Abdallah Eteleeb

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BACKGROUND Long noncoding RNAs (lncRNAs) are an emerging class of relatively underexplored oncogenic molecules with biological and clinical significance. Current inadequacies for stratifying patients with aggressive disease presents a strong rationale to systematically identify lncRNAs as clinical predictors in localized prostate cancer. OBJECTIVE To(More)
Poly (ADP-ribose) polymerase-1 (PARP1) is a nuclear enzyme involved in DNA repair, chromatin remodeling and gene expression. PARP1 interactions with chromatin architectural multi-protein complexes (i.e. nucleosomes) alter chromatin structure resulting in changes in gene expression. Chromatin structure impacts gene regulatory processes including(More)
High-throughput mRNA sequencing (also known as RNA-Seq) promises to be the technique of choice for studying transcriptome profiles. This technique provides the ability to develop precise methodologies for transcript and gene expression quantification, novel transcript and exon discovery, and splice variant detection. One of the limitations of current(More)
Normalization is an essential step with considerable impact on high-throughput RNA sequencing (RNA-seq) data analysis. Although there are numerous methods for read count normalization, it remains a challenge to choose an optimal method due to multiple factors contributing to read count variability that affects the overall sensitivity and specificity. In(More)
Detection of differentially expressed (DE) genes across conditions within RNA-Seq datasets yields insight into the differences in biological processes at work in these conditions. Most methods available for discovering DE genes use statistical methods that model the data based on counting reads that map to individual genes. However, the distribution of(More)
Results Computational analyses of the novel UTR sequences, focusing on RNA-binding protein (RNAbp) interaction motifs revealed strongly over-represented RNAbps with known roles in nervous system pathologies. We consider the implications of 3’UTR transcript extension and protein interaction in the context of axonal plasticity and the consequences of(More)
Affymetrix<sup>&#x00AE;</sup> GeneChip<sup>&#x00AE;</sup> micro array design defines probe sets consisting of 11, 16, or 20 distinct 25 base pair (BP) probes for determining mRNA expression for a specific gene, which may be covered by one or more probe sets. Each probe has a corresponding perfect match (PM) and mismatch (MM) set. Traditional analytical(More)
Specialized chromatin structures such as nucleosomes with specific histone modifications decorate exons in eukaryotic genomes, suggesting a functional connection between chromatin organization and the regulation of pre-mRNA splicing. Through profiling the functional location of Poly (ADP) ribose polymerase, we observed that it is associated with the(More)
Background Neurons interact with, and are influenced by, tissues that are remote from the cell body. For example, sensory neuron cell bodies are located within peri-spinal ganglia but are connected to both the spinal cord and skin via their axons projecting through dorsal roots and peripheral nerves. Biochemical signals from anatomical compartments (spinal(More)
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