Nameeta Shah

Learn More
O⁶-methylguanine DNA-methyltransferase (MGMT) promoter methylation has been identified as a potential prognostic marker for glioblastoma patients. The relationship between the exact site of promoter methylation and its effect on gene silencing, and the patient's subsequent response to therapy, is still being defined. The aim of this study was to(More)
MOTIVATION The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing number of genomic sequence datasets being generated for an ever-increasing number of organisms. To be efficient these visualization algorithms must(More)
BACKGROUND Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of(More)
Genomes of hundreds of species have been sequenced to date, and many more are being sequenced. As more and more sequence data sets become available, and as the challenge of comparing these massive " billion basepair DNA sequences " becomes substantial, so does the need for more powerful tools supporting the exploration of these data sets. Similarity score(More)
Technological advancements are constantly increasing the size and complexity of data resulting from microarray experiments. This fact has led biologists to ask complex questions, which the existing, fully automated analyses are often not adequate to answer. We present GeneBox, an interactive tool for two-dimensional and three-dimensional visualization of(More)
RNA-seq has spurred important gene fusion discoveries in a number of different cancers, including lung, prostate, breast, brain, thyroid and bladder carcinomas. Gene fusion discovery can potentially lead to the development of novel treatments that target the underlying genetic abnormalities. In this study, we provide comprehensive view of gene fusion(More)
Recent studies in the field of comparative genomics demonstrate that multi-species DNA comparison presents a powerful method for discovering functional genomic sequences. Similarity across large evolutionary distances usually reveals conserved, and, by inference, important biological features. Expanding the capabilities of computational tools designed for(More)
The authors report a case of multicentric glioblastoma multiforme (GBM) in which all 4 tumor foci were resected and evaluated using both comparative genomic hybridization array and RNA sequencing. Genetic analysis showed that the tumors shared a common origin, although each had its own unique set of genetic aberrations. The authors note that the genetic(More)