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Sequences lacking molecular function annotations have limited research value, so automated approaches for annotating molecular function are used to smooth over this deficiency. Whereas massive erroneous prediction results that may reduce the reliability and utility of these methods is non-ignorable in protein function prediction. Approaches combined phylogenomics and mathematical inference have been...
Exploring and identifying novel aging genes has been the current area of interest in Gerontology. A variety of techniques have been proposed to identify the genes that affect the centenarians and the focus is on the study of genes of interest affecting older population. However the study of aging related pathways using computational methods has not been discussed explicitly so far. In this paper,...
When designing a cloud infrastructure, it is critical to ensure beforehand that the system will be able to offer the desired level of QoS (Quality of Service). Our attention is focused here on efficient QoS accessing to a biological database in cloud computing systems. Our group developed two software applications that address important biological problems, Biblio-MetReS and Homol-MetReS. Biblio-MetReS...
In the embryo development problem for the Drosophila melanogaster, a set of molecules known as mor-phogens are responsible for the embryo segmentation. These morphogens are encoded by different genes, including the GAP genes, maternal coordination genes and pair-rule genes. One of the maternal coordination genes encodes the Bicoid morphogen, which is the responsible for the development of the Drosophila...
BLAST[1] (Basic Local Alignment Search Tool) is a suite of programs used to identify similarity between genetic sequences. It is one of the most widely used tools in Bioinformatics. In recent years, with the size of gene and protein sequence database increasing exponentially, BLAST has become both a data-intensive and a computation-intensive application. How to run BLAST rapidly with low cost has...
Information Extraction is an activity of examine text for information relevant to some interest. Information extraction needs depth analysis than simple key word searches. The information extraction system recognizes and extracts knowledge from a massive literature and extracted knowledge is accumulated in a knowledge base. Many conventional automatic information extraction approaches using Natural...
Proteins have very important role in cellular processes. Proteins doesn't work alone, rather they interact together to perform various cellular events. Protein protein interaction means physical contact between two or more proteins as a result of certain biochemical events. There are several examples for protein interactions. Cell transduction, cell metabolism, muscle contraction are some of them...
Cardiomyopathies are a group of genetically heterogeneous myocardial diseases. In primary cardiomyopathies, hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) are usually autosomal dominant inherited. Network modules are often used to analyze biological insights of some diseases. In this article, we firstly collected pathogenic proteins of HCM and DCM from the PubMed database using...
Occurrence of high imbalance in real-world domains is a direct result of rarity of interesting events, which results in skewed datasets. Without dataset rebalancing, the learning algorithm will encounter extremely low minority class samples therefore it gets biased towards the majority class in the classification tasks. Hence properly handling the imbalanced dataset is a crucial issue in the pattern...
Protein is the primary element of organism and takes part in almost all the biological processes such as metabolism and neurological regulation. Generally, proteins are interacting with each other while they exert biological role in vivo. The exploration upon protein-protein interactions (PPIs) of the specific biological process could provide valuable information to the study of the relevant field...
Although a number of sequence database search tools and post-database search algorithms for filtering target PSMs have been developed, the discrepancy among the output PSMs is usually significant, remaining a few disputable PSMs. We employ a SVM-based learning model to search the optimal weight for each target PSM and develop a new score system, C-Ranker, to rank all target PSMs. Compared with PeptideProphet...
Proteins are the functional subunits of a cell which interact with each other to carry out biological processes. Protein interaction networks form the backbone of the research in molecular and systems biology. Although there are available methods to mine protein interactions and their detection methods from the biological literature, the accuracy of these methods is quite low. In this study, we applied...
The Chinese genebank contains 6169 wild soybean (Glycine soja) accessions collected from 25 provinces. In this study, leaf shape and a suite of other morphological characteristics were analyzed in order to examine the relationship between leaf shape and other characteristics of wild soybeans. The accessions were classified into the following six groups based on leaf shape: accessions with round leaves,...
There are currently several biological databases related to proteins depending on the information we are interested to extract. Therefore, since a heterogeneous set of features will be needed (domains, structures, ontology terms, etc), several quite different databases should be consulted. The handling of different databases can become difficult, as each database could provide a different nomenclature...
Computer-aided drug design techniques are important assets in pharmaceutical industry because of their support for research and development of new drugs. Molecular docking (MD) predicts specific compound's binding modes within the active site of target proteins. Since MD is a time-consuming process, existing approaches reduce the number of receptors or ligands in docking by evaluating only small sets...
In NVR which is an NMR protein structure based assignment program, only N15 labeled data has been used until now due to the cost of acquiring C13 labeled data. Besides, in score function of NVR program, manually set parameters have been used for different proteins while calculating assignment probability of atoms. Nowadays, triple resonance experiments are standardized and obtaining C13 labeled data...
Primary sequence motif extraction from protein amino sequences is a field of growing importance in bioinformatics due to its relevance to both sequential and structural analysis. Many approaches for motif extraction include two limitations: a reliance on discovering an existing, known protein homologue to perform motif extraction or structural analysis, and an assumed motif length. This work would...
Network theory has been used for modeling biological data as well as social networks, transportation logistics, business transcripts, and many other types of data sets. Identifying important features/parts of these networks for a multitude of applications is becoming increasingly significant as the need for big data analysis techniques grows. When analyzing a network of protein-protein interactions...
Objectives: In order to better understand the synergetic activities of radix aconite lateralis praeparata (Fuzi)-rheum officinale (Dahuang) herb pairs. Material and methods: The target proteins of Fuzi and Dahuang were retrieved from PubChem database and were uploaded to ingenuity pathway analysis (IPA) platform. Then we carried out molecular network analysis and canonical pathway analysis. Finally,...
Acne is the most common chronic inflammatory skin disease in adolescents and young adults. Many Chinese herbal medicines (CHMs) have been used in the treatment of acne and were proved to be effective and safe. There is growing need to investigate which CHMs are the most frequently prescribed herbs used to treatment acne and what were the molecular mechanisms of therapeutic effects of these CHMs. So...
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