M A Newton

Summary

Affiliation: University of Wisconsin
Country: USA

Publications

  1. pmc A conditional predictive p-value to compare a multinomial with an overdispersed multinomial in the analysis of T-cell populations
    Qinglin Pei
    Department of Statistics, University of Wisconsin, Madison, WI 53706, USA
    Biostatistics 15:129-39. 2014
  2. pmc Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis
    Mohana Ray
    Department of Chemistry, UW Biotechnology Center, University of Wisconsin Madison, Madison, WI 53706, USA
    BMC Genomics 14:505. 2013
  3. ncbi request reprint Detecting differential gene expression with a semiparametric hierarchical mixture method
    Michael A Newton
    Department of Statistics, University of Wisconsin Madison, 1210 West Dayton St, Madison, WI 53706 1685, USA
    Biostatistics 5:155-76. 2004
  4. ncbi request reprint On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data
    M A Newton
    Department of Statistics, University of Wisconsin, Madison, WI 53792, USA
    J Comput Biol 8:37-52. 2001
  5. ncbi request reprint A statistical test of the hypothesis that polyclonal intestinal tumors arise by random collision of initiated clones
    Michael A Newton
    Department of Statistics, University of Wisconsin Madison, 1300 University Avenue, Madison, Wisconsin 53706, USA
    Biometrics 62:721-7. 2006
  6. ncbi request reprint Inferring the location and effect of tumor suppressor genes by instability-selection modeling of allelic-loss data
    M A Newton
    Department of Statistics, University of Wisconsin Madison, 1210 West Dayton Street, Madison, Wisconsin 53706 1685, USA
    Biometrics 56:1088-97. 2000
  7. ncbi request reprint On the statistical analysis of allelic-loss data
    M A Newton
    Department of Biostatistics, University of Wisconsin Madison, Clinical Science Center 53792, USA
    Stat Med 17:1425-45. 1998
  8. pmc Genetic loci controlling breast cancer susceptibility in the Wistar-Kyoto rat
    H Lan
    McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin 53792, USA
    Genetics 157:331-9. 2001
  9. ncbi request reprint On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles
    C M Kendziorski
    Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53703, USA
    Stat Med 22:3899-914. 2003
  10. pmc A resistant genetic background leading to incomplete penetrance of intestinal neoplasia and reduced loss of heterozygosity in ApcMin/+ mice
    A R Shoemaker
    McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 95:10826-31. 1998

Collaborators

Detail Information

Publications29

  1. pmc A conditional predictive p-value to compare a multinomial with an overdispersed multinomial in the analysis of T-cell populations
    Qinglin Pei
    Department of Statistics, University of Wisconsin, Madison, WI 53706, USA
    Biostatistics 15:129-39. 2014
    ..The procedure has a simple interpretation, requires fewer modeling assumptions than would be required of a fully Bayesian analysis, and has reasonable operating characteristics as evidenced empirically and by asymptotic analysis. ..
  2. pmc Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis
    Mohana Ray
    Department of Chemistry, UW Biotechnology Center, University of Wisconsin Madison, Madison, WI 53706, USA
    BMC Genomics 14:505. 2013
    ..In this context, high throughput, single molecule platforms like Optical Mapping offer a unique perspective...
  3. ncbi request reprint Detecting differential gene expression with a semiparametric hierarchical mixture method
    Michael A Newton
    Department of Statistics, University of Wisconsin Madison, 1210 West Dayton St, Madison, WI 53706 1685, USA
    Biostatistics 5:155-76. 2004
    ..Compared to several competing methodologies, the proposed methodology exhibits good operating characteristics in a simulation study, on the analysis of spike-in data, and in a cross-validation calculation...
  4. ncbi request reprint On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data
    M A Newton
    Department of Statistics, University of Wisconsin, Madison, WI 53792, USA
    J Comput Biol 8:37-52. 2001
    ..Significant gene expression changes are identified by deriving the posterior odds of change within a similar model. The methods are tested via simulation and are applied to a panel of Escherichia coli microarrays...
  5. ncbi request reprint A statistical test of the hypothesis that polyclonal intestinal tumors arise by random collision of initiated clones
    Michael A Newton
    Department of Statistics, University of Wisconsin Madison, 1300 University Avenue, Madison, Wisconsin 53706, USA
    Biometrics 62:721-7. 2006
    ..Bayesian analysis yields the posterior distribution of the number of heterotypic tumors, from which p-values are computed to test random collision...
  6. ncbi request reprint Inferring the location and effect of tumor suppressor genes by instability-selection modeling of allelic-loss data
    M A Newton
    Department of Statistics, University of Wisconsin Madison, 1210 West Dayton Street, Madison, Wisconsin 53706 1685, USA
    Biometrics 56:1088-97. 2000
    ..Parametric bootstrap and Bayesian computations are also developed. Data from three allelic-loss studies are reanalyzed to illustrate the methods...
  7. ncbi request reprint On the statistical analysis of allelic-loss data
    M A Newton
    Department of Biostatistics, University of Wisconsin Madison, Clinical Science Center 53792, USA
    Stat Med 17:1425-45. 1998
    ..We illustrate these methods on allelic-loss data from induced rat mammary tumours and human bladder cancers...
  8. pmc Genetic loci controlling breast cancer susceptibility in the Wistar-Kyoto rat
    H Lan
    McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin 53792, USA
    Genetics 157:331-9. 2001
    ..In addition, we identified an interaction between Mcs8 and a region on chromosome 6 termed Mcsm1 (modifier of Mcs), which had no significant main effect on mammary cancer susceptibility in this genetic analysis...
  9. ncbi request reprint On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles
    C M Kendziorski
    Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53703, USA
    Stat Med 22:3899-914. 2003
    ..The methodology is used in a study of mammary cancer in the rat, where four distinct patterns of expression are possible...
  10. pmc A resistant genetic background leading to incomplete penetrance of intestinal neoplasia and reduced loss of heterozygosity in ApcMin/+ mice
    A R Shoemaker
    McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 95:10826-31. 1998
    ..The means by which Apc function is inactivated is affected by genetic background. Possible scenarios are discussed...
  11. ncbi request reprint Bayesian phylogenetic inference via Markov chain Monte Carlo methods
    B Mau
    Department of Statistics, University of Wisconsin Madison, 53706 1685, USA
    Biometrics 55:1-12. 1999
    ..The algorithm mixes well in both examples from random starting trees, generating reproducible estimates and credible sets for the path of evolution...
  12. pmc Genetic identification of multiple loci that control breast cancer susceptibility in the rat
    L A Shepel
    Department of Human Oncology, University of Wisconsin Madison, Madison, Wisconsin 53792, USA
    Genetics 149:289-99. 1998
    ..The isolation of the Mcs genes may help elucidate novel mechanisms of carcinogenesis, provide information important for human breast cancer risk estimation, and also provide unique drug discovery targets for breast cancer prevention...
  13. ncbi request reprint In vivo mutant frequency of thioguanine-resistant T-cells in the peripheral blood and lymph nodes of melanoma patients
    M R Albertini
    Department of Medicine, University of Wisconsin, Madison, WI 53792, USA
    Mutat Res 476:83-97. 2001
    ..Further studies will characterize the functional reactivity of hprt mutant isolates against melanoma-related antigens...
  14. ncbi request reprint Intestinal neoplasia in the ApcMin mouse: independence from the microbial and natural killer (beige locus) status
    W F Dove
    Laboratory of Genetics, University of Wisconsin, Madison 53706, USA
    Cancer Res 57:812-4. 1997
    ..In parallel, we have found that C57BL/6-ApcMin/+ mice mutated at the beige locus, which controls natural killer activity, are also unaltered in adenoma multiplicity...
  15. ncbi request reprint p16/pRb pathway alterations are required for bypassing senescence in human prostate epithelial cells
    D F Jarrard
    Department of Toxicology, University of Wisconsin Comprehensive Cancer Center and Medical School, Madison 53792, USA
    Cancer Res 59:2957-64. 1999
    ..Our results further indicate that inactivation of the p16/pRb pathway alone is not sufficient to immortalize HPECs and that additional genetic alterations are required for this process...
  16. pmc Clonal expansions of 6-thioguanine resistant T lymphocytes in the blood and tumor of melanoma patients
    Mark R Albertini
    Medical Service, William S Middleton Memorial Veterans Hospital, Madison, Wisconsin 53705, USA
    Environ Mol Mutagen 49:676-87. 2008
    ....
  17. ncbi request reprint On estimating the polyclonal fraction in lineage-marker studies of tumor origin
    Michael A Newton
    Department of Statistics, University of Wisconsin Madison, Madison, WI 53706, USA
    Biostatistics 7:503-14. 2006
    ..On data from several published studies, our estimates of the polyclonal fraction are substantially smaller than Novelli's ratio...
  18. pmc Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae
    Chang Yi Wu
    Department of Nutritional Sciences, University of Wisconsin Madison, Madison, WI 53706, USA
    BMC Genomics 9:370. 2008
    ..We previously used transcriptome profiling with DNA microarrays to identify 46 potential Zap1 target genes in the yeast genome. In this new study, we used complementary methods to identify additional Zap1 target genes...
  19. ncbi request reprint Chemoprevention of spontaneous intestinal adenomas in the Apc Min mouse model by the nonsteroidal anti-inflammatory drug piroxicam
    R F Jacoby
    Department of Medicine Division of Gastroenterology, University of Wisconsin, Madison, Wisconsin 53792, USA
    Cancer Res 56:710-4. 1996
    ..The Min mouse model demonstrates that the nonsteroidal anti-inflammatory drug piroxicam has strong biological and therapeutic effects, potentially useful for prevention of the early adenoma stage of tumor development...
  20. pmc The intestinal epithelium and its neoplasms: genetic, cellular and tissue interactions
    W F Dove
    McArdle Laboratory for Cancer Research, University of Wisconsin, Madison 53706, USA
    Philos Trans R Soc Lond B Biol Sci 353:915-23. 1998
    ....
  21. pmc Discovery and validation of colonic tumor-associated proteins via metabolic labeling and stable isotopic dilution
    Edward L Huttlin
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 106:17235-40. 2009
    ..Our work demonstrates the power of metabolic labeling combined with stable isotopic dilution as an integrated strategy for the identification and validation of differentially expressed proteins using rodent models of human disease...
  22. pmc Statistical use of argonaute expression and RISC assembly in microRNA target identification
    Stephen A Stanhope
    Department of Statistics, University of Wisconsin Madison, Madison, Wisconsin, USA
    PLoS Comput Biol 5:e1000516. 2009
    ....
  23. pmc Polyclonality of familial murine adenomas: analyses of mouse chimeras with low tumor multiplicity suggest short-range interactions
    Andrew T Thliveris
    McArdle Laboratory for Cancer Research, Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 102:6960-5. 2005
    ..These statistical calculations indicate that the familial adenomas of the Apc(Min/+) mouse may commonly form through interactions between clones as close as 1-2 crypt diameters apart...
  24. ncbi request reprint Genome-wide expression profiling reveals EBV-associated inhibition of MHC class I expression in nasopharyngeal carcinoma
    Srikumar Sengupta
    Institute for Molecular Virology, McArdle Laboratory for Cancer Research, University of Wisconsin Madison, Madison, WI 53706, USA
    Cancer Res 66:7999-8006. 2006
    ....
  25. pmc Fundamental differences in cell cycle deregulation in human papillomavirus-positive and human papillomavirus-negative head/neck and cervical cancers
    Dohun Pyeon
    McArdle Laboratory for Cancer Research, University of Wisconsin Madison, Madison, WI 53706, USA
    Cancer Res 67:4605-19. 2007
    ....
  26. pmc MicroRNA 29c is down-regulated in nasopharyngeal carcinomas, up-regulating mRNAs encoding extracellular matrix proteins
    Srikumar Sengupta
    Institute for Molecular Virology, Howard Hughes Medical Institute, McArdle Laboratory for Cancer Research, Departments of Statistics and Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53076, USA
    Proc Natl Acad Sci U S A 105:5874-8. 2008
    ..Thus, we identify eight miRNAs differentially expressed in NPC and demonstrate the involvement of one in regulating genes involved in metastasis...
  27. pmc Reproducibility of tumor volume measurement at microCT colonography in living mice
    Benjamin Y Durkee
    Department of Medical Physics, 1400 University Avenue, University of Wisconsin, Madison, WI 53706, USA
    Acad Radiol 15:334-41. 2008
    ..The precision and accuracy of volumetric measurements were determined to assess whether changes in tumor volume over time were readily detectable...
  28. pmc High-resolution human genome structure by single-molecule analysis
    Brian Teague
    The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706 1580, USA
    Proc Natl Acad Sci U S A 107:10848-53. 2010
    ..We also describe thousands of new variants with sizes ranging from kb to Mb...
  29. ncbi request reprint Genes involved in DNA repair and nitrosamine metabolism and those located on chromosome 14q32 are dysregulated in nasopharyngeal carcinoma
    Lori E Dodd
    National Cancer Institute, 6120 Executive Boulevard, Room 7062, Rockville, MD 20852, USA
    Cancer Epidemiol Biomarkers Prev 15:2216-25. 2006
    ..Our results suggest that nitrosamine activation and DNA repair are important in NPC. The consistent down-regulation of expression on chromosome 14q32 suggests loss of heterozygosity in this region...