Vahid H. Gazestani

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Integrating expression data with gene interactions in a network is essential for understanding the functional organization of the cells. Consequently, knowledge of interaction types in biological networks is important for data interpretation. Signing of Regulatory Networks (SIREN) plugin for Cytoscape is an open-source Java tool for discrimination of(More)
The human Y chromosome contains a small number of genes that play a critical role in the determination of male-specific organs. Today's advances have provided valuable resources for defining the functions of this chromosome in both normal and cancerous prostates. Despite the fact that generation of high-throughput expression data is becoming usual; the(More)
Morphological and metabolic changes in the life cycle of Trypanosoma brucei are accomplished by precise regulation of hundreds of genes. In the absence of transcriptional control, RNA-binding proteins (RBPs) shape the structure of gene regulatory maps in this organism, but our knowledge about their target RNAs, binding sites, and mechanisms of action is far(More)
DRBD13 RNA-binding protein (RBP) regulates the abundance of AU-rich element (ARE)-containing transcripts in trypanosomes. Here we show that DRBD13 regulates RBP6, the developmentally critical protein in trypanosomatids. We also show DRBD13-specific regulation of transcripts encoding cell surface coat proteins including GPEET2, variable surface glycoprotein(More)
The functions of the majority of trypanosomatid-specific proteins are unknown, hindering our understanding of the biology and pathogenesis of Trypanosomatida. While protein-protein interactions are highly informative about protein function, a global map of protein interactions and complexes is still lacking for these important human parasites. Here,(More)
BACKGROUND Prostate cancer is one of the most widespread cancers in men and is fundamentally a genetic disease. Identifying regulators in cancer using novel systems biology approaches will potentially lead to new insight into this disease. It was sought to address this by inferring gene regulatory networks (GRNs). Moreover, dynamical analysis of GRNs can(More)
Knowledge of interaction types in biological networks is important for understanding the functional organization of the cell. Currently information-based approaches are widely used for inferring gene regulatory interactions from genomics data, such as gene expression profiles; however, these approaches do not provide evidence about the regulation type(More)
Trypanosoma brucei is a vector-borne parasite with intricate life cycle that can cause serious diseases in humans and animals. This pathogen relies on fine regulation of gene expression to respond and adapt to variable environments, with implications in transmission and infectivity. However, the involved regulatory elements and their mechanisms of actions(More)
BACKGROUND Prostate cancer, a serious genetic disease, has known as the first widespread cancer in men, but the molecular changes required for the cancer progression has not fully understood. Availability of high-throughput gene expression data has led to the development of various computational methods, for identification of the critical genes, have(More)
Post-transcriptionally added RNA 3' nucleotide extensions, or tails, impose numerous regulatory effects on RNAs, including effects on RNA turnover and translation. However, efficient methods for in-depth tail profiling of a transcript of interest are still lacking, hindering available knowledge particularly of tail populations that are highly heterogeneous.(More)