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After introducing the platforms, applications and advances in next generation sequencing technologies the author will discuss his involvement with several genome sequencing initiatives, focusing more closely on the tammar wallaby genome project. The Baylor College of Medicine, Australian Government and University of Connecticut teamed together (under the KanGO consortium) as part of an international...
The use of short interfering RNA (siRNA) is an emerging powerful method for gene silencing. siRNA is a short RNA sequence that targets mRNA and causes the sequence-specific degradation of the mRNA. Despite its importance, few efforts have been made to develop algorithms and computational tools to detect genes controlled by siRNA process. This paper introduces an algorithm that uses an intelligent...
We present a novel algorithm to estimate genome-wide gene networks consisting of more than 20,000 genes from gene expression data using nonparametric Bayesian networks. Due to the difficulty of learning Bayesian network structures, existing algorithms cannot be applied to more than a few thousand genes. Our algorithm overcomes this limitation by repeatedly estimating subnetworks in parallel for genes...
RNA interference (RNAi) is a widely used method for gene function analyses in a variety of organisms. Establishment of a large-scale, high-throughput platform for analysing gene function may require development of an RNAi microarray system using reverse transfection. Here, we show that shRNA is more effective in microarray gene silencing compared to siRNA. Endogenous mammalian genes are suppressed...
Many characteristics of functional synthetic siRNAs have been identified. Our three-phase algorithm was developed to design siRNA on a whole-genome scale based on these characteristics. When this algorithm was applied to design shRNAs, the validated success rate was over 70%, which was almost double the rate reported for TRC library. This indicates that the designs of siRNA and shRNA may share the...
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