ArticleGenome biology2022
SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Antibiotic-induced gut microbiome remodeling reduces neuroinflammation in traumatic brain injury.Communications biology · 2026Article
- Review
- Genomic phylogeny, taxonomic classification, genetic landscape, and antibiotic resistance of clinicalFrontiers in microbiology · 2026Article
- ADAPT: a programme for the advanced detection of AI-enabled pathogenic threats.Frontiers in bioengineering and biotechnology · 2026Article
- Beyond sequence similarity: toward function-based screening of nucleic acid synthesis.Frontiers in bioengineering and biotechnology · 2026Article
- Gut microbiome remodeling by antibiotics reduces neuroinflammation in traumatic brain injury.Research square · 2025Article
- De novo virulence feature discovery and risk assessment in Klebsiella pneumoniae based on microbial genome vectorization.Communications biology · 2025Article
- New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern.Journal of biomedical semantics · 2025Article
- Annotation of Functions of Sequences of Concern and Its Relevance to the New Biosecurity Regulatory Framework in the United States.Applied biosafety : journal of the American Biological Safety Association · 2024Article
- Practical Questions for Securing Nucleic Acid Synthesis.Applied biosafety : journal of the American Biological Safety Association · 2024Article
- Enhancing Gene Synthesis Security: An Updated Framework for Synthetic Nucleic Acid Screening and the Responsible Use of Synthetic Biological Materials.Applied biosafety : journal of the American Biological Safety Association · 2024Review
- Microbial biofilms on macroalgae harbour diverse integron gene cassettes.Microbiology (Reading, England) · 2024Article
- Review
- Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease.Scientific reports · 2022Article
- SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning.Genome biology · 2022Article
- KOMB: K-core based de novo characterization of copy number variation in microbiomes.Computational and structural biotechnology journal · 2022Article
- Article
Corrections and comments
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Authors and funding
14 authors.
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Abstract
The COVID-19 pandemic has emphasized the importance of accurate detection of known and emerging pathogens. However, robust characterization of pathogenic sequences remains an open challenge. To address this need we developed SeqScreen, which accurately characterizes short nucleotide sequences using taxonomic and functional labels and a customized set of curated Functions of Sequences of Concern (FunSoCs) specific to microbial pathogenesis. We show our ensemble machine learning model can label protein-coding sequences with FunSoCs with high recall and precision. SeqScreen is a step towards a novel paradigm of functionally informed synthetic DNA screening and pathogen characterization, available for download at www.gitlab.com/treangenlab/seqscreen .
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