Sahar Al Seesi

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Massively parallel whole transcriptome sequencing, commonly referred to as RNA-Seq, has become the technology of choice for performing gene expression profiling. However, reconstruction of full-length novel transcripts from RNA-Seq data remains challenging due to the short read length delivered by most existing sequencing technologies. We propose a novel(More)
The mutational repertoire of cancers creates the neoepitopes that make cancers immunogenic. Here, we introduce two novel tools that identify, with relatively high accuracy, the small proportion of neoepitopes (among the hundreds of potential neoepitopes) that protect the host through an antitumor T cell response. The two tools consist of (a) the numerical(More)
A major application of RNA-Seq is to perform differential gene expression analysis. Many tools exist to analyze differentially expressed genes in the presence of biological replicates. Frequently, however, RNA-Seq experiments have no or very few biological replicates and development of methods for detecting differentially expressed genes in these scenarios(More)
Formal grammars have been employed in biology to solve various important problems. In particular, grammars have been used to model and predict RNA structures. Two such grammars are Simple Linear Tree Adjoining Grammars (SLTAGs) and Extended SLTAGs (ESLTAGs). Performances of techniques that employ grammatical formalisms critically depend on the efficiency of(More)
High throughput RNA sequencing (RNA-Seq) can generate whole transcriptome information at the single transcript level providing a powerful tool with multiple interrelated applications including transcriptome reconstruction and quantification. The sequences of novel transcripts can be reconstructed from deep RNA-Seq data, but this is computationally(More)
Cancer immunotherapy uses one’s own immune system to fight cancerous cells. As immune system is hard-wired to distinguish self and non-self, cancer immunotherapy is predicted to target cancerous cells specifically, therefore is less toxic than chemotherapy and radiation therapy, two major treatments for cancer. Cancer immunologists have spent decades to(More)
Assessing pathway activity levels is a plausible way to quantify metabolic differences between various conditions. This is usually inferred from microarray expression data. Wide availability of NGS technology has triggered a demand for bioinformatics tools capable of analyzing pathway activity directly from RNA-Seq data. In this paper we introduce XPathway,(More)