AIMC Topic: Genome, Viral

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Improving viral annotation with artificial intelligence.

mBio Sep 4, 2024
Viruses of bacteria, "phages," are fundamental, poorly understood components of microbial community structure and function. Additionally, their dependence on hosts for replication positions phages as unique sensors of ecosystem features and environme...
Humans Artificial Intelligence Molecular Sequence Annotation Bacteriophages Metagenome High-Throughput Nucleotide Sequencing Metagenomics Genome, Viral
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Machine Learning Using Template-Based-Predicted Structure of Haemagglutinin Predicts Pathogenicity of Avian Influenza.

Journal of microbiology and biotechnology Aug 6, 2024
Deep learning presents a promising approach to complex biological classifications, contingent upon the availability of well-curated datasets. This study addresses the challenge of analyzing three-dimensional protein structures by introducing a novel ...
Neural Networks, Computer Hemagglutinins Genome, Viral Hemagglutinin Glycoproteins, Influenza Virus Influenza A virus Deep Learning Principal Component Analysis Computational Biology Machine Learning Animals Influenza in Birds Neuraminidase Algorithms Birds
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Genome composition-based deep learning predicts oncogenic potential of HPVs.

Frontiers in cellular and infection microbiology Jul 22, 2024
Human papillomaviruses (HPVs) account for more than 30% of cancer cases, with definite identification of the oncogenic role of viral and genes. However, the identification of high-risk HPV genotypes has largely relied on lagged biological explorati...
Papillomavirus E7 Proteins Deep Learning Oncogene Proteins, Viral Genotype Papillomaviridae Carcinogenesis Humans Genome, Viral Papillomavirus Infections
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Deepvirusclassifier: a deep learning tool for classifying SARS-CoV-2 based on viral subtypes within the coronaviridae family.

BMC bioinformatics Jul 5, 2024
PURPOSE: In this study, we present DeepVirusClassifier, a tool capable of accurately classifying Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral sequences among other subtypes of the coronaviridae family. This classification is ach...
Humans Neural Networks, Computer COVID-19 Genome, Viral Coronaviridae SARS-CoV-2 Deep Learning
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Assessment and classification of COVID-19 DNA sequence using pairwise features concatenation from multi-transformer and deep features with machine learning models.

SLAS technology May 23, 2024
The 2019 novel coronavirus (renamed SARS-CoV-2, and generally referred to as the COVID-19 virus) has spread to 184 countries with over 1.5 million confirmed cases. Such a major viral outbreak demands early elucidation of taxonomic classification and ...
Sequence Analysis, DNA Genome, Viral COVID-19 SARS-CoV-2 Computational Biology DNA, Viral Deep Learning Humans Machine Learning
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HostNet: improved sequence representation in deep neural networks for virus-host prediction.

BMC bioinformatics Dec 1, 2023
BACKGROUND: The escalation of viruses over the past decade has highlighted the need to determine their respective hosts, particularly for emerging ones that pose a potential menace to the welfare of both human and animal life. Yet, the traditional me...
Humans Neural Networks, Computer Animals Viruses Genomics Genome, Viral
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Coot-Lion optimized deep learning algorithm for COVID-19 point mutation rate prediction using genome sequences.

Computer methods in biomechanics and biomedical engineering Sep 5, 2023
In this study, a deep quantum neural network (DQNN) based on the Lion-based Coot algorithm (LBCA-based Deep QNN) is employed to predict COVID-19. Here, the genome sequences are subjected to feature extraction. The fusion of features is performed usin...
Genome, Viral Mutation Rate Point Mutation Algorithms SARS-CoV-2 Deep Learning Humans COVID-19
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Benchmarking machine learning robustness in Covid-19 genome sequence classification.

Scientific reports Mar 13, 2023
The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome-millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of traditional ap...
Genome, Viral Viral Proteins Machine Learning Research Design COVID-19 SARS-CoV-2 Computer Simulation Sequence Analysis, RNA
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New proposal of viral genome representation applied in the classification of SARS-CoV-2 with deep learning.

BMC bioinformatics Mar 11, 2023
BACKGROUND: In December 2019, the first case of COVID-19 was described in Wuhan, China, and by July 2022, there were already 540 million confirmed cases. Due to the rapid spread of the virus, the scientific community has made efforts to develop techn...
Humans Deep Learning COVID-19 Genomics SARS-CoV-2 Genome, Viral
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A deep learning approach reveals unexplored landscape of viral expression in cancer.

Nature communications Feb 11, 2023
About 15% of human cancer cases are attributed to viral infections. To date, virus expression in tumor tissues has been mostly studied by aligning tumor RNA sequencing reads to databases of known viruses. To allow identification of divergent viruses ...
Deep Learning Humans High-Throughput Nucleotide Sequencing Neoplasms Genome, Viral Viruses
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