The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Applications of genome‐scale metabolic reconstructions
Open accessAbstract
The availability and utility of genome-scale metabolic reconstructions have exploded since the first genome-scale reconstruction was published a decade ago. Reconstructions have now been built for a wide variety of organisms, and have been used toward five major ends: (1) contextualization of high-throughput data, (2) guidance of metabolic engineering, (3) directing hypothesis-driven discovery, (4) interrogation of multi-species relationships, and (5) network property discovery. In this review, we examine the many uses and future directions of genome-scale metabolic reconstructions, and we highlight trends and opportunities in the field that will make the greatest impact on many fields of biology.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
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-citationToward Automatic Reconstruction of a Highly Resolved Tree of Life
Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., & Bork, P. (2006) · Science · doi:10.1126/science.1123061 · Cited by 1,663
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-citationHerrgård, 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×
“As the applications of E. coli genome-scale models have been reviewed earlier in detail (Feist and Palsson, 2008), we specifically exclude E. coli from this review, and instead focus on the many other target organisms that have been studied.”
BackgroundSelf-citationThe Edinburgh human metabolic network reconstruction and its functional analysis
Ma, H., Sorokin, A., Mazein, A., Selkov, A., Selkov, E., Demin, O., & Goryanin, I. (2007) · Molecular Systems Biology · doi:10.1038/msb4100177 · Cited by 435
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-citationFormulating genome‐scale kinetic models in the post‐genome era
Jamshidi, N., & Palsson, B. Ø. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.8 · Cited by 180
Self-citationA genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189
Suthers, P. F., Dasika, M. S., Kumar, V. S., Denisov, G., Glass, J. I., & Maranas, C. D. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000285 · Cited by 144
Cited by
What is flux balance analysis?
Orth, J. D., Thiele, I., & Palsson, B. Ø. (2010) · Nature Biotechnology · doi:10.1038/nbt.1614 · Cited by 3,903
Self-citationSimultaneous epitope and transcriptome measurement in single cells
Stoeckius, M., Hafemeister, C., Stephenson, W., Houck-Loomis, B., Chattopadhyay, P. K., Swerdlow, H., Satija, R., & Smibert, P. (2017) · Nature Methods · doi:10.1038/nmeth.4380 · Cited by 3,098
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-citationInteractome Networks and Human Disease
Vidal, M., Cusick, M. E., & Barabási, A.-L. (2011) · Cell · doi:10.1016/j.cell.2011.02.016 · Cited by 1,771
A community-driven global reconstruction of human metabolism
Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2488 · Cited by 1,019
Self-citation
Metadata
- Authors
- Oberhardt, M. A., Palsson, B. Ø., & Papin, J. A.
- Venue
- Molecular Systems Biology
- Published
- 2009-01
- Volume
- 5
- Issue
- 1
- Pages
- 320-320
- ISSN
- 1744-4292 (ISSN-L)
- OpenAlex
- W2098824895
- Cited by
- 828
- References
- 9
- FWCI
- 27.85
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Applications of genome‐scale metabolic reconstructions. https://app.cochat.ai/papers/10.1038/msb.2009.77
- The paper
- Oberhardt, M. A., Palsson, B. Ø., & Papin, J. A. (2009). Applications of genome‐scale metabolic reconstructions. Molecular Systems Biology. https://doi.org/10.1038/msb.2009.77
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
