The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Computational tools for the synthetic design of biochemical pathways
Open accessOverview
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
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
Production of the antimalarial drug precursor artemisinic acid in engineered yeast
Ro, D.-K., Paradise, E. M., Ouellet, M., Fisher, K. J., Newman, K. L., Ndungu, J. M., Ho, K. A., Eachus, R. A., Ham, T. S., Kirby, J., et al. (2006) · Nature · doi:10.1038/nature04640 · Cited by 2,805
The Pfam protein families database
Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., Gavin, O. L., Gunasekaran, P., Ceric, G., Forslund, K., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp985 · Cited by 2,694
Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
Atsumi, S., Hanai, T., & Liao, J. C. (2008) · Nature · doi:10.1038/nature06450 · Cited by 1,945
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
High-throughput generation, optimization and analysis of genome-scale metabolic models
Henry, C. S., DeJongh, M., Best, A. A., Frybarger, P. M., Linsay, B., & Stevens, R. L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1672 · Cited by 1,090
Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome
Neumann, H., Wang, K., Davis, L., Garcia-Alai, M., & Chin, J. W. (2010) · Nature · doi:10.1038/nature08817 · Cited by 622
Five hard truths for synthetic biology
Kwok, R. (2010) · Nature · doi:10.1038/463288a · Cited by 442
Engineering Escherichia coli for production of functionalized terpenoids using plant P450s
Chang, M. C. Y., Eachus, R. A., Trieu, W., Ro, D.-K., & Keasling, J. D. (2007) · Nature Chemical Biology · doi:10.1038/nchembio875 · Cited by 364
Dietrich, J. A., Yoshikuni, Y., Fisher, K. J., Woolard, F. X., Ockey, D., McPhee, D. J., Renninger, N. S., Chang, M. C. Y., Baker, D., & Keasling, J. D. (2009) · ACS Chemical Biology · doi:10.1021/cb900006h · Cited by 186
Cited by
COBRApy: COnstraints-Based Reconstruction and Analysis for Python
Ebrahim, A., Lerman, J. A., Palsson, B. O., & Hyduke, D. R. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-74 · Cited by 1,378
Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications
Wu, G., Yan, Q., Jones, J. A., Tang, Y. J., Fong, S. S., & Koffas, M. A. G. (2016) · Trends in Biotechnology · doi:10.1016/j.tibtech.2016.02.010 · Cited by 666
Synthetic Biology and Metabolic Engineering
Stephanopoulos, G. (2012) · ACS Synthetic Biology · doi:10.1021/sb300094q · Cited by 274
Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities
Hu, R., Zhao, H., Xu, X., Wang, Z., Yu, K., Shu, L., Yan, Q., Wu, B., Mo, C., He, Z., et al. (2021) · Environment International · doi:10.1016/j.envint.2021.106560 · Cited by 176
Programming biological operating systems: genome design, assembly and activation.
Gibson, D. G. (2014) · Nature Methods · doi:10.1038/nmeth.2894 · Cited by 65
Metadata
- Authors
- Medema, M. H., van Raaphorst, R., Takano, E., & Breitling, R.
- Venue
- Nature Reviews Microbiology
- Published
- 2012-01-23
- Volume
- 10
- Issue
- 3
- Pages
- 191-202
- ISSN
- 1740-1526 (ISSN-L)
- 1740-1534
- OpenAlex
- W1964232618
- Cited by
- 226
- References
- 10
- FWCI
- 2.00
- Type
- journal article
- Language
- en
- Open access
- green
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: Computational tools for the synthetic design of biochemical pathways. https://app.cochat.ai/papers/10.1038/nrmicro2717
- The paper
- Medema, M. H., van Raaphorst, R., Takano, E., & Breitling, R. (2012). Computational tools for the synthetic design of biochemical pathways. Nature Reviews Microbiology. https://doi.org/10.1038/nrmicro2717
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.
