AIMC Topic: Metagenomics
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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...
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...
PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolutional Neural Networks to Predict Host Phenotype From Metagenomic Data.
IEEE journal of biomedical and health informatics
May 11, 2020
Accurate prediction of the host phenotype from a metagenomic sample and identification of the associated microbial markers are important in understanding potential host-microbiome interactions related to disease initiation and progression. We introdu...
A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type.
PLoS computational biology
May 11, 2020
The microbiome is a new frontier for building predictors of human phenotypes. However, machine learning in the microbiome is fraught with issues of reproducibility, driven in large part by the wide range of analytic models and metagenomic data types ...
Big data in IBD: big progress for clinical practice.
Gut
Feb 28, 2020
IBD is a complex multifactorial inflammatory disease of the gut driven by extrinsic and intrinsic factors, including host genetics, the immune system, environmental factors and the gut microbiome. Technological advancements such as next-generation se...
Microbial Decolorization of Triazo Dye, Direct Blue 71: An Optimization Approach Using Response Surface Methodology (RSM) and Artificial Neural Network (ANN).
BioMed research international
Feb 18, 2020
The release of wastewater from textile dyeing industrial sectors is a huge concern with regard to pollution as the treatment of these waters is truly a challenging process. Hence, this study investigates the triazo bond Direct Blue 71 (DB71) dye deco...
Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes.
Microbiome
Feb 11, 2020
BACKGROUND: Microorganisms in activated sludge (AS) play key roles in the wastewater treatment processes. However, their ecological behaviors and differences from microorganisms in other environments have mainly been studied using the 16S rRNA gene t...
Prediction of microbial communities for urban metagenomics using neural network approach.
Human genomics
Oct 22, 2019
BACKGROUND: Microbes are greatly associated with human health and disease, especially in densely populated cities. It is essential to understand the microbial ecosystem in an urban environment for cities to monitor the transmission of infectious dise...
A machine learning-based service for estimating quality of genomes using PATRIC.
BMC bioinformatics
Oct 3, 2019
BACKGROUND: Recent advances in high-volume sequencing technology and mining of genomes from metagenomic samples call for rapid and reliable genome quality evaluation. The current release of the PATRIC database contains over 220,000 genomes, and curre...
Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples.
Biology direct
Aug 20, 2019
BACKGROUND: The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacteria...
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