Research Article

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2017 Feb 23
Algorithms; Amino acid sequence; Amino acids; Animals; binding sites; Computational biology; Databases, Protein; Humans; Hydrophobic and Hydrophilic Interactions; Models, Theoretical; Neural Networks, Computer; Phosphorylation; Proteins; Reproducibility of Results; Support vector machine

Phosphorylation is an important part of post-translational modifications of proteins, and is essential for many biological activities. Phosphorylation and dephosphorylation can regulate signal transduction, gene expression, and cell cycle regulation in many cellular processes. Phosphorylation is extremely important for both basic research and drug discovery to rapidly and correctly identify ... more

R.Z. Han; D. Wang; Y.H. Chen; L.K. Dong; Y.L. Fan
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Female; Gene frequency; Genetic markers; Humans; Immunologic Factors; Intravitreal Injections; Macular Degeneration; male; Polymorphism, Genetic; Precision Medicine; Proteins; Ranibizumab; Sequence Analysis, DNA; Treatment outcome

Age-related macular degeneration (AMD) is a leading cause of blindness in developed countries. The ARMS2 gene has been found to be associated with AMD. Currently, intravitreal ranibizumab (IVR) treatment is one of the widely used treatments for neovascular AMD. The aim of this study was to investigate the association between the genotype of ARMS2 rs10490924 polymorphism and IVR treatment ... more

H. Bardak; Y. Bardak; Y. Ercalik; T. Kumral; S. Imamoglu; M. Gunay; H. Ozbas; O. Bagci
2017 Mar 15
Amino acid sequence; Animals; Base Sequence; Chickens; Eimeria tenella; Escherichia coli; Gene expression; HSP70 Heat-Shock Proteins; Hydrophobic and Hydrophilic Interactions; Protozoan Proteins; Sequence Analysis, DNA

Members of the Eimeria genus are protozoan parasites of the subphylum Apicomplexa (Eimeriidae family), and belong to the coccidia group. Eimeria tenella is one of the most pathogenic species owing to its ability to penetrate the mucosa, and cause inflammation and damage. It is an obligate intracellular parasite that causes disease by destroying the host cells during multiplication. Heat shock ... more

A.L.G. Bogado; G.F. Martins; J.P. Sasse; daS. Guimarães; J.L. Garcia
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cluster analysis; Genes, Plant; Manihot; Phylogeny; Polymorphism, Single Nucleotide; Sequence alignment; Sequence Analysis, DNA; Starch

The distribution and frequency of single nucleotide polymorphisms (SNPs) can help to understand changes associated with characteristics of interest. We aimed to evaluate nucleotide diversity in six genes involved in starch biosynthesis in cassava using a panel of 96 unrelated accessions. The genes were sequenced, aligned, and used to obtain values for nucleotide diversity (π), segregating ... more

L.M. Vasconcelos; A.C. Brito; C.D. Carmo; E.J. Oliveira
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Bacteria; Bacterial Proteins; Computational biology; Databases, Protein; Gene Ontology; Humans; Protein Interaction Mapping

Since the first assembled genomes, gene sequences alone have not been sufficient to understand complex metabolic processes involving several genes, each playing distinct roles. To identify their roles, a network of interactions, wherein each gene is a node, should be created. Edges connecting nodes are evidence of interaction, for instance, of gene products coexisting in the same cellular ... more

G.S. Oliveira; A.R. Santos
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Computational biology; Gene Regulatory Networks; Humans; Models, Genetic; Models, Statistical; Translational Medical Research

A salient problem in translational genomics is the use of gene regulatory networks to determine therapeutic intervention strategies. Theoretically, in a complete network, the optimal policy performs better than the suboptimal policy. However, this theory may not hold if we intervene in a system based on a control policy derived from imprecise inferred networks, especially in the small-sample ... more

X.Z. Zan; W.B. Liu; M.X. Hu; L.Z. Shen
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Computational biology; Gene expression profiling; Humans; Models, Statistical; Reproducibility of Results

Microarray gene expression technology provides a systematic approach to patient classification. However, microarray data pose a great computational challenge owing to their large dimensionality, small sample sizes, and potential correlations among genes. A recent study has shown that gene-gene correlations have a positive effect on the accuracy of classification models, in contrast to some ... more

M. Pan; J. Zhang
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Animals; Cetacea; DNA Barcoding, Taxonomic; Electron Transport Complex IV; Endangered species; Genetic markers; Reference Standards; Sequence alignment

Molecular identification is very useful in cases where morphology-based species identification is not possible. Examples for its application in cetaceans include the identification of carcasses of stranded animals in advanced state of decomposition and body parts that are illegally traded. One DNA region that is often used for molecular identification is the Folmer region of the mitochondrial ... more

L.H.O. Falcão; A.S. Campos; J.E.P. Freitas; M.A.A. Furtado-Neto; V.V. Faria
2017 Jan 23
Female; Genetic predisposition to disease; High-Throughput Nucleotide Sequencing; Humans; Macular Degeneration; male; Proteins; Risk; Turkey

Age-related macular degeneration (AMD) is the leading cause of blindness in developed countries. It is a complex disease with both genetic and environmental risk factors. To improve clinical management of this condition, it is important to develop risk assessment and prevention strategies for environmental influences, and establish a more effective treatment approach. The aim of the present ... more

H. Bardak; M. Gunay; Y. Ercalik; Y. Bardak; H. Ozbas; O. Bagci
2017 Feb 23
Adult; DNA, Viral; Female; Genotype; Hepatitis B Antibodies; Hepatitis B e Antigens; Hepatitis B Surface Antigens; Hepatitis B virus; Hepatitis B, Chronic; Host-Pathogen Interactions; Humans; male; Middle Aged; Polymerase chain reaction; Sequence Analysis, DNA; Virus Activation; Virus Replication; Young Adult

Concurrent detection of hepatitis B surface antigen (HBsAg) and anti-HBs antibody or hepatitis B surface E antigen (HBeAg) and anti-HBe antibody in patients with chronic hepatitis B (CHB) infection is well established. However, the clinical implications of these proteins remain largely unknown. In this study, demographic, clinical, and laboratory data from 124,865 patients with chronic CHB ... more

Y. Xiang; P. Chen; J.R. Xia; L.P. Zhang

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