The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
The comprehensive microbial resource
Open accessAbstract
The Comprehensive Microbial Resource or CMR (http://cmr.jcvi.org) provides a web-based central resource for the display, search and analysis of the sequence and annotation for complete and publicly available bacterial and archaeal genomes. In addition to displaying the original annotation from GenBank, the CMR makes available secondary automated structural and functional annotation across all genomes to provide consistent data types necessary for effective mining of genomic data. Precomputed homology searches are stored to allow meaningful genome comparisons. The CMR supplies users with over 50 different tools to utilize the sequence and annotation data across one or more of the 571 currently available genomes. At the gene level users can view the gene annotation and underlying evidence. Genome level information includes whole genome graphical displays, biochemical pathway maps and genome summary data. Comparative tools display analysis between genomes with homology and genome alignment tools, and searches across the accessions, annotation, and evidence assigned to all genes/genomes are available. The data and tools on the CMR aid genomic research and analysis, and the CMR is included in over 200 scientific publications. The code underlying the CMR website and the CMR database are freely available for download with no license restrictions.
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Citations
Cites
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Highways of gene sharing in prokaryotes
Beiko, R. G., Harlow, T. J., & Ragan, M. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504068102 · Cited by 535
Cited by
Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M., Dale, J. M., Lee, T. J., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., et al. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp043 · Cited by 694
Karp, P. D., Paley, S., & Romero, P. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s225 · Cited by 661
Highways of gene sharing in prokaryotes
Beiko, R. G., Harlow, T. J., & Ragan, M. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504068102 · Cited by 535
A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter
Finucane, M. M., Sharpton, T. J., Laurent, T. J., & Pollard, K. S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0084689 · Cited by 321
Koch, G., Yepes, A., Förstner, K. U., Wermser, C., Stengel, S. T., Modamio, J., Ohlsen, K., Foster, K. R., & Lopez, D. (2014) · Cell · doi:10.1016/j.cell.2014.06.046 · Cited by 211
The Stepwise Evolution of Early Life Driven by Energy Conservation
Ferry, J. G. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msk014 · Cited by 123
Critical assessment of genome-scale metabolic networks: the need for a unified standard
Ravikrishnan, A., & Raman, K. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv003 · Cited by 87
Rioux, S., Neyt, C., Di Paolo, E., Turpin, L., Charland, N., Labbé, S., Mortier, M.-C., Mitchell, T. J., Feron, C., Martin, D., et al. (2011) · Microbiology · doi:10.1099/mic.0.042184-0 · Cited by 75
Dibrova, D. V., Galperin, M. Y., & Mulkidjanian, A. Y. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq234 · Cited by 70
Clinton, B., Warden, A. C., Haboury, S., Easton, C. J., Kotsonis, S., Taylor, M. C., Oakeshott, J. G., Russell, R. J., & Scott, C. (2011) · Biocatalysis and Biotransformation · doi:10.3109/10242422.2011.578740 · Cited by 31
Metadata
- Authors
- Davidsen, T., Beck, E., Ganapathy, A., Montgomery, R., Zafar, N., Yang, Q., Madupu, R., Goetz, P., Galinsky, K., White, O., & Sutton, G.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-11-05
- Volume
- 38
- Issue
- suppl_1
- Pages
- D340-D345
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1984345785
- Cited by
- 487
- References
- 2
- FWCI
- 17.52
- Type
- journal article
- Language
- en
- Open access
- gold
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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.
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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.
