The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies
Open accessAbstract
EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignments that has been extended to include assignments based on both the large and small subunit RNA marker genes and to encompass all cellular micro-organisms. We also describe the addition of metagenomic assembly as a new analysis service. Our pilot studies have produced over 2400 assemblies from datasets in the public domain. From these assemblies, we have produced a searchable, non-redundant protein database of over 50 million sequences. To provide improved access to the data stored within the resource, we have developed a programmatic interface that provides access to the analysis results and associated sample metadata. Finally, we have integrated the results of a series of statistical analyses that provide estimations of diversity and sample comparisons.
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Cites
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
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Complex archaea that bridge the gap between prokaryotes and eukaryotes
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An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis
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Protein structure determination using metagenome sequence data
Ovchinnikov, S., Park, H., Varghese, N., Huang, P.-S., Pavlopoulos, G. A., Kim, D. E., Kamisetty, H., Kyrpides, N. C., & Baker, D. (2017) · Science · doi:10.1126/science.aah4043 · Cited by 520
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Cited by
UniProt: a worldwide hub of protein knowledge
The UniProt Consortium (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1049 · Cited by 7,698
Potter, S. C., Luciani, A., Eddy, S. R., Park, Y., Lopez, R., & Finn, R. D. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky448 · Cited by 2,607
Self-citationInterPro in 2019: improving coverage, classification and access to protein sequence annotations
Mitchell, A. L., Attwood, T. K., Babbitt, P. C., Blum, M., Bork, P., Bridge, A., Brown, S. D., Chang, H.-Y., El-Gebali, S., Fraser, M. I., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1100 · Cited by 1,426
Self-citationA unified catalog of 204,938 reference genomes from the human gut microbiome
Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0603-3 · Cited by 1,367
Self-citationA new genomic blueprint of the human gut microbiota
Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D. (2019) · Nature · doi:10.1038/s41586-019-0965-1 · Cited by 1,314
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Metadata
- Authors
- Mitchell, A. L., Scheremetjew, M., Denise, H., Potter, S., Tarkowska, A., Qureshi, M., Salazar, G. A., Pesseat, S., Boland, M. A., Hunter, F. M. I., ten Hoopen, P., Alako, B., Amid, C., Wilkinson, D. J., Curtis, T. P., Cochrane, G., & Finn, R. D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-10-23
- Volume
- 46
- Issue
- D1
- Pages
- D726-D735
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2766822634
- Cited by
- 210
- References
- 7
- FWCI
- 9.22
- Type
- journal article
- Language
- en
- Open access
- gold
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- Mitchell, A. L., Scheremetjew, M., Denise, H., Potter, S., Tarkowska, A., Qureshi, M., Salazar, G. A., Pesseat, S., Boland, M. A., Hunter, F. M. I., ten Hoopen, P., Alako, B., Amid, C., Wilkinson, D. J., Curtis, T. P., Cochrane, G., & Finn, R. D. (2018). EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx967
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