Current Bioinformatics - Volume 15, Issue 5, 2020

Pathway analysis integrates most of the computational tools for the investigation of high-level and complex human diseases. In the field of bioinformatics research, biological pathways analysis is an important part of systems biology. The molecular complexities of biological pathways are difficult to understand in human diseases, which can be explored through pathway analysis. In this review, we describe essential informa Read More

Background: Carboxylation is one of the most biologically important post-translational modifications and occurs on lysine, arginine, and glutamine residues of a protein. Among all these three, the covalent attachment of the carboxyl group with the lysine side chain is the most frequent and biologically important type of carboxylation. For studying such biological functions, it is essential to correctly determine the lysine sites s Read More

Background: Medical test orders can display the physiological functions of patients by using medical means. The medical staff determines the patient's condition through medical test orders and completes the treatment. However, for most patients and their families, there are so many terminologies in the medical test list and they are inconvenient to understand and query, which would affect the patients’ cognition and Read More

Background: Antioxidant Response Elements (ARE) play a key role in the expression of Nrf2 target genes by regulating the Keap1-Nrf2-ARE pathway, which offers protection against toxic agents and oxidative stress-induced diseases. Objective: To develop a database of putative AREs for all the genes in the zebrafish genome. This database will be helpful for researchers to investigate Nrf2 regulatory mechanisms in detail. Read More

Background: Bioinformatics software for RNA-seq analysis has a high computational requirement in terms of the number of CPUs, RAM size, and processor characteristics. Specifically, de novo transcriptome assembly demands large computational infrastructure due to the massive data size, and complexity of the algorithms employed. Comparative studies on the quality of the transcriptome yielded by de novo assemblers hav Read More

Background: In the last years, similarity searching has gained wide popularity as a method for performing Ligand-Based Virtual Screening (LBVS). This screening technique functions by making a comparison of the target compound’s features with that of each compound in the database of compounds. It is well known that none of the individual similarity measures could provide the best performances each time pertaining to Read More

Background: Hotspots are those residues that contribute major free energy of binding in protein-protein interactions. Protein functions are frequently dependent on hotspot residues. At present, hotspot residues are always identified by Alanine scanning mutagenesis technology, which is costly, time-consuming and laborious. Objective: Therefore, more accurate and efficient methods have to be developed to identify prote Read More

Background: Aegilops tauschii is a wild relative of bread wheat. This species has been reported as the donor of bread wheat D genome. There are also several reports that mentioned the importance of Ae. tauschii in biotic and abiotic stress tolerance. On the other hands, miRNAs have been reported as the essential regulatory elements in stress response. Objective: Therefore, it is important to discover novel miRNAs involved Read More

Background: White Blood Cell (WBC) image segmentation plays a key role in cell morphology analysis. However, WBC segmentation is still a challenging task due to the diversity of WBCs under different staining conditions. Objective: In this paper, we propose a novel WBC segmentation method based on color component combination and contour fitting to segment WBC images accurately. Methods: Specifically, the propo Read More

Background: The microbiome plays a very important role in many physiological processes including metabolism, inflammation, homeostasis and many biological pathways. Therefore, dysbiosis of the microbiome disrupts these pathways in different ways that may result in causing cancer. There is a complex connection between the microbiome and cancer. The human bodies are continuously exposed to microbial cells, bot Read More

Background: Some natural pancreatic lipase inhibitors with fewer side effects are proposed. As a traditional Chinese medicine, Shuangdan Capsule (SDC) has been used for the treatment of higher lipid in blood, which is mainly composed by Radix Salviae and Peony skin. Objective: This work is aimed to investigate the molecular mechanism of the constituents from this SDC against metabolic disorders, the molecular flexibility an Read More

Background: Thermophilic proteins can maintain good activity under high temperature, therefore, it is important to study thermophilic proteins for the thermal stability of proteins. Objective: In order to solve the problem of low precision and low efficiency in predicting thermophilic proteins, a prediction method based on feature fusion and machine learning was proposed in this paper. Methods: For the selected thermophilic dat Read More

Background: The rhizosphere microbiota are of vital importance for plant growth and health in terrestrial ecosystems. There have been extensive studies aiming to identify the microbial communities as well as their relationship with host plants in different soil types. Objective: In the present study, we have employed the high-throughput sequencing technology to investigate the composition and structure of rhizosphere micro Read More