2011 IEEE International Conference on Systems Biology (ISB)最新文献_第6页

An edge based core-attachment method to detect protein complexes in PPI networks 一种基于边缘的核连接检测蛋白复合物的方法

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033123

Yu Wang, Lin Gao, Zhe Chen

{"title":"An edge based core-attachment method to detect protein complexes in PPI networks","authors":"Yu Wang, Lin Gao, Zhe Chen","doi":"10.1109/ISB.2011.6033123","DOIUrl":"https://doi.org/10.1109/ISB.2011.6033123","url":null,"abstract":"Characterization and identification of protein complexes in protein-protein interaction (PPI) networks is important in understanding cellular processes. With the core-attachment concept, a novel core-attachment algorithm is proposed by characterizing the protein complex core from the perspective of edges. We reinvite a protein complex core to be a set of closely interrelated edges rather than a set of interrelated proteins. We first identify the edges must belong to a core, and then partition these edges to extract cores. After that, we select the attachments for each complex core to form a protein complex. Finally, we evaluate the performance of our algorithm by applying it on two different yeast PPI networks. The experimental results show that our algorithm outperforms the MCL, CPM, CoAch in terms of number of precisely predicted protein complexes, localization as well as GO semantic similarity. Our proposed method is validated as an effective algorithm in identifying protein complexes and can provide more insights for future biological study. It proves that edge community is a better topological characterization of protein complex.","PeriodicalId":355056,"journal":{"name":"2011 IEEE International Conference on Systems Biology (ISB)","volume":"64 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129508863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Identifying biomarkers for acupuncture treatment via an optimization model 通过优化模型确定针灸治疗的生物标志物

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033172

Yong Wang, Qiao-feng Wu, Cheng Chen, Xian-Zhong Yan, S. Yu, Xiang-Sun Zhang, F. Liang

引用次数: 3

The early warning signal of complex diseases based on the network transition entropy 基于网络转移熵的复杂疾病预警信号

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033179

Rui Liu, Luonan Chen, K. Aihara

引用次数: 0

A general shape equation for local regular structure of biomolecular chains 生物分子链局部规则结构的一般形状方程

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033146

Liu Hong, J. Lei

引用次数: 0

Global analysis of a general HBV infection model 一般HBV感染模型的全局分析

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033171

X. Zhuo

{"title":"Global analysis of a general HBV infection model","authors":"X. Zhuo","doi":"10.1109/ISB.2011.6033171","DOIUrl":"https://doi.org/10.1109/ISB.2011.6033171","url":null,"abstract":"Mathematical models have been used to understand the factors that govern infectious disease progression in viral infections. Two basic models of within-host viral infection, proposed by Nowak et. al. and Perelson et. al. respectively, have been widely used in the studies of HBV and HIV infections. However, the loss term of viral particles when it enters the target cells are both ignored by these two models. Leenheer and Smith provided a general virus dynamic model with the loss term of viral particles, which make the above two basic models only be special cases. But the basic reproduction numbers of all above models are proportional to the number of total cells of the host's organ prior to the infection(when used for HBV infection) or the normal target cell level(when used for HIV infection). On the other hand, the global asymptotically stable condition of the endemic equilibrium about Leenheer and Smith's model is related to the initial value of the growth function of uninfected cell. In this paper, we formulate an amended Leenheer and Smith's model with standard incidence, the basic reproduction numbers were no more dependent on the number of total cells of the host's organ. If the basic reproduction number of virus is less than one, the infection-free equilibrium is globally asymptotically stable and the virus is cleared; if the basic reproduction number is great than one, then the virus persist in the host, and solutions approach either an endemic equilibrium or a periodic orbit. The periodic orbit can be ruled out in some cases but not in general. The globally asymptotically stable condition of the endemic equilibrium is only determined by the model parameters.","PeriodicalId":355056,"journal":{"name":"2011 IEEE International Conference on Systems Biology (ISB)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130990981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Protein interaction prediction for mouse pdz domains using dipeptide composition features 利用二肽组成特征预测小鼠pdz结构域的蛋白质相互作用

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033143

Songyot Nakariyakul, Zhiping Liu, Luonan Chen

引用次数: 1

Evolutionary sequence divergence predicts protein sub-cellular localization signals 进化序列分化预测蛋白质亚细胞定位信号

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033170

Yoshinori Fukasawa, R. Leung, S. Tsui, P. Horton

引用次数: 2

Predicting MicroRNA targets by integrating sequence and expression data in cancer 通过整合MicroRNA在癌症中的序列和表达数据来预测其靶标

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033158

Naifang Su, Yufu Wang, M. Qian, Minghua Deng

{"title":"Predicting MicroRNA targets by integrating sequence and expression data in cancer","authors":"Naifang Su, Yufu Wang, M. Qian, Minghua Deng","doi":"10.1109/ISB.2011.6033158","DOIUrl":"https://doi.org/10.1109/ISB.2011.6033158","url":null,"abstract":"Gene regulation is a key factor in gaining a full understanding of molecular biology. microRNA (miRNA), a novel class of non-coding RNA, has recently been found to be one crucial class of post-transactional regulators, and play important parts in cancer. One essential step to understand the regulatory effect of miRNAs is the reliable prediction of their target mRNAs. Typically, the predictions are solely based on sequence information, which unavoidably have high false detection rates. Here we develop a new algorithm called HCTarget, which predict miRNA targets by integrating the typical algorithm and the paired expression profiles of miRNA and mRNA. HCTarget formulates a linear model to characterize the relationship between mRNA and miRNA, and use a Markov Chain Monto Carlo algorithm to learn the target probabilities. When applying HCtarget to the expression data in multiple myeloma, we predict target genes for ten cancer related miRNAs. The experimental verification and a loss of function study of hsa-miR-16 validate our predictions. Compared with the previous approaches, our target sets have increased functional enrichment. Meanwhile, our predicted target pair hsa-miR-19b and SULF1 plays an important role in multiple myeloma. Therefore, HCtarget is a reliable and effective approach to predict miRNA target genes, and could improve our comprehensive understanding of gene regulation.","PeriodicalId":355056,"journal":{"name":"2011 IEEE International Conference on Systems Biology (ISB)","volume":"63 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123685134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Kinetics of muller's ratchet from adaptive landscape viewpoint 适应性景观视角下穆勒棘轮动力学研究

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-09-19 DOI: 10.1109/ISB.2011.6033116

Shuyun Jiao, Yanbo Wang, Bo Yuan, P. Ao

引用次数: 3

Identifying positional homologs as bidirectional best hits of sequence and gene context similarity 定位同源物作为序列和基因上下文相似性的双向最佳命中点

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-09-01 DOI: 10.1109/isb.2011.6033141

Melvin Zhang, Hon Wai Leong

引用次数: 2