The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Identifying biologically relevant differences between metagenomic communities
Abstract
Motivation: Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can highlight the influence of ecological factors on patterns of microbial life in a wide range of habitats. Statistical hypothesis tests can help us distinguish ecological influences from sampling artifacts, but knowledge of only the P-value from a statistical hypothesis test is insufficient to make inferences about biological relevance. Current reporting practices for pairwise comparative metagenomics are inadequate, and better tools are needed for comparative metagenomic analysis. Results: We have developed a new software package, STAMP, for comparative metagenomics that supports best practices in analysis and reporting. Examination of a pair of iron mine metagenomes demonstrates that deeper biological insights can be gained using statistical techniques available in our software. An analysis of the functional potential of ‘Candidatus Accumulibacter phosphatis’ in two enhanced biological phosphorus removal metagenomes identified several subsystems that differ between the A.phosphatis stains in these related communities, including phosphate metabolism, secretion and metal transport. Availability: Python source code and binaries are freely available from our website at http://kiwi.cs.dal.ca/Software/STAMP Contact: beiko@cs.dal.ca Supplementary information: Supplementary data are available at Bioinformatics online.
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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444
Statistical significance for genomewide studies
Storey, J. D., & Tibshirani, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1530509100 · Cited by 9,692
Human gut microbes associated with obesity
Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227
Functional metagenomic profiling of nine biomes
Dinsdale, E. A., Edwards, R. A., Hall, D., Angly, F., Breitbart, M., Brulc, J. M., Furlan, M., Desnues, C., Haynes, M., Li, L., et al. (2008) · Nature · doi:10.1038/nature06810 · Cited by 980
Willner, D., Furlan, M., Haynes, M., Schmieder, R., Angly, F. E., Silva, J., Tammadoni, S., Nosrat, B., Conrad, D., & Rohwer, F. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007370 · Cited by 441
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Metagenomic biomarker discovery and explanation
Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011) · Genome Biology · doi:10.1186/gb-2011-12-6-r60 · Cited by 16,192
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116
Self-citationLiu, P., Wu, L., Peng, G., Han, Y., Tang, R., Ge, J., Zhang, L., Jia, L., Yue, S., Zhou, K., et al. (2019) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2019.05.008 · Cited by 669
Microbiota and host determinants of behavioural phenotype in maternally separated mice
De Palma, G., Blennerhassett, P., Lu, J., Deng, Y., Park, A. J., Green, W., Denou, E., Silva, M. A., Santacruz, A., Sanz, Y., et al. (2015) · Nature Communications · doi:10.1038/ncomms8735 · Cited by 517
Mitra, A., MacIntyre, D. A., Lee, Y. S., Smith, A., Marchesi, J. R., Lehne, B., Bhatia, R., Lyons, D., Paraskevaidis, E., Li, J. V., et al. (2015) · Scientific Reports · doi:10.1038/srep16865 · Cited by 498
Metadata
- Authors
- Parks, D. H., & Beiko, R. G.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-02-03
- Volume
- 26
- Issue
- 6
- Pages
- 715-721
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2149202898
- Cited by
- 947
- References
- 7
- FWCI
- 14.77
- Type
- journal article
- Language
- en
- Open access
- closed
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