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Proliferating dynamic modeling in systems biology studies
Molecular BioSystems, 2011Michael L. Blinov introduces this themed issue on Computational Biology which includes topics discussed during the ‘Advanced Modeling & Simulation Techniques’ workshop at the 11th International Conference on Systems Biology (ICSB 2010) in Edinburgh last year.
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Systems Biology Modeling of Nonlinear Cancer Dynamics
2017Systems Biology represents nowadays a promising standard framework for natural and human sciences to attack complicated problems involving Life. Here a particular application of such a program is discussed in the case of Cancer, by using a basic toy model for solid tumor spread for framing together two apparently different conceptual leading paradigms ...
Christian, Cherubini +2 more
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Nonhomogeneous Dynamic Bayesian Networks in Systems Biology
2011Dynamic Bayesian networks (DBNs) have received increasing attention from the computational biology community as models of gene regulatory networks. However, conventional DBNs are based on the homogeneous Markov assumption and cannot deal with inhomogeneity and nonstationarity in temporal processes.
Sophie, Lèbre +2 more
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Dynamical Systems in Biology: A Short Introduction
2019The contributions to this textbook are based on a summer school on Dynamics of Biological Systems as part of the series “Seminaire de Mathematiques Superieures,” which was held at the University of Alberta in June 2016. The lectures cover a wide variety of topics and it would be presumptuous to assume that all readers are equally familiar with all the ...
Thomas Hillen, Mark A. Lewis
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Absolute systems biology – measuring dynamics of protein modifications
Trends in Biotechnology, 2003Mass spectrometry is already established as the method of choice for protein identification. Hitherto, a major limitation of mass spectrometry was the inability to quantitate protein levels. With the development of novel methods, such as the AQUA method by Gerber et al., this hurdle has finally been overcome, unleashing the power of mass spectrometry ...
Chaerkady, Raghothama, Akhilesh, Pandey
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Beyond standardization: dynamic software infrastructures for systems biology
Nature Reviews Genetics, 2007Progress in systems biology is seriously hindered by slow production of suitable software infrastructures. Biologists need infrastructure that easily connects to work that is done in other laboratories, for which standardization is helpful. However, the infrastructure must also accommodate the specifics of their biological system, but appropriate ...
Morris A, Swertz, Ritsert C, Jansen
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Independent Dynamics Hybrid Automata in Systems Biology
2005Independent Dynamics Hybrid Automata (IDA) describe a new class of hybrid automata that extends decidable O-minimal automata by further allowing identity resets. We define the condi- tions under which reachability is decidable over IDA. These conditions involve the satisfiability of first-order formulæ that limit the interval of time we need to ...
CASAGRANDE A +3 more
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Systems Biology of Genome Structure and Dynamics
2018Our view of the packed genome inside a nucleus has evolved greatly over the past decade. Aided by novel experimental and bioinformatic analysis techniques and detailed computational models, fundamental insights into the structure and dynamics of chromosomes have been gained.
Zahra Fahmi +2 more
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High-Confidence Predictions in Systems Biology Dynamic Models
2014No
Alejandro Fernández Villaverde +6 more
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Nonlinear Dynamical Systems in Mechanics and Biology.
1995Abstract : This grant was in its final no-cost extension during academic year 1994-5. Following the PIi's move to Princeton University, te remaining funds on the grant were administered under Cornell,/Princeton Subcontract 20188-5423. They were to partially support the PI, Philip Holmes, during the academic year and summer 1995, and to support visiting
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