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It is well-known that obesity has a marked effect on many of the routinely used laboratory parameters. An obvious example is the serum level of various blood lipids: hyperlipidemia, hypercholesteremia are often observed in obese people. Our research aimed to provide a more thorough understanding of the effects of obesity on laboratory parameters, concentrating on every laboratory parameter, not just...
Summary form only given: Viruses have been implicated as the causative agents for a variety of cancers as well as diseases of the major physiological systems (e.g., nervous, respiratory, immune, reproductive, etc.), and viral infections have consistently ranked among the leading causes of death worldwide. Although viruses exhibit extreme biological diversity, plainly evidenced by the Baltimore classification...
Influenza is one of the most important emerging and reemerging infectious diseases, causing high morbidity and mortality in communities (epidemic) and worldwide (pandemic). Here, Classification of human vs. non-human influenza, and subtyping of human influenza viral strains virus is done based on Profile Hidden Markov Models. The classical ways of determining influenza viral subtypes depend mainly...
Glioblastoma is the most aggressive form of brain cancer. Transcriptional aberrations may play an important role in etiology of glioblastoma, which might be caused through genomic alterations: nucleotide mutation, copy number variation, DNA mythelation. Here, we explored another possible mechanism involving cooperative deregulation of microRNAs (miRNAs) and transcription factors (TFs). Several miRNA-TF...
We developed a procedure for indentifying transcriptional master regulators (MRs) related to special biological phenomena, such as diseases, in conjunction with network screening and inference. Network screening is a system for detecting activated transcriptional regulatory networks under particular conditions, based on the estimation of the graph structure consistency with the measured data. Since...
Most loci discovered through genome-wide association analyses are predicted to affect gene expression, the integrative approach of genome-wide analysis with gene expression data is becoming essential procedure for discovering genetic effect of disease development. Many studies have been performed to discover significant SNP-gene associations, but most of them are limited to consider only cis-associations...
Conotoxins show prospects for being potent pharmaceuticals in the treatment of some serious disease. Accurate prediction of conotoxin superfamily would have many important applications in biological research and clinical medicine. In this study, we propose a novel dHKNN method to predict conotoxin superfamily. Firstly, we extract the protein's sequential features composed of physicochemical properties,...
Several flaviviruses are important human pathogens, including dengue virus, a disease against which neither a vaccine nor specific antiviral therapies currently exist. QSAR study was carried out with the purpose of searching new competitive dengue inhibitors with similar properties to the existence inhibitors (i.e. data set). The approach began with the development of rigorously validated QSAR model...
Local gene network pattern (LGNP) is a useful tool to display complex relationship between multiple genes. A diabetes-specific local gene network (LGN) was constructed with 29 genes (including 9 diabetes susceptibility genes and 20 extra genes to join them) that participate in 30 biological pathways. Further analysis indicated diabetes-specific LGN has close relations with carbohydrate metabolism,...
Bioinformatics is an interesting combination of biology and computational sciences, which help scientists and researchers to do more biological experiments to improve the life of living being. Gene expression is fundamental biological basics of cell biology. It is also responsible for genetic as well as physical or biochemical characteristics of an organism. The study of gene expression analysis helps...
In this paper an assay for the detection of genes associated with rheumatoid arthritis (RA) and multiple sclerosis, using polymerase chain reaction (PCR) and sequence specific oligonucleotide probes (SSOP) is presented, in order to be further applied in a portable Lab-On-Chip (LOC) device. A substantial part of these reagents were based on the literature (11th International Histocompatibility Workshop,...
This paper addresses mutational events that give rise to differing response to drugs focusing on Rac1, a protein that has been recognized as a target for drug design for cardiovascular disease due its regulatory role of angiogenesis. Rac1 has been considered with reference to Single Nucleotide Polymorphism (SNP), which has become of great value for personalized medicine. We have considered four variation...
Inspired by recent discovery that human disease phenome shows a modular organization on the genetic landscape, we introduce a network-module based method towards phenotype-genotype association inference and disease-gene identification. This approach integrates protein-protein interaction network, phenotype similarity network and known phenotype-genotype associations, and then decomposes the resulted...
Abstract-We present a novel Bayesian network (BN) to classify strains of Mycobacterium tuberculosis complex (MTBC) into six major genetic lineages using mycobacterial interspersed repetitive units (MIRUs), a high-throughput biomarker. MTBC is the causative agent of tuberculosis (TB), which remains one of the leading causes of disease and morbidity world-wide. DNA fingerprinting methods such as MIRU...
This paper describes an approach to providing computer-interpretable logical definitions for the terms of the Human Phenotype Ontology (HPO) using PATO, the ontology of phenotypic qualities, to link terms of the HPO to the anatomic and other entities that are affected by abnormal phenotypic qualities. This approach will allow improved computerized reasoning as well as a facility to compare phenotypes...
We combine text mining with methods of systems biology for the first time, to predict functional networks for therapeutic mechanisms of Traditional Chinese Medicine in rheumatoid arthritis. The text mining results indicated rheumatoid arthritis highly associated with Tripterygium wilfordii, and eleven genes associated with both. Protein interaction information for these genes from databases and Literature...
It has been commonly accepted that protein-protein interaction network contains valuable information for elucidation of biological processes. Such information, which is difficult to be identified from traditional genetic studies, is important for uncovering the mechanisms of complex diseases such as cancers. In this study, we performed a systematic analysis of global network characteristics for the...
The Gene Ontology (GO) was widely used to annotate gene products, which provide a new way to analyze the relationship between the gene products. Many approaches based on GO were proposed to measure the functional similarity of gene products. In order to improve the accuracy, we proposed a novel method, MUI, to measure functional similarity of gene products combining the information of the interactions...
HPAI A (H5N1) is an avian disease. It is commonly known as "avian influenza" or "bird flu" because of highly pathogenic avian influenza virus of type A of subtype H5N1. It has made great progress in the research on the Avian Influenza A. This paper makes use of the Z curve method to visualize and analyze DNA sequences of H5N1. Z curve is a three- dimensional space curve constituting...
One of the principal features of DNA microarrays is the volume of quantitative data that they generate. As a result, the major challenges in the field are how to handle, interpret and make use of these data. Currently, there are a large number of tools available which perform statistical analysis for constructing a significant gene set from the microarray data. There are others who given a set of...
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