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Interdisciplinary Sciences, Computational Life Sciences

Juanjuan Kang, Yewei Fang, Pengcheng Yao, Ning Li, Qiang Tang, Jian Huang
Neuropeptides (NPs) are short secreted peptides produced mainly in the nervous system and digestive system. They activate signaling cascades to control a wide range of biological functions, such as metabolism, sensation, and behavior. NPs are typically produced from a larger NP precursor (NPP) which includes a signal peptide sequence, one or more NP sequences, and other sequences. With the drastic growth of unknown protein sequences generated in the post-genomic age, it is highly desired to develop computational methods for identifying NPP rapidly and efficiently...
March 10, 2018: Interdisciplinary Sciences, Computational Life Sciences
Mili Nailwal, Jenabhai B Chauhan
BACKGROUND: DEAD-box helicase 3, Y-linked (DBY) is a candidate gene of the AZF region which is involved in spermatogenesis process. Mutations in the DBY gene may disrupt the spermatogenesis and lead to infertility in men. Identification of functionally neutral mutation from the disease-causing mutation is the biggest challenge in human genetic variation analysis. Owing to the importance of DBY in male infertility, functional analysis was carried out to reveal the association between genetic mutation and phenotypic variation through various in silico approaches...
March 8, 2018: Interdisciplinary Sciences, Computational Life Sciences
Haixin Ai, Xuewei Wu, Mengyuan Qi, Li Zhang, Huan Hu, Qi Zhao, Jian Zhao, Hongsheng Liu
In recent years, new strains of influenza virus such as H7N9, H10N8, H5N6 and H5N8 had continued to emerge. There was an urgent need for discovery of new anti-influenza virus drugs as well as accurate and efficient large-scale inhibitor screening methods. In this study, we focused on six influenza virus proteins that could be anti-influenza drug targets, including neuraminidase (NA), hemagglutinin (HA), matrix protein 1 (M1), M2 proton channel (M2), nucleoprotein (NP) and non-structural protein 1 (NS1). Structure-based molecular docking was utilized to identify potential inhibitors for these drug targets from 13144 compounds in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform...
March 2, 2018: Interdisciplinary Sciences, Computational Life Sciences
Mingming Zhang, Hongbo Mu, Ruijie Zhang, Shenkui Liu, Imshik Lee
Salt stress is a common abiotic stress in agricultural production, which is affected by multiple genes and environmental factors. Although transcriptome analyses have detected some salt-related genes in Arabidopsis thaliana, these genes are often major genes and can not adequately explain the molecular mechanism of salt tolerance. Some genes related to salt stress, but does not reach significant threshold in gene expression analysis (called modest effect genes), are often ignored. Therefore, we took full account of the role of modest effect genes and performed a pathway-based analysis of three gene microarray datasets to identify the pathways related to salt stress...
February 28, 2018: Interdisciplinary Sciences, Computational Life Sciences
Caroline König, René Alquézar, Alfredo Vellido, Jesús Giraldo
G-protein-coupled receptors (GPCRs) are a large and diverse super-family of eukaryotic cell membrane proteins that play an important physiological role as transmitters of extracellular signal. In this paper, we investigate Class C, a member of this super-family that has attracted much attention in pharmacology. The limited knowledge about the complete 3D crystal structure of Class C receptors makes necessary the use of their primary amino acid sequences for analytical purposes. Here, we provide a systematic analysis of distinct receptor sequence segments with regard to their ability to differentiate between seven class C GPCR subtypes according to their topological location in the extracellular, transmembrane, or intracellular domains...
February 19, 2018: Interdisciplinary Sciences, Computational Life Sciences
Ankita Awasthi, Vikrant Nain, Rekha Puria
mTOR regulates multiple cellular processes that are critical for proper maintenance of cell growth and development. However, mechanisms and factors responsible for transcriptional regulation of mTOR are partially known. To identify different transcription factor binding sites in promoter region of mTOR, we performed in silico phylogenetic foot printing analysis of diverse set of human orthologs. Phylogenetic tree for the orthologs was generated to establish the evolutionary relationships among them. Conserved binding sites among the species were predicted by tool MEME...
February 6, 2018: Interdisciplinary Sciences, Computational Life Sciences
Agnieszka Cecotka, Joanna Polanska
Alteration of DNA methylation level in cancer diseases leads to deregulation of gene expression-silencing of tumor suppressor genes and enhancing of protooncogenes. There are several tools devoted to the problem of identification of CpG sites' demethylation but majority of them focuses on single site level and does not allow for quantification of region methylation changes. The aim was to create an adaptive algorithm supporting detection of differentially methylated CpG sites and genomic regions specific for acute myeloid leukemia...
February 5, 2018: Interdisciplinary Sciences, Computational Life Sciences
D A Adeniyi, Z Wei, Y Yang
A wealth of data are available within the health care system, however, effective analysis tools for exploring the hidden patterns in these datasets are lacking. To alleviate this limitation, this paper proposes a simple but promising hybrid predictive model by suitably combining the Chi-square distance measurement with case-based reasoning technique. The study presents the realization of an automated risk calculator and death prediction in some life-threatening ailments using Chi-square case-based reasoning (χ2 CBR) model...
January 30, 2018: Interdisciplinary Sciences, Computational Life Sciences
A Sreeja, U Krishnakumar, K P Vinayan
Interaction of multiple genetic variants is a major challenge in the development of effective treatment strategies for complex disorders. Identifying the most promising genes enhances the understanding of the underlying mechanisms of the disease, which, in turn leads to better diagnostic and therapeutic predictions. Categorizing the disease genes into meaningful groups even helps in analyzing the correlated phenotypes which will further improve the power of detecting disease-associated variants. Since experimental approaches are time consuming and expensive, computational methods offer an accurate and efficient alternative for analyzing gene-disease associations from vast amount of publicly available genomic information...
January 30, 2018: Interdisciplinary Sciences, Computational Life Sciences
Baomin Li, Fenglei Yang
As a simulation of human expression recognition, the studies on automatic expression recognition expect to draw useful enlightenment through close, accurate observation on human expression processing via advanced devices. Eye-trackers are mostly used devices that are technically designed to obtain eye-movement data. However, due to the discrepancy between target faces, across-target analysis is limited in these studies, and this much reduces the chance of finding the latent eye-behavior patterns. Through the utilization of correspondences between targets, this study achieves an across-target analysis to explore the attention pattern in expression recognition...
January 30, 2018: Interdisciplinary Sciences, Computational Life Sciences
Noé Vázquez, Cristina P Vieira, Bárbara S R Amorim, André Torres, Hugo López-Fernández, Florentino Fdez-Riverola, José L R Sousa, Miguel Reboiro-Jato, Jorge Vieira
When changes at few amino acid sites are the target of selection, adaptive amino acid changes in protein sequences can be identified using maximum-likelihood methods based on models of codon substitution (such as codeml). Although such methods have been employed numerous times using a variety of different organisms, the time needed to collect the data and prepare the input files means that tens or hundreds of coding regions are usually analyzed. Nevertheless, the recent availability of flexible and easy to use computer applications that collect relevant data (such as BDBM) and infer positively selected amino acid sites (such as ADOPS), means that the entire process is easier and quicker than before...
January 30, 2018: Interdisciplinary Sciences, Computational Life Sciences
Jamal Shamsara
5-Alpha-reductase 2 is an interesting pharmaceutical target for the treatment of several diseases, including prostate cancer, benign prostatic hyperplasia, male pattern baldness, acne, and hirsutism. One of the main approaches in computer aided drug design is structure-based drug discovery. However, the experimental 3D structure of 5-alpha-reductase 2 is not available at present. Therefore, a homology modeling method and molecular dynamics simulation were used to develop a reliable model of 5-alpha-reductase 2 for inhibitor pose prediction and virtual screening...
January 30, 2018: Interdisciplinary Sciences, Computational Life Sciences
Zhiyong Pei, Jielin Liu, Manjiao Liu, Wenchao Zhou, Pengcheng Yan, Shaojun Wen, Yubao Chen
Essential hypertension (EH) has become a major chronic disease around the world. To build a risk-predicting model for EH can help to interpose people's lifestyle and dietary habit to decrease the risk of getting EH. In this study, we constructed a EH risk-predicting model considering both environmental and genetic factors with support vector machine (SVM). The data were collected through Epidemiological investigation questionnaire from Beijing Chinese Han population. After data cleaning, we finally selected 9 environmental factors and 12 genetic factors to construct the predicting model based on 1200 samples, including 559 essential hypertension patients and 641 controls...
January 29, 2018: Interdisciplinary Sciences, Computational Life Sciences
José A Castellanos-Garzón, Juan Ramos, Daniel López-Sánchez, Juan F de Paz, Juan M Corchado
This paper proposes an ensemble framework for gene selection, which is aimed at addressing instability problems presented in the gene filtering task. The complex process of gene selection from gene expression data faces different instability problems from the informative gene subsets found by different filter methods. This makes the identification of significant genes by the experts difficult. The instability of results can come from filter methods, gene classifier methods, different datasets of the same disease and multiple valid groups of biomarkers...
January 8, 2018: Interdisciplinary Sciences, Computational Life Sciences
Yong-Kai Wei, Xiao-Miao Zhao, Meng-Meng Li, Jing-Xin Yu, Selvaraj Gurudeeban, Yan-Fei Hu, Guang-Fu Ji, Dong-Qing Wei
Aflatoxins are sequential of derivatives of coumarin and dihydrofuran with similar chemical structures and well-known carcinogenic agent. Many studies performed to detoxify aflatoxins, but the result is not ideal. Therefore, we studied structural, infrared spectrum, mechanical, and optical properties of these compounds in the aim of perspective physics. Mulliken charge distributions and infrared spectral analysis performed to understand the structural difference between the basic types of aflatoxins. In addition, the effect of pressure, different polarized, and incident directions on their structural changes was determined...
December 27, 2017: Interdisciplinary Sciences, Computational Life Sciences
Lijun Tang, Nan Zhou
Single-cell RNA sequencing (RNA-seq) allows the analysis of gene expression with high resolution. The intrinsic defects of this promising technology imports technical noise into the single-cell RNA-seq data, increasing the difficulty of accurate downstream inference. Normalization is a crucial step in single-cell RNA-seq data pre-processing. SCnorm is an accurate and efficient method that can be used for this purpose. An R implementation of this method is currently available. On one hand, the R package possesses many excellent features from R...
December 26, 2017: Interdisciplinary Sciences, Computational Life Sciences
Ana Helena Tavares, Jakob Raymaekers, Peter J Rousseeuw, Raquel M Silva, Carlos A C Bastos, Armando Pinho, Paula Brito, Vera Afreixo
In this work, we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance distributions are considered, and it is found that the peak dissimilarity works best in this setting. We report the existence of reverse complementary word pairs with very dissimilar distance distributions, as well as word pairs with very similar distance distributions even when both distributions are irregular and contain strong peaks...
March 2018: Interdisciplinary Sciences, Computational Life Sciences
Ming Zheng, Shugong Zhang, You Zhou, Guixia Liu
Inferring gene regulatory networks (GRNs) is a challenging computational task in system biology. Many inference algorithms have been proposed along with related modifications to various problems. Every algorithm has its own advantages and drawbacks. In particular, the efficiency of each algorithm is not as good as people expect. A novel inference algorithm is proposed in this paper that can be divided into two parts. In the first part, the pre-computational part, two tasks must be accomplished: singular value decomposition for solution space determination and the threshold restriction method for redundant edge deletion...
March 2018: Interdisciplinary Sciences, Computational Life Sciences
Deshun Sun, Fei Liu
In this paper, a hepatitis B virus (HBV) model with an incubation period and delayed state and control variables is firstly proposed. Furthermore, the combination treatment is adopted to have a longer-lasting effect than mono-therapy. The equilibrium points and basic reproduction number are calculated, and then the local stability is analyzed on this model. We then present optimal control strategies based on the Pontryagin's minimum principle with an objective function not only to reduce the levels of exposed cells, infected cells and free viruses nearly to zero at the end of therapy, but also to minimize the drug side-effect and the cost of treatment...
December 19, 2017: Interdisciplinary Sciences, Computational Life Sciences
Gautam Anand, Sangeeta Yadav, Aiman Tanveer, Jeya Nasim, Nitish K Singh, Amit K Dubey, Dinesh Yadav
The polygalacturonases (PG) is one of the important members of pectin-degrading glycoside hydrolases of the family GH28. In plants, PG represents multigene families associated with diverse processes. In the present study, an attempt has been made to investigate the diversity of PG genes among monocots and dicots with respect to phylogeny, gene duplication and subcellular localization to get an insight into the evolutionary and functional attributes. The genome-wide assessment of Medicago truncatula, Vitis vinifera Sorghum bicolor, and Oryza sativa L...
December 14, 2017: Interdisciplinary Sciences, Computational Life Sciences
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