Grant Number:	5R01CA064364-11 Interpret this number
Primary Investigator:	Newton, Michael
Organization:	University Of Wisconsin-Madison
Project Title:	Statistical Methods for Molecular Cancer Data
Fiscal Year:	2006

DESCRIPTION (provided by applicant): Challenging questions are raised by the measurement of genomic and transcriptional aberrations in cancer cells. In a broad sense, answering these questions will further our understanding of cancer biology, guide more sensitive diagnosis, and ultimately improve therapy. These questions present clear opportunities for the development of statistical methods, since many sources of variation affect the measurements, and these need to be properly accommodated so that relevant biological signals can be detected. The four specific aims of the proposed project react to the demand for better statistical methods to study dependencies in multivariate profiles of genomic aberration and to study patterns of differential gene expression. Motivated by recent innovations in the stochastic modeling of genomic aberrations, the first three specific aims will extend and fully evaluate the model-based instability-selection approach to data analysis. The fourth aim focuses on new methodology to characterize patterns of differential gene expression among multiple groups. The proposed research merges advanced stochastic modeling techniques and tools from statistical computing to provide useful statistical methods for oncologists who study cancer at the molecular level.




Enrichment of melanoma-associated T cells in 6-thioguanine-resistant T cells from metastatic melanoma patients.
Authors: Zuleger C.L. , Newton M.A. , Ma X. , Ong I.M. , Pei Q. , Albertini M.R. .
Source: Melanoma Research, 2019-05-23 00:00:00.0; , .
EPub date: 2019-05-23 00:00:00.0.
PMID: 31135600
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Statistical significance of optical map alignments.
Authors: Sarkar D. , Goldstein S. , Schwartz D.C. , Newton M.A. .
Source: Journal Of Computational Biology : A Journal Of Computational Molecular Cell Biology, 2012 May; 19(5), p. 478-92.
PMID: 22506568
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Longitudinal assessment of colonic tumor fate in mice by computed tomography and optical colonoscopy.
Authors: Durkee B.Y. , Shinki K. , Newton M.A. , Iverson C.E. , Weichert J.P. , Dove W.F. , Halberg R.B. .
Source: Academic Radiology, 2009 Dec; 16(12), p. 1475-82.
PMID: 19896065
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Statistical use of argonaute expression and RISC assembly in microRNA target identification.
Authors: Stanhope S.A. , Sengupta S. , den Boon J. , Ahlquist P. , Newton M.A. .
Source: Plos Computational Biology, 2009 Sep; 5(9), p. e1000516.
PMID: 19779550
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MicroRNA 29c is down-regulated in nasopharyngeal carcinomas, up-regulating mRNAs encoding extracellular matrix proteins.
Authors: Sengupta S. , den Boon J.A. , Chen I.H. , Newton M.A. , Stanhope S.A. , Cheng Y.J. , Chen C.J. , Hildesheim A. , Sugden B. , Ahlquist P. .
Source: Proceedings Of The National Academy Of Sciences Of The United States Of America, 2008-04-15 00:00:00.0; 105(15), p. 5874-8.
EPub date: 2008-04-15 00:00:00.0.
PMID: 18390668
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Fundamental differences in cell cycle deregulation in human papillomavirus-positive and human papillomavirus-negative head/neck and cervical cancers.
Authors: Pyeon D. , Newton M.A. , Lambert P.F. , den Boon J.A. , Sengupta S. , Marsit C.J. , Woodworth C.D. , Connor J.P. , Haugen T.H. , Smith E.M. , et al. .
Source: Cancer Research, 2007-05-15 00:00:00.0; 67(10), p. 4605-19.
PMID: 17510386
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Genes involved in DNA repair and nitrosamine metabolism and those located on chromosome 14q32 are dysregulated in nasopharyngeal carcinoma.
Authors: Dodd L.E. , Sengupta S. , Chen I.H. , den Boon J.A. , Cheng Y.J. , Westra W. , Newton M.A. , Mittl B.F. , McShane L. , Chen C.J. , et al. .
Source: Cancer Epidemiology, Biomarkers & Prevention : A Publication Of The American Association For Cancer Research, Cosponsored By The American Society Of Preventive Oncology, 2006 Nov; 15(11), p. 2216-25.
PMID: 17119049
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A statistical test of the hypothesis that polyclonal intestinal tumors arise by random collision of initiated clones.
Authors: Newton M.A. , Clipson L. , Thliveris A.T. , Halberg R.B. .
Source: Biometrics, 2006 Sep; 62(3), p. 721-7.
PMID: 16984313
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Genome-wide expression profiling reveals EBV-associated inhibition of MHC class I expression in nasopharyngeal carcinoma.
Authors: Sengupta S. , den Boon J.A. , Chen I.H. , Newton M.A. , Dahl D.B. , Chen M. , Cheng Y.J. , Westra W.H. , Chen C.J. , Hildesheim A. , et al. .
Source: Cancer Research, 2006-08-15 00:00:00.0; 66(16), p. 7999-8006.
PMID: 16912175
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Polyclonality Of Familial Murine Adenomas: Analyses Of Mouse Chimeras With Low Tumor Multiplicity Suggest Short-range Interactions
Authors: Thliveris A.T. , Halberg R.B. , Clipson L. , Dove W.F. , Sullivan R. , Washington M.K. , Stanhope S. , Newton M.A. .
Source: Proceedings Of The National Academy Of Sciences Of The United States Of America, 2005-05-10 00:00:00.0; 102(19), p. 6960-5.
PMID: 15870186
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Lack of association between EBV and breast carcinoma.
Authors: Perrigoue J.G. , den Boon J.A. , Friedl A. , Newton M.A. , Ahlquist P. , Sugden B. .
Source: Cancer Epidemiology, Biomarkers & Prevention : A Publication Of The American Association For Cancer Research, Cosponsored By The American Society Of Preventive Oncology, 2005 Apr; 14(4), p. 809-14.
PMID: 15824148
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Genetic determination of susceptibility to estrogen-induced mammary cancer in the ACI rat: mapping of Emca1 and Emca2 to chromosomes 5 and 18.
Authors: Gould K.A. , Tochacek M. , Schaffer B.S. , Reindl T.M. , Murrin C.R. , Lachel C.M. , VanderWoude E.A. , Pennington K.L. , Flood L.A. , Bynote K.K. , et al. .
Source: Genetics, 2004 Dec; 168(4), p. 2113-25.
PMID: 15611180
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Detecting differential gene expression with a semiparametric hierarchical mixture method.
Authors: Newton M.A. , Noueiry A. , Sarkar D. , Ahlquist P. .
Source: Biostatistics (oxford, England), 2004 Apr; 5(2), p. 155-76.
PMID: 15054023
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On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles.
Authors: Kendziorski C.M. , Newton M.A. , Lan H. , Gould M.N. .
Source: Statistics In Medicine, 2003-12-30 00:00:00.0; 22(24), p. 3899-914.
PMID: 14673946
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On Differential Variability Of Expression Ratios: Improving Statistical Inference About Gene Expression Changes From Microarray Data
Authors: Newton M.A. , Kendziorski C.M. , Richmond C.S. , Blattner F.R. , Tsui K.W. .
Source: Journal Of Computational Biology : A Journal Of Computational Molecular Cell Biology, 2001; 8(1), p. 37-52.
PMID: 11339905
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Inferring the location and effect of tumor suppressor genes by instability-selection modeling of allelic-loss data.
Authors: Newton M.A. , Lee Y. .
Source: Biometrics, 2000 Dec; 56(4), p. 1088-97.
PMID: 11129465
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A Resistant Genetic Background Leading To Incomplete Penetrance Of Intestinal Neoplasia And Reduced Loss Of Heterozygosity In Apcmin/+ Mice
Authors: Shoemaker A.R. , Moser A.R. , Midgley C.A. , Clipson L. , Newton M.A. , Dove W.F. .
Source: Proceedings Of The National Academy Of Sciences Of The United States Of America, 1998-09-01 00:00:00.0; 95(18), p. 10826-31.
PMID: 9724789
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On The Statistical Analysis Of Allelic-loss Data
Authors: Newton M.A. , Gould M.N. , Reznikoff C.A. , Haag J.D. .
Source: Statistics In Medicine, 1998-07-15 00:00:00.0; 17(13), p. 1425-45.
PMID: 9695190
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