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Enhanced construction of gene regulatory networks using hub gene information
Yu, Donghyeon,Lim, Johan,Wang, Xinlei,Liang, Faming,Xiao, Guanghua BioMed Central 2017 BMC bioinformatics Vol.18 No.1
<P><B>Background</B></P><P>Gene regulatory networks reveal how genes work together to carry out their biological functions. Reconstructions of gene networks from gene expression data greatly facilitate our understanding of underlying biological mechanisms and provide new opportunities for biomarker and drug discoveries. In gene networks, a gene that has many interactions with other genes is called a hub gene, which usually plays an essential role in gene regulation and biological processes. In this study, we developed a method for reconstructing gene networks using a partial correlation-based approach that incorporates prior information about hub genes. Through simulation studies and two real-data examples, we compare the performance in estimating the network structures between the existing methods and the proposed method.</P><P><B>Results</B></P><P>In simulation studies, we show that the proposed strategy reduces errors in estimating network structures compared to the existing methods. When applied to <I>Escherichia coli</I>, the regulation network constructed by our proposed ESPACE method is more consistent with current biological knowledge than the SPACE method. Furthermore, application of the proposed method in lung cancer has identified hub genes whose mRNA expression predicts cancer progress and patient response to treatment.</P><P><B>Conclusions</B></P><P>We have demonstrated that incorporating hub gene information in estimating network structures can improve the performance of the existing methods.</P>
Review of Biological Network Data and Its Applications
Yu, Donghyeon,Kim, MinSoo,Xiao, Guanghua,Hwang, Tae Hyun Korea Genome Organization 2013 Genomics & informatics Vol.11 No.4
Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.
Genomic analysis of Sheldrake origin goose hemorrhagic polyomavirus, China
Chunhe Wan,Cuiteng Chen,Longfei Cheng,Rongchang Liu,Guanghua Fu,Shaohua Shi,Hongmei Chen,Qiuling Fu,Yu Huang 대한수의학회 2018 Journal of Veterinary Science Vol.19 No.6
Goose hemorrhagic polyomavirus (GHPV) is not a naturally occurring infection in geese in China; however, GHPV infection has been identified in Pekin ducks, a domestic duck species. Herein, we investigated the prevalence of GHPV in five domestic duck species (Liancheng white ducks, Putian black ducks, Shan Sheldrake, Shaoxing duck, and Jinyun Sheldrake) in China. We determined that the Jinyun Sheldrake duck species could be infected by GHPV with no clinical signs, whereas no infection was identified in the other four duck species. We sequenced the complete genome of the Jinyun Sheldrake origin GHPV. Genomic data comparison suggested that GHPVs share a conserved genomic structure, regardless of the host (duck or geese) or region (Asia or Europe). Jinyun Sheldrake origin GHPV genomic characterization and epidemiological studies will increase our understanding of potential heterologous reservoirs of GHPV.
Behavior Characteristics of Hydrogen and its Isotope in Molten Salt of LiF-NaF-KF (FLiNaK)
Youshi Zeng,Wenguan Liu,WeiLiu,Yuan Qian,Nan Qian,Xiaoling Wu,Yu Huang,Shengwei Wu,Guanghua Wang 한국원자력학회 2019 Nuclear Engineering and Technology Vol.51 No.2
Experimental studies to investigate the behaviors of hydrogen in molten FLiNaK (LiF-NaF-KF) have beenconducted at 500e700 C. On the basis of previous studies, the diffusivity and solubility of hydrogen inFLiNaK have been revised, and the expressions can be correlated to the following Arrhenius equations:DH2 ¼ 1.62 10 5exp ( 48.20 103/Rg$T) [m2/s] and SH2 ¼ 1.03 10 4exp ( 14.96 103/Rg$T) [mol-H2/m3/Pa], respectively. The behavior characteristics of deuterium in FLiNaK were studied and comparedwith the hydrogen behaviors in FLiNaK. The results showed the behaviors of deuterium were consistencewith the behaviors of hydrogen in FLiNaK. The difference between hydrogen and deuterium has not beenobserved upon the experimental research of the behavior characteristics of hydrogen and deuterium inFLiNaK, which suggested the results obtained here might apply equally to the behavior characteristics oftritium in FLiNaK.
Regulating the magnetic anisotropy by Hf thickness and heat treatment in Pt/Co/Hf films
Li Minghua,Zhang Shijie,Wang Shuanghai,Li Yongzeng,Liu Lu,Chen Yu,Shi Hui,Yu Guanghua 한국물리학회 2022 Current Applied Physics Vol.34 No.-
Pt/Co/Hf multilayers were prepared by magnetron sputtering, and the magnetic anisotropy was effectively regulated by Hf thickness and heat treatment in Pt/Co/Hf films. The interface microstructures were characterized. The influence of the interface microstructure on magnetic properties was studied. The results show that the magnetic anisotropy in Pt/Co/Hf films is closely related to the interface microstructure, which is influenced by Hf thickness and the heat treatment temperature. Microstructure analysis shows that after the Pt(3)/Co(1.5)/Hf (1) film is heat-treated, the CoOx content increases, more CoPt(111) forms, the interface is smoother and sharper, and the roughness of the Co/Hf interface decreases. Several factors work together to cause the magnetic anisotropy of the sample to change from in-plane magnetic anisotropy (IMA)to perpendicular magnetic anisotropy (PMA).