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For: Wu S, Chen Y, Li Z, Li J, Zhao F, Su X. Towards multi-label classification: Next step of machine learning for microbiome research. Comput Struct Biotechnol J 2021;19:2742-2749. [PMID: 34093989 PMCID: PMC8131981 DOI: 10.1016/j.csbj.2021.04.054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 11/22/2022]  Open
Number Cited by Other Article(s)
1
Dakal TC, Xu C, Kumar A. Advanced computational tools, artificial intelligence and machine-learning approaches in gut microbiota and biomarker identification. FRONTIERS IN MEDICAL TECHNOLOGY 2025;6:1434799. [PMID: 40303946 PMCID: PMC12037385 DOI: 10.3389/fmedt.2024.1434799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 10/16/2024] [Indexed: 05/02/2025]  Open
2
Bakir-Gungor B, Temiz M, Canakcimaksutoglu B, Yousef M. Prediction of colorectal cancer based on taxonomic levels of microorganisms and discovery of taxonomic biomarkers using the Grouping-Scoring-Modeling (G-S-M) approach. Comput Biol Med 2025;187:109813. [PMID: 39929003 DOI: 10.1016/j.compbiomed.2025.109813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 01/09/2025] [Accepted: 02/05/2025] [Indexed: 02/12/2025]
3
Jiang Y, Liao D, Zhu Q, Lu YY. PhyloMix: enhancing microbiome-trait association prediction through phylogeny-mixing augmentation. Bioinformatics 2025;41:btaf014. [PMID: 39799515 PMCID: PMC11849959 DOI: 10.1093/bioinformatics/btaf014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 12/14/2024] [Accepted: 01/09/2025] [Indexed: 01/15/2025]  Open
4
Su Q, Lau RI, Liu Q, Li MKT, Yan Mak JW, Lu W, Lau ISF, Lau LHS, Yeung GTY, Cheung CP, Tang W, Liu C, Ching JYL, Cheong PK, Chan FKL, Ng SC. The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome. Cell Host Microbe 2024;32:651-660.e4. [PMID: 38657605 DOI: 10.1016/j.chom.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/28/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024]
5
Ibrahimi E, Lopes MB, Dhamo X, Simeon A, Shigdel R, Hron K, Stres B, D’Elia D, Berland M, Marcos-Zambrano LJ. Overview of data preprocessing for machine learning applications in human microbiome research. Front Microbiol 2023;14:1250909. [PMID: 37869650 PMCID: PMC10588656 DOI: 10.3389/fmicb.2023.1250909] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/22/2023] [Indexed: 10/24/2023]  Open
6
Zhang W, Fan X, Shi H, Li J, Zhang M, Zhao J, Su X. Comprehensive Assessment of 16S rRNA Gene Amplicon Sequencing for Microbiome Profiling across Multiple Habitats. Microbiol Spectr 2023;11:e0056323. [PMID: 37102867 PMCID: PMC10269731 DOI: 10.1128/spectrum.00563-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/10/2023] [Indexed: 04/28/2023]  Open
7
An Improved Diagnostic of the Mycobacterium tuberculosis Drug Resistance Status by Applying a Decision Tree to Probabilities Assigned by the CatBoost Multiclassifier of Matrix Metalloproteinases Biomarkers. Diagnostics (Basel) 2022;12:diagnostics12112847. [PMID: 36428907 PMCID: PMC9688965 DOI: 10.3390/diagnostics12112847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022]  Open
8
Acharjee A, Singh U, Choudhury SP, Gkoutos GV. The diagnostic potential and barriers of microbiome based therapeutics. Diagnosis (Berl) 2022;9:411-420. [PMID: 36000189 DOI: 10.1515/dx-2022-0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/03/2022] [Indexed: 02/07/2023]
9
Chen Y, Su X. Search-based health status detection and disease classification using species-level profiles of metagenomes. MEDICINE IN MICROECOLOGY 2022. [DOI: 10.1016/j.medmic.2021.100048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]  Open
10
Chen Y, Li J, Zhang Y, Zhang M, Sun Z, Jing G, Huang S, Su X. Parallel-Meta Suite: Interactive and rapid microbiome data analysis on multiple platforms. IMETA 2022;1:e1. [PMID: 38867729 PMCID: PMC10989749 DOI: 10.1002/imt2.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2024]
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