Discovering non-coding RNA elements in Drosophila 3' untranslated regions

The Non-Coding RNA (ncRNA) elements in the 3′ Untranslated Regions (3′-UTRs) are known to participate in the genes’ post-transcriptional regulations. Inferring co-expression patterns of the genes through clustering these 3′-UTR ncRNA elements will provide invaluable insights for studying their biological functions. In this paper, we propose an improved RNA structural clustering pipeline. Benchmark of the new pipeline on Rfam data demonstrates over 10% performance improvements compared to the traditional hierarchical clustering pipeline. By applying the new clustering pipeline to 3′-UTRs of Drosophila melanogaster’s genome, we have successfully identified 184 ncRNA clusters with 91.3% accuracy. One of these clusters corresponds to genes that are preferentially expressed in male Drosophila. Another cluster contains genes that are responsible for the functions of septate junction in epithelial cells. These discoveries encourage more studies on novel post-transcriptional regulation mechanisms

Discovering Non-Coding Rna Elements In Drosophila 3′ Untranslated Regions

The Non-Coding RNA (ncRNA) elements in the 3′ Untranslated Regions (3′-UTRs) are known to participate in the genes\u27 post-transcriptional regulations. Inferring co-expression patterns of the genes through clustering these 3′-UTR ncRNA elements will provide invaluable insights for studying their biological functions. In this paper, we propose an improved RNA structural clustering pipeline. Benchmark of the new pipeline on Rfam data demonstrates over 10% performance improvements compared to the traditional hierarchical clustering pipeline. By applying the new clustering pipeline to 3′-UTRs of Drosophila melanogaster\u27s genome, we have successfully identified 184 ncRNA clusters with 91.3% accuracy. One of these clusters corresponds to genes that are preferentially expressed in male Drosophila. Another cluster contains genes that are responsible for the functions of septate junction in epithelial cells. These discoveries encourage more studies on novel post-transcriptional regulation mechanisms. Copyright © 2014 Inderscience Enterprises Ltd

Discovering Non-Coding Rna Elements In Drosophila 3′ Untranslated Regions

The problem of finding parameters of an adaptive quadratic spiking neuron model in order to fit data derived from in vitro embryonic rat motoneurons is addressed. Since the model does not fit the shape of the experimental action potential, we utilize a correlation based technique to extract input-independent spike areas, and pre-distort these areas such that they conform to the model assumptions. Simulation results show that the spike train is accurately predicted. © 2012 IEEE