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MOTIVATION Mass spectrometry yields complex functional data for which the features of scientific interest are peaks. A common two-step approach to analyzing these data involves first extracting and quantifying the peaks, then analyzing the resulting matrix of peak quantifications. Feature extraction and quantification involves a number of interrelated(More)
MOTIVATION One of the key limitations for proteomic studies using 2-dimensional gel electrophoresis (2DE) is the lack of rapid, robust and reproducible methods for detecting, matching and quantifying protein spots. The most commonly used approaches involve first detecting spots and drawing spot boundaries on individual gels, then matching spots across gels(More)
MOTIVATION In contrasting levels of gene expression between groups of SAGE libraries, the libraries within each group are often combined and the counts for the tag of interest summed, and inference is made on the basis of these larger 'pseudolibraries'. While this captures the sampling variability inherent in the procedure, it fails to allow for normal(More)
MOTIVATION There has been much interest in using patterns derived from surface-enhanced laser desorption and ionization (SELDI) protein mass spectra from serum to differentiate samples from patients both with and without disease. Such patterns have been used without identification of the underlying proteins responsible. However, there are questions as to(More)
MOTIVATION DNA methylation is a key epigenetic modification that can modulate gene expression. Over the past decade, a lot of studies have focused on profiling DNA methylation and investigating its alterations in complex diseases such as cancer. While early studies were mostly restricted to CpG islands or promoter regions, recent findings indicate that many(More)
UNLABELLED We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter settings, experimentally determined to work well in most situations. These values, if desired, can be changed by the user. PrepMS is a(More)
Clustering of gene expression data collected across time is receiving growing attention in the biological literature since time-course experiments allow one to understand dynamic biological processes and identify genes governed by the same processes. It is believed that genes demonstrating similar expression profiles over time might give an informative(More)
Duane's retraction syndrome (DRS) is a congenital eye movement disorder characterized by marked limitation or absence of abduction, variable limitation of adduction, and narrowing of the palpebral fissure with retraction of the globe on attempted adduction. We have recently recorded and quantitated ocular motility in five patients with unilateral DRS. In(More)
Despite recent progress in "shotgun" peptide separation by integrated liquid chromatography and mass spectrometry (LC/MS), proteome coverage and reproducibility are still limited with this approach and obtaining enough replicate runs for biomarker discovery is a challenge. For these reasons, recent research demonstrates that there is a continuing need for(More)
BACKGROUND Reports conflict as to whether Tourette syndrome (TS) confers deficits in executive function. This study's aim was to evaluate executive function in youths with TS using oculomotor tasks while controlling for confounds of tic severity, age, medication, and severity of comorbid disorders. METHOD Four saccade tasks requiring the executive(More)