The DOI matches its Crossref record; 51 of the 51 references it cites were found in a registry or an index.
Genomic mining of prokaryotic repressors for orthogonal logic gates
Open accessAbstract
Genetic circuits perform computational operations based on interactions between freely diffusing molecules within a cell. When transcription factors are combined to build a circuit, unintended interactions can disrupt its function. Here, we apply “part mining” to build a library of 73 TetR-family repressors gleaned from prokaryotic genomes. The operators of a subset were determined using an in vitro method and this information was used to build synthetic promoters. The promoters and repressors were screened for cross-reactions. Of these, 16 were identified that both strongly repress their cognate promoter (5- to 207-fold) and do not interact with other promoters. Each repressor:promoter pair was converted to a NOT gate and characterized. Used as a set of 16 NOR gates, there are >1054 circuits that could be built by changing the pattern of input and output promoters. This represents a large set of compatible gates that can be used to construct user-defined circuits.
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
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.022 · Cited by 5,016
Tight control of gene expression in mammalian cells by tetracycline-responsive promoters.
Gossen, M., & Bujard, H. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.12.5547 · Cited by 4,943
A synthetic oscillatory network of transcriptional regulators
Elowitz, M. B., & Leibler, S. (2000) · Nature · doi:10.1038/35002125 · Cited by 4,630
Construction of a genetic toggle switch in Escherichia coli
Gardner, T. S., Cantor, C. R., & Collins, J. J. (2000) · Nature · doi:10.1038/35002131 · Cited by 4,268
MEME: discovering and analyzing DNA and protein sequence motifs
Bailey, T. L., Williams, N., Misleh, C., & Li, W. W. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl198 · Cited by 2,670
FACS-optimized mutants of the green fluorescent protein (GFP)
Cormack, B. P., Valdivia, R. H., & Falkow, S. (1996) · Gene · doi:10.1016/0378-1119(95)00685-0 · Cited by 2,620
Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors
Boch, J., Scholze, H., Schornack, S., Landgraf, A., Hahn, S., Kay, S., Lahaye, T., Nickstadt, A., & Bonas, U. (2009) · Science · doi:10.1126/science.1178811 · Cited by 2,470
Automated design of synthetic ribosome binding sites to control protein expression
Salis, H. M., Mirsky, E. A., & Voigt, C. A. (2009) · Nature Biotechnology · doi:10.1038/nbt.1568 · Cited by 1,844
Self-citationLutz, R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.6.1203 · Cited by 1,693
Foundations for engineering biology
Endy, D. (2005) · Nature · doi:10.1038/nature04342 · Cited by 1,511
Cited by
Genetic circuit design automation
Nielsen, A. A. K., Der, B. S., Shin, J., Vaidyanathan, P., Paralanov, V., Strychalski, E. A., Ross, D., Densmore, D., & Voigt, C. A. (2016) · Science · doi:10.1126/science.aac7341 · Cited by 1,020
Self-citationLarge-scale de novo DNA synthesis: technologies and applications
Kosuri, S., & Church, G. M. (2014) · Nature Methods · doi:10.1038/nmeth.2918 · Cited by 869
Permanent genetic memory with >1-byte capacity
Yang, L., Nielsen, A. A. K., Fernandez-Rodriguez, J., McClune, C. J., Laub, M. T., Lu, T. K., & Voigt, C. A. (2014) · Nature Methods · doi:10.1038/nmeth.3147 · Cited by 243
Self-citationRealizing the potential of synthetic biology
Church, G. M., Elowitz, M. B., Smolke, C. D., Voigt, C. A., & Weiss, R. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3767 · Cited by 226
Self-citationBervoets, I., & Charlier, D. (2019) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuz001 · Cited by 180
Metadata
- Authors
- Stanton, B. C., Nielsen, A. A. K., Tamsir, A., Clancy, K., Peterson, T., & Voigt, C. A.
- Venue
- Nature Chemical Biology
- Published
- 2013-12-08
- Volume
- 10
- Issue
- 2
- Pages
- 99-105
- ISSN
- 1552-4450 (ISSN-L)
- 1552-4469
- OpenAlex
- W1973256834
- Cited by
- 379
- References
- 51
- FWCI
- 11.97
- 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: Genomic mining of prokaryotic repressors for orthogonal logic gates. https://app.cochat.ai/papers/10.1038/nchembio.1411
- The paper
- Stanton, B. C., Nielsen, A. A. K., Tamsir, A., Clancy, K., Peterson, T., & Voigt, C. A. (2014). Genomic mining of prokaryotic repressors for orthogonal logic gates. Nature Chemical Biology. https://doi.org/10.1038/nchembio.1411
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.
