AIMC Topic: DNA Barcoding, Taxonomic
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Review of the genus Shilovia Makarchenko (Diptera: Chironomidae: Diamesinae: Boreoheptagyiini) from the mountains of Central Asia, with morphological description and DNA barcoding of known species.
Zootaxa
Dec 15, 2020
Chironomids of the genus Shilovia Makarchenko (Diamesinae, Boreoheptagyiini) from the mountains of Central Asia are revised using both morphological characters and molecular data. Illustrated descriptions of the adult male Shilovia xinhuawangi sp. no...
Scalable classification of organisms into a taxonomy using hierarchical supervised learners.
Journal of bioinformatics and computational biology
Oct 29, 2020
Accurately identifying organisms based on their partially available genetic material is an important task to explore the phylogenetic diversity in an environment. Specific fragments in the DNA sequence of a living organism have been defined as DNA ba...
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 ...
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