AIMC Topic: Metagenomics

Clear Filters Showing 61 to 70 of 132 articles

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...
Microbiota Metagenomics Metagenome Machine Learning Cities Humans
View on PubMed DOI

Deep learning for HGT insertion sites recognition.

BMC genomics Dec 29, 2020
BACKGROUND: Horizontal Gene Transfer (HGT) refers to the sharing of genetic materials between distant species that are not in a parent-offspring relationship. The HGT insertion sites are important to understand the HGT mechanisms. Recent studies in m...
Deep Learning Metagenomics Genome Gene Transfer, Horizontal Phylogeny Base Sequence
View on PubMed DOI

Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data.

Biology direct Dec 10, 2020
BACKGROUND: The advent of metagenomic sequencing provides microbial abundance patterns that can be leveraged for sample origin prediction. Supervised machine learning classification approaches have been reported to predict sample origin accurately wh...
Microbiota Metagenomics Metagenome RNA, Ribosomal, 16S Supervised Machine Learning
View on PubMed DOI

A machine learning framework to determine geolocations from metagenomic profiling.

Biology direct Nov 23, 2020
BACKGROUND: Studies on metagenomic data of environmental microbial samples found that microbial communities seem to be geolocation-specific, and the microbiome abundance profile can be a differentiating feature to identify samples' geolocations. In t...
Humans Machine Learning Cities Geography Metagenome Microbiota Metagenomics
View on PubMed DOI

Deep learning in next-generation sequencing.

Drug discovery today Oct 12, 2020
Next-generation sequencing (NGS) methods lie at the heart of large parts of biological and medical research. Their fundamental importance has created a continuously increasing demand for processing and analysis methods of the data sets produced, addr...
Humans Neural Networks, Computer Biomedical Research High-Throughput Nucleotide Sequencing Metagenomics Deep Learning
View on PubMed DOI

Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life.

BMC bioinformatics Sep 21, 2020
BACKGROUND: It is a computational challenge for current metagenomic classifiers to keep up with the pace of training data generated from genome sequencing projects, such as the exponentially-growing NCBI RefSeq bacterial genome database. When new ref...
Genome, Bacterial Metagenome Bacteria Gastrointestinal Microbiome Bayes Theorem Metagenomics Sequence Analysis, DNA Humans Machine Learning Algorithms
View on PubMed DOI

Metatranscriptomics reveals the gene functions and metabolic properties of the major microbial community during Chinese Sichuan Paocai fermentation.

Food microbiology Jul 3, 2020
Chinese Sichuan Paocai (CSP) is one of the world's best-known fermented vegetables with a large presence in the Chinese market. The dynamic microbial community is the main contributor to Paocai fermentation. However, little is known about the ecologi...
Vegetables Brassica Enterobacteriaceae Lactobacillaceae Metagenomics Fermented Foods Transcriptome Microbiota Food Microbiology China Fermentation
View on PubMed DOI

Predicting host taxonomic information from viral genomes: A comparison of feature representations.

PLoS computational biology May 26, 2020
The rise in metagenomics has led to an exponential growth in virus discovery. However, the majority of these new virus sequences have no assigned host. Current machine learning approaches to predicting virus host interactions have a tendency to focus...
Algorithms Viruses Area Under Curve Caudovirales Nucleotides Sequence Analysis, DNA Linear Models Bacteria Genome, Viral Metagenomics Databases, Factual Computational Biology Phylogeny Support Vector Machine
View on PubMed DOI

CHEER: HierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning.

Methods (San Diego, Calif.) May 23, 2020
The fast accumulation of viral metagenomic data has contributed significantly to new RNA virus discovery. However, the short read size, complex composition, and large data size can all make taxonomic analysis difficult. In particular, commonly used a...
Deep Learning Metagenomics RNA Viruses Classification
View on PubMed DOI

Oral microbiome-systemic link studies: perspectives on current limitations and future artificial intelligence-based approaches.

Critical reviews in microbiology May 21, 2020
In the past decade, there has been a tremendous increase in studies on the link between oral microbiome and systemic diseases. However, variations in study design and confounding variables across studies often lead to inconsistent observations. In th...
Metagenomics Disease Diagnosis Microbiota Mouth Neural Networks, Computer Arthritis, Rheumatoid Artificial Intelligence Humans Pancreatic Neoplasms Female Pregnancy Diabetes Mellitus, Type 2 Atherosclerosis
View on PubMed DOI
Popular Topics
Recent Journals