AIMC Topic: Metagenomics
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Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.
Genome research
Feb 14, 2025
Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations...
Effects of data transformation and model selection on feature importance in microbiome classification data.
Microbiome
Jan 4, 2025
BACKGROUND: Accurate classification of host phenotypes from microbiome data is crucial for advancing microbiome-based therapies, with machine learning offering effective solutions. However, the complexity of the gut microbiome, data sparsity, composi...
Interpretation of machine learning-based prediction models and functional metagenomic approach to identify critical genes in HBCD degradation.
Journal of hazardous materials
Dec 25, 2024
Hexabromocyclododecane (HBCD) poses significant environmental risks, and identifying HBCD-degrading microbes and their enzymatic mechanisms is challenging due to the complexity of microbial interactions and metabolic pathways. This study aimed to ide...
Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study.
NPJ biofilms and microbiomes
Dec 19, 2024
Sex differences in the gut microbiome have been examined previously, but results are inconsistent, often due to small sample sizes. We investigated sex and menopausal differences in the gut microbiome in a large multi-ethnic population cohort study, ...
Interpretation knowledge extraction for genetic testing via question-answer model.
BMC genomics
Nov 9, 2024
BACKGROUND: Sequencing-based genetic testing is widely used in biomedical research, including pathogenic microorganism detection with metagenomic next-generation sequencing (mNGS). The application of sequencing results to clinical diagnosis and treat...
Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production.
mSystems
Oct 10, 2024
UNLABELLED: The increasing knowledge of microbial ecology in food products relating to quality and safety and the established usefulness of machine learning algorithms for anomaly detection in multiple scenarios suggests that the application of micro...
Understanding the mechanism of microplastic-associated antibiotic resistance genes in aquatic ecosystems: Insights from metagenomic analyses and machine learning.
Water research
Oct 2, 2024
The pervasive presence of microplastics (MPs) in aquatic systems facilitates the transmission of antibiotic resistance genes (ARGs), thereby posing risks to ecosystems and human well-being. However, owing to variations in environmental backgrounds an...
Untargeted Metabolomics and Soil Community Metagenomics Analyses Combined with Machine Learning Evaluation Uncover Geographic Differences in Ginseng from Different Locations.
Journal of agricultural and food chemistry
Sep 20, 2024
C.A. Meyer, known as the "King of Herbs," has been used as a nutritional supplement for both food and medicine with the functions of relieving fatigue and improving immunity for thousands of years in China. In agricultural planting, soil environment...
CCPred: Global and population-specific colorectal cancer prediction and metagenomic biomarker identification at different molecular levels using machine learning techniques.
Computers in biology and medicine
Sep 17, 2024
Colorectal cancer (CRC) ranks as the third most common cancer globally and the second leading cause of cancer-related deaths. Recent research highlights the pivotal role of the gut microbiota in CRC development and progression. Understanding the comp...
Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities.
Trends in microbiology
Sep 12, 2024
Increasing evidence suggests that the human microbiome plays an important role in cancer risk and treatment. Untargeted 'omics' techniques have accelerated research into microbiome-cancer interactions, supporting the discovery of novel associations a...
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