Current Bioinformatics - Volume 11, Issue 1, 2016

With recent development of bioinformatics, the importance of understanding protein function has been widely acknowledged. Most proteins perform their functions by interacting with other proteins. Hence, it is urgent to explore the protein-protein interaction (PPI). At present, the prediction of PPIs is still a tough problem. Despite the fact that a variety of computational methods have been proposed to identify PPIs; Read More

Boolean network is a powerful tool for the study of gene regulatory networks, and dynamics of a Boolean network is mainly determined by its attractors. In this study, a new approach to construct Boolean network is proposed based on biochemical reaction differential equations. We attempt to investigate gene regulatory networks by means of comparing the experimental results from relevant literature with the attra Read More

B-cell epitope, also known as antigenic determinant, is part of an antigen recognized by the B-cells. The capability of an antibody to recognize epitopes is widely utilized in numerous biomedical applications including immunodetection and immunotherapeutics. Identification of immunogenic regions helps to understand the mechanisms of the immune system and guide the related applications. In contrast with laborious and ti Read More

Cercis gigantea is one of the most beautiful garden trees. It is part of the Cercis genus in the subfamily Caesalpinioideae of Leguminosae. However, little genetic information of C. gigantea is available. In the present study, the C. gigantea transcriptome was subjected to RNA sequencing. This generated large expression datasets suitable for functional genomic analysis. Some 55.5 million high-quality clean reads were collected. Read More

Characterization of cancer related genes is important and challenging in both biomedicine and computational biology. As one of the leading causes of cancer mortality worldwide, lung cancer accounts for over one million deaths each year. Generally, lung cancer can be assigned to small-cell lung cancer (SCLC) and non-small-cell lung cancer (NSCLC). Although great advances have been made in lung cancer detection and trea Read More

Breast cancer, the most prevalent cancer in women, develops from breast tissue. Its incidence has increased in recent years due to environmental risk factors. Thus, it is urgent to uncover the mechanism underlying breast cancer to design effective treatments. Identification of all breast cancer-related genes is one way to help elucidate the underlying breast cancer mechanism. In this study, a computational method was built an Read More

Gene expression level changes in cancer patients have been studied for a long time and have proven to be useful in classifying patients, predicting drug response, etc. But factors that control the gene expression in pathological conditions are still unclear. Identifying the putative causal factors could greatly help in understanding the mechanisms of cancer development and progression. It is believed that the microRNA, methylati Read More

In this paper, we have performed virtual screening of compounds to identify potential inhibitors against the Penicillin Binding Protein 2B (PBP2B) of the resistant 5204 strain of Streptococcus pneumoniae. We have considered 1,677,620 compounds from ZINC database for virtual screening workflow of Schrödinger suite software to identify potential inhibitors that are capable of binding to mutated resistant 5204-PBP2B. Initia Read More

A structure-activity relationship (SAR) dataset was generated for a set of acetylcholinesterase inhibitors using Adaboost and physicochemical parameters. After calculation, it is found that the ACC of SAR model is 99.51 by using 10-fold cross-validation test, while 99.35% for independent test set. Based on the SAR prediction model, bakuchiol is predicted to be an acetylcholinesterase inhibitor. Fluorescence was used to inv Read More

The development of cancer evolves gene mutations according to the somatic mutation theory. The identification and prediction of the cancer-associated genes is one of the most important aims in cancer research. We apply four centrality metrics (degree, betweenness, closeness and PageRank) to prioritize and predict the candidate cancer-associated genes in the human signaling network. We find that the genes with Read More

Frameworks for metabolic engineering have been successfully applied in combination with pre- and post-processing algorithms on genome-wide metabolic models. However, genetic engineering methods with a particular focus on understanding results from multiple perspectives and combining automated and human design are still lacking. To this end, we adopt a multi-objective genetic design technique to find the opt Read More

This paper deals with the relations among structural, topological, and chemical properties of the E. coli proteome from the vantage point of the solubility/aggregation propensity of proteins. Each E. coli protein is initially represented according to its known folded 3D shape. This step involves representing the available E. coli proteins in terms of graphs. We first analyze those graphs by considering pure topological characteriza Read More

Gene fusion is a key factor in sarcomas, lymphomas, leukemias and so on. In order to help biologist to discover the target of the treatment, we developed VFP to predict gene-fusion from single-end RNA-sequencing reads. VFP employs seed index strategy and octal encoding operations for sequence alignments. By using several rules to score and filter the potential fusion genes, VFP could detect known and novel fusions thr Read More

Terpenes are the major component of essential oils biosynthesized in various plant species. The essential oils are widely used as natural flavouring agents, food additives, perfumery and pharmaceuticals. The terpenes are of many types based on presence of numbers of isoprene units i.e. mono (C10), sesqui (C15), di (C20), tri (C30) and tetra (C40). The monoterpenes are diverse in nature and useful for plants and human. Monot Read More

The development of high-throughput screening for protein-protein interaction (PPI) is currently utilized for detailed experimentation and the formulation of biological hypotheses. Comprehensive and concrete PPI networks of domestic animals are urgently needed because of their considerable economic value. We constructed the PPI networks of chickens, cattle, dogs, horses, and rabbits using the InParanoid metho Read More

The discovery of microRNAs (miRs) in the 1990's spawned a genre of research which has thrown light on the involvement of these small non-coding RNAs in several developmental pathways and diseases, one of which happens to be cancer. While algorithms which predict the binding of miRNAs to their targets are abundant, the same is not true for the association of miRNAs to targets which can be implicated in cancer. Machine l Read More