ArticleNature biotechnology2022
Designing sensitive viral diagnostics with machine learning.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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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
57 citing papers in PubMed.
- Multiplexed detection of febrile infections using CARMEN.Nature communications · 2025Trial
- Streamlined CRISPR-based assays for detection and subtyping of H5 and H7 avian influenza.iScience · 2026Article
- A rapid, inexpensive diagnostic for bacterial pathogen and resistance detection in resource-limited settings.Science advances · 2026Article
- RNA structure modulates Cas13 activity and enables mismatch detection.Nature biotechnology · 2026Article
- Convergence of Soft Electronics and Artificial Intelligence: From Materials to Intelligent Systems.Nano-micro letters · 2026Review
- Beyond DNA editing: how Cas13 redefined programmable RNA manipulation and what still limits its therapeutic promise.Nucleic acids research · 2026Review
- Intersegmental transfers drive target search in an RNA-targeting CRISPR system.bioRxiv : the preprint server for biology · 2026Article
- Machine Learning for CRISPR-Based Diagnostics.International journal of molecular sciences · 2026Review
- Rapid development and field evaluation of a portable CRISPR-based assay for Mpox during the 2025 Sierra Leone outbreak.Nature communications · 2026Article
- CasCADE: CasMicrobiology spectrum · 2026Article
- Review
- DeepTYLCV: An interpretable and experimentally validated AI model for predicting virulence of different tomato yellow leaf curl virus strains.Plant communications · 2026Article
- A kinetic approach for mapping seed regions of CRISPR ribonucleoprotein and improving specificity.Nucleic acids research · 2026Article
- Adaptation of the multiplexed CRISPR-Cas13 CARMEN RVP assay for longitudinal detection of respiratory pathogens from air samples.Applied and environmental microbiology · 2026Article
- Genomic diversity analysis enables development of pan-Dengue Toehold RNA sensors.PLoS neglected tropical diseases · 2026Article
- Programmable kinetic barcoding for multiplexed RNA detection with Cas13a.Nature biomedical engineering · 2026Article
- Challenges and Solutions in pgRNA Measurement: Toward Improved Monitoring of Hepatitis B Therapy.Pathogens (Basel, Switzerland) · 2026Review
- Proteomics in the Diagnosis of Viral and Pathogenic Infections.Advances in experimental medicine and biology · 2026Review
- The Emergence of a CRISPR-Cas Revolution in Ecology: Applications, Challenges, and an Ecologist's Overview of the Toolbox.Molecular ecology resources · 2026Review
- CRISPR-based point-of-care diagnostics for viral hepatitis: from molecular design to clinical implementation.Frontiers in bioengineering and biotechnology · 2026Review
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Design of nucleic acid-based viral diagnostics typically follows heuristic rules and, to contend with viral variation, focuses on a genome's conserved regions. A design process could, instead, directly optimize diagnostic effectiveness using a learned model of sensitivity for targets and their variants. Toward that goal, we screen 19,209 diagnostic-target pairs, concentrated on CRISPR-based diagnostics, and train a deep neural network to accurately predict diagnostic readout. We join this model with combinatorial optimization to maximize sensitivity over the full spectrum of a virus's genomic variation. We introduce Activity-informed Design with All-inclusive Patrolling of Targets (ADAPT), a system for automated design, and use it to design diagnostics for 1,933 vertebrate-infecting viral species within 2 hours for most species and within 24 hours for all but three. We experimentally show that ADAPT's designs are sensitive and specific to the lineage level and permit lower limits of detection, across a virus's variation, than the outputs of standard design techniques. Our strategy could facilitate a proactive resource of assays for detecting pathogens.
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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.