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-citationGreenblum, S., Turnbaugh, P. J., & Borenstein, E. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1116053109 · Cited by 821
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
Lewis, N. E., Nagarajan, H., & Palsson, B. O. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2737 · Cited by 779
Self-citationMultidimensional Optimality of Microbial Metabolism
Schuetz, R., Zamboni, N., Zampieri, M., Heinemann, M., & Sauer, U. (2012) · Science · doi:10.1126/science.1216882 · Cited by 420
Robinson, J. L., Kocabaş, P., Wang, H., Cholley, P.-E., Cook, D., Nilsson, A., Anton, M., Ferreira, R., Domenzain, I., Billa, V., et al. (2020) · Science Signaling · doi:10.1126/scisignal.aaz1482 · Cited by 442
Self-citationDetailing the optimality of photosynthesis in cyanobacteria through systems biology analysis
Nogales, J., Gudmundsson, S., Knight, E. M., Palsson, B. O., & Thiele, I. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1117907109 · Cited by 301
Self-citationReconstructing organisms in silico: genome-scale models and their emerging applications
Fang, X., Lloyd, C. J., & Palsson, B. O. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-00440-4 · Cited by 292
Self-citationIn silico method for modelling metabolism and gene product expression at genome scale
Lerman, J. A., Hyduke, D. R., Latif, H., Portnoy, V. A., Lewis, N. E., Orth, J. D., Schrimpe-Rutledge, A. C., Smith, R. D., Adkins, J. N., Zengler, K., et al. (2012) · Nature Communications · doi:10.1038/ncomms1928 · Cited by 266
Self-citationPereira, S., Kildegaard, H. F., & Andersen, M. R. (2018) · Biotechnology Journal · doi:10.1002/biot.201700499 · Cited by 214
Machine learning for biochemical engineering: A review
Mowbray, M., Savage, T., Wu, C., Song, Z., Cho, B. A., Del Rio-Chanona, E. A., & Zhang, D. (2021) · Biochemical Engineering Journal · doi:10.1016/j.bej.2021.108054 · Cited by 188
Aung, H. W., Henry, S. A., & Walker, L. P. (2013) · Industrial Biotechnology · doi:10.1089/ind.2013.0013 · Cited by 156
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1
Sigurdsson, M. I., Jamshidi, N., Steingrimsson, E., Thiele, I., & Palsson, B. Ø. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-140 · Cited by 154
Self-citationModeling metabolism of the human gut microbiome
Magnúsdóttir, S., & Thiele, I. (2018) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2017.12.005 · Cited by 127
Metabolic network modeling of microbial communities
Biggs, M. B., Medlock, G. L., Kolling, G. L., & Papin, J. A. (2015) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1308 · Cited by 124
Self-citationUsing the reconstructed genome-scale human metabolic network to study physiology and pathology
Bordbar, A., & Palsson, B. O. (2012) · Journal of Internal Medicine · doi:10.1111/j.1365-2796.2011.02494.x · Cited by 115
Self-citationA systems biology approach to studying the role of microbes in human health
Thiele, I., Heinken, A., & Fleming, R. M. (2013) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2012.10.001 · Cited by 114
Imam, S., Schäuble, S., Valenzuela, J., López García de Lomana, A., Carter, W., Price, N. D., & Baliga, N. S. (2015) · The Plant Journal · doi:10.1111/tpj.13059 · Cited by 96
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
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
Nitrogen-use efficiency in maize (Zea mays L.): from ‘omics’ studies to metabolic modelling
Simons, M., Saha, R., Guillard, L., Clement, G., Armengaud, P., Canas, R., Maranas, C. D., Lea, P. J., & Hirel, B. (2014) · Journal of Experimental Botany · doi:10.1093/jxb/eru227 · Cited by 87
Machado, D., Herrgård, M. J., & Rocha, I. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005140 · Cited by 82
Genome scale models of yeast: towards standardized evaluation and consistent omic integration
Sánchez, B. J., & Nielsen, J. (2015) · Integrative Biology · doi:10.1039/c5ib00083a · Cited by 75
Pilalis, E., Chatziioannou, A., Thomasset, B., & Kolisis, F. (2011) · Biotechnology and Bioengineering · doi:10.1002/bit.23107 · Cited by 62
Systems biology perspectives on minimal and simpler cells
Xavier, J. C., Patil, K. R., & Rocha, I. (2014) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00050-13 · Cited by 58
Genome-scale models in human metabologenomics
Mardinoglu, A., & Palsson, B. Ø. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-024-00768-0 · Cited by 54
Self-citationYoshikawa, K., Aikawa, S., Kojima, Y., Toya, Y., Furusawa, C., Kondo, A., & Shimizu, H. (2015) · PLOS ONE · doi:10.1371/journal.pone.0144430 · Cited by 39
Nogiec, C., Burkart, A., Dreyfuss, J. M., Lerin, C., Kasif, S., & Patti, M.-E. (2015) · Molecular Metabolism · doi:10.1016/j.molmet.2014.12.012 · Cited by 34
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
Population FBA predicts metabolic phenotypes in yeast
Labhsetwar, P., Melo, M. C. R., Cole, J. A., & Luthey-Schulten, Z. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005728 · Cited by 21
Integrative characterization of the near‐minimal bacterium Mesoplasma florum
Matteau, D., Lachance, J., Grenier, F., Gauthier, S., Daubenspeck, J. M., Dybvig, K., Garneau, D., Knight, T. F., Jacques, P., & Rodrigue, S. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209844 · Cited by 16
“…of organisms, offering phenotypic predictions capabilities useful in a wide-range of applications from omics data integration to metabolic engineering (Oberhardt et al , 2009; Durot et al , 2009; Bordbar et al , 2014; O’Brien et al , 2015; Ebrahim et al , 2016; Kim et al , 2016; Gu et al , 2019).”
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
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.