The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
Open accessAbstract
Recovery of ribosomal small subunit genes by assembly of short read community DNA sequence data generally fails, making taxonomic characterization difficult. Here, we solve this problem with a novel iterative method, based on the expectation maximization algorithm, that reconstructs full-length small subunit gene sequences and provides estimates of relative taxon abundances. We apply the method to natural and simulated microbial communities, and correctly recover community structure from known and previously unreported rRNA gene sequences. An implementation of the method is freely available at https://github.com/csmiller/EMIRGE.
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Cites
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Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891
Community structure and metabolism through reconstruction of microbial genomes from the environment
Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature · doi:10.1038/nature02340 · Cited by 2,417
Self-citationDethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
Huse, S. M., Welch, D. M., Morrison, H. G., & Sogin, M. L. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02193.x · Cited by 1,346
Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products
Gloor, G. B., Hummelen, R., Macklaim, J. M., Dickson, R. J., Fernandes, A. D., MacPhee, R., & Reid, G. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015406 · Cited by 330
Metagenomic Sequencing of an In Vitro-Simulated Microbial Community
Morgan, J. L., Darling, A. E., & Eisen, J. A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010209 · Cited by 248
Cited by
Poretsky, R., Rodriguez-R, L. M., Luo, C., Tsementzi, D., & Konstantinidis, K. T. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093827 · Cited by 684
PhyloSift: phylogenetic analysis of genomes and metagenomes
Darling, A. E., Jospin, G., Lowe, E., Matsen, F. A., Bik, H. M., & Eisen, J. A. (2014) · PeerJ · doi:10.7717/peerj.243 · Cited by 631
Chng, K. R., Tay, A. S. L., Li, C., Ng, A. H. Q., Wang, J., Suri, B. K., Matta, S. A., McGovern, N., Janela, B., Wong, X. F. C. C., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.106 · Cited by 388
Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor
Nobu, M. K., Narihiro, T., Rinke, C., Kamagata, Y., Tringe, S. G., Woyke, T., & Liu, W.-T. (2015) · The ISME Journal · doi:10.1038/ismej.2014.256 · Cited by 403
phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes
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Metadata
- Authors
- Miller, C. S., Baker, B. J., Thomas, B. C., Singer, S. W., & Banfield, J. F.
- Venue
- Genome Biology
- Published
- 2011-05
- Volume
- 12
- Issue
- 5
- Pages
- R44-R44
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2153137490
- Cited by
- 347
- References
- 9
- FWCI
- 6.23
- Type
- journal article
- Language
- en
- Open access
- gold
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- Miller, C. S., Baker, B. J., Thomas, B. C., Singer, S. W., & Banfield, J. F. (2011). EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biology. https://doi.org/10.1186/gb-2011-12-5-r44
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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