The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli
Open accessAbstract
The recent flood of genomic ([13][1]), transcriptomic ([29][2]), and other high-throughput data ([21][3], [33][4], [45][5]) makes the need to interpret this information in a systemic fashion increasingly pressing. The construction of in silico models represents a way to interpret these data and
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Citations
Cites
Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network
Förster, J., Famili, I., Fu, P., Palsson, B. Ø., & Nielsen, J. (2003) · Genome Research · doi:10.1101/gr.234503 · Cited by 1,069
Self-citationEscherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
Ibarra, R. U., Edwards, J. S., & Palsson, B. O. (2002) · Nature · doi:10.1038/nature01149 · Cited by 857 · cited 6×
“It has also been found that some carbon sources do no initially support optimal behavior, although limited adaptive evolution data do suggest that over time E. coli adjusts its metabolic fluxes to find the optimal solution (26; S. S. Fong and B. O. Palsson, unpublished data).”
BackgroundMethodInfluentialSelf-citationMetabolic network structure determines key aspects of functionality and regulation
Stelling, J., Klamt, S., Bettenbrock, K., Schuster, S., & Gilles, E. D. (2002) · Nature · doi:10.1038/nature01166 · Cited by 802
Metabolic modelling of microbes: the flux‐balance approach
Edwards, J. S., Covert, M., & Palsson, B. (2002) · Environmental Microbiology · doi:10.1046/j.1462-2920.2002.00282.x · Cited by 365
Self-citation
Cited by
Integrating high-throughput and computational data elucidates bacterial networks
Covert, M. W., Knight, E. M., Reed, J. L., Herrgard, M. J., & Palsson, B. O. (2004) · Nature · doi:10.1038/nature02456 · Cited by 792
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
Self-citationMetabolomics and systems biology: making sense of the soup
KELL, D. (2004) · Current Opinion in Microbiology · doi:10.1016/j.mib.2004.04.012 · Cited by 529
Famili, I., Förster, J., Nielsen, J., & Palsson, B. O. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2235812100 · Cited by 353
Self-citationNetwork Context and Selection in the Evolution to Enzyme Specificity
Nam, H., Lewis, N. E., Lerman, J. A., Lee, D.-H., Chang, R. L., Kim, D., & Palsson, B. O. (2012) · Science · doi:10.1126/science.1216861 · Cited by 277
Self-citationIt Is All about MetabolicFluxes
Nielsen, J. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.24.7031-7035.2003 · Cited by 236
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli
Feist, A. M., Zielinski, D. C., Orth, J. D., Schellenberger, J., Herrgard, M. J., & Palsson, B. Ø. (2010) · Metabolic Engineering · doi:10.1016/j.ymben.2009.10.003 · Cited by 238
Self-citationFlux Balance Analysis of Photoautotrophic Metabolism
Shastri, A. A., & Morgan, J. A. (2005) · Biotechnology Progress · doi:10.1021/bp050246d · Cited by 205
Modeling formalisms in Systems Biology
Machado, D., Costa, R. S., Rocha, M., Ferreira, E. C., Tidor, B., & Rocha, I. (2011) · AMB Express · doi:10.1186/2191-0855-1-45 · Cited by 189
Mathematical models in microbial systems biology
Stelling, J. (2004) · Current Opinion in Microbiology · doi:10.1016/j.mib.2004.08.004 · Cited by 164
Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation
Macklin, D. N., Ahn-Horst, T. A., Choi, H., Ruggero, N. A., Carrera, J., Mason, J. C., Sun, G., Agmon, E., DeFelice, M. M., Maayan, I., et al. (2020) · Science · doi:10.1126/science.aav3751 · Cited by 151
Growth and Maintenance of Escherichia coli Laboratory Strains
Tuttle, A. R., Trahan, N. D., & Son, M. S. (2021) · Current Protocols · doi:10.1002/cpz1.20 · Cited by 140
Flux-Balance Modeling of Plant Metabolism
Sweetlove, L. J., & Ratcliffe, R. G. (2011) · Frontiers in Plant Science · doi:10.3389/fpls.2011.00038 · Cited by 137
Growth, metabolic partitioning, and the size of microorganisms
Kempes, C. P., Dutkiewicz, S., & Follows, M. J. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1115585109 · Cited by 132
Kinetic modelling of plant metabolic pathways
Rohwer, J. M. (2012) · Journal of Experimental Botany · doi:10.1093/jxb/ers080 · Cited by 106
Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling
Wodke, J. A. H., Puchałka, J., Lluch‐Senar, M., Marcos, J., Yus, E., Godinho, M., Gutiérrez‐Gallego, R., dos Santos, V. A. P. M., Serrano, L., Klipp, E., et al. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.6 · Cited by 89
Predicting Gene Essentiality Using Genome-Scale in Silico Models
Joyce, A. R., & Palsson, B. Ø. (2008) · Methods in Molecular Biology™ · doi:10.1007/978-1-59745-321-9_30 · Cited by 87
Self-citationCheng, Y., Schlosser, P., Hertel, J., Sekula, P., Oefner, P. J., Spiekerkoetter, U., Mielke, J., Freitag, D. F., Schmidts, M., GCKD Investigators, et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20877-8 · Cited by 37
Microbiome modeling: a beginner's guide
Lange, E., Kranert, L., Krüger, J., Benndorf, D., & Heyer, R. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1368377 · Cited by 21
Metadata
- Authors
- Reed, J. L., & Palsson, B. Ø.
- Venue
- Journal of Bacteriology
- Publisher
- American Society for Microbiology
- Published
- 2003-05
- Volume
- 185
- Issue
- 9
- Pages
- 2692-2699
- ISSN
- 0021-9193 (ISSN-L)
- 1098-5530
- OpenAlex
- W2122638857
- Cited by
- 301
- References
- 4
- FWCI
- 7.72
- Type
- journal article
- Language
- en
- Open access
- green
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