Genomes and Genes
M A Newton
Affiliation: University of Wisconsin
- A conditional predictive p-value to compare a multinomial with an overdispersed multinomial in the analysis of T-cell populationsQinglin 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. ..
- Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysisMohana 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...
- Detecting differential gene expression with a semiparametric hierarchical mixture methodMichael 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...
- On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray dataM 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...
- A statistical test of the hypothesis that polyclonal intestinal tumors arise by random collision of initiated clonesMichael 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...
- Inferring the location and effect of tumor suppressor genes by instability-selection modeling of allelic-loss dataM 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...
- On the statistical analysis of allelic-loss dataM 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...
- Genetic loci controlling breast cancer susceptibility in the Wistar-Kyoto ratH 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...
- On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profilesC 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...
- A resistant genetic background leading to incomplete penetrance of intestinal neoplasia and reduced loss of heterozygosity in ApcMin/+ miceA 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...
- Bayesian phylogenetic inference via Markov chain Monte Carlo methodsB 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...
- Genetic identification of multiple loci that control breast cancer susceptibility in the ratL 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...
- In vivo mutant frequency of thioguanine-resistant T-cells in the peripheral blood and lymph nodes of melanoma patientsM 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...
- Intestinal neoplasia in the ApcMin mouse: independence from the microbial and natural killer (beige locus) statusW 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...
- p16/pRb pathway alterations are required for bypassing senescence in human prostate epithelial cellsD 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...
- Clonal expansions of 6-thioguanine resistant T lymphocytes in the blood and tumor of melanoma patientsMark R Albertini
Medical Service, William S Middleton Memorial Veterans Hospital, Madison, Wisconsin 53705, USA
Environ Mol Mutagen 49:676-87. 2008....
- On estimating the polyclonal fraction in lineage-marker studies of tumor originMichael 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...
- Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiaeChang 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...
- Chemoprevention of spontaneous intestinal adenomas in the Apc Min mouse model by the nonsteroidal anti-inflammatory drug piroxicamR 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...
- The intestinal epithelium and its neoplasms: genetic, cellular and tissue interactionsW 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....
- Discovery and validation of colonic tumor-associated proteins via metabolic labeling and stable isotopic dilutionEdward 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...
- Statistical use of argonaute expression and RISC assembly in microRNA target identificationStephen A Stanhope
Department of Statistics, University of Wisconsin Madison, Madison, Wisconsin, USA
PLoS Comput Biol 5:e1000516. 2009....
- Polyclonality of familial murine adenomas: analyses of mouse chimeras with low tumor multiplicity suggest short-range interactionsAndrew 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...
- Genome-wide expression profiling reveals EBV-associated inhibition of MHC class I expression in nasopharyngeal carcinomaSrikumar Sengupta
Institute for Molecular Virology, McArdle Laboratory for Cancer Research, University of Wisconsin Madison, Madison, WI 53706, USA
Cancer Res 66:7999-8006. 2006....
- Fundamental differences in cell cycle deregulation in human papillomavirus-positive and human papillomavirus-negative head/neck and cervical cancersDohun Pyeon
McArdle Laboratory for Cancer Research, University of Wisconsin Madison, Madison, WI 53706, USA
Cancer Res 67:4605-19. 2007....
- MicroRNA 29c is down-regulated in nasopharyngeal carcinomas, up-regulating mRNAs encoding extracellular matrix proteinsSrikumar 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...
- Reproducibility of tumor volume measurement at microCT colonography in living miceBenjamin 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...
- High-resolution human genome structure by single-molecule analysisBrian 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...
- Genes involved in DNA repair and nitrosamine metabolism and those located on chromosome 14q32 are dysregulated in nasopharyngeal carcinomaLori 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...