhang Y, Xuan J, de Los Reyes BG, Clarke R, Ressom H. Network motif-based identification of breast cancer susceptibility genes. Conference Proceedings IEEE Engineering in Medicine and Biology Society 1:5696-9, 2008.

Befekadu GK, Tadesse MG, Hathout Y, Ressom H. Multi-class alignment of LC-MS data using probabilistic-based mixture regression models. Conference Proceedings IEEE Engineering in Medicine and Biological Society1:4094-4097, 2008.

Ressom H, Varghese RS, Goldman L, Loffredo C, Abdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Goldman R. Analysis of MALDI-TOF mass spectrometry data for detection of glycan biomarkers. Pacific Symposium on Biocomputing 216-227, 2008.

Ressom H, Varghese RS, Goldman L, An Y, Loffredo C, Abdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Drake SK, Goldman R. Analysis of MALDI-TOF mass spectrometry data for discovery of peptide and glycan biomarkers of hepatocellular carcinoma. Journal of Proteome Research 7(2):603-610, 2008.

Varghese RS, Goldman L, An Y, Loffredo C, Abdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Drake SK, Goldman R, Ressom H. Integrated peptide and glycan biomarker discovery using MALDI-TOF mass spectrometry. Conference Proceedings IEEE Engineering in Medical and Biological Soc 1:3791-4, 2008.