ArticleNature biotechnology2023
Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 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
50 citing papers in PubMed, 89 citations in OpenAlex.
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- Human wastewater contamination drives the emergence of multidrug-resistant bacteria in the Galápagos marine ecosystem.Nature communications · 2026Article
- Clinical application of an Asian Screening Array-based preimplantation genetic testing workflow for various genetic disorders.Orphanet journal of rare diseases · 2026Article
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- Flexible and rapid validation of structural variation using adaptive sampling.European journal of human genetics : EJHG · 2026Article
- Adaptation of custom capture sequencing panels to the Oxford Nanopore MinION platform.Molecular biology reports · 2026Article
- Recovery and microbial host assignment of mobile genetic elements in complex microbiomes: insights from a spiked gut sample.mSystems · 2026Article
- Sequenoscope: a modular tool for nanopore adaptive sequencing analytics and beyond.Access microbiology · 2026Article
- The molecular revolution in fungal diagnostics: bridging gaps across clinical, agricultural, and environmental mycology.Mycology · 2026Review
- Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance.bioRxiv : the preprint server for biology · 2025Article
- Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.BMC medical genomics · 2025Article
- Targeted sequencing and iterative assembly of near-complete genomes.Nature communications · 2025Article
- Introduction of whole genome sequencing as NHS standard of care for glioma patients in two neurosurgical oncology centres: West Midlands.BJC reports · 2025Article
- Empowering low-crosstalk, dynamic-decision random access of DNA storage via 384-multiplexed nanopore signatures.Nature communications · 2025Article
- Dynamic sensor selection for biomarker discovery.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A comprehensive benchmarking of adaptive sampling tools for nanopore sequencing.Genome biology · 2025Article
- Article
- Real-time genomic characterization of pediatric acute leukemia using adaptive sampling.Leukemia · 2025Article
- Prospective, multicenter validation of a platform for rapid molecular profiling of central nervous system tumors.Nature medicine · 2025Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Nanopore sequencers can select which DNA molecules to sequence, rejecting a molecule after analysis of a small initial part. Currently, selection is based on predetermined regions of interest that remain constant throughout an experiment. Sequencing efforts, thus, cannot be re-focused on molecules likely contributing most to experimental success. Here we present BOSS-RUNS, an algorithmic framework and software to generate dynamically updated decision strategies. We quantify uncertainty at each genome position with real-time updates from data already observed. For each DNA fragment, we decide whether the expected decrease in uncertainty that it would provide warrants fully sequencing it, thus optimizing information gain. BOSS-RUNS mitigates coverage bias between and within members of a microbial community, leading to improved variant calling; for example, low-coverage sites of a species at 1% abundance were reduced by 87.5%, with 12.5% more single-nucleotide polymorphisms detected. Such data-driven updates to molecule selection are applicable to many sequencing scenarios, such as enriching for regions with increased divergence or low coverage, reducing time-to-answer.
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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.