David N. Stivers

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Metaplastic breast cancers (MBC) are aggressive, chemoresistant tumors characterized by lineage plasticity. To advance understanding of their pathogenesis and relatedness to other breast cancer subtypes, 28 MBCs were compared with common breast cancers using comparative genomic hybridization, transcriptional profiling, and reverse-phase protein arrays and(More)
Using the generalized stepwise mutation model, we propose a method of estimating the relative mutation rates of microsatellite loci, grouped by the repeat motif. Applying ANOVA to the distributions of the allele sizes at microsatellite loci from a set of populations, grouped by repeat motif types, we estimated the effect of population size differences and(More)
A major goal of microarray experiments is to determine which genes are differentially expressed between samples. Differential expression has been assessed by taking ratios of expression levels of different samples at a spot on the array and flagging spots (genes) where the magnitude of the fold difference exceeds some threshold. More recent work has(More)
Since the first characterization of the population genetic properties of repeat polymorphisms, the number of short tandem repeat (STR) loci validated for forensic use has now grown to at least 13. Worldwide variations of allele frequencies at these loci have been studied, showing that variations of interpopulation diversity at these loci do not compromise(More)
Microarray experiments involve many steps, including spotting cDNA, extracting RNA, labeling targets, hybridizing, scanning, and analyzing images. Each step introduces variability, confounding our ability to obtain accurate estimates of the biological differences between samples. We ran repeated experiments using high-density cDNA microarray membranes(More)
Y-box protein 1 (YB-1) is a multifunctional DNA/RNA-binding protein that regulates transcription and translation. The specificity of YB-1's RNA binding and its consequences are unknown. Because expression and subcellular localization of YB-1 have been reported to be important in breast cancer, we determined the specificity and functional impact of YB-1(More)
OBJECTIVE To compare the transcriptosome of early-passage nonlesional dermal fibroblasts from systemic sclerosis (SSc) patients with diffuse disease and matched normal controls in order to gain further understanding of the gene activation patterns that occur in early disease. METHODS Total RNA was isolated from early-passage fibroblasts obtained from(More)
We have analyzed the CTG repeat length and the neighboring Alu insertion/deletion (+/-) polymorphism in DNA samples from 16 ethnically and geographically diverse human populations to understand the evolutionary dynamics of the myotonic dystrophy-associated CTG repeat. Our results show that the CTG repeat length is variable in human populations. Although the(More)
Suggested molecular mechanisms for the generation of new tandem repeats of simple sequences indicate that the microsatellite loci evolve via some of forward-backward mutation. We provide a mathematical basis for suggesting a measure of genetic distance between populations based on microsatellite variation. Our results indicate that such a genetic distance(More)
PURPOSE The purpose of this study was to determine whether comprehensive transcriptional profiles (TPs) can be obtained from single-passage fine-needle aspirations (FNAs) of breast cancer and to explore whether profiles capture routine clinicopathological parameters. EXPERIMENTAL DESIGN Expression profiles were available on 38 patients with stage I-III(More)