Systems Biology: Properties of Reconstructed Networks

By Bernhard O. Palsson. 2006

876 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/dcd584781175eea0d74504cb96db399cba8809dd

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Citations in the corpus

Genome-scale models of bacterial metabolism: reconstruction and applications (2008, methodology): “One of the primary uses of genome-scale metabolic models is the prediction of growth phenotypes (Price et al., 2004; Palsson, 2006).”
Flux balance analysis of biological systems: applications and challenges (2009, neutral): “flux balance models [16].”
Petri Nets for Systems and Synthetic Biology (2008, background): “There are corresponding notions in systems biology, called chemical moieties, elementary modes and extreme pathways, which are elaborated in the setting of biochemical networks in [ Pal06 ].”
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology (2008, background): “The first is a qualitative stage in which are listed all the reactions that are known to occur in the system or organism of interest; in the modern era, and especially for metabolic networks, these reaction lists are often derived in part from genomic annotation”
Revealing networks from dynamics: an introduction (2014, background): “As an example, many constituents of protein and gene interaction networks are well characterized but how they interact and which pathways are relevant for suitable functioning is not well understood [1, 2].”
Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli (2013, background): “Genomescale models (GEMs) are a structured format of such a knowledge base that can be used to perform computational and quantitative queries to answer various questions about the capabilities of organisms and their likely phenotypic states (Palsson, 2006; Orth et al, 2010).”
Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes (2015, neutral): “Flux balance analysis (157), a tool from”
Towards multidimensional genome annotation (2006, background): “These high-quality reconstructions can be used as the basis for computation of phenotypic traits, and they represent a key step in the development of the burgeoning field of systems biolog”
Gut microbiota functions: metabolism of nutrients and other food components (2017, background): “1 3 and curated and validated against the available literature [145].”
A protocol for generating a high-quality genome-scale metabolic reconstruction (2010, background): “Examples for simple or more complex Type III pathways in metabolic networks can be found else-where 67,68 .”
Nonequilibrium Thermodynamics of Chemical Reaction Networks: Wisdom from Stochastic Thermodynamics (2016, background): “Conservation laws identify conserved quantities L ≡ `σ Z , called components [23, 25], which satisfy”