AIMC Topic: Genome, Viral
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A Machine Learning Approach for MicroRNA Precursor Prediction in Retro-transcribing Virus Genomes.
Journal of integrative bioinformatics
Dec 22, 2016
Identification of microRNA (miRNA) precursors has seen increased efforts in recent years. The difficulty in experimental detection of pre-miRNAs increased the usage of computational approaches. Most of these approaches rely on machine learning especi...
Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time.
Nucleic acids research
Feb 8, 2025
In infected individuals, viruses are present as a population consisting of dominant and minor variant genomes. Most databases contain information on the dominant genome sequence. Since the emergence of SARS-CoV-2 in late 2019, variants have been sele...
Unveiling the ghost: machine learning's impact on the landscape of virology.
The Journal of general virology
Jan 1, 2025
The complexity and speed of evolution in viruses with RNA genomes makes predictive identification of variants with epidemic or pandemic potential challenging. In recent years, machine learning has become an increasingly capable technology for address...
VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification.
Briefings in bioinformatics
Nov 22, 2024
This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus ide...
Mutation prediction in the SARS-CoV-2 genome using attention-based neural machine translation.
Mathematical biosciences and engineering : MBE
May 20, 2024
Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) has been evolving rapidly after causing havoc worldwide in 2020. Since then, it has been very hard to contain the virus owing to its frequently mutating nature. Changes in its genome lead t...
RNAVirHost: a machine learning-based method for predicting hosts of RNA viruses through viral genomes.
GigaScience
Jan 2, 2024
BACKGROUND: The high-throughput sequencing technologies have revolutionized the identification of novel RNA viruses. Given that viruses are infectious agents, identifying hosts of these new viruses carries significant implications for public health a...
Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants.
GigaScience
Jan 2, 2024
BACKGROUND: Phage therapy, reemerging as a promising approach to counter antimicrobial-resistant infections, relies on a comprehensive understanding of the specificity of individual phages. Yet the significant diversity within phage populations prese...
IPEV: identification of prokaryotic and eukaryotic virus-derived sequences in virome using deep learning.
GigaScience
Jan 2, 2024
BACKGROUND: The virome obtained through virus-like particle enrichment contains a mixture of prokaryotic and eukaryotic virus-derived fragments. Accurate identification and classification of these elements are crucial to understanding their roles and...
Accurate and fast clade assignment via deep learning and frequency chaos game representation.
GigaScience
Dec 28, 2022
BACKGROUND: Since the beginning of the coronavirus disease 2019 pandemic, there has been an explosion of sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, making it the most widely sequenced virus in the history. S...
DeePVP: Identification and classification of phage virion proteins using deep learning.
GigaScience
Aug 11, 2022
BACKGROUND: Many biological properties of phages are determined by phage virion proteins (PVPs), and the poor annotation of PVPs is a bottleneck for many areas of viral research, such as viral phylogenetic analysis, viral host identification, and ant...
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