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Interdisciplinary Sciences, Computational Life Sciences

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https://www.readbyqxmd.com/read/29313209/an-ensemble-framework-coping-with-instability-in-the-gene-selection-process
#1
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
https://www.readbyqxmd.com/read/29282626/detoxification-of-aflatoxins-on-prospective-approach-effect-on-structural-mechanical-and-optical-properties-under-pressures
#2
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
https://www.readbyqxmd.com/read/29280088/visnormsc-a-graphical-user-interface-to-normalize-single-cell-rna-sequencing-data
#3
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
https://www.readbyqxmd.com/read/29260504/modeling-and-control-of-a-delayed-hepatitis-b-virus-model-with-incubation-period-and-combination-treatment
#4
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
https://www.readbyqxmd.com/read/29243204/genome-wide-assessment-of-polygalacturonases-like-pgl-genes-of-medicago-truncatula-sorghum-bicolor-vitis-vinifera-and-oryza-sativa-using-comparative-genomics-approach
#5
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
https://www.readbyqxmd.com/read/29236214/neural-network-modeling-of-ache-inhibition-by-new-carbazole-bearing-oxazolones
#6
Levent Cavas, Gamze Topcam, Cevher Gundogdu-Hizliates, Yavuz Ergun
Acetylcholine esterase (AChE) is one of the targeted enzymes in the therapy of important neurodegenerative diseases such as Alzheimer's disease. Many studies on carbazole- and oxazolone-based compounds have been conducted in the last decade due to the importance of these compounds. New carbazole-bearing oxazolones were synthesized from several carbazole aldehydes and p-nitrobenzoyl glycine as AChE inhibitors by the Erlenmeyer reaction in the present study. The inhibitory effects of three carbazole-bearing oxazolone derivatives on AChE were studied in vitro and the experimental results were modeled using artificial neural network (ANN)...
December 13, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29236213/structural-probing-screening-and-structure-based-drug-repositioning-insights-into-the-identification-of-potential-cox-2-inhibitors-from-selective-coxibs
#7
Uma Devi Bommu, Kranthi Kumar Konidala, Rishika Pamanji, Suneetha Yeguvapalli
The rate-limiting enzyme cyclooxygenase-2 (COX-2) is considered as an insightful prognostic target for non-small cell lung cancer (NSCLC) therapy. Now, administration and prolonged utilization of selective COX-2 inhibitors (COXIBs) towards moderating the NSCLC has been associated with different side effects. In the present study, we focused on the structure-based drug repositioning approaches for predicting therapeutic potential de novo candidates for human COX-2. Due to discrepancies in the eminence of x-ray diffraction structures, creates a big barrier in drug discovery approach...
December 13, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29214497/comparing-reverse-complementary-genomic-words-based-on-their-distance-distributions-and-frequencies
#8
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...
December 6, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29204795/inferring-gene-regulatory-networks-based-on-a-hybrid-parallel-genetic-algorithm-and-the-threshold-restriction-method
#9
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...
December 4, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29196984/identification-of-disease-critical-genes-using-collective-meta-heuristic-approaches-an-application-to-preeclampsia
#10
Surama Biswas, Subarna Dutta, Sriyankar Acharyya
Identifying a small subset of disease critical genes out of a large size of microarray gene expression data is a challenge in computational life sciences. This paper has applied four meta-heuristic algorithms, namely, honey bee mating optimization (HBMO), harmony search (HS), differential evolution (DE) and genetic algorithm (basic version GA) to find disease critical genes of preeclampsia which affects women during gestation. Two hybrid algorithms, namely, HBMO-kNN and HS-kNN have been newly proposed here where kNN (k nearest neighbor classifier) is used for sample classification...
December 1, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29147967/association-of-inflammatory-bowel-disease-with-arthritis-evidence-from-in-silico-gene-expression-patterns-and-network-topological-analysis
#11
Anukriti Verma, Pallavi Somvanshi, Shafiul Haque, Bhawna Rathi, Shivani Sharda
Inflammatory bowel disease (IBD) is an idiopathic prolonged ailment accountable for inflammatory conditions of the intestine. Moreover, arthritis is responsible for joints' stiffness and painful inflammation. IBD shows certain articular extra-intestinal manifestations associating IBD with arthritis. IBD associated arthritis is found to be linked with ankylosing spondylitis (AS). The present study insights for the potential and putative drug targets and biomarkers of IBD associated with arthritis using in silico approaches...
November 17, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29143920/distinguishing-the-disease-associated-snps-based-on-composition-frequency-analysis
#12
Wenling Li, Menglong Li, Xuemei Pu, Yanzhi Guo
Single-nucleotide polymorphism (SNP) is a basical variation in genome. When SNPs occur at the binding sites of microRNA, they can influence the binding efficiency, cause a fluctuation of the mRNA in vivo, and thus arouse posttranscriptional level abnormality. Therefore, SNP has a strong correlation with diseases. Although enormous SNPs have been experimentally identified, only a tiny proportion of them are truly disease-associated SNPs (dSNPs) that relate to microRNA modification and then are involved in disease causing process...
November 16, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29128919/genome-wide-prediction-of-potential-vaccine-candidates-for-campylobacter-jejuni-using-reverse-vaccinology
#13
Richa Jain, Sarita Singh, Santosh Kumar Verma, Ankit Jain
Campylobacteriosis is a deadly disease which has developed resistance to most of the available chemotherapeutic agents. Although various studies provide evidence of acquired immunity following exposure to Campylobacter jejuni, no effective vaccine has been developed, still. Hence, there is an urgent need to identify potential vaccine candidates for Campylobacter species. In the proposed study, Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168) was taken and computational approach was employed to screen C...
November 11, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29110287/a-novel-hypergraph-based-genetic-algorithm-hgga-built-on-unimodular-and-anti-homomorphism-properties-for-dna-sequencing-by-hybridization
#14
V Swaminathan, Gangothri Rajaram, V Abhishek, Boosi Shashank Reddy, K Kannan
The sequencing by hybridization (SBH) of determining the order in which nucleotides should occur on a DNA string is still under discussion for enhancements on computational intelligence although the next generation of DNA sequencing has come into existence. In the last decade, many works related to graph theory-based DNA sequencing have been carried out in the literature. This paper proposes a method for SBH by integrating hypergraph with genetic algorithm (HGGA) for designing a novel analytic technique to obtain DNA sequence from its spectrum...
November 6, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29103184/in-silico-evaluation-of-variable-ph-on-the-binding-of-epidermal-growth-factor-receptor-ectodomain-to-its-ligand-through-molecular-dynamics-simulation-in-tumors
#15
Inderpal Singh, Gurvinder Singh, Vijeshwar Verma, Shashank Singh, Ratna Chandra
Many aggressive and metastatic cancer cell types show Warburg Effect; therefore, it is a possible adaptation helping cancer cells to rapidly divide and utilize the glycolytic intermediates for biosynthesis of ribose sugars (for nucleotide biosynthesis), fatty acid synthesis (lipids for membrane synthesis), NADPH (cellular currency for reductive biosynthesis) and lactate. This in due course results in decrease of extracellular pH, leading to acidic tumor micro-environment. EGFR is a crucial cell surface signaling receptor implicated in cancer cell survival and progression...
November 4, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29098594/a-comprehensive-computational-analysis-of-mycobacterium-genomes-pinpoints-the-genes-co-occurring-with-ycze-a-membrane-protein-coding-gene-under-the-putative-control-of-a-mocr-and-predicts-its-function
#16
Teresa Milano, Sebastiana Angelaccio, Angela Tramonti, Martino Luigi di Salvo, Isabel Nogues, Roberto Contestabile, Stefano Pascarella
Bacterial proteins belonging to the YczE family are predicted to be membrane proteins of yet unknown function. In many bacterial species, the yczE gene coding for the YczE protein is divergently transcribed with respect to an adjacent transcriptional regulator of the MocR family. According to in silico predictions, proteins named YczR are supposed to regulate the expression of yczE genes. These regulators linked to the yczE genes are predicted to constitute a subfamily within the MocR family. To put forward hypotheses amenable to experimental testing about the possible function of the YczE proteins, a phylogenetic profile strategy was applied...
November 2, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29094320/rare-diseases-drug-discovery-and-informatics-resource
#17
REVIEW
Mingzhu Zhao, Dong-Qing Wei
A rare disease refers to any disease with very low prevalence individually. Although the impacted population is small for a single disease, more than 6000 rare diseases affect millions of people across the world. Due to the small market size, high cost and possibly low return on investment, only in recent years, the research and development of rare disease drugs have gradually risen globally, in several domains including gene therapy, enzyme replacement therapy, and drug repositioning. Due to the complex etiology and heterogeneous symptoms, there is a large gap between basic research and patient unmet needs for rare disease drug discovery...
November 1, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29094319/an-innovative-framework-for-bioimage-annotation-and-studies
#18
Patrizia Vizza, Giuseppe Tradigo, Pietro Hiram Guzzi, Rosario Curia, Loredana Sisca, Filippo Aiello, Gionata Fragomeni, Mario Cannataro, Giuseppe Lucio Cascini, Pierangelo Veltri
The collection and analysis of clinical data are needed to investigate diseases and to define medical protocols and treatments. Bioimages, medical annotations and patient history are clinical data acquired and studied to perform a correct diagnosis and to propose an appropriate therapy. Currently, hospital departments manage these data using legacy systems which do not often allow data integration among different departments or health structures. Thus, in many cases clinical information sharing and exchange are difficult to implement...
November 1, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29094318/discovery-of-t-cell-driven-subunit-vaccines-from-zika-virus-genome-an-immunoinformatics-approach
#19
Dibyabhaba Pradhan, Monika Yadav, Rashi Verma, Noor Saba Khan, Lingaraja Jena, Arun Kumar Jain
The recent outbreaks of Zika virus and the absence of a specific therapy have necessitated to identify T-cell-stimulating antigenic peptides as potential subunit vaccine candidates. The translated ssRNA (+) genome of Zika virus was explored in EMBOSS antigenic and VaxiJen to predict 63 peptides as potential antigens. Three MHC-II binding peptide prediction tools, viz. NetMHCIIpan, PREDIVAC and immune epitope database (IEDB) were employed in consensus on 63 antigenic peptides to propose 14 T-helper cell epitopes...
November 1, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29090372/insight-into-a-transcriptional-adaptor-zinc-finger-encoded-by-a-putative-protein-in-the-white-spot-syndrome-virus-genome
#20
Malathi Shekar, Moleyur Nagarajappa Venugopal
The transcriptional adaptor zinc (TAZ) fingers are a specialized class of zinc finger domains reported to exist only in eukaryotic transcriptional coactivator proteins. A putative protein within the shrimp white spot syndrome virus (WSSV) encodes for a TAZ domain, which is unique as no virus so far has been reported for the presence of this domain. Our study shows the viral TAZ domain to be similar to TAZ2 rather than TAZ1 domain of eukaryotic CREB-binding proteins and its paralog p300 proteins. Furthermore, as with eukaryotic TAZ2 domain which interacts and binds to several transcriptional factors including the p53 tumor suppressor protein, an in silico docking study of the WSSV-TAZ and the shrimp p53 transcriptional factor showed the two protein domains to be involved in a protein-protein interaction...
October 31, 2017: Interdisciplinary Sciences, Computational Life Sciences
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