C M Kendziorski
Affiliation: University of Wisconsin
- Statistical methods for expression quantitative trait loci (eQTL) mappingC M Kendziorski
Department of Biostatistics and Medical Informatics, University of Wisconsin Madison, Madison, Wisconsin 53703, USA
Biometrics 62:19-27. 2006..The MOM model is also the only one capable of finding two genome regions previously shown to be involved in diabetes...
- Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysisMelissa R Christopherson
Department of Bacteriology, University of Wisconsin Madison, 5159 Microbial Sciences Building, 1550 Linden Drive, Madison, WI 53706 1521, USA
BMC Genomics 15:1066. 2014..Here, we used a combination of comparative genomics, fermentation analyses, and transcriptomics to further clarify the cellulolytic and fermentative potential of R. albus 7...
- Statistical methods for gene set co-expression analysisYounjeong Choi
Department of Statistics, University of Wisconsin Madison, Madison, WI 53706, USA
Bioinformatics 25:2780-6. 2009..However, such methods are not able to identify many relevant classes of differentially regulated genes. One important example concerns differentially co-expressed (DC) genes...
- 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...
- Gene expression profiling of aging reveals activation of a p53-mediated transcriptional programMichael G Edwards
Department of Genetics and Medical Genetics, University of Wisconsin, Madison, WI, USA
BMC Genomics 8:80. 2007..We have used high density oligonucleotide arrays and novel statistical methods to identify specific transcriptional classes that may uncover biological processes that play a central role in mammalian aging...
- 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...
- The efficiency of pooling mRNA in microarray experimentsC M Kendziorski
Department of Biostatistics and Medical Informatics, University of Wisconsin, 6729 Medical Sciences Center, 1300 University Avenue, Madison, WI 53792, USA
Biostatistics 4:465-77. 2003..As such, the results should be generally applicable to a number of technologies provided sufficient pre-processing and normalization methods are available and applied...
- Mapping baroreceptor function to genome: a mathematical modeling approachC M Kendziorski
Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706, USA
Genetics 160:1687-95. 2002..The phenotypes are then used in a quantitative trait loci (QTL) mapping study to identify a potential genetic basis of this controller...
- An efficient method for identifying statistical interactors in gene association networksAlina Andrei
Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, 1300 University Avenue, Madison, WI 53706 1510, USA
Biostatistics 10:706-18. 2009..Practical advantages are demonstrated in analyses of data from a breast cancer study...
- A review of statistical methods for expression quantitative trait loci mappingChristina Kendziorski
Department of Biostatistics and Medical Informatics, University of Wisconsin, 1300 University Avenue 6729 MSC, Madison, WI 53706, USA
Mamm Genome 17:509-17. 2006..In this article we review these principles and methods and discuss the open questions most likely to yield significant progress toward increasing the amount of meaningful information obtained from eQTL mapping experiments...
- On the utility of pooling biological samples in microarray experimentsC Kendziorski
Department of Biostatistics and Medical Informatics and McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53703, USA
Proc Natl Acad Sci U S A 102:4252-7. 2005..The realized benefits in this case do not outweigh the price paid for loss of individual specific information. Pooling is beneficial when many subjects are pooled, provided that independent samples contribute to multiple pools...
- 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 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...
- Microarray analysis of BeWo and JEG3 trophoblast cell lines: identification of differentially expressed transcriptsD W Burleigh
Wisconsin National Primate Research Center, University of Wisconsin Medical School, 1220 Capitol Court, Madison, WI 53715 1299, USA
Placenta 28:383-9. 2007..These data suggest that BeWo and JEG3 cell lines, and perhaps other trophoblast cell lines, are sufficiently dissimilar from each other such that they will be differentially suited for specific experimental paradigms...
- Combined expression trait correlations and expression quantitative trait locus mappingHong Lan
Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
PLoS Genet 2:e6. 2006..The combined analysis is more sensitive compared with linkage mapping alone...
- Liver gene expression analysis reveals endoplasmic reticulum stress and metabolic dysfunction in SCD1-deficient mice fed a very low-fat dietMatthew T Flowers
Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
Physiol Genomics 33:361-72. 2008....
- Genetic networks of liver metabolism revealed by integration of metabolic and transcriptional profilingChristine T Ferrara
Sarah W Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina, United States of America
PLoS Genet 4:e1000034. 2008..Thus, the methods described here have the potential to reveal regulatory networks that contribute to chronic, complex, and highly prevalent diseases and conditions such as obesity and diabetes...
- A statistical framework for expression quantitative trait loci mappingMeng Chen
Pfizer Global Research and Development, Groton, Connecticut 06340, USA
Genetics 177:761-71. 2007..Evaluations are based on simulation studies and a study of diabetes in mice...
- A unified approach for simultaneous gene clustering and differential expression identificationMing Yuan
School of Industrial and Systems Engineering, Georgia Institute of Technology, 765 Ferst Drive NW, Atlanta, Georgia 30332, USA
Biometrics 62:1089-98. 2006..The improvement over existing methods is illustrated in both our simulation results and a case study...
- A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibilityMark P Keller
Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53076, USA
Genome Res 18:706-16. 2008....
- Identification of novel modifier loci of Apc Min affecting mammary tumor developmentHua Wang
Department of Human Oncology, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin 53792, USA
Cancer Res 67:11226-33. 2007..None of these modifiers is associated with intestinal tumor susceptibility, which indicates that these modifiers act on tumor development in a tissue-specific manner...
- Gene expression profiling in INS-1 cells overexpressing thioredoxin-interacting proteinAlexandra H Minn
Department of Medicine, University of Wisconsin Madison, WI, USA
Biochem Biophys Res Commun 336:770-8. 2005..Thus, aside from regulating the cellular redox, TXNIP does modulate overall gene transcription and thereby may further enhance beta-cell death and impair insulin secretion...
- Exenatide blocks JAK1-STAT1 in pancreatic beta cellsFrancesca M Couto
Department of Medicine, University of Wisconsin, Madison, WI, USA
Metabolism 56:915-8. 2007..Thus, these findings suggest that Ex-4 treatment may also be beneficial in type 1 diabetes mellitus, where it may help protect beta cells from cytokine-induced cell death by inhibiting JAK1-STAT1...