BACKGROUND: RNAs play key roles in cells through the interactions with proteins known as the RNA-binding proteins (RBP) and their binding motifs enable crucial understanding of the post-transcriptional regulation of RNAs. How the RBPs correctly recog...
Journal of bioinformatics and computational biology
Jan 9, 2017
Piwi-interacting RNAs (piRNAs) were recently discovered as endogenous small noncoding RNAs. Some recent research suggests that piRNAs may play an important role in cancer. So the precise identification of human piRNAs is a significant work. In this p...
Journal of integrative bioinformatics
Dec 22, 2016
The performance of many learning and data mining algorithms depends critically on suitable metrics to assess efficiency over the input space. Learning a suitable metric from examples may, therefore, be the key to successful application of these algor...
IEEE/ACM transactions on computational biology and bioinformatics
May 3, 2016
The transcription factors (TFs) can activate or suppress gene expression by binding to specific sites, hence are crucial regulatory elements for transcription. Recently, series of discriminative motif finders have been tailored to offering promising ...
Identifying discriminative motifs underlying the functionality and evolution of organisms is a major challenge in computational biology. Machine learning approaches such as support vector machines (SVMs) achieve state-of-the-art performances in genom...
IEEE transactions on neural networks and learning systems
Jun 9, 2015
Self-organizing map (SOM)-based motif mining, despite being a promising approach for problem solving, mostly fails to offer a consistent interpretation of clusters with respect to the mixed composition of signal and noise in the nodes. The main reaso...
Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtai...
Polyadenylation is the process of addition of poly(A) tail to mRNA 3' ends. Identification of motifs controlling polyadenylation plays an essential role in improving genome annotation accuracy and better understanding of the mechanisms governing gene...
DNA, beyond its canonical B-form double helix, adopts various alternative conformations, among which the i-motif, emerging in cytosine-rich sequences under acidic conditions, holds significant biological implications in transcription modulation and t...
SUMMARY: Cis-acting mRNA elements play a key role in the regulation of mRNA stability and translation efficiency. Revealing the interactions of these elements and their impact plays a crucial role in understanding the regulation of the mRNA translati...
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