ArticleNAR genomics and bioinformatics2020
Identifying microbial species by single-molecule DNA optical mapping and resampling statistics.
Article in NAR genomics and bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
15 citing papers in PubMed.
- Harnessing Methyltransferase-Guided Targeting for Sequence-Specific Proximity Labeling of DNA.Angewandte Chemie (International ed. in English) · 2026Article
- DeepMAP: Deep CNN Classifiers Applied to Optical Mapping for Fast and Precise Species-Level Metagenomic Analysis.ACS omega · 2025Article
- Sequencing and Optical Genome Mapping for the Adventurous Chemist.Chemical & biomedical imaging · 2024Review
- Optical Mapping: Detecting Genomic Resistance Cassettes in MRSA.ACS omega · 2024Article
- OM2Seq: learning retrieval embeddings for optical genome mapping.Bioinformatics advances · 2024Article
- The potential of including the microbiome as biomarker in population-based health studies: methods and benefits.Frontiers in public health · 2024Review
- Design of optimal labeling patterns for optical genome mapping via information theory.Bioinformatics (Oxford, England) · 2023Article
- DeepOM: single-molecule optical genome mapping via deep learning.Bioinformatics (Oxford, England) · 2023Article
- Fast and simple super-resolution with single images.Scientific reports · 2022Article
- A simple cut and stretch assay to detect antimicrobial resistance genes on bacterial plasmids by single-molecule fluorescence microscopy.Scientific reports · 2022Article
- Article
- Self-contained and modular structured illumination microscope.Biomedical optics express · 2021Article
- Article
- Combining dense and sparse labeling in optical DNA mapping.PloS one · 2021Article
- Cultivation-Free Typing of Bacteria Using Optical DNA Mapping.ACS infectious diseases · 2020Article
Corrections and comments
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Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to provide an unbiased view into the composition of complex viromes and/or microbiomes. To fully enable mapping-based metagenomics, sensitivity and specificity of DNA map analysis and identification need to be improved. Using detailed simulations and experimental data, we first demonstrate how fluorescence imaging of surface stretched, sequence specifically labeled DNA fragments can yield highly sensitive identification of targets. Second, a new analysis technique is introduced to increase specificity of the analysis, allowing even closely related species to be resolved. Third, we show how an increase in resolution improves sensitivity. Finally, we demonstrate that these methods are capable of identifying species with long genomes such as bacteria with high sensitivity.
Identifiers
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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.