Biostatistics & Bioinformatics Shared Resource

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Collins BT, Erickson K, Reichner CA, Collins SP, Gagnon GJ, Dieterich S, McRae DA, Zhang Y, Yousefi S, Levy E, Chang T, Jamis-Dow C, Banovac F, Anderson ED. Radical stereotactic radiosurgery with real-time tumor motion tracking in the treatment of small peripheral lung tumors. Radiation Oncology 2:39, 2007.

Gagnon GJ, Henderson FC, Gehan E, Sanford D, Collins BT, Moulds JC, Dritschilo A. Cyberknife radiosurgery for breast cancer spine metastases: a matched-pair analysis. Cancer 110(8):1796-1802, 2007.

Goldman R, Ressom HW, Abdel-Hamid M, Goldman L, Wang A, Varghese RS, An Y, Loffredo CA, Drake SK, Eissa SA, Gouda I, Ezzat S, Seillier-Moiseiwitsch F. Candidate markers for the detection of hepatocellular carcinoma in low molecular weight fraction of serum. Carcinogenesis 28(10):2149-53, 2007.

Gomez BP, Riggins RB, Shajahan AN, Klimach U, Wang A, Crawford AC, Zhu Y, Zwart A, Wang M, Clarke R. Human X-box binding protein-1 confers both estrogen independence and antiestrogen resistance in breast cancer cell lines. FASEB J 21(14):4013-4027, 2007.

Kim JS, Lee C, Bonifant CL, Ressom H, Waldman T. Activation of p53-dependent growth suppression in human cells by mutations in PTEN or PIK3CA. Molecular Cell Biolology, 27(2):662-677, 2007.

Lehnes K, Winder AD, Alfonso C, Kasid N, Simoneaux M, Summe H, Morgan E, Iann M, Duncan J, Eagan M, Tavaluc R, Evans CH, Russell R, Wang A, Hu F, Stoica A. The effect of estradiol on in vivo tumorigenesis is modulated by the human epidermal growth factor receptor 2/phosphatidylinositol 3-kinase/Akt1 pathway. Endocrinology 148(3):1171-1180, 2007.

Marshall JL, Gehan E. The development of novel agents for the treatment of colorectal cancer. Clinical Advances in Hematology and Oncology 5(3):167-172, 2007.

Martin MB, Reiter R, Johnson M, Shah MS, Iann MC, Singh B, Richards JK, Wang A, Stoica A. Effects of tobacco smoke condensate on estrogen. Endocrinology 148(10):4676-4686, 2007.

Saha D, Davidson B, Wang A, Pollock A, Orden RA, Goldman R. Quantification of DNA repair capacity in whole blood of patients with head and neck cancer and Hhealthy donors by comet assay. Mutation Research 28:2149-2153, 2007.

Shajahan AN, Wang A, Decker M, Minshall RD, Liu MC, Clarke R. Caveolin-1 tyrosine phosphorylation enhances paclitaxel-mediated cytotoxicity 3. J Biol Chem 282(8):5934-5943, 2007.

White AM, Banovac F, Yousefi S, Slack R, Spies JB. Uterine fibroid embolization: The utility of aortography in detecting ovarian artery collateral supply. Radiology 244(1):291-298, 2007.

Xu J, Gao M, Fan S, Meng Q, Goldberg ID, Abounader R, Ressom H, Laterra JJ, Rosen EM. Effect of Akt inhibition on scatter factor-regulated gene expression in DU-145 human prostate cancer cells. Oncogene 26(20):2925-38, 2007.

Casimiro M, Rodriguez O, Pootrakul L, Fricke S, Ostrowski M, Hung MC, Rabbani S, Datar R, Cote R, Pestell R, Albanese C. ErbB-2 induces the cyclin D1 gene in prostate epithelial Cells in vitro and in vivo. Cancer Research 7(9):4364-72, 2007.

Espinoza LA, Smulson ME, Chen Z. Prolonged poly(ADP-ribose) polymerase-1 activity regulates JP-8-induced sustained cytokine expression in alveolar macrophages. Free Radic Biol Med 42:1430-1440, 2007.

Ganesan N, Kato S, Bowman ED, Shields PG. N-7-Alkyl-2'-Deoxyguanosine as surrogate biomarkers for N-nitrosamine exposure in human lung. Int. J. Canc. Prev. 2(4):265-277, 2007.

Hilakivi-Clarke L. Nutritional modulation of terminal end buds: its relevance to breast cancer prevention. Curr Cancer Drug Targets 7(5):465-474, 2007.

Khan G, Penttinen P, Cabanes A, Foxworth A, Chezek A, Mastropole K, Yu B, Smeds A, Halttunen T, Good C, Makela S, Hilakivi-Clarke L. Maternal flaxseed diet during pregnancy or lactation increases female rat offspring's susceptibility to carcinogen-induced mammary tumorigenesis. Reprod Toxicol 23(3):397-406, 2007.

Ma Y, Hu C, Riegel AT, Fan S, Rosen EM. Growth factor signaling pathways modulate BRCA1 repression of estrogen receptor-alpha activity. Mol Endocrinol 21(8):1905-1923, 2007.

Nie L. Convergence rate of MLE in generalized linear and nonlinear mixed-effects models: Theory and applications. Journal of Statistical Planning and Inference 137:1787-1804, 2007.

Wang A. The analysis of bivariate truncated data using the Clayton copula model. The International Journal of Biostatistics 3:1, Article 8, 2007.

Nie L. Optimal designs for linear mixed-effects models. Journal of Mathematical Science 1:1-15, 2007.

Ahn C, Koch GG, Paynter L, Preisser J, Seillier-Moiseiwitsch F. Log-linear models for mutations in the HIV genome. Journal of Statistical Planning and Inference 137:3227-3239, 2007.

Karnoub M, Sen PK, Seillier-Moiseiwitsch F. Are there correlated genomic substitutions? In: Advances in Statistical Methods for the Health Sciences - Applications to Cancer and AIDS Studies, Genome Sequence Analysis, and Survival Analysis, Auget J-L, Balkrishnan N, Mesbah M, Molenberghs G (editors), Statistics for Industry and Technology, pp. 491-515, Birkhäuser, Boston, 2007.

Li R, Nie L. A new estimation procedure for partially nonlinear model via a mixed effects approach. Canadian Journal of Statistics 35:399-411, 2007.

Nie L, Wu G, Culley D, Scholten J, Zhang W. (2007) Integrative analysis of transcriptomic and proteomic data: Challenges, solutions and applications. Critical Reviews in Biotechnology 27(2):63-75, 2007.

Ressom H, Varghese RS, Drake SK, Hortin GL, Abdel-Hamid M, Loffredo C, Goldman R. Peak selection from MALDI-TOF mass spectra using ant colony optimization. Bioinformatics 23(5): 619-626, 2007.

Scholten JC, Culley DE, Nie L, Munn JK, Chow L, Broockman J, Zhang W. Development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and Its responses to oxidative stress. Biochemical and Biophysical Research Communication 358(2):571-577, 2007.

Wu G, Nie L, Freeland S. The effects of differential gene expression on coding sequence features: Analysis by one-way ANOVA. Biochemical and Biophysical Research Communication 358(4):1108-1113, 2007.

Zhang W, Culley D, Nie L, Scholten J. Comparative transcriptome analysis of Desulfovibrio Vulgaris grown in planktonic culture and mature biofilm on a steel surface. Applied Microbiology and Biotechnology 76:447-457, 2007.

Bebu I, Seillier-Moiseiwitsch F, Liu H. Semiparametric RMA Background Correction for Oligonucleotide Arrays. In: Proceedings of the IEEE 7th International Conference on Bioinformatics and Bioengineering (BIBE), pp. 1404-1408, Boston, Massachusetts, 2007.

Cheng C, Yun KY, Ressom H, Mohanty B, Bajic VB, Jia Y, Yun SJ, de los Reyes BG. Reactive oxygen species trigger a regulatory moduleiInvolved in the early responses of rice seedlings to cold stress. BMC Genomics 8:175, 2007.

Li X. Knowledge based, data driven and object-relational workflow management for microarray processing pipeline. In: Proceedings of 2007 International Conference on Cybernetics and Information Technologies, Systems, and Applications, Volume III, International Institute of Informatics and Systemic, pp.204-209, 2007.

Kahn AB, Ryan MC, Liu H, Zeeberg BR, Jamison DC, Weinstein JN. SpliceMiner: A high-throughput database implementation of the NCBI evidence viewer for microarray splice variant analysis. BMC Bioinformatics 8(1):75, 2007.

Tisnado DM, Adams JL, Liu H, Damberg CL, Hu A, Chen WP, Kahn KL. Does concordance between data sources vary by medical organization type? Am J Manag Care 13(6 Part 1):289-296, 2007.

Koru AG, Zhang D, Liu H. Effect of coupling on defect proneness in evolutionary open-source software development. In: Proceedings of Open Source Software (OSS, pp.271-276, 2007.

Koru AG, Zhang D, Liu H. Modeling the effect of size on defect proneness for open-source software.In: Proceeding of Predictor Models in Software Engineering (PROMISE), pp.115-124, 2007.

Liu H, Torii M. Mapping gene/protein names in free text to biomedical databases. In: Proceedings of the Seventh IEEE International Conference on Data Mining Workshops (ICDMW), pp.101-106, 2007.

Liu H, Torii M, Hu ZZ, Wu C. Gene mention and gene normalization based on machine learning and online resources. In: Proceedings of the Second BioCreative Challenge Evaluation Workshop, pp.135-140, 2007.

Liu H, Zeeberg BR, Qu G, Koru AG, Ferrucci A, Kahn A, Ryan MC, Nuhanovic A, Munson PJ, Reinhold WC, Kane DW, Weinstein JN. AffyProbeMiner: A web resource for computing or retrieving accurately redefined Affymetrix probe sets. Bioinformatics 23(18):2385-2390, 2007.

Musavi MT, Ressom H, Srirangam S, Natarajan P, Virnstein RW, Morris LJ, Tweedale W. Neural network-based light attenuation model for monitoring seagrass population in the Indian River lagoon. Journal of Intelligent Information Systems 29:63-77, 2007.

Natale DA, Arighi CN, Barker WC, Blake J, Chang TC, Hu ZZ, Liu H, Smith B, Wu C. Framework for a protein ontology. BMC Bioinformatics 8 Suppl 9:S1, 2007.

Torii M, Hu ZZ, Song M, Wu C, Liu H. A comparison study on algorithms of detecting long forms for short forms in biomedical text. BMC Bioinformatics 8 Suppl 9:S5, 2007.

Torii M, Liu H. Semantic category assignment for long forms extracted from text. In: Proceedings of the American Medical Informatics Association (AMIA), pp.731-735, 2007.

Torii M, Liu H. Classifier ensemble for biomedical document retrieval. In: Proceedings of the 2nd International Symposium on Languages in Biology and Medicine, Volume 319, Paper 5, 2007.