AIMC Topic: Genome, Viral

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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...
Genotype Papillomavirus Infections Carcinogenesis Humans Deep Learning Papillomaviridae Papillomavirus E7 Proteins Genome, Viral Oncogene Proteins, Viral
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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...
Deep Learning Humans Genome, Viral Neural Networks, Computer Coronaviridae COVID-19 SARS-CoV-2
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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 ...
Genome, Viral DNA, Viral Machine Learning Sequence Analysis, DNA COVID-19 Humans Deep Learning Computational Biology SARS-CoV-2
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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...
Genomics Genome, Viral Viruses Neural Networks, Computer Animals Humans
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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...
Deep Learning Genome, Viral Point Mutation Mutation Rate Algorithms SARS-CoV-2 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...
Machine Learning Research Design Computer Simulation COVID-19 Viral Proteins SARS-CoV-2 Genome, Viral 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...
COVID-19 SARS-CoV-2 Genomics Genome, Viral Deep Learning Humans
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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 ...
Humans Viruses High-Throughput Nucleotide Sequencing Genome, Viral Neoplasms Deep Learning
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Can machines learn the mutation signatures of SARS-CoV-2 and enable viral-genotype guided predictive prognosis?

Journal of molecular biology Jun 11, 2022
MOTIVATION: Continuous emergence of new variants through appearance/accumulation/disappearance of mutations is a hallmark of many viral diseases. SARS-CoV-2 variants have particularly exerted tremendous pressure on global healthcare system owing to t...
Machine Learning COVID-19 SARS-CoV-2 Mutation Severity of Illness Index Genome, Viral Humans Genotype
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PhageLeads: Rapid Assessment of Phage Therapeutic Suitability Using an Ensemble Machine Learning Approach.

Viruses Feb 8, 2022
The characterization of therapeutic phage genomes plays a crucial role in the success rate of phage therapies. There are three checkpoints that need to be examined for the selection of phage candidates, namely, the presence of temperate markers, anti...
Phage Therapy Genome, Viral Bacteria Viral Proteins Bacteriophages Humans Bacterial Infections Bacterial Physiological Phenomena Lysogeny Machine Learning
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