A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

By Markus J. Herrgård, Neil Swainston, Paul D. Dobson, Warwick B. Dunn, K. Arğa, Mikko Arvas, Nils Blüthgen, S. Borger, R. Costenoble, Matthias Heinemann and 24 more. Nature Biotechnology, 2008

617 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/41c727788468a01017451f711b5e42dee3717ed5

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Fueling the future with fungal genomics (2011, background): “(Herrgard et al. 2008; Andersen et al. 2008) to predict genes whose deletion or overexpression”
The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum (2013, methodology): “The native model format for the RAVEN Toolbox follows the format of the yeast consensus metabolic network [27], but models in the COBRA Toolbox format can also be imported [21].”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, methodology): “Database http://hmdb.ca Wishart et al., 2009 BRENDA Comprehensive enzyme data resource http://brenda-enzymes.info Scheer et al., 2011 YeastNet Yeast metabolic network http://comp-sys-bio.org/yeastnet Herrgard et al., 2008 iMAT another metabolic network construction and analysis tools Several metabol”
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions (2010, background): “Because of the great effort involved, there have been attempts to partially automate the process [25-31] and split work through collaboration [32].”
Advances in plant disease and pest management (2010, background): “Genomescale metabolic reconstructions are already available for a range of species (Oberhardt et al. 2009), including yeast (Herrgård et al. 2008) and other fungi of industrial importance (Andersen et al. 2008), and within the next few years should also extend to some pests and pathogens.”
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease (2011, background): “As our understanding of the human microbiome improves, better models can be constructed, potentially using the collective effort of the research community (51, 52).”
ChEBI in 2016: Improved services and an expanding collection of metabolites (2015, background): “ChEBI is widely used for many different purposes including as a source of stable unique identifiers for chemicals in annotations in a wide range of bioinformatics databases, including as of recently UniProt for references to chemicals as cofactors, (4) and systems biology models (5,6).”
Single-Cell Metabolomics: Analytical and Biological Perspectives (2013, background): “Even for model organisms such as yeast [the size of the yeastmetabolome is 1168 compounds (90, 91); in the yeast metabolome database, www.”
Environments that Induce Synthetic Microbial Ecosystems (2010, methodology): “Although several metabolites downstream of the ade8 reaction might restore flux through the rest of the adenine biosynthesis pathway, based on the stoichiometric model [40] only PAP and HXAN can be reversibly transported.”
Chapter 1. General introduction (2015, neutral): “…books Built by scientists, for scientists 12.2% 117,000 130M TOP 1%154 4,400 Chapter 1 General Introduction: Advances in Hepatic Surgery J.H.M.B. Stoot, R.J.S. Coelen, J.L.A. van Vugt and C.H.C. Dejong Additional information is available at the end of the chapter http://dx.doi.org/10.5772/54710”