AIMC Topic: Metagenomics

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EnsDeepDP: An Ensemble Deep Learning Approach for Disease Prediction Through Metagenomics.

IEEE/ACM transactions on computational biology and bioinformatics Apr 3, 2023
A growing number of studies show that the human microbiome plays a vital role in human health and can be a crucial factor in predicting certain human diseases. However, microbiome data are often characterized by the limited samples and high-dimension...
Humans Deep Learning Microbiota Metagenomics Machine Learning Algorithms
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Unlocking the microbial studies through computational approaches: how far have we reached?

Environmental science and pollution research international Mar 15, 2023
The metagenomics approach accelerated the study of genetic information from uncultured microbes and complex microbial communities. In silico research also facilitated an understanding of protein-DNA interactions, protein-protein interactions, docking...
Microbiota Metagenomics Proteomics DNA Artificial Intelligence
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The need for an integrated multi-OMICs approach in microbiome science in the food system.

Comprehensive reviews in food science and food safety Jan 12, 2023
Microbiome science as an interdisciplinary research field has evolved rapidly over the past two decades, becoming a popular topic not only in the scientific community and among the general public, but also in the food industry due to the growing dema...
Multiomics Metabolomics Metagenomics Microbiota Humans Artificial Intelligence
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RNN-VirSeeker: A Deep Learning Method for Identification of Short Viral Sequences From Metagenomes.

IEEE/ACM transactions on computational biology and bioinformatics Jun 3, 2022
Viruses are the most abundant biological entities on earth, and play vital roles in many aspects of microbial communities. As major human pathogens, viruses have caused huge mortality and morbidity to human society in history. Metagenomic sequencing ...
Deep Learning Microbiota Metagenomics Humans Viruses Metagenome
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MarkerML - Marker Feature Identification in Metagenomic Datasets Using Interpretable Machine Learning.

Journal of molecular biology Apr 18, 2022
Identification of environment specific marker-features is one of the key objectives of many metagenomic studies. It aims to identify such features in microbiome datasets that may serve as markers of the contrasting or comparable states. Hypothesis te...
Metagenomics Datasets as Topic Metagenome Machine Learning Reproducibility of Results Internet Use Humans
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WalkIm: Compact image-based encoding for high-performance classification of biological sequences using simple tuning-free CNNs.

PloS one Apr 15, 2022
The classification of biological sequences is an open issue for a variety of data sets, such as viral and metagenomics sequences. Therefore, many studies utilize neural network tools, as the well-known methods in this field, and focus on designing cu...
Research Design Data Collection Neural Networks, Computer Metagenomics
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Multimodal deep learning applied to classify healthy and disease states of human microbiome.

Scientific reports Jan 17, 2022
Metagenomic sequencing methods provide considerable genomic information regarding human microbiomes, enabling us to discover and understand microbial diseases. Compositional differences have been reported between patients and healthy people, which co...
Diabetes Mellitus, Type 2 Liver Cirrhosis Metagenome Healthy Volunteers Inflammatory Bowel Diseases Humans Metagenomics Genome, Microbial Microbiota Colorectal Neoplasms Deep Learning
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Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer.

Scientific reports Jan 10, 2022
Gut microbiome is gaining interest because of its links with several diseases, including colorectal cancer (CRC), as well as the possibility of being used to obtain non-intrusive predictive disease biomarkers. Here we performed a meta-analysis of 104...
Colorectal Neoplasms Gastrointestinal Microbiome Metagenomics Adenoma Humans Machine Learning
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NGS read classification using AI.

PloS one Dec 22, 2021
Clinical metagenomics is a powerful diagnostic tool, as it offers an open view into all DNA in a patient's sample. This allows the detection of pathogens that would slip through the cracks of classical specific assays. However, due to this unspecific...
Metagenome Bacteria Algorithms DNA Metagenomics DNA, Bacterial High-Throughput Nucleotide Sequencing Viruses Humans DNA, Viral Animals Neural Networks, Computer
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Metagenomic Sequencing Analysis for Acne Using Machine Learning Methods Adapted to Single or Multiple Data.

Computational and mathematical methods in medicine Nov 13, 2021
The human health status can be assessed by the means of research and analysis of the human microbiome. Acne is a common skin disease whose morbidity increases year by year. The lipids which influence acne to a large extent are studied by metagenomic ...
Metagenome Canonical Correlation Analysis Face Acne Vulgaris Humans Microbiota Lipids Machine Learning Metagenomics Principal Component Analysis Case-Control Studies Skin Computational Biology
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