Search-based health status detection and disease classification using species-level profiles of metagenomes

Halfvarson, 2017, Dynamics of the human gut microbiome in inflammatory bowel disease, Nat. Microbiol., 2, 1, 10.1038/nmicrobiol.2017.4 Vázquez-Baeza, 2018, Guiding longitudinal sampling in IBD cohorts, Gut, 67, 1743, 10.1136/gutjnl-2017-315352 Baxter, 2016, Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions, Genome Med, 8, 1, 10.1186/s13073-016-0290-3 Knight, 2018, Best practices for analysing microbiomes, Nat Rev Microbiol, 16, 410, 10.1038/s41579-018-0029-9 Sun, 2019, A microbiome-based index for assessing skin health and treatment effects for atopic dermatitis in children, mSystems, 4, 10.1128/mSystems.00293-19 Teng, 2015, Prediction of early childhood caries via spatial-temporal variations of oral microbiota, Cell Host Microbe, 18, 296, 10.1016/j.chom.2015.08.005 Cammarota, 2020, Gut microbiome, big data and machine learning to promote precision medicine for cancer, Nat Rev Gastroenterol Hepatol, 17, 635, 10.1038/s41575-020-0327-3 Duvallet, 2017, Meta-analysis of gut microbiome studies identifies disease-specific and shared responses, Nat Commun, 8, 1, 10.1038/s41467-017-01973-8 Wirbel, 2019, Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer, Nat Med, 25, 679, 10.1038/s41591-019-0406-6 Jackson, 2018, Gut microbiota associations with common diseases and prescription medications in a population-based cohort, Nat Commun, 9, 1, 10.1038/s41467-018-05184-7 Wu, 2021, Towards multi-label classification: next step of machine learning for microbiome research, Comput Struct Biotechnol J, 10.1016/j.csbj.2021.04.054 Su, 2020, Multiple-disease detection and classification across cohorts via microbiome search, mSystems, 5, 10.1128/mSystems.00150-20 Su, 2018, Identifying and predicting novelty in microbiome studies, mBio, 9, 10.1128/mBio.02099-18 Jing, 2020, Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level, Bioinformatics, 36, 2308, 10.1093/bioinformatics/btz910 Su, 2012, Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data, Bioinformatics, 28, 2493, 10.1093/bioinformatics/bts470 Jing, 2021, Microbiome search engine 2: a platform for taxonomic and functional search of global microbiomes on the whole-microbiome level, mSystems, 6, 10.1128/mSystems.00943-20 Truong, 2015, MetaPhlAn2 for enhanced metagenomic taxonomic profiling, Nat Methods, 12, 902, 10.1038/nmeth.3589 Su, 2021, Elucidating the beta-diversity of the microbiome: from global alignment to local alignment, mSystems, 6, 10.1128/mSystems.00363-21