AIMC Topic: Metagenome

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Environmental adaptations in metagenomes revealed by deep learning.

BMC biology Aug 11, 2025
BACKGROUND: Deep learning has emerged as a powerful tool in the analysis of biological data, including the analysis of large metagenome data. However, its application remains limited due to high computational costs, model complexity, and difficulty e...
Adaptation, Physiological Environment Metagenome Deep Learning
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Metagenomics-Toolkit: the flexible and efficient cloud-based metagenomics workflow featuring machine learning-enabled resource allocation.

NAR genomics and bioinformatics Jul 17, 2025
The metagenome analysis of complex environments with thousands of datasets, such as those in the Sequence Read Archive, requires substantial computational resources for it to be completed within a reasonable time frame. Efficient use of infrastructur...
Workflow Metagenomics Cloud Computing Machine Learning Software Metagenome
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Extensive novel diversity and phenotypic associations in the dromedary camel microbiome are revealed through deep metagenomics and machine learning.

PloS one Jul 17, 2025
The dromedary camel, also known as one-humped camel or Arabian camel, is iconic and economically important to Arabian society. Its contemporary importance in commerce and transportation, along with the historical and modern use of its milk and meat p...
Microbiota Phenotype Metagenome Machine Learning Metagenomics Camelus Animals Gastrointestinal Microbiome
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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...
Humans Metagenome Gastrointestinal Microbiome Machine Learning Parkinson Disease
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Exploring deep learning in phage discovery and characterization.

Virology Apr 29, 2025
Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The d...
Computational Biology Metagenomics Genome, Viral Algorithms Deep Learning Metagenome Bacteriophages Neural Networks, Computer
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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...
Adenoma Microbiota Proof of Concept Study Dysbiosis Cell-Free Nucleic Acids Metagenome Colorectal Neoplasms Male Feces Gastrointestinal Microbiome Middle Aged Female Aged Adult Humans
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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...
Humans Machine Learning Metagenome Genes, Bacterial Bacteria Computational Biology Anti-Bacterial Agents Metagenomics Drug Resistance, Bacterial
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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...
Eukaryota Metagenome Ruminants Fungi Animals Gastrointestinal Microbiome Metagenomics Deep Learning Databases, Protein Rumen Computational Biology
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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...
Bacteria Gastrointestinal Microbiome Microbiota Algorithms Humans Biomarkers Machine Learning Metagenomics Metagenome
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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...
Metagenomics Soil Microbiology Machine Learning Metagenome Hydrocarbons, Brominated Bacteria Soil Pollutants Biodegradation, Environmental
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