Current Bioinformatics - Volume 11, Issue 3, 2016

MicroRNAs (miRNAs) are small noncoding RNAs that regulate cellular functions by finely controlling the transcription and translation efficiency of their targets. Understanding the functions of miRNAs entails predicting the targets of miRNAs and dissecting the miRNA–messenger RNA regulatory network. An increasing number of computational methods for rapidly screening miRNA potential targets have been developed with the i Read More

The discovery of molecular prognostic cancer biomarkers is still a major scientific challenge. Some methodologies have been proposed to generate novel model biomarkers for clinical outcome using gene expression as predictors but involve some drawbacks. For example, (i) they heavily depend on a rank of the initial univariate relation to survival times, (ii) are unable to generate compact multivariate predictors, (iii) are based on Read More

Ortholog clusters are very important for functional annotation and studies in comparative and evolutionary genomics. Their accuracy is, therefore, of considerable significance. However, it is very hard to calculate the accuracy of ortholog clusters because it takes too much time to compare every gene between both ortholog clusters due to huge search space in many clusters. This study presents a fast comparison algorithm Read More

Rapidly developing next-generation sequencing technologies significantly promote metagenomics research, yet also present extreme challenges in the analysis of metagenomic data. Metagenomic samples can contain thousands of microbial species, thus, sequencing datasets can contain fragments from thousands of different genomes. Therefore, clustering the sequencing reads with their original genomes, namely, binnin Read More

Benzopyrone derivatives (Coumarins) are well known inhibitors of P-glycoprotein (P-gp) mediated efflux. The high expression level of these efflux proteins promotes the growth of breast cancer stem cells (CSCs). The activity of breast CSCs is directly affected by the inhibition of efflux proteins by benzopyrone derivatives. Ligand based pharmacophoric study and structure based docking studies have been exploited for assessing Read More

The phytohormone ethylene plays essential physiological roles throughout the life cycle of plants, mainly via promoting ripening and senescence of fruits and flowers. Accompanying the sharp climacteric increase in ethylene production, there is a surge of 1-aminocyclopropane-1-carboxylate (ACC) synthase (ACS) and ACC oxidase (ACO) activities. ACS converts S-adenosyl-L-methionine (SAM) to ACC, whereas ACO converts AC Read More

Misfolding of proteins results in amyloidosis: a condition where amyloid motifs build up in neuronal tissues leading to life threatening organ failures. Hence understanding the underlying cause of incorrect folding of proteins is significant followed by the identification of such peptide motifs. This research effort proposes a distinctive ensemble approach by taking advantage of diverse fusion of structural information and sequence Read More

Identification of differentially expressed genes (DEG) in transcriptomic analyses is one of the important tasks to find out significantly activated/deactivated pathways. Outliers and/or the missing values are commonly observed in microarray data; however, most available statistical methods did not deal with these issues and, therefore, their analytical results were frequently skewed and deteriorated. Here, we develo Read More

As the length of sequencing read increasing, greater bioinformation is demanded from longread aligner. The short-read aligner is often widely used to make alignment very fast and accurate, but the approach is ill-suited to finding longer, gapped alignments with long indels. A wide variety of alignment algorithms and aligners have been subsequently developed over the past few years. In this article, we survey the theoretical f Read More

Drug resistance is a major problem for non-small cell lung cancer (NSCLC) treatment due to mutations in patients’ DNA sequences. It is now possible to obtain the human genome information easily based on the high-throughput sequencing technology, so personalized medicine can become a reality. Based on mutation data of 168 patients with stage IIIB and IV NSCLC. We use computational method to predict the ho Read More