Research Article

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12/19/2016
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
2/23/2017
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
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
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
4/5/2017
Arthritis, Rheumatoid; Gene expression profiling; Humans; Models, Genetic; Monte Carlo method; Signal transduction; Transcriptome

We attempted to identify significant pathway cross-talk in rheumatoid arthritis (RA) by the Monte Carlo cross-validation (MCCV) method. We therefore obtained and preprocessed the gene expression profile of RA. MCCV involves identifying differentially expressed genes (DEGs), identifying differential pathways (DPs), calculating the discriminating score (DS) of the pathway cross-talk, and random ... more

W. Song; Y.M. Zhang; T. Ma; J. Wang; K.Z. Wang
12/23/2016
Fruit; Gene expression profiling; Gene Expression Regulation, Plant; Mutation; Prunus persica; Transcriptome

Fruit ripening is a complex developmental process, the details of which remain largely unknown in fleshy fruits. In this paper, the fruit flesh of two peach varieties, "Zhongyou9" (a nectarine; Prunus persica L. Batsch) and its mutant "Hongyu", was analyzed by RNA-seq technology during two stages of ripening at 20-day intervals. One hundred and eighty significant upregulated and two hundred ... more

H.F. Pan; Y. Sheng; Z.H. Gao; H.L. Chen; Y.J. Qi; X.K. Yi; G.H. Qin; J.Y. Zhang
1/23/2017
Animal Feed; Animals; Chickens; Female; Gene expression; Gene expression profiling; Meat Products; Muscles

Chicken meat quality is becoming increasingly important among breeders and consumers. To understand the effect of feeding conditions on chicken meat quality, we investigated the profiles of genes expressed in chicken breast muscle. Using RNA sequencing, we identified 336, 321, and 387 differentially expressed genes among Chengkou, Daninghe, and Qingjiaoma chickens under scatter- and captivity- ... more

G.L. Gao; C. Wang; X.Z. Zhao; H.W. Wang; Q. Li; J. Li; K.S. Zhang; H. Zhong; Q.G. Wang
2/16/2017
Animals; Gene expression profiling; Gene Expression Regulation; Genetic markers; Oligonucleotide Array Sequence Analysis; Phenotype; Quantitative trait loci; Sheep; Wool

Fiber diameter is a useful indicator of wool traits and it is the main determinant of wool quality and value. A comparative study was conducted to analyze the abundance and expression of 13 candidate genes using expression profile microarray analysis and to identify novel molecular markers associated with wool traits to provide a molecular basis for improving wool quality in sheep. Genes ... more

Y.Z. Tian; T. Usman; K.C. Tian; J. Di; X.X. Huang; X.M. Xu; H. Tulafu; W.W. Wu; X.F. Fu; Y. Bai; M. Tuerxun; A. Maimaiti
3/15/2017
Animals; Breeding; Cells, Cultured; Female; Gene expression profiling; Gene Expression Regulation; Goats; Oocytes; Oogenesis; Single-Cell Analysis; Transcriptome

Juvenile in vitro embryo transfer is an important animal reproductive technology that can shorten the generation interval of livestock, explore the reproductive potential of dams with excellent genetic traits, accelerate genetic progress and production efficiency of the herd, and provide a wealth of genetic resources for livestock breeding. However, oocytes from kids do not develop as well as ... more

X.Y. Yin; G.H. Cheng; H.Y. Guo; Q. Wang; Y.J. Li; H. Zhang
3/30/2017
Brassica; China; Chromosome Mapping; Flowers; Gene expression profiling; Genes, Plant; Plant Proteins; seeds

Pak choi is a highly nutritious vegetable that is widely grown in China, Southeast Asia, and other parts of the world. Because it reproduces by seed, it is very important to understand the mechanism of floral organ development. Therefore, using the Chinese cabbage genome as a reference, this study analyzed the expression profiles of shoot apex genes at flower bud differentiation stages 1 and 5 ... more

H.X. Song; A.M. Ping; M.X. Sun; X.H. Qi; M.Y. Gao; X.Y. Xu; Z.J. Zhu; M.L. Li; L.P. Hou

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