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2013 7th International Conference on Systems Biology (ISB)最新文献

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Hopf bifurcation and Turing instability in a modified Leslie-Gower prey-predator model 改进Leslie-Gower捕食-捕食模型的Hopf分岔和图灵不稳定性
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623798
Yan Meng, Guangwu Wen, L. Min
{"title":"Hopf bifurcation and Turing instability in a modified Leslie-Gower prey-predator model","authors":"Yan Meng, Guangwu Wen, L. Min","doi":"10.1109/ISB.2013.6623798","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623798","url":null,"abstract":"In this paper, we study a modified Leslie-Gower prey-predator model in the presence of nonlinear harvesting in prey subject to the Neumann boundary condition. Our results reveal the conditions on the parameters so that the periodic solution exist surrounding the interior equilibrium. Furthermore, the direction of Hopf bifurcation and the stability of bifurcated periodic solutions are investigated. For the model with the Neumann boundary condition, Turing instability of the interior equilibrium solution is studied. In particular, Turing instability region regarding the parameters is established. Numerical simulations are carried out to demonstrate the results obtained.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"46 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133821086","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
Accelerating processing speed in pathway research based on GPU 加快了GPU在路径研究中的处理速度
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623797
Bo Liao, Ting Yao, Xiong Li
{"title":"Accelerating processing speed in pathway research based on GPU","authors":"Bo Liao, Ting Yao, Xiong Li","doi":"10.1109/ISB.2013.6623797","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623797","url":null,"abstract":"Genome-wide association study (GWAS) has become an effective and successful method to identify disease loci by considering SNPs independently. However, it may be invalid for uncovering the disease loci that not reaching a stringent genome-wide significance threshold. As a result, multi-SNP GWAS is developing rapidly as a complement to traditional GWAS. However, the high computational cost becomes a major limitation for it. The graphical processing unit (GPU) is a programmable graphics processor which has powerful parallel computing ability. And with the development, GPUs have been feasible for many scientific studies. Hence, we are motivated to use GPUs for pathway-based GWAS to improve computational efficiency. The experiment results attained showed the speed-up ratio can reach up to more than 160.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121833369","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
Rank-based interolog mapping for predicting proteinprotein interactions between genomes 基于秩的基因组间互作图谱预测
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623794
Yu-Shu Lo, Chun-Chen Chen, K. Hsu, Jinn-Moon Yang
{"title":"Rank-based interolog mapping for predicting proteinprotein interactions between genomes","authors":"Yu-Shu Lo, Chun-Chen Chen, K. Hsu, Jinn-Moon Yang","doi":"10.1109/ISB.2013.6623794","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623794","url":null,"abstract":"As rapidly increasing number of sequenced genomes, the methods for predicting protein-protein interactions (PPIs) from one organism to another is becoming important. Best-match and generalized interolog mapping methods have been proposed for predicting (PPIs). However, best-match mapping method suffers from low coverage of the total interactome, because of using only best matches. Generalized interolog mapping method may predict unreliable interologs at a certain similarity cutoff, because of the homologs differed in subcellular compartment, biological process, or function from the query protein. Here, we propose a new “rank-based interolog mapping” method, which uses the pairs of proteins with high sequence similarity (E-value<;10-10) and ranked by BLASTP E-value in all possible homologs to predict interologs. First, we evaluated “rank-based interolog mapping” on predicting the PPIs in yeast. The accuracy at selecting top 5 and top 10 homologs are 0.17, and 0.12, respectively, and our method outperformed generalized interolog mapping method (accuracy=0.04) with the joint E-value<;10-70. Furthermore, our method was used to predict PPIs in four organisms, including worm, fly, mouse, and human. In addition, we used Gene Ontology (GO) terms to analyzed PPIs, which reflect cellular component, biological process, and molecular function, inferred by rank-based mapping method. Our rank-based mapping method can predict more reliable interactions under a given percentage of false positives than the best-match and generalized interolog mapping methods. We believe that the rank-based mapping method is useful method for predicting PPIs in a genome-wide scale.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"65 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122030156","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
Dynamical behaviour of an anti-HBV infection therapy model with time-delayed immune response 具有时滞免疫应答的抗hbv感染治疗模型的动力学行为
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623799
X. Zhuo, Yongmei Su
{"title":"Dynamical behaviour of an anti-HBV infection therapy model with time-delayed immune response","authors":"X. Zhuo, Yongmei Su","doi":"10.1109/ISB.2013.6623799","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623799","url":null,"abstract":"Mathematical models have been used to understand the factors that govern infectious disease progression in viral infections. In this paper, based on the standard mass action incidence, an anti-HBV therapy model with time-delayed immune response is set up. The time-delay is used to describe the period of time for antigenic stimulation to generate CTLs. The globally asymptotically stable analysis of the infection-free equilibrium is given in the paper. Some conditions for Hopf bifurcation around endemic equilibrium to occur are also obtained by using the time delay as a bifurcation parameter.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122190068","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
DMS model calibration using Genetic Algorithm 基于遗传算法的DMS模型标定
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623785
B. Qu, A. Gabric, Jiaojiao Xi
{"title":"DMS model calibration using Genetic Algorithm","authors":"B. Qu, A. Gabric, Jiaojiao Xi","doi":"10.1109/ISB.2013.6623785","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623785","url":null,"abstract":"Recent researchers suggested Dimethyl sulphide (DMS) flux emission in Arctic Ocean plays an important role for the global warming. A Genetic Algorithm (GA) method was developed and used in calibrating the DMS model parameters in Barents Sea in Arctic Ocean (70-80N, 30-35E). Two-step GA calibrations were performed. First step was to calibrate the most sensitive parameters based on Chlorophyll_a (CHL) satellite SeaWIFS 8-day data. DMS model was then calibrated for another 5 most sensitive parameters. The best fitness was as good as -0.76 for CHL calibration in 1998-2002. The GA proved an efficient tool in the multiple-parameter calibration task. Model simulations indicate significant inter-annual variation in the CHL amount leading to significant inter-annual variability in the observed and modeled production of DMS and DMS flux in the study region in Arctic Ocean.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127758805","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
Cell commitment motif composed of progenitor-specific TF and fate-decision motif 由祖特异性TF和命运决定基序组成的细胞承诺基序
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623811
Tongpeng Wang, Peipei Zhou, Ruiqi Wang
{"title":"Cell commitment motif composed of progenitor-specific TF and fate-decision motif","authors":"Tongpeng Wang, Peipei Zhou, Ruiqi Wang","doi":"10.1109/ISB.2013.6623811","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623811","url":null,"abstract":"Mutual-inhibition motif is frequently-occuring motif in transcriptional regulatory networks for cell lineage commitment. Stable attractors represent cell commitment state. But how progenitor-specific transcription factors stabilize progenitor cells and commit them to different cell fates remains unexplained. In this paper we represent the motif for cell commitment, composed of mutual-inhibition motif and progenitor-specific transcription factor, and develop associated mathematical model. In the analysis of bifurcation and dynamical simulation, the model could exhibit multiple steady stable states and transition between them, cooresponding to progenitor, committed cell state and different commitment processes. Furthermore, we demonstrate that different commitment patterns, for example that of hematopoitic stem cell and neural stem cell, could be represented with different bifurcation features.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"230 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121541280","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
Mining disease associated biomarker networks from PubMed 从PubMed中挖掘疾病相关的生物标志物网络
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623786
Zhong Huang
{"title":"Mining disease associated biomarker networks from PubMed","authors":"Zhong Huang","doi":"10.1109/ISB.2013.6623786","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623786","url":null,"abstract":"Disease related biomarker discovery is the critical step to realize the future personalized medicine and has been an important research area. With exponential growing of biomedical knowledge deposited in PubMed database, it is now an essential step to mine PubMed for biomarker-disease associations to support the laboratory research and clinical validation. We constructed list of human diseases that are most frequently associated with biomarker in literatures by text mining. Top ranked neurology diseases were then used to extract associated genes from PubMed using context sensitive information retrieval methods. Associated genes were then integrated into pathways and subject to network biomarker analysis. Our approach identifies both known and potential biomarkers for 3 neurodegenerative diseases.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115975061","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: 3
Anti-rheumatic effects of Tripterygium wilfordii Hook F in a network perspective 雷公藤抗风湿病作用的网络研究
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623810
Haiyang Fang, Tinghong Yang, Yichuan Wang, Weidong Zhang, Yang Ga, J. Zhao, Yi Zhang
{"title":"Anti-rheumatic effects of Tripterygium wilfordii Hook F in a network perspective","authors":"Haiyang Fang, Tinghong Yang, Yichuan Wang, Weidong Zhang, Yang Ga, J. Zhao, Yi Zhang","doi":"10.1109/ISB.2013.6623810","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623810","url":null,"abstract":"Rheumatoid arthritis (RA) is a chronic disease that affects the joints, often those in a person's wrists, fingers, and feet. In contrast to FDA-approved anti-RA drugs, Tripterygium wilfordii Hook F (TwHF), a traditional Chinese medicine (TCM), featured as multi-targeting, have been acknowledged with notable anti-RA effects although the pharmacology is unclear. In this work, we investigated the therapeutic mechanisms of TwHF at protein network level. First, RA-associated genes, the protein targets of FDA approved anti-RA drugs and TwHF were collected. Then we mapped the protein targets of TwHF on the drug-target network of FDA approved anti-RA drugs and KEGG RA pathway, based on these information and resources. Furthermore, we quantitatively analyzed the anti-rheumatic effect of TwHF and compared it with those of FDA approved anti-RA drugs by a network based anti-rheumatic effect score. Our study suggests that TwHF may function as a combination of disease-modifying anti-rheumatic drug and non-steroidal anti-inflammatory drug and its anti-rheumatic power could be comparable with that of anti-inflammatory agents. This study may facilitate our understanding of the RA treatment by TwHF from the perspective of network systems and it may suggest new approach for the study of TCM pharmacology.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115986271","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
Global stability of the SEIR epidemic model with infectivityin both latent period and infected period 潜伏期和感染期具有传染性的SEIR流行病模型的全局稳定性
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623790
Yu Zhang, Zefeng Ren
{"title":"Global stability of the SEIR epidemic model with infectivityin both latent period and infected period","authors":"Yu Zhang, Zefeng Ren","doi":"10.1109/ISB.2013.6623790","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623790","url":null,"abstract":"An epidemic model with infectivity and recovery in both latent and infected period is introduced. Utilizing the LaSalle invariance principle and Bendixson criterion,the basic reproduction number is found, we prove that the disease-free equilibrium is globally asymptotically stable when the basic reproduction number is less than one. The disease-free equilibrium is unstable and the unique positive equilibrium is globally asymptotically stable when the basic reproduction number is greater than one. Numerical simulations support our conclusions.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131683281","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
Anti-cancer effect of aloe emodin on breast cancer cells, MCF-7 芦荟大黄素对乳腺癌细胞MCF-7的抗癌作用
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623802
I. M. Amin, S. H. Sheikh Abdul Kadir, N. M. Rosdy, R. Siran, N. Hasani
{"title":"Anti-cancer effect of aloe emodin on breast cancer cells, MCF-7","authors":"I. M. Amin, S. H. Sheikh Abdul Kadir, N. M. Rosdy, R. Siran, N. Hasani","doi":"10.1109/ISB.2013.6623802","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623802","url":null,"abstract":"Phytochemicals of some plants are believed to have natural anti-proliferative properties to various cancer cells. Thus, they might have the potential as alternative choice for contemporary treatment as the latter are usually associated with many unpleasant side effects. The aim of this study is to investigate the possible anti-cancer effect of aloe emodin (AE; 1,8-Dihydroxy-3-hydro-xymethyl-anthraquinone) on estrogenpositive breast cancer cells, MCF-7. We were able to demonstrate the efficiency of AE, an antraquinone derivatives which are present in Aloe Vera leaves, in limiting the proliferation effect of MCF-7 cells in a dose and time dependent manner using WST-1 assay. Our preliminary result suggests that AE could be a promising natural candidate for future pharmacological study, targeting in breast cancer prevention strategies.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129111914","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
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