Current Bioinformatics - Volume 10, Issue 1, 2015

It is well known that the mutations in BRCA1 or BRCA2 gene can cause the hereditary breast cancer. However, it is a tedious and expensive task to identify the mutant genes that impact breast cancer due to the large number of genes and very small number of samples. Furthermore, the expressive energy of the subset of genes in comparison to that of one individual gene at a time is considered to have a profound influen Read More

Classification for enzymes is essential for understanding the functions of organisms because it is directly related to the knowledge about which specific target it acts on, as well as to its catalytic process. Hence, it is crucial to use an accurate and robust approach to correctly map the enzyme in specific enzyme family class that it is belong to. In this research, a protein-protein interaction (PPI) network-based method was develo Read More

Prediction and identification of cancer related genes are among of the most challenging and important problems in bioinformatics and biomedicine. Colorectal cancer (CRC), the second most commonly diagnosed cancer worldwide, is a major cause of cancer-related death. Knowledge of CRC-related genes may help to make an early detection of CRC and develop gene-targeted treatment schemes to significantly improve a pati Read More

Hepatocellular carcinoma (HCC) is the most common type of liver cancer worldwide and mostly occurs in viral hepatitis endemic areas such as China. Knowledge of HCC-related genes may lead to an early detection of HCC and develop molecularly targeted therapeutics, reducing mortality and improving a patient’s prognosis significantly. Therefore, it is valuable and important for us to identify common characters of HCC rel Read More

Drosophila circadian rhythm is an interesting topic for researchers and a lot of mathematic models have been constructed. Most of the studies of circadian rhythm are based upon the interactive positive and negative feedback loops controlling the circadian clock. Recently many studies have shown that microRNAs (miRNAs) have important effects on the circadian clock. In this paper, we present a detailed mathematic model o Read More

Recently several experiments have shown that REST is bound to the chromatin of miR-21, and miR-21 inhibits the self-renewal of mouse embryonic stem (ES) cells by decreasing the expression of SOX2, NANOG and OCT4. Thus, REST is believed to be a core transcription factor together with miR-21 to regulate differentiation and self-renewal of ES cells. In this paper, a mathematical model is established for investigating the roles o Read More

A computational systems biology representation was utilized for understanding the molecular and metabolic behaviors of heavy metal assimilation system in the genome Methanosarcina barkeri str. Fusaro. A known functional protein of this system was identified by text mining. A combined functional annotation approach was employed to discover the missing proteins with unknown function. Herein, assimilation systems of c Read More

In an effort to accelerate translational bioinformatics research, this study presents a universal software tool, named as Sequence Relation Drawing program (SRD). It can be used to dynamically visualize the relationship between molecular sequences and their categories based on undirected graphs in similarity analysis of gene and protein sequences. SRD consists of two components: a Window-based application and a comput Read More

Intracellular Ca2+ transients have been shown to be induced by ultrasound in various types of cells and Ca2+ plays an important role in cell recovery after sonoporation. To achieve a complete understanding of Ca2+ dynamics during insonation and get clues for suitable parameters of ultrasound to accelerate its clinical application, a new model of ultrasound-induced Ca2+ dynamics has been developed. In the model, e Read More

GO (Gene Ontology) analysis is a technology which shows the enrichment and distribution of genes based on Gene Ontology databases. It has been widely used in the researches on target genes of biological compounds and medicines. However, the associations among target genes, as well as the associations among biological processes, molecular functions and cellular components were not cleared by the enrichment and distr Read More

Annonaceous acetogenins (Annonin-I, IV, VI, VIII &XVI) were tested for their insecticidal property against the dusky cotton bug Oxycarenus laetus Kirby. Bioinformatics approach using PASS indicated Annonin-I to have the highest phosphatase inhibition and toxic activity. The structure of the target (ND1) was modeled using the Robetta server. The Molecular docking of the ligands to the active site of ND1 was carried out using Read More

This paper proposes an efficient method to solve the DNA fragment assembly problem using Adaptive Particle Swarm Optimization (APSO). The DNA fragment assembly for shotgun sequencing has been under study with great significance and complexity. It refers to the arrangement of the fragments in an accurate sequence. This fragment assembly problem is an NP-hard combinatorial optimization problem. In this paper, t Read More

Lacking of diagnostic biomarker for early diagnosis leads to the poor survival rate of lung squamous cell carcinoma (LUSC). Nowadays, development of high throughput technologies provides a critical timing for identifying molecular biomarkers by integrating multifactorial data. In this work, we have integrated the survival data and multifactorial data (transcription factors, microRNAs and gene ontology terms) to an Read More

To facilitate the similarities/dissimilarities analysis of the protein sequences, we introduce a novel approach based on the recurrence quantification analysis (RQA), in which, based on a selected pair of physicochemical properties of amino acids, the primary structure of proteins is considered as two time series, with the amino acid order playing the role of subsequent time intervals, and then, we adopt RQA to analyze these two ti Read More