AIMC Topic: DNA Barcoding, Taxonomic
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Its2vec: Fungal Species Identification Using Sequence Embedding and Random Forest Classification.
BioMed research international
May 27, 2020
Fungi play essential roles in many ecological processes, and taxonomic classification is fundamental for microbial community characterization and vital for the study and preservation of fungal biodiversity. To cope with massive fungal barcode data, t...
Machine learning approaches outperform distance- and tree-based methods for DNA barcoding of Pterocarpus wood.
Planta
Mar 1, 2019
Machine-learning approaches (MLAs) for DNA barcoding outperform distance- and tree-based methods on identification accuracy and cost-effectiveness to arrive at species-level identification of wood. DNA barcoding is a promising tool to combat illegal ...
Metabarcoding and machine learning analysis of environmental DNA in ballast water arriving to hub ports.
Environment international
Jan 17, 2019
While ballast water has long been linked to the global transport of invasive species, little is known about its microbiome. Herein, we used 16S rRNA gene sequencing and metabarcoding to perform the most comprehensive microbiological survey of ballast...
funbarRF: DNA barcode-based fungal species prediction using multiclass Random Forest supervised learning model.
BMC genetics
Jan 7, 2019
BACKGROUND: Identification of unknown fungal species aids to the conservation of fungal diversity. As many fungal species cannot be cultured, morphological identification of those species is almost impossible. But, DNA barcoding technique can be empl...
Molecular phylogenetic investigations of Triops granarius (Lucas, 1864 (Branchiopoda: Notostraca) from the type locality of the former Apus orientalis Tiwari, 1952 and three other localities in the Western Ghats of India.
Zootaxa
Dec 14, 2018
We investigated the phylogenetic position of Triops granarius populations from four localities in the Western Ghats using partial sequences of three mitochondrial genes (COI, 12S rRNA and 16S rRNA) publicly available on the GenBank database. One of t...
Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring.
Trends in microbiology
Dec 13, 2018
Genomics is fast becoming a routine tool in medical diagnostics and cutting-edge biotechnologies. Yet, its use for environmental biomonitoring is still considered a futuristic ideal. Until now, environmental genomics was mainly used as a replacement ...
Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.
PLoS computational biology
Nov 20, 2018
Multiplexing, the simultaneous sequencing of multiple barcoded DNA samples on a single flow cell, has made Oxford Nanopore sequencing cost-effective for small genomes. However, it depends on the ability to sort the resulting sequencing reads by barco...
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 ...
FuzzyID2: A software package for large data set species identification via barcoding and metabarcoding using hidden Markov models and fuzzy set methods.
Molecular ecology resources
Dec 10, 2017
Species identification through DNA barcoding or metabarcoding has become a key approach for biodiversity evaluation and ecological studies. However, the rapid accumulation of barcoding data has created some difficulties: for instance, global enquirie...
Predicting the Ecological Quality Status of Marine Environments from eDNA Metabarcoding Data Using Supervised Machine Learning.
Environmental science & technology
Jul 25, 2017
Monitoring biodiversity is essential to assess the impacts of increasing anthropogenic activities in marine environments. Traditionally, marine biomonitoring involves the sorting and morphological identification of benthic macro-invertebrates, which ...
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