If you use MIMOSA2 in a publication, please cite:
Noecker, C., Eng, A., Muller, E., and Borenstein, E. (2022). MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data. Bioinformatics btac003. https://doi.org/10.1093/bioinformatics/btac003
MIMOSA2 uses several other R packages, bioinformatics tools, and databases. Depending on the settings for your MIMOSA2 analysis, you may also need to cite the following:
Rfit: Kloke, J.D. and Mckean, J.W. (2012), Rfit: Rank-based estimation for linear models, The R Journal, 4, 57–64.
vsearch: Rognes, T., Flouri, T., Nichols, B., Quince, C., and Mahé, F. (2016). VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584.
PICRUSt: 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). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotech 31, 814–821.
MetaboAnalystR: Chong, J., Soufan, O., Li, C., Caraus, I., Li, S., Bourque, G., Wishart, D.S., and Xia, J. (2018). MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. Nucleic Acids Research.
AGORA: Magnúsdóttir, S., Heinken, A., Kutt, L., Ravcheev, D.A., Bauer, E., Noronha, A., Greenhalgh, K., Jäger, C., Baginska, J., Wilmes, P., et al. (2016). Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nature Biotechnology.
CarveMe/embl_gems: Machado, D., Andrejev, S., Tramontano, M., and Patil, K.R. (2018). Fast automated reconstruction of genome-scale metabolic models for microbial species and communities. Nucleic Acids Research 46, 7542–7553.
KEGG: Kanehisa, M., and Goto, S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28, 27–30.
For questions about MIMOSA2, please email elbo [at] tauex.tau.ac.il .
If you find a bug or problem with the web application, please open a GitHub issue at www.github.com/borenstein-lab/MIMOSA2shiny. If you encounter a problem with the R package, please open an issue at www.github.com/borenstein-lab/mimosa2.