AIMC Topic: DNA Barcoding, Taxonomic

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Illuminating Entomological Dark Matter with DNA Barcodes in an Era of Insect Decline, Deep Learning, and Genomics.

Annual review of entomology Dec 19, 2024
Most insects encountered in the field are initially entomological dark matter in that they cannot be identified to species while alive. This explains the enduring quest for efficient ways to identify collected specimens. Morphological tools came firs...
Animals Entomology Insecta DNA Barcoding, Taxonomic Deep Learning Genomics Biodiversity
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Integrating external stressors in supervised machine learning algorithm achieves high accuracy to predict multi-species biological integrity index of aquaculture wastewater.

Journal of hazardous materials Oct 30, 2024
Monitoring and predicting the environmental impact of wastewater is essential for sustainable aquaculture. The environmental DNA metabarcoding-integrated supervised machine learning (SML) algorithm is an alternative method for ecological quality asse...
Supervised Machine Learning DNA Barcoding, Taxonomic Animals Environmental Monitoring Aquaculture Wastewater Algorithms
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Development of a two-layer machine learning model for the forensic application of legal and illegal poppy classification based on sequence data.

Forensic science international. Genetics May 22, 2024
Poppies are beneficial plants with a variety of applications, including medicinal, edible, ornamental, and industrial purposes. Some Papaver species are forensically significant plants because they contain opium, a narcotic substance. Internationally...
Machine Learning Sequence Analysis, DNA DNA Barcoding, Taxonomic Genetic Markers Papaver DNA, Plant Forensic Genetics
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New deep learning-based methods for visualizing ecosystem properties using environmental DNA metabarcoding data.

Molecular ecology resources Sep 13, 2023
Environmental DNA (eDNA) metabarcoding provides an efficient approach for documenting biodiversity patterns in marine and terrestrial ecosystems. The complexity of these data prevents current methods from extracting and analyzing all the relevant eco...
Ecosystem Deep Learning Environmental Monitoring Biodiversity DNA Barcoding, Taxonomic DNA, Environmental
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Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks.

Proceedings of the National Academy of Sciences of the United States of America Aug 26, 2022
Taxonomic classification, that is, the assignment to biological clades with shared ancestry, is a common task in genetics, mainly based on a genome similarity search of large genome databases. The classification quality depends heavily on the databas...
Deep Learning Genomics DNA Software Algorithms DNA Barcoding, Taxonomic Base Sequence Genome
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DeepBarcoding: Deep Learning for Species Classification Using DNA Barcoding.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
DNA barcodes with short sequence fragments are used for species identification. Because of advances in sequencing technologies, DNA barcodes have gradually been emphasized. DNA sequences from different organisms are easily and rapidly acquired. There...
DNA Barcoding, Taxonomic Neural Networks, Computer Deep Learning Sequence Analysis, DNA DNA
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DiversityScanner: Robotic handling of small invertebrates with machine learning methods.

Molecular ecology resources Dec 23, 2021
Invertebrate biodiversity remains poorly understood although it comprises much of the terrestrial animal biomass, most species and supplies many ecosystem services. The main obstacle is specimen-rich samples obtained with quantitative sampling techni...
DNA Barcoding, Taxonomic Invertebrates Robotics Robotic Surgical Procedures Biodiversity Animals Humans Ecosystem Machine Learning
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Domain-Scan: Combinatorial Sero-Diagnosis of Infectious Diseases Using Machine Learning.

Frontiers in immunology Feb 10, 2021
The presence of pathogen-specific antibodies in an individual's blood-sample is used as an indication of previous exposure and infection to that specific pathogen (e.g., virus or bacterium). Measurement of the diagnostic antibodies is routinely achie...
DNA, Recombinant HIV Envelope Protein gp160 Hepatitis C Antigens HIV Antibodies AIDS Serodiagnosis Amino Acid Sequence Humans Base Sequence Antigen-Antibody Reactions Oligonucleotides Polymerase Chain Reaction Machine Learning HIV Core Protein p24 Hepatitis C Hepatitis C Antibodies Peptide Library Communicable Diseases Serologic Tests Genetic Vectors Peptide Fragments HIV Infections High-Throughput Nucleotide Sequencing Epitopes 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...
Chironomidae DNA Barcoding, Taxonomic Phylogeny Animals Bayes Theorem Male Diptera
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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...
Algorithms Animals Birds Classification Chiroptera Phylogeny Databases, Genetic Rodentia Deep Learning Ferns Fungi Support Vector Machine DNA Barcoding, Taxonomic
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