The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Use and abuse of correlation analyses in microbial ecology
Open accessAbstract
Correlation analyses are often included in bioinformatic pipelines as methods for inferring taxon–taxon interactions. In this perspective, we highlight the pitfalls of inferring interactions from covariance and suggest methods, study design considerations, and additional data types for improving high-throughput interaction inferences. We conclude that correlation, even when augmented by other data types, almost never provides reliable information on direct biotic interactions in real-world ecosystems. These bioinformatically inferred associations are useful for reducing the number of potential hypotheses that we might test, but will never preclude the necessity for experimental validation.
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Cites
Tackling the widespread and critical impact of batch effects in high-throughput data
Leek, J. T., Scharpf, R. B., Bravo, H. C., Simcha, D., Langmead, B., Johnson, W. E., Geman, D., Baggerly, K., & Irizarry, R. A. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2825 · Cited by 2,196
Sparse and Compositionally Robust Inference of Microbial Ecological Networks
Kurtz, Z. D., Müller, C. L., Miraldi, E. R., Littman, D. R., Blaser, M. J., & Bonneau, R. A. (2015) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004226 · Cited by 1,799
Perturbation Experiments in Community Ecology: Theory and Practice
Bender, E. A., Case, T. J., & Gilpin, M. E. (1984) · Ecology · doi:10.2307/1939452 · Cited by 1,245
Diet dominates host genotype in shaping the murine gut microbiota
Carmody, R. N., Gerber, G. K., Luevano, J. M., Gatti, D. M., Somes, L., Svenson, K. L., & Turnbaugh, P. J. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2014.11.010 · Cited by 1,103
Community Structure Follows Simple Assembly Rules in Microbial Microcosms
Friedman, J., Higgins, L. M., & Gore, J. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0109 · Cited by 557
Cited by
Lekberg, Y., Arnillas, C. A., Borer, E. T., Bullington, L. S., Fierer, N., Kennedy, P. G., Leff, J. W., Luis, A. D., Seabloom, E. W., & Henning, J. A. (2021) · Nature Communications · doi:10.1038/s41467-021-23605-y · Cited by 319
Linking soil fungi to bacterial community assembly in arid ecosystems
Jiao, S., Chu, H., Zhang, B., Wei, X., Chen, W., & Wei, G. (2022) · iMeta · doi:10.1002/imt2.2 · Cited by 284
Lyu, X., Nuhu, M., Candry, P., Wolfanger, J., Betenbaugh, M., Saldivar, A., Zuniga, C., Wang, Y., & Shrestha, S. (2024) · Journal of Industrial Microbiology and Biotechnology · doi:10.1093/jimb/kuae025 · Cited by 53
Metadata
- Authors
- Carr, A., Diener, C., Baliga, N. S., & Gibbons, S. M.
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-06-28
- Volume
- 13
- Issue
- 11
- Pages
- 2647-2655
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- OpenAlex
- W2955206482
- Cited by
- 289
- References
- 5
- FWCI
- 20.47
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Carr, A., Diener, C., Baliga, N. S., & Gibbons, S. M. (2019). Use and abuse of correlation analyses in microbial ecology. The ISME Journal. https://doi.org/10.1038/s41396-019-0459-z
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