In this repository, you will find the references used in my presentation for the DMG symposium “Practical applications of metagenomics towards typing”. The title of my presentation is You must choose, but choose wisely: Model-based approaches for microbial community analysis and data integration. The references stored here provide further reading and support for the concepts discussed in my presentation. In addition to the references, I also included links to tutorials for the methods I discussed in my presentation. I hope to make it easier for you to apply the model-based approaches for analysis of -omics data.

References (in order of appearance)

Jia, Dini-Andreote, Salles. ISME COMMUN. 2, 96 (2022) - Jia, X., Dini-Andreote, F. & Salles, J.F. Unravelling the interplay of ecological processes structuring the bacterial rare biosphere. ISME COMMUN. 2, 96 (2022). https://doi.org/10.1038/s43705-022-00177-6

McLaren, Willis, Callahan. Elife. 2019 - Michael R McLaren, Amy D Willis, Benjamin J Callahan (2019) Consistent and correctable bias in metagenomic sequencing experiments eLife 8:e46923 https://doi.org/10.7554/eLife.46923

McLaren et al. biorxiv. 2022 - Michael R. McLaren, Jacob T. Nearing, Amy D. Willis, Karen G. Lloyd, Benjamin J. Callahan bioRxiv 2022.08.19.504330; doi: https://doi.org/10.1101/2022.08.19.504330

Dimitrov et al. PeerJ. 2017 - Dimitrov, Mauricio R., et al. "Successive DNA extractions improve characterization of soil microbial communities." PeerJ 5 (2017): e2915.

Willis & Martin. Biostatistics. 2022 - Amy D Willis, Bryan D Martin, Estimating diversity in networked ecological communities, Biostatistics, Volume 23, Issue 1, January 2022, Pages 207–222, https://doi.org/10.1093/biostatistics/kxaa015

Manor & Borenstein. Genome Biology. 2015 - Manor, O., Borenstein, E. MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome. Genome Biol 16, 53 (2015). https://doi.org/10.1186/s13059-015-0610-8

Mardis. Annu. Rev. Genom. Human Genet. 2008 - Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 2008;9:387-402. doi: 10.1146/annurev.genom.9.081307.164359. PMID: 18576944.

Gloor & Reid. Can. J. Microbiol. 2016 - Gregory B. Gloor and Gregor Reid. Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data. Canadian Journal of Microbiology. 62(8): 692-703. https://doi.org/10.1139/cjm-2015-0821

Leite & Kuramae. SBB. 2020 - Leite, Márcio FA, and Eiko E. Kuramae. "You must choose, but choose wisely: Model-based approaches for microbial community analysis." Soil Biology and Biochemistry 151 (2020): 108042. https://doi.org/10.1016/j.soilbio.2020.108042

Warton et al. Methods Ecol. Evol. 2012 - Warton, David I., Stephen T. Wright, and Yi Wang. "Distance‐based multivariate analyses confound location and dispersion effects." Methods in Ecology and Evolution 3.1 (2012): 89-101.

Warton & Hui. Methods Ecol. Evol. 2017 - Warton, David I., and Francis KC Hui. "The central role of mean‐variance relationships in the analysis of multivariate abundance data: A response to Roberts (2017)." Methods in Ecology and Evolution 8.11 (2017): 1408-1414. https://doi.org/10.1111/2041-210X.12843

Warton et al. TREE. 2015 - Warton DI, Blanchet FG, O'Hara RB, Ovaskainen O, Taskinen S, Walker SC, Hui FKC. So Many Variables: Joint Modeling in Community Ecology. Trends Ecol Evol. 2015 Dec;30(12):766-779. doi: 10.1016/j.tree.2015.09.007. Epub 2015 Oct 28. PMID: 26519235.

Ovaskainen et al. Ecol. 2017 - Ovaskainen, Otso, et al. "How to make more out of community data? A conceptual framework and its implementation as models and software." Ecology letters 20.5 (2017): 561-576. https://doi.org/10.1111/ele.12757

Zhou et al. Environ. microbiome. 2021 - Zhou, X., Leite, M.F.A., Zhang, Z. et al. Facilitation in the soil microbiome does not necessarily lead to niche expansion. Environmental Microbiome 16, 4 (2021). https://doi.org/10.1186/s40793-021-00373-2

Clark et al. Ecol. Monogr. 2017 - Clark, James S., et al. "Generalized joint attribute modeling for biodiversity analysis: Median‐zero, multivariate, multifarious data." Ecological Monographs 87.1 (2017): 34-56. https://doi.org/10.1002/ecm.1241

Bossolani et al. SBB. 2021 - Bossolani, João W., et al. "Modulation of the soil microbiome by long-term Ca-based soil amendments boosts soil organic carbon and physicochemical quality in a tropical no-till crop rotation system." Soil Biology and Biochemistry 156 (2021): 108188. https://doi.org/10.1016/j.soilbio.2021.108188