ArticleScientific reports2021
PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment.Bioinformatics (Oxford, England) · 2024Article
- Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya.BMC genomics · 2022Article
- Integrated COVID-19 Predictor: Differential expression analysis to reveal potential biomarkers and prediction of coronavirus using RNA-Seq profile data.Computers in biology and medicine · 2022Article
- Enabling Artificial Intelligence for Genome Sequence Analysis of COVID-19 and Alike Viruses.Interdisciplinary sciences, computational life sciences · 2022Article
- Article
- Sequencing meets machine learning to fight emerging pathogens: A preview.Patterns (New York, N.Y.) · 2022Article
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Authors and funding
5 authors.
Funding
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Abstract
Viral co-infections occur in COVID-19 patients, potentially impacting disease progression and severity. However, there is currently no dedicated method to identify viral co-infections in patient RNA-seq data. We developed PACIFIC, a deep-learning algorithm that accurately detects SARS-CoV-2 and other common RNA respiratory viruses from RNA-seq data. Using in silico data, PACIFIC recovers the presence and relative concentrations of viruses with > 99% precision and recall. PACIFIC accurately detects SARS-CoV-2 and other viral infections in 63 independent in vitro cell culture and patient datasets. PACIFIC is an end-to-end tool that enables the systematic monitoring of viral infections in the current global pandemic.
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Registered trials
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