Current Bioinformatics - Volume 14, Issue 7, 2019

Background: The advent of the Single-Molecule Real-time (SMRT) Isoform Sequencing (Iso-Seq) has paved the way to obtain longer full-length transcripts. This method was found to be much superior in identifying full-length splice variants and other post-transcriptional events as compared to the Next Generation Sequencing (NGS)-based short read sequencing (RNA-Seq). Several different bioinformatics tools to analyze the I Read More

Background: Blattella germanica is a widespread urban invader insect that can spread numerous types of human pathogens, including bacteria, fungi, and protozoa. Despite the medical significance of B. germanica, the genetic diversity of this species has not been investigated across its wide geographical distribution in China. Objective: In this study, the genetic variation of B. germanica was evaluated in central China. Method Read More

Background: Studies of Positively Selected Genes (PSGs) in microorganisms and mammals have provided insights into the dynamics of genome evolution and the genetic basis of differences between species by using whole genome-wide scans. Systematic investigations and comparisons of PSGs in plants, however, are still limited. Objective: A systematic comparison of PSGs between the genomes of two cotton species, Goss Read More

Background: Chickpea is a nutritional rich premier pulse crop but its production encounters setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance. Objective: The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea in response to herbicide stress and decipher their interacting partners. Methods: For this purpose, transcriptome Read More

Background: Plants respond to various stresses at the same time. Recent studies show that interactions of various phytohormones can play important roles in response to stresses. Objective: Although many studies have been done about the effects of the individual hormones, little information exists about the crosstalk among the hormone signalling pathways in plants. Methods: In this work, the weighted gene co-ex Read More

Background: As one of the most important reversible protein post-translation modification types, ubiquitination plays a significant role in the regulation of many biological processes, such as cell division, signal transduction, apoptosis and immune response. Protein ubiquitination usually occurs when ubiquitin molecule is attached to a lysine on a target protein, which is also known as “lysine ubiquitination”. Objective: In or Read More

Background: Long noncoding RNAs (lncRNAs) are endogenous noncoding RNAs, arbitrarily longer than 200 nucleotides, that play critical roles in diverse biological processes. LncRNAs exist in different genomes ranging from animals to plants. Objective: PlncRNADB is a searchable database of lncRNA sequences and annotation in plants. Methods: We built a pipeline for lncRNA prediction in plants, providing a convenient utility fo Read More

Background: The BLAST (Basic Local Alignment Search Tool) algorithm has been widely used for sequence similarity searching. Analogously, the public phenotype images must be efficiently retrieved using biological images as queries and identify the phenotype with high similarity. Due to the accumulation of genotype-phenotype-mapping data, a system of searching for similar phenotypes is not available due to the bottleneck Read More

Background: Rice straw as a plant photosynthesis product, is a valuable renewable resource and it contains protein, fat, cellulose, hemicellulose, lignin and ash. It has received wide attention for biogas can solve both the energy and environment problems. Objective: To improve the degradation rate of rice straw in aerobic and anaerobic bi-phase fermentation process. Methods: Different aerobic methods were adopt Read More

Background: Phospholipase D (PLD)is closely related to browning and senescence of postharvest longan fruit. Objective: This study investigated the effects of 2-butanol (a PLD inhibitor) on the expression and regulation of PLD during storage of longan fruit at a low temperature. Methods: Senescence-related quality indices showed that the 2-butanol-treated fruit presented lower pericarp browning index, pulp breakdown in Read More

Background: Lung cancer is one of the common malignant tumors. The successful diagnosis of lung cancer depends on the accuracy of the image obtained from medical imaging modalities. Objective: The fusion of CT and PET is combining the complimentary and redundant information both images and can increase the ease of perception. Since the existing fusion method sare not perfect enough, and the fusion effect remain Read More

Objective: Biomedical data can be de-identified via micro-aggregation achieving k - anonymity privacy. However, the existing micro-aggregation algorithms result in low similarity within the equivalence classes, and thus, produce low-utility anonymous data when dealing with a sparse biomedical dataset. To balance data utility and anonymity, we develop a novel microaggregation framework. Methods: Combining a den Read More

Background: At present, due to the limitation of hardware, software and network transmission performance, the medical diagnosis of medical CT image equipment is easy to be carried out based on the wrong image. In addition, due to the complex structure of human organs and unpredictable lesion location, it is difficult to judge the reliability of medical CT images, spatial localization of the lesion, two-dimensional Read More