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EURASIP Journal on Bioinformatics and Systems Biology最新文献

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Inference of dynamic biological networks based on responses to drug perturbations 基于药物扰动响应的动态生物网络推理
EURASIP Journal on Bioinformatics and Systems Biology Pub Date : 2014-09-25 DOI: 10.1186/s13637-014-0014-1
Noah E. Berlow, L. Davis, C. Keller, R. Pal
{"title":"Inference of dynamic biological networks based on responses to drug perturbations","authors":"Noah E. Berlow, L. Davis, C. Keller, R. Pal","doi":"10.1186/s13637-014-0014-1","DOIUrl":"https://doi.org/10.1186/s13637-014-0014-1","url":null,"abstract":"","PeriodicalId":227594,"journal":{"name":"EURASIP Journal on Bioinformatics and Systems Biology","volume":"2014 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131182518","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: 8
Optimal cancer prognosis under network uncertainty 网络不确定性下的最优癌症预后
EURASIP Journal on Bioinformatics and Systems Biology Pub Date : 2014-09-20 DOI: 10.1186/s13637-014-0020-3
Mohammadmahdi R. Yousefi, Lori A. Dalton
{"title":"Optimal cancer prognosis under network uncertainty","authors":"Mohammadmahdi R. Yousefi, Lori A. Dalton","doi":"10.1186/s13637-014-0020-3","DOIUrl":"https://doi.org/10.1186/s13637-014-0020-3","url":null,"abstract":"","PeriodicalId":227594,"journal":{"name":"EURASIP Journal on Bioinformatics and Systems Biology","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133936564","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: 13
Wavelet analysis of frequency chaos game signal: a time-frequency signature of the C. elegans DNA 频率混沌博弈信号的小波分析:线虫DNA的时频特征
EURASIP Journal on Bioinformatics and Systems Biology Pub Date : 2014-09-12 DOI: 10.1186/s13637-014-0016-z
Imen Messaoudi, A. Oueslati, Z. Lachiri
{"title":"Wavelet analysis of frequency chaos game signal: a time-frequency signature of the C. elegans DNA","authors":"Imen Messaoudi, A. Oueslati, Z. Lachiri","doi":"10.1186/s13637-014-0016-z","DOIUrl":"https://doi.org/10.1186/s13637-014-0016-z","url":null,"abstract":"","PeriodicalId":227594,"journal":{"name":"EURASIP Journal on Bioinformatics and Systems Biology","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127773096","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: 12
Template-based intervention in Boolean network models of biological systems 基于模板的干预生物系统布尔网络模型
EURASIP Journal on Bioinformatics and Systems Biology Pub Date : 2014-07-19 DOI: 10.1186/s13637-014-0011-4
Michael P. Verdicchio, Seungchan Kim
{"title":"Template-based intervention in Boolean network models of biological systems","authors":"Michael P. Verdicchio, Seungchan Kim","doi":"10.1186/s13637-014-0011-4","DOIUrl":"https://doi.org/10.1186/s13637-014-0011-4","url":null,"abstract":"","PeriodicalId":227594,"journal":{"name":"EURASIP Journal on Bioinformatics and Systems Biology","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132413108","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
Gene regulatory network inference and validation using relative change ratio analysis and time-delayed dynamic Bayesian network 基于相对变化率分析和时滞动态贝叶斯网络的基因调控网络推断与验证
EURASIP Journal on Bioinformatics and Systems Biology Pub Date : 2014-07-16 DOI: 10.1186/s13637-014-0012-3
Pengcheng Li, P. Gong, Haoni Li, E. Perkins, Nan Wang, Chaoyang Zhang
{"title":"Gene regulatory network inference and validation using relative change ratio analysis and time-delayed dynamic Bayesian network","authors":"Pengcheng Li, P. Gong, Haoni Li, E. Perkins, Nan Wang, Chaoyang Zhang","doi":"10.1186/s13637-014-0012-3","DOIUrl":"https://doi.org/10.1186/s13637-014-0012-3","url":null,"abstract":"","PeriodicalId":227594,"journal":{"name":"EURASIP Journal on Bioinformatics and Systems Biology","volume":"46 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114729135","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: 14
Using the minimum description length principle to reduce the rate of false positives of best-fit algorithms 利用最小描述长度原理降低最佳拟合算法的误报率
EURASIP Journal on Bioinformatics and Systems Biology Pub Date : 2014-07-03 DOI: 10.1186/s13637-014-0013-2
Jie Fang, Hongjia Ouyang, Liangzhong Shen, E. Dougherty, Wenbin Liu
{"title":"Using the minimum description length principle to reduce the rate of false positives of best-fit algorithms","authors":"Jie Fang, Hongjia Ouyang, Liangzhong Shen, E. Dougherty, Wenbin Liu","doi":"10.1186/s13637-014-0013-2","DOIUrl":"https://doi.org/10.1186/s13637-014-0013-2","url":null,"abstract":"","PeriodicalId":227594,"journal":{"name":"EURASIP Journal on Bioinformatics and Systems Biology","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130218990","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
Modelling Transcriptional Regulation with a Mixture of Factor Analyzers and Variational Bayesian Expectation Maximization 因子分析和变分贝叶斯期望最大化的混合转录调节建模
EURASIP Journal on Bioinformatics and Systems Biology Pub Date : 2009-04-12 DOI: 10.1186/1687-4153-2009-601068
K. Lin, D. Husmeier
{"title":"Modelling Transcriptional Regulation with a Mixture of Factor Analyzers and Variational Bayesian Expectation Maximization","authors":"K. Lin, D. Husmeier","doi":"10.1186/1687-4153-2009-601068","DOIUrl":"https://doi.org/10.1186/1687-4153-2009-601068","url":null,"abstract":"","PeriodicalId":227594,"journal":{"name":"EURASIP Journal on Bioinformatics and Systems Biology","volume":"85 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131084794","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: 8
Adaptive Dynamics of Regulatory Networks: Size Matters 调节网络的自适应动力学:大小问题
EURASIP Journal on Bioinformatics and Systems Biology Pub Date : 2009-02-03 DOI: 10.1186/1687-4153-2009-618502
D. Repsilber, T. Martinetz, M. Björklund
{"title":"Adaptive Dynamics of Regulatory Networks: Size Matters","authors":"D. Repsilber, T. Martinetz, M. Björklund","doi":"10.1186/1687-4153-2009-618502","DOIUrl":"https://doi.org/10.1186/1687-4153-2009-618502","url":null,"abstract":"","PeriodicalId":227594,"journal":{"name":"EURASIP Journal on Bioinformatics and Systems Biology","volume":"124 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122847627","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: 7
Integrating Biosystem Models Using Waveform Relaxation 利用波形松弛整合生物系统模型
EURASIP Journal on Bioinformatics and Systems Biology Pub Date : 2008-11-10 DOI: 10.1155/2008/308623
Linzhong Li, R. Seymour, S. Baigent
{"title":"Integrating Biosystem Models Using Waveform Relaxation","authors":"Linzhong Li, R. Seymour, S. Baigent","doi":"10.1155/2008/308623","DOIUrl":"https://doi.org/10.1155/2008/308623","url":null,"abstract":"Modelling in systems biology often involves the integration of component models into larger composite models. How to do this systematically and efficiently is a significant challenge: coupling of components can be unidirectional or bidirectional, and of variable strengths. We adapt the waveform relaxation (WR) method for parallel computation of ODEs as a general methodology for computing systems of linked submodels. Four test cases are presented: (i) a cascade of unidirectionally and bidirectionally coupled harmonic oscillators, (ii) deterministic and stochastic simulations of calcium oscillations, (iii) single cell calcium oscillations showing complex behaviour such as periodic and chaotic bursting, and (iv) a multicellular calcium model for a cell plate of hepatocytes. We conclude that WR provides a flexible means to deal with multitime-scale computation and model heterogeneity. Global solutions over time can be captured independently of the solution techniques for the individual components, which may be distributed in different computing environments.","PeriodicalId":227594,"journal":{"name":"EURASIP Journal on Bioinformatics and Systems Biology","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115528740","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
Assessing the Exceptionality of Coloured Motifs in Networks 网络中有色母题的异常性评价
EURASIP Journal on Bioinformatics and Systems Biology Pub Date : 2008-10-26 DOI: 10.1186/1687-4153-2009-616234
Sophie Schbath, Vincent Lacroix, M. Sagot
{"title":"Assessing the Exceptionality of Coloured Motifs in Networks","authors":"Sophie Schbath, Vincent Lacroix, M. Sagot","doi":"10.1186/1687-4153-2009-616234","DOIUrl":"https://doi.org/10.1186/1687-4153-2009-616234","url":null,"abstract":"","PeriodicalId":227594,"journal":{"name":"EURASIP Journal on Bioinformatics and Systems Biology","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132974396","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: 36
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