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Nonsense-mediated mRNA decay (NMD) is a eukaryotic mechanism of RNA surveillance that selectively eliminates aberrant transcripts coding for potentially deleterious proteins. NMD also functions in the normal repertoire of gene expression. In Saccharomyces cerevisiae, hundreds of endogenous RNA Polymerase II transcripts achieve steady-state levels that(More)
Next-generation sequencing (NGS) technology generates millions of short reads, which provide valuable information for various aspects of cellular activities and biological functions. A key step in NGS applications (e.g., RNA-Seq) is to map short reads to correct genomic locations within the source genome. While most reads are mapped to a unique location, a(More)
RNA sequencing (RNA-seq) has become a major tool for biomedical research. A key step in analyzing RNA-seq data is to infer the origin of short reads in the source genome, and for this purpose, many read alignment/mapping software programs have been developed. Usually, the majority of mappable reads can be mapped to one unambiguous genomic location, and(More)
We present the Optimizing Control Variate (OCV) estimator, a new estimator for Monte Carlo rendering. Based upon a deterministic sampling framework, OCV allows multiple importance sampling functions to be combined in one algorithm. Its optimizing nature addresses a major problem with control variate estimators for rendering: users supply a generic(More)
MOTIVATION The classification of samples using gene expression profiles is an important application in areas such as cancer research and environmental health studies. However, the classification is usually based on a small number of samples, and each sample is a long vector of thousands of gene expression levels. An important issue in parametric modeling(More)
An important application of microarray gene expression data is classification of treatments. One pioneering work in this area is by Golub et al. (1999) who classified samples into three types of leukemia using oligonucleotide microarrays. Recently, with more applications appearing in the literature, researchers began to realize the importance of(More)