Foundations of Phylogenetic Systematics by Johann-Wolfgang Wägele

By Johann-Wolfgang Wägele

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Eng. Life Sci. 8, 467–476. Edwards JS, Faeder JR, Hlavacek WS, Jiang Y, Nemenman I and Wall ME 2007 q-bio 2007: a watershed moment in modern biology. Mol. Syst. Biol. 3, 148. Endy D and Brent R 2001 Modelling cellular behaviour. Nature 409, 391–395. Faeder JR, Blinov ML, Goldstein B and Hlavacek WS 2005 Rule-based modeling of biochemical networks. Complexity 10, 22–41. Faeder JR, Blinov ML and Hlavacek WS 2009 Rule-based modeling of biochemical systems with BioNetGen. Methods Mol. Biol. 500, 113–167.

2009). A signaling protein is typically composed of multiple functional components or sites. e. they depend on site-specific details. For example, many protein– protein interactions are regulated by phosphorylation (Pawson and Kofler 2009). It is difficult to document and/or visualize the contextual dependencies of molecular interactions in a way that is both clear and precise. Online resources, such as NetPath (Kandasamy et al. ELM (Dinkel et al. 2011) and Reactome (Matthews et al. g. a list of sites of phosphorylation), comments, and literature citations.

Mallavarapu A, Thomson M, Ullian B and Gunawardena J 2009 Programming with models: modularity and abstraction provide powerful capabilities for systems biology. J. R. Soc. Interface 6, 257–270. Two Challenges of Systems Biology 13 Mariotto AB, Robin Yabroff K, Shao Y, Feuer EJ and Brown ML 2011 Projections of the cost of cancer care in the United States: 2010–2020. J. Natl. Cancer Inst. 103, 117–128. Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L and D’Eustachio P 2009 Reactome knowledge base of human biological pathways and processes.

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