AIMC Topic: Metagenomics

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XenoBug: machine learning-based tool to predict pollutant-degrading enzymes from environmental metagenomes.

NAR genomics and bioinformatics Jun 1, 2025
Application of machine learning-based methods to identify novel bacterial enzymes capable of degrading a wide range of xenobiotics offers enormous potential for bioremediation of toxic and carcinogenic recalcitrant xenobiotics such as pesticides, pla...
Machine Learning Metagenomics Xenobiotics Metagenome Bacteria Environmental Pollutants Biodegradation, Environmental
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Early-life and concurrent predictors of the healthy adolescent microbiome in a cohort study.

Genome medicine May 8, 2025
BACKGROUND: The microbiome of adolescents is poorly understood, as are factors influencing its composition. We aimed to describe the healthy adolescent microbiome and identify early-life and concurrent predictors of its composition.
Child Male Humans Gastrointestinal Microbiome Feces Female Metagenomics Adolescent Cohort Studies
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A review of neural networks for metagenomic binning.

Briefings in bioinformatics Mar 4, 2025
One of the main goals of metagenomic studies is to describe the taxonomic diversity of microbial communities. A crucial step in metagenomic analysis is metagenomic binning, which involves the (supervised) classification or (unsupervised) clustering o...
Metagenomics Metagenome Machine Learning Deep Learning Humans Neural Networks, Computer
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PharaCon: a new framework for identifying bacteriophages via conditional representation learning.

Bioinformatics (Oxford, England) Mar 4, 2025
MOTIVATION: Identifying bacteriophages (phages) within metagenomic sequences is essential for understanding microbial community dynamics. Transformer-based foundation models have been successfully employed to address various biological challenges. Ho...
Metagenomics Bacteriophages Algorithms Bacteria Machine Learning Software
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Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning.

Microbial genomics Mar 1, 2025
Diabetes mellitus is a complex metabolic disorder and one of the fastest-growing global public health concerns. The gut microbiota is implicated in the pathophysiology of various diseases, including diabetes. This study utilized 16S rRNA metagenomic ...
Humans Male Middle Aged Diabetes Mellitus, Type 2 Machine Learning Female Adult Supervised Machine Learning Metagenomics Metagenome Bacteria Diabetes Mellitus, Type 1 Support Vector Machine Gastrointestinal Microbiome RNA, Ribosomal, 16S
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VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification.

Briefings in bioinformatics Nov 22, 2024
This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus ide...
Viral Proteins Eukaryota Metagenome Metagenomics Genome, Viral Viruses Convolutional Neural Networks Computational Biology Humans Neural Networks, Computer Artificial Intelligence
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MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework.

Briefings in bioinformatics Sep 23, 2024
The gut microbiota plays a vital role in human health, and significant effort has been made to predict human phenotypes, especially diseases, with the microbiota as a promising indicator or predictor with machine learning (ML) methods. However, the a...
Deep Learning ROC Curve Computational Biology Liver Cirrhosis Gastrointestinal Microbiome Phenotype Autism Spectrum Disorder Inflammatory Bowel Diseases Humans Metagenomics Machine Learning Metagenome
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DeepCheck: multitask learning aids in assessing microbial genome quality.

Briefings in bioinformatics Sep 23, 2024
Metagenomic analyses facilitate the exploration of the microbial world, advancing our understanding of microbial roles in ecological and biological processes. A pivotal aspect of metagenomic analysis involves assessing the quality of metagenome-assem...
Metagenomics Metagenome Genome, Microbial Machine Learning Software Deep Learning
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Deep learning methods in metagenomics: a review.

Microbial genomics Apr 1, 2024
The ever-decreasing cost of sequencing and the growing potential applications of metagenomics have led to an unprecedented surge in data generation. One of the most prevalent applications of metagenomics is the study of microbial environments, such a...
Microbiota Humans Metagenomics Deep Learning Metagenome Gastrointestinal Microbiome
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CoCoPyE: feature engineering for learning and prediction of genome quality indices.

GigaScience Jan 2, 2024
BACKGROUND: The exploration of the microbial world has been greatly advanced by the reconstruction of genomes from metagenomic sequence data. However, the rapidly increasing number of metagenome-assembled genomes has also resulted in a wide variation...
Computational Biology Metagenomics Metagenome Software Machine Learning Genomics
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