ReviewInfection and immunity2022
Categorizing Sequences of Concern by Function To Better Assess Mechanisms of Microbial Pathogenesis.
Review in Infection and immunity, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed, 20 citations in OpenAlex.
- Discerning dangerous gain of function: most gain of function (GoF) research does not involve infectious microbes.Frontiers in bioengineering and biotechnology · 2026Review
- Beyond sequence similarity: toward function-based screening of nucleic acid synthesis.Frontiers in bioengineering and biotechnology · 2026Article
- ADAPT: a programme for the advanced detection of AI-enabled pathogenic threats.Frontiers in bioengineering and biotechnology · 2026Article
- A perspective and demonstration of an approach to screening synthetic nucleic acid orders containing short nucleic acid sequences.Frontiers in bioengineering and biotechnology · 2026Article
- The Case for Limiting "Sequences of Concern" to Those with Demonstrated Pathogenic Function.Applied biosafety : journal of the American Biological Safety Association · 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
- Responsible AI in biotechnology: balancing discovery, innovation and biosecurity risks.Frontiers in bioengineering and biotechnology · 2025Review
- 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
- A Sensitivity Study for Interpreting Nucleic Acid Sequence Screening Regulatory and Guidance Documentation: Toward a Foundational Synthetic Nucleic Acid Sequence Screening Framework.Applied biosafety : journal of the American Biological Safety Association · 2024Article
- Developing a Common Global Baseline for Nucleic Acid Synthesis Screening.Applied biosafety : journal of the American Biological Safety Association · 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
- Function-based classification of hazardous biological sequences: Demonstration of a new paradigm for biohazard assessments.Frontiers in bioengineering and biotechnology · 2022Article
- Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To identify sequences with a role in microbial pathogenesis, we assessed the adequacy of their annotation by existing controlled vocabularies and sequence databases. Our goal was to regularize descriptions of microbial pathogenesis for improved integration with bioinformatic applications. Here, we review the challenges of annotating sequences for pathogenic activity. We relate the categorization of more than 2,750 sequences of pathogenic microbes through a controlled vocabulary called Functions of Sequences of Concern (FunSoCs). These allow for an ease of description by both humans and machines. We provide a subset of 220 fully annotated sequences in the supplemental material as examples. The use of this compact (∼30 terms), controlled vocabulary has potential benefits for research in microbial genomics, public health, biosecurity, biosurveillance, and the characterization of new and emerging pathogens.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.