AIMC Topic: Metagenomics
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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...
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 ...
TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
PLoS computational biology
Oct 29, 2021
We have developed the program TwinCons, to detect noisy signals of deep ancestry of proteins or nucleic acids. As input, the program uses a composite alignment containing pre-defined groups, and mathematically determines a 'cost' of transforming one ...
AI for the collective analysis of a massive number of genome sequences: various examples from the small genome of pandemic SARS-CoV-2 to the human genome.
Genes & genetic systems
Sep 27, 2021
In genetics and related fields, huge amounts of data, such as genome sequences, are accumulating, and the use of artificial intelligence (AI) suitable for big data analysis has become increasingly important. Unsupervised AI that can reveal novel know...
A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data.
Journal of visualized experiments : JoVE
Sep 25, 2021
A variety of biological sequence classification tasks, such as species classification, gene function classification and viral host classification, are expected processes in many metagenomic data analyses. Since metagenomic data contain a large number...
MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly.
BMC bioinformatics
Jun 2, 2021
BACKGROUND: The increasing use of whole metagenome sequencing has spurred the need to improve de novo assemblers to facilitate the discovery of unknown species and the analysis of their genomic functions. MetaVelvet-SL is a short-read de novo metagen...
Combining natural language processing and metabarcoding to reveal pathogen-environment associations.
PLoS neglected tropical diseases
Apr 7, 2021
Cryptococcus neoformans is responsible for life-threatening infections that primarily affect immunocompromised individuals and has an estimated worldwide burden of 220,000 new cases each year-with 180,000 resulting deaths-mostly in sub-Saharan Africa...
Distinguishing between recent balancing selection and incomplete sweep using deep neural networks.
Molecular ecology resources
Apr 5, 2021
Balancing selection is an important adaptive mechanism underpinning a wide range of phenotypes. Despite its relevance, the detection of recent balancing selection from genomic data is challenging as its signatures are qualitatively similar to those l...
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Genome biology
Mar 30, 2021
The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software is scarce, and overoptimistic evaluation and limited cross-study generalization are prevailing i...
Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences.
Scientific reports
Feb 25, 2021
Alterations in the human microbiome have been observed in a variety of conditions such as asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and human health. The fusion of artificial inte...
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