AIMC Topic: Metagenome
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Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease.
Nature communications
May 7, 2025
There is strong interest in using the gut microbiome for Parkinson's disease (PD) diagnosis and treatment. However, a consensus on PD-associated microbiome features and a multi-study assessment of their diagnostic value is lacking. Here, we present a...
Microbiome and fragmentation pattern of blood cell-free DNA and fecal metagenome enhance colorectal cancer micro-dysbiosis and diagnosis analysis: a proof-of-concept study.
mSystems
Apr 29, 2025
Colorectal cancer (CRC) is the third most common cancer, and it can be prevented by performing early screening. As a hallmark of cancer, the human microbiome plays important roles in the occurrence and development of CRC. Recently, the blood microbio...
DRAMMA: a multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data.
Microbiome
Mar 7, 2025
BACKGROUND: Antibiotics are essential for medical procedures, food security, and public health. However, ill-advised usage leads to increased pathogen resistance to antimicrobial substances, posing a threat of fatal infections and limiting the benefi...
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...
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...
Improving viral annotation with artificial intelligence.
mBio
Sep 4, 2024
Viruses of bacteria, "phages," are fundamental, poorly understood components of microbial community structure and function. Additionally, their dependence on hosts for replication positions phages as unique sensors of ecosystem features and environme...
Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data.
Gut microbes
Jul 7, 2024
The gut microbiome, linked significantly to host diseases, offers potential for disease diagnosis through machine learning (ML) pipelines. These pipelines, crucial in modeling diseases using high-dimensional microbiome data, involve selecting profile...
Discovery of antimicrobial peptides in the global microbiome with machine learning.
Cell
Jun 5, 2024
Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine-learning-based approach to predict antimicrobial peptides (AMPs) within the global microbiome and leverage a vast dataset of 63,410 metagenomes and...
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