AIMC Topic: Metagenome
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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 ...
SquiggleNet: real-time, direct classification of nanopore signals.
Genome biology
Oct 27, 2021
We present SquiggleNet, the first deep-learning model that can classify nanopore reads directly from their electrical signals. SquiggleNet operates faster than DNA passes through the pore, allowing real-time classification and read ejection. Using 1 ...
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...
Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14.
Proteins
Aug 17, 2021
The trRosetta structure prediction method employs deep learning to generate predicted residue-residue distance and orientation distributions from which 3D models are built. We sought to improve the method by incorporating as inputs (in addition to se...
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...
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...
MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning.
BMC bioinformatics
Jan 18, 2021
BACKGROUND: Diverse microbiome communities drive biogeochemical processes and evolution of animals in their ecosystems. Many microbiome projects have demonstrated the power of using metagenomics to understand the structures and factors influencing th...
Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge.
Biology direct
Jan 4, 2021
BACKGROUND: Composition of microbial communities can be location-specific, and the different abundance of taxon within location could help us to unravel city-specific signature and predict the sample origin locations accurately. In this study, the wh...
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