AIMC Topic: Metagenomics

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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 ...
Deep Learning Evolution, Molecular Bacterial Proteins Conserved Sequence Sequence Analysis, Protein Archaeal Proteins Metagenomics RNA, Ribosomal Sequence Alignment
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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...
Genome, Viral Time Factors Computational Biology RNA, Transfer Cluster Analysis Codon Usage Mutation Metagenomics Genome, Human Humans Artificial Intelligence SARS-CoV-2
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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...
Humans Algorithms Deep Learning Metagenomics Metagenome
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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...
Algorithms Deep Learning Genomics Software Metagenome Sequence Analysis, DNA High-Throughput Nucleotide Sequencing Metagenomics
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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...
RNA, Ribosomal, 18S Cryptococcus neoformans Environmental Microbiology Natural Language Processing Trees Metagenomics Ecosystem Models, Theoretical Soil Microbiology Humans Machine Learning
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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...
Haplotypes Metagenomics Neural Networks, Computer Phenotype Genomics
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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...
Humans Machine Learning Software Microbiota ROC Curve Metagenomics Computational Biology Confounding Factors, Epidemiologic Metagenome Meta-Analysis as Topic Workflow Crohn Disease Gastrointestinal Microbiome Databases, Genetic Models, Statistical
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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...
Metagenome Middle Aged Deep Learning Computational Biology Humans Young Adult Artificial Intelligence Metagenomics Adult Data Analysis Smokers Aging Menopause Phenotype Skin Female Microbiota Aged Biodiversity
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Machine learning for the analysis of multi-omics data.

Methods (San Diego, Calif.) Feb 9, 2021
Metagenomics Genomics Epigenomics Proteomics Machine Learning Gene Expression Profiling
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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...
Humans RNA, Ribosomal, 16S Machine Learning Metagenomics Phenotype Metagenome
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