2011 IEEE International Conference on Systems Biology (ISB)最新文献_第2页

Application of an improved K-means algorithm in gene expression data analysis 改进的K-means算法在基因表达数据分析中的应用

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033126

Qian Ren, X. Zhuo

引用次数: 8

Analysis of gene expression profile triggered by signal peptide of eosinophil cationic protein 嗜酸性阳离子蛋白信号肽触发基因表达谱分析

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033145

Yu-Shu Liu, Chung-Hsaio Chao, Hao-Teng Chang, M. Chang, Yong Wang, Tun-Wen Pai

{"title":"Analysis of gene expression profile triggered by signal peptide of eosinophil cationic protein","authors":"Yu-Shu Liu, Chung-Hsaio Chao, Hao-Teng Chang, M. Chang, Yong Wang, Tun-Wen Pai","doi":"10.1109/ISB.2011.6033145","DOIUrl":"https://doi.org/10.1109/ISB.2011.6033145","url":null,"abstract":"The signal peptide of eosinophil cationic protein (ECPsp) is known to play an important role in translocating ECP to extracellular space. However, we previously discovered that ECPsp has a novel function of inhibiting microbial growth and regulating the gene expression of tumor growth factor-alpha (TGF-α) and epidermal growth factor receptor (EGFR) in mammalian cells. In the present study, we first generated a DNA microarray dataset, which showed that ECPsp up-regulated inflammatory molecules including cytokines, chemokines, interferon-induced molecules, and Toll-like receptors. We then generated a function linkage network by integrating the microarray dataset with the KEGG pathway database, and discovered that STAT1, an important factor regulating cytokine expression and release, served as a hub to connect the pathways of cytokine stimulation (TGF-α and EGFR) and inflammatory responses. Furthermore, integrating the ECPsp interactome dataset with the functional linkage network elucidated that STAT1 served as a hub to connect 3 functional clusters, including cell proliferation and survival, protein translational regulation, and inflammatory responses. Our approach involving experimental and computational systems biology provided predicted pathways and potential regulation for further characterization of the novel function of ECPsp under inflammatory conditions.","PeriodicalId":355056,"journal":{"name":"2011 IEEE International Conference on Systems Biology (ISB)","volume":"188 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":"125844492","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: 0

Heavy metal tolerance of an antarctic bacterial Strain O5 and its antioxidant enzyme activity changes induced by Cu2+ Cu2+对南极菌株O5重金属耐受性及抗氧化酶活性的影响

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033169

Min Wang, Guangfeng Kan, Cuijuan Shi, Qiuju Xie, Yingying Huang, Zhenhuan Lei

{"title":"Heavy metal tolerance of an antarctic bacterial Strain O5 and its antioxidant enzyme activity changes induced by Cu2+","authors":"Min Wang, Guangfeng Kan, Cuijuan Shi, Qiuju Xie, Yingying Huang, Zhenhuan Lei","doi":"10.1109/ISB.2011.6033169","DOIUrl":"https://doi.org/10.1109/ISB.2011.6033169","url":null,"abstract":"Under the heavy metal polluted circumstances, microorganisms certainly have some changes in terms of species, quantity, community structure and diversity to adapt the environments. Now, many heavy metal tolerant microbe groups have been studied. In the study, a heavy metal tolerant and psychrophilic bacterium strain from Antarctica was screened. Based on 16S rDNA sequence analysis, this strain belongs to Planococcus, named as Planococcus sp. O5. The capacity of antimetal of Planococcus sp. O5 is Pb2+ > Cu2+ > Hg2+ > Cd2+ > Zn2+, and the MICs is 320 mg/L, 130 mg/L, 80 mg/L, 80 mg/L and 40 mg/L, respectively. Lipid peroxidation (indicated by malonydialdehyde content) happened in strain O5 induced with Cu2+. At the same time, the antioxidation enzyme activity (such as SOD, POD and CAT) had stimulus-controlled improvement, which is a certain protection against heavy metals. Therefore, as an important feature adapting the stress environments, the activity of antimetal, can reflect the adaptive strategy of microorganism to some extent. This paper studied the activity of antimetal and antioxidation of a bacterial strain, which can help us better understand the bacteria how to adapt the extreme environments.","PeriodicalId":355056,"journal":{"name":"2011 IEEE International Conference on Systems Biology (ISB)","volume":"79 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":"125986318","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: 1

Finding optimal control policy by using dynamic programming in conjunction with state reduction 将动态规划与状态约简相结合，寻找最优控制策略

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033165

X. Chen, W. Ching

引用次数: 5

The calibration method research for biology image 生物图像标定方法研究

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033128

Zilong Liu, Wenli Liu, Rui Chen, Yu Wang, N. Liao

引用次数: 0

A dynamical method to extract communities induced by low or middle-degree nodes 中低度节点诱导群落的动态提取方法

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033175

Junhua Zhang, Zhiping Liu, Xiang-Sun Zhang, Luonan Chen

引用次数: 1

Stability analysis and simulation of an anti-HBV therapy mathematical model with time-delay immune response 具有时滞免疫应答的抗hbv治疗数学模型的稳定性分析与仿真

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033163

Yongmei Su, L. Min

引用次数: 0

Discriminative random field approach to prediction of protein residue contacts 判别随机场方法预测蛋白残基接触

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033167

M. Kamada, M. Hayashida, Jiangning Song, T. Akutsu

{"title":"Discriminative random field approach to prediction of protein residue contacts","authors":"M. Kamada, M. Hayashida, Jiangning Song, T. Akutsu","doi":"10.1109/ISB.2011.6033167","DOIUrl":"https://doi.org/10.1109/ISB.2011.6033167","url":null,"abstract":"Understanding of interactions of proteins is important to reveal networks and functions of molecules. Many investigations have been conducted to analyze interactions and contacts between residues. It is supported that residues at interacting sites have co-evolved with those at the corresponding residues in the partner protein to keep the interactions between the proteins. Therefore, mutual information (MI) between residues calculated from multiple sequence alignments of homologous proteins is considered to be useful for identifying contact residues in interacting proteins. In our previous work, we proposed a prediction method for protein-protein interactions using mutual information and conditional random fields (CRFs), and confirmed its usefulness. The discriminative random field (DRF) is a special type of CRFs, and can recognize some specific characteristic regions in an image. Since the matrix consisted of mutual information between residues in two interacting proteins can be regarded as an image, we propose a prediction method for protein residue contacts using DRF models with mutual information. To validate our method, we perform computational experiments for several interactions between Pfam domains. The results suggest that the proposed DRF-based method with MI is useful for predicting protein residue contacts compared with that using the corresponding Markov random field (MRF) model.","PeriodicalId":355056,"journal":{"name":"2011 IEEE International Conference on Systems Biology (ISB)","volume":"7 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":"123212019","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: 6

Neural fate decisions mediated by notch-delta signaling 缺口- δ信号介导的神经命运决定

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033174

Ruiqi ang, Kaihui Liu, Luonan Chen

引用次数: 1

Phenotype-difference oriented identification of molecular functions for diabetes progression in Goto-Kakizaki rat 以表型差异为导向的Goto-Kakizaki大鼠糖尿病进展分子功能鉴定

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033130

Guanying Piao, Bangguo Qian, Shigeru Saito, Zhiping Liu, Tao Zeng, Yong Wang, Jiarui Wu, Huarong Zhou, Luonan Chen, K. Horimoto

{"title":"Phenotype-difference oriented identification of molecular functions for diabetes progression in Goto-Kakizaki rat","authors":"Guanying Piao, Bangguo Qian, Shigeru Saito, Zhiping Liu, Tao Zeng, Yong Wang, Jiarui Wu, Huarong Zhou, Luonan Chen, K. Horimoto","doi":"10.1109/ISB.2011.6033130","DOIUrl":"https://doi.org/10.1109/ISB.2011.6033130","url":null,"abstract":"In general, molecular signatures of diseases are estimated by comparing the two sets of molecular data measured for the samples with distinctive phenotypes, and then molecular functions of the diseases are characterized by the following analyses of the signatures. Unfortunately, ambiguous relationships between molecular signatures and functions are observed in some cases, due to a posteriori justification from molecular level to phenotype level. Here, we propose a method for detecting molecular functions of the disease by a deductive justification from phenotype level to molecular level, and illustrate its performance by applying our method to the gene expression and phenotype data sets for diabetes progression in Goto-Kakizaki rat. By our method, the functions identified by the previous studies were well covered, and furthermore, some implications for molecular mechanisms were obtained. Our phenotype-difference oriented method provides some clues to bridge directly a gap between molecular signatures and phenotype data in diabetes.","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":"133998979","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: 2