Research Article

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3/15/2017
Amino acid sequence; Base Sequence; Computational biology; Databases, Genetic; Humans; Models, Molecular; Open Reading Frames; Precision Medicine; Proteins; Sequence alignment; Sequence Analysis, DNA

Technological advancements in recent years have promoted a marked progress in understanding the genetic basis of phenotypes. In line with these advances, genomics has changed the paradigm of biological questions in full genome-wide scale (genome-wide), revealing an explosion of data and opening up many possibilities. On the other hand, the vast amount of information that has been generated ... more

W.J.S. Diniz; F. Canduri
1/23/2017
Biomarkers, Tumor; Colonic Neoplasms; Humans; Models, Theoretical; Reproducibility of Results; Support vector machine

We aimed to evaluate the specificity of 12 tumor markers related to colon carcinoma and identify the most sensitive index. Bhattacharyya distance was used to evaluate the index. Then, different index combinations were used to establish a support vector machine (SVM) diagnosis model of malignant colon carcinoma. The accuracy of the model was checked. High accuracy was assumed to indicate the ... more

W.Y. Yang; G. Shi; L.P. Wu; S.T. Wei; Y.N. Huang; L.X. Tan; R.Z. Yang; C.X. Yan; E.T. Guo; H.Y. Wang; J.Z. Tong; Y. Dong; D.Z. Han
12/19/2016
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
1/23/2017
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
3/15/2017
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
06/29/2017
Amino acids; Animals; Collagen; Fish Proteins; Gadiformes; Protein Denaturation; Protein Subunits; Skin

Acid and pepsin-soluble collagen (ASC and PSC, respectively) were extracted from cod (Gadus macrocephaius) skin, and yields of 37.36 and 55.96% were obtained for ASC and PSC, respectively. The total yield of ASC and PSC was 93.92%, based on the lyophilized dry weight, which is higher than that obtained from other sources. Electrophoresis revealed that both ASC and PSC consisted of two ... more

Y. Shu; H. Ren; R. Ao; W.C. Qi; Z.S. Zhang
12/19/2016
Computational biology; Gene Regulatory Networks; Humans; Models, Genetic; Models, Statistical; Translational Research, Biomedical

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
1/23/2017
Animals; Biomarkers; Cell line; G-Protein-Coupled Receptor Kinase 2; Humans; Mechanical Phenomena; Mice; Osteoblasts; Phosphorylation; Receptors, Purinergic P2Y2; Signal transduction

Bone desensitization after mechanical loading is essential for bone to adapt to its mechanical environment. However, the desensitization mechanism is unknown. Previous studies suggest that G protein-coupled receptors (GPCRs), including P2Y and parathyroid hormone receptors, play important roles in osteoblast mechanobiology. Thus, for the present research, we examined the role of G protein- ... more

Y. Xing; Y. Gu; X. Shan; L. Wang; J. You
3/30/2017
Amino acids; Crop Production; Crops, Agricultural; Edible Grain; Food Analysis; Genetic association studies; Genotype; seeds; Statistics as Topic; Zea mays

The objective of this study was to evaluate the effects of multicollinearity under two methods of canonical correlation analysis (with and without elimination of variables) in maize (Zea mays L.) crop. Seventy-six maize genotypes were evaluated in three experiments, conducted in a randomized block design with three replications, during the 2009/2010 crop season. Eleven agronomic variables ( ... more

B.M. Alves; C. Filho; C. Burin
12/19/2016
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

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