Protein coding regions prediction is a very important but overlooked subtask for tasks such as of complete gene structure, coding/noncoding RNA. Many machine learning methods have been proposed this problem, they first encode biological sequence into numerical values and then feed them classifier final prediction. However, encoding schemes directly influence the classifier's capability to captu...

Background: Exonic splice enhancers are sequences embedded within exons which promote and regulate the splicing of the transcript in which they are located. A class of exonic splice enhancers are the SR proteins, which are thought to mediate interactions between splicing factors bound to the 5’ and 3’ splice sites. Method and results: We present a novel strategy for analysing proteincoding sequ...

Recent years have witnessed new innovation in Bayesian techniques to adjust for unmeasured confounding. A challenge with existing methods is that the user is often required to elicit prior distributions for high-dimensional parameters that model competing bias scenarios. This can render the methods unwieldy. In this paper, we propose a novel methodology to adjust for unmeasured confounding that...

Studies of various mRNAs have revealed that changes in the abundance of transcripts, through mRNA degradation, act as a critical step in the control of various biological pathways. Similarly, the regulation of non-coding RNA (ncRNA) levels is also considered to be important for their biological functions; however, far less is known about the mechanisms and biological importance of ncRNA turnove...

Post-transcriptional regulation of stem cell differentiation is far from being completely understood. Changes in protein levels are not fully correlated with corresponding changes in mRNAs; the observed differences might be partially explained by post-transcriptional regulation mechanisms, such as alternative polyadenylation. This would involve changes in protein binding, transcript usage, miRN...

With unprecedented increase in next generation sequencing technologies, there has been a persistent interest on transcript profiles of long non-coding RNAs (lncRNAs) and protein-coding genes forming an interaction network. Apart from protein-protein interaction (PPI), gene network models such as Weighted Gene Co-expression Network Analysis (WGCNA) are used to functionally annotate lncRNAs in id...

A single transcript sometimes codes for more than one product. In bacteria, and in a few exceptional animal lineages, many genes are organized into operons: clusters of open reading frames that are transcribed together in a single polycistronic transcript. However, polycistronic transcripts are rare in eukaryotes. One notable exception is that of miRNAs (microRNAs), small RNAs that regulate gen...

Increasing evidence indicates that long non-coding RNAs (lncRNAs) can act as crucial regulators of tumor progression. In the present study, UXT-AS1 was found to be significantly upregulated in colorectal cancer (CRC) and high expression levels of UXT-AS1 were significantly associated with poor prognosis in CRC patients. In addition, upregulation of UXT-AS1 resulted in inhibition of cell apoptos...

BACKGROUND Azithromycin, an antibiotic used for multiple infectious disorders, exhibits anti-inflammatory effects, but the molecular basis for this activity is not well characterized. Azithromycin inhibits IL-1β-mediated inflammation that is dependent, in part, on inflammasome activity. Here, we investigated the effects of azithromycin on the NACHT, LRR, and PYD domains-containing protein 3 (NA...