Computational modeling of genetic and biochemical networks

By James M. Bower, H. Bolouri. 2001

483 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/976f1fa332dcb4ef4f3cb60d19e56a307a8f2f0f

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In Molecular Biology

Citations in the corpus

From Boolean to probabilistic Boolean networks as models of genetic regulatory networks (2002, background): “There have been a number of excellent survey papers on modeling and simulation of genetic regulatory networks [12]–[14] as well as a recent book [15].”
Comparing Stars: On Approximating Graph Edit Distance (2009, background): “For example, World Wide Web can be considered as a graph whose vertices correspond to static pages and edges correspond to links between pages[7]; in chem-informatics, labelled graphs are suited to express the connectivity of chemical compounds[29]; in bioinformatics, collections of DNA segments in ”
Modeling and Simulation of Genetic Regulatory Systems: A Literature Review (2002, unknown): “Recently, a collection of introductory chapters covering some of the methods discussed below appeared (Bower and Bolouri, 2001).”
A computational algebra approach to the reverse engineering of gene regulatory networks. (2003, background): “For more thorough reviews the reader can consult, e.g., (Bower and Bolouri, 2001) or (de Jong, 2002).”
Integration from proteins to organs: the Physiome Project (2003, methodology): “A more reasonable approach is therefore to develop models for a more limited range of spatial and temporal scales and to develop techniques to link the parameters of this hierarchy of models (see, for example, recent texts on computational biolog”
PopSGD: Decentralized Stochastic Gradient Descent in the Population Model (2019, background): “The population model, introduced by [8], is one of the standard models of distributed computing, and has proved a useful abstraction for modeling settings from wireless sensor networks [40, 21], to gene regulatory networks [16], and chemical reaction networks [18].”