The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
Open accessAbstract
Background: Genome-scale metabolic reconstructions under the Constraint Based Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the metabolic capabilities of organisms and interpreting experimental data. As the number of such reconstructions and analysis methods increases, there is a greater need for data uniformity and ease of distribution and use. Description: We describe BiGG, a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest. Conclusions: BiGG addresses a need in the systems biology community to have access to high quality curated metabolic models and reconstructions. It is freely available for academic use at http://bigg.ucsd.edu.
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Cites
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., et al. (2011) · Nature Protocols · doi:10.1038/nprot.2011.308 · Cited by 1,835
Self-citationA protocol for generating a high-quality genome-scale metabolic reconstruction
Thiele, I., & Palsson, B. Ø. (2010) · Nature Protocols · doi:10.1038/nprot.2009.203 · Cited by 1,789
Self-citationE-CELL: software environment for whole-cell simulation
Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T. S., Matsuzaki, Y., Miyoshi, F., Saito, K., Tanida, S., Yugi, K., Venter, J. C., et al. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.1.72 · Cited by 764
Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1492 · Cited by 588
Self-citationThe growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
Feist, A. M., & Palsson, B. Ø. (2008) · Nature Biotechnology · doi:10.1038/nbt1401 · Cited by 545 · cited 1×
“Case studies have been reviewed in [10].”
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Cited by
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., et al. (2011) · Nature Protocols · doi:10.1038/nprot.2011.308 · Cited by 1,835
Self-citationKBase: The United States Department of Energy Systems Biology Knowledgebase
(2018) · doi:10.1038/nbt.4163 · Cited by 1,624
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
King, Z. A., Lu, J., Dräger, A., Miller, P., Federowicz, S., Lerman, J. A., Ebrahim, A., Palsson, B. O., & Lewis, N. E. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1049 · Cited by 938
Self-citationPopularity versus similarity in growing networks
Papadopoulos, F., Kitsak, M., Serrano, M. Á., Boguñá, M., & Krioukov, D. (2012) · Nature · doi:10.1038/nature11459 · Cited by 634
Metabolite concentrations, fluxes and free energies imply efficient enzyme usage
Park, J. O., Rubin, S. A., Xu, Y.-F., Amador-Noguez, D., Fan, J., Shlomi, T., & Rabinowitz, J. D. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2077 · Cited by 453
Bosi, E., Monk, J. M., Aziz, R. K., Fondi, M., Nizet, V., & Palsson, B. Ø. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1523199113 · Cited by 266
Self-citationEssential metabolism for a minimal cell
Breuer, M., Earnest, E. E., Merryman, C., Wise, K. S., Sun, L., Lynott, M. R., Hutchison, C. A., Smith, H. O., Lapek, J. D., Gonzalez, D. J., et al. (2019) · eLife · doi:10.7554/elife.36842 · Cited by 190
“Metabolite and reaction IDs were matched to BiGG IDs (Schellenberger et al., 2010; King et al., 2016) when possible, otherwise IDs akin to BiGG IDs were assigned.”
MethodMoretti, S., Martin, O., Van Du Tran, T., Bridge, A., Morgat, A., & Pagni, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1117 · Cited by 162
Redox balance is key to explaining full vs. partial switching to low-yield metabolism
van Hoek, M. J., & Merks, R. M. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-22 · Cited by 131
A Caenorhabditis elegans genome-scale metabolic network model
Yilmaz, L. S., & Walhout, A. J. M. (2016) · Cell Systems · doi:10.1016/j.cels.2016.04.012 · Cited by 88
Vazquez, A., & Oltvai, Z. N. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019538 · Cited by 70
“Large scale model The large scale model of cell metabolism included the set of metabolic reactions listed in the Table S1, which were compiled from the BiGG database [42].”
MethodInvestigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model
Islam, M. A., Zengler, K., Edwards, E. A., Mahadevan, R., & Stephanopoulos, G. (2015) · Integrative Biology · doi:10.1039/c5ib00095e · Cited by 41
A genome-scale database and reconstruction of Caenorhabditis elegans metabolism
Gebauer, J., Gentsch, C., Mansfeld, J., Schmeißer, K., Waschina, S., Brandes, S., Klimmasch, L., Zamboni, N., Zarse, K., Schuster, S., et al. (2016) · Cell Systems · doi:10.1016/j.cels.2016.04.017 · Cited by 33
The chemical interactome space between the human host and the genetically defined gut metabotypes
Jacobsen, U. P., Nielsen, H. B., Hildebrand, F., Raes, J., Sicheritz-Ponten, T., Kouskoumvekaki, I., & Panagiotou, G. (2013) · The ISME Journal · doi:10.1038/ismej.2012.141 · Cited by 24
A biochemical network modeling of a whole-cell
Burke, P. E. P., Campos, C. B. D. L., Costa, L. D. F., & Quiles, M. G. (2020) · Scientific Reports · doi:10.1038/s41598-020-70145-4 · Cited by 18
Network spectra for drug-target identification in complex diseases: new guns against old foes
Rai, A., Shinde, P., & Jalan, S. (2018) · Applied Network Science · doi:10.1007/s41109-018-0107-y · Cited by 12
Metadata
- Authors
- Schellenberger, J., Park, J. O., Conrad, T. M., & Palsson, B. Ø.
- Venue
- BMC Bioinformatics
- Published
- 2010-04-29
- Volume
- 11
- Issue
- 1
- Pages
- 213-213
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W2075283200
- Cited by
- 583
- References
- 5
- FWCI
- 20.20
- Type
- journal article
- Language
- en
- Open access
- gold
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