AIMC Topic: Metagenomics

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Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring.

Molecular ecology resources Aug 3, 2018
Biodiversity monitoring is the standard for environmental impact assessment of anthropogenic activities. Several recent studies showed that high-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) could overcome many limitations ...
Biomarkers Computer Simulation Bacteria Metagenomics DNA Barcoding, Taxonomic RNA, Ribosomal Eukaryota Environmental Monitoring Supervised Machine Learning Biodiversity
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Deep learning models for bacteria taxonomic classification of metagenomic data.

BMC bioinformatics Jul 9, 2018
BACKGROUND: An open challenge in translational bioinformatics is the analysis of sequenced metagenomes from various environmental samples. Of course, several studies demonstrated the 16S ribosomal RNA could be considered as a barcode for bacteria cla...
Metagenome RNA, Ribosomal, 16S Databases, Genetic Metagenomics Neural Networks, Computer Algorithms Reproducibility of Results Bacteria Deep Learning Models, Genetic Time Factors
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Tracking antibiotic resistance gene pollution from different sources using machine-learning classification.

Microbiome May 24, 2018
BACKGROUND: Antimicrobial resistance (AMR) has been a worldwide public health concern. Current widespread AMR pollution has posed a big challenge in accurately disentangling source-sink relationship, which has been further confounded by point and non...
Anti-Bacterial Agents Animals China Bacteria Humans Machine Learning High-Throughput Nucleotide Sequencing Sewage Metagenomics Gastrointestinal Microbiome Soil Microbiology Drug Resistance, Microbial
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Phylogenetic convolutional neural networks in metagenomics.

BMC bioinformatics Mar 8, 2018
BACKGROUND: Convolutional Neural Networks can be effectively used only when data are endowed with an intrinsic concept of neighbourhood in the input space, as is the case of pixels in images. We introduce here Ph-CNN, a novel deep learning architectu...
Support Vector Machine Databases, Genetic Principal Component Analysis Inflammatory Bowel Diseases Reproducibility of Results Phylogeny Metagenomics Data Analysis Algorithms Humans Neural Networks, Computer
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Gene Prediction in Metagenomic Fragments with Deep Learning.

BioMed research international Nov 8, 2017
Next generation sequencing technologies used in metagenomics yield numerous sequencing fragments which come from thousands of different species. Accurately identifying genes from metagenomics fragments is one of the most fundamental issues in metagen...
Models, Statistical Metagenomics Genes, Bacterial Bacteria Databases, Genetic Sequence Analysis, DNA Machine Learning
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Phenotype Prediction from Metagenomic Data Using Clustering and Assembly with Multiple Instance Learning (CAMIL).

IEEE/ACM transactions on computational biology and bioinformatics Oct 4, 2017
The recent advent of Metagenome Wide Association Studies (MGWAS) provides insight into the role of microbes on human health and disease. However, the studies present several computational challenges. In this paper, we demonstrate a novel, efficient, ...
Cluster Analysis Metagenomics Metagenome Humans Machine Learning Phenotype
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SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare?

BMC genomics Mar 14, 2017
BACKGROUND: A key step in microbiome sequencing analysis is read assignment to taxonomic units. This is often performed using one of four taxonomic classifications, namely SILVA, RDP, Greengenes or NCBI. It is unclear how similar these are and how to...
Algorithms Phylogeny Bacteria Microbiota Metagenomics RNA, Ribosomal, 16S Databases, Genetic Gene Ontology Archaea
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Prediction of virus-host infectious association by supervised learning methods.

BMC bioinformatics Mar 14, 2017
BACKGROUND: The study of virus-host infectious association is important for understanding the functions and dynamics of microbial communities. Both cellular and fractionated viral metagenomic data generate a large number of viral contigs with missing...
Genome, Viral Likelihood Functions Viruses Models, Theoretical Support Vector Machine DNA, Viral ROC Curve Metagenomics Bacteria Host-Pathogen Interactions Sequence Analysis, DNA Logistic Models Bayes Theorem Reproducibility of Results
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Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights.

PLoS computational biology Jul 11, 2016
Shotgun metagenomic analysis of the human associated microbiome provides a rich set of microbial features for prediction and biomarker discovery in the context of human diseases and health conditions. However, the use of such high-resolution microbia...
Machine Learning Software Inflammatory Bowel Diseases Obesity Humans Colorectal Neoplasms Metagenome Metagenomics Computational Biology Gastrointestinal Microbiome
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Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes.

PloS one Apr 22, 2016
The rapid improvement of next-generation sequencing performance now enables us to analyze huge sample sets with more than ten thousand specimens. However, DNA extraction can still be a limiting step in such metagenomic approaches. In this study, we a...
Metagenomics Adsorption Hot Temperature Principal Component Analysis Robotics Dental Plaque Humans DNA, Bacterial Liquid Phase Microextraction Male High-Throughput Nucleotide Sequencing RNA, Ribosomal, 16S Microbiota Pilot Projects Sequence Analysis, DNA
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