全部文献期刊会议图书|学者科研项目
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作者:... Yu Xin , Sontag Eduardo , Levine Arnold
来源:[J].BMC Bioinformatics(IF 3.024), 2009, Vol.10 (1), pp.111
摘要:Abstract Background A computational method (called p53HMM) is presented that utilizes Profile Hidden Markov Models (PHMMs) to estimate the relative binding affinities of putative p53 response elements (REs), both p53 single-sites and cluster-sites. These models incorporate a nove...
作者:... Li Yi , Sontag Eduardo , Bleris Leonidas
来源:[J].Proceedings of the National Academy of Sciences(IF 9.737), 2015, Vol.112 (41), pp.12893-12898
摘要:Significance We used a combination of computational and theoretical approaches coupled to synthetic biology experimentation in mammalian cells to study direct and indirect connectivities in biological networks. After subjecting benchmark circuits to a range of perturbations, we r...
作者:Sontag Eduardo , Gennaro Maria L
来源:[J].PLoS computational biology(IF 4.867), 2016, Vol.12 (2), pp.e1004741
摘要:Understanding how dynamical responses of biological networks are constrained by underlying network topology is one of the fundamental goals of systems biology. Here we employ monotone systems theory to formulate a theorem stating necessary conditions for non-monotonic time-r...
作者:Sontag Eduardo , Veliz-Cuba Alan ...
来源:[J].Biophysical journal, 2008, Vol.95 (2), pp.518-26
摘要:Feedback loops play an important role in determining the dynamics of biological networks. To study the role of negative feedback loops, this article introduces the notion of distance-to-positive-feedback which, in essence, captures the number of independent negative feedback loop...
作者:Prabakaran Sudhakaran , Gunawardena Jeremy , Sontag Eduardo
来源:[J].Biophysical journal, 2014, Vol.106 (12), pp.2720-8
摘要:Mathematical models are extensively employed to understand physicochemical processes in biological systems. In the absence of detailed mechanistic knowledge, models are often based on network inference methods, which in turn rely upon perturbations to nodes by biochemical means. ...
作者:... Adadey Asa , Sontag Eduardo , Benenson Yaakov
来源:[J].Molecular systems biology(IF 11.34), 2011, Vol.7, pp.519
摘要:Natural and synthetic biological networks must function reliably in the face of fluctuating stoichiometry of their molecular components. These fluctuations are caused in part by changes in relative expression efficiency and the DNA template amount of the network-coding genes. Gen...
作者:... Yu Xin , Sontag Eduardo , Levine Arnold
来源:[J].BMC bioinformatics(IF 3.024), 2009, Vol.10, pp.111
摘要:BACKGROUND(#br)A computational method (called p53HMM) is presented that utilizes Profile Hidden Markov Models (PHMMs) to estimate the relative binding affinities of putative p53 response elements (REs), both p53 single-sites and cluster-sites. These models incorporate a novel "Co...
作者:... Enciso German Andres , Sontag Eduardo , Zhang Yi
来源:[J].Bio Systems(IF 1.581), 2007, Vol.90 (1), pp.161-78
摘要:A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions which are optimal in an appropriate sense. I...
作者:... Kholodenko Boris N , Levy Ronald M , Sontag Eduardo
来源:[J].Journal of theoretical biology(IF 2.351), 2005, Vol.232 (3), pp.427-41
摘要:One of the fundamental problems of cell biology is the understanding of complex regulatory networks. Such networks are ubiquitous in cells and knowledge of their properties is essential for the understanding of cellular behavior. In earlier work (Kholodenko et al. (PNAS 99: 12841...
作者:Hamadeh Abdullah , Ingalls Brian , Sontag Eduardo
来源:[J].Journal of the Royal Society, Interface, 2013, Vol.10 (80), pp.20120935
摘要:The chemotaxis pathway of the bacterium Rhodobacter sphaeroides shares many similarities with that of Escherichia coli. It exhibits robust adaptation and has several homologues of the latter's chemotaxis proteins. Recent theoretical results have correctly predicted that the E. co...

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