{"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}
{"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}
{"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}
{"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}
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}
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}
{"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}
{"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}
{"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}
{"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}