ArticleCell reports methods2021
Probe design for simultaneous, targeted capture of diverse metagenomic targets.
Article in Cell reports methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 12 papers.
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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.
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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
12 citing papers in PubMed, 15 citations in OpenAlex.
- Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical sample types, with analysis of paired bronchoalveolar lavage fluid and blood samples.Microbiology spectrum · 2026Article
- A Roadmap for Using Hybridisation Capture-Based Target Enrichment of Ancient Environmental DNA in Palaeoecology.Molecular ecology resources · 2026Review
- Optimisation and validation of capture mNGS for predicting antimicrobial resistance.EBioMedicine · 2026Article
- Hybridization capture increases on-target nanopore sequencing of plant RNA tobamovirus- derived cDNA libraries.Frontiers in microbiology · 2026Article
- Enrichment techniques for clinical metagenomics.Frontiers in cellular and infection microbiology · 2026Review
- Clinical implement of Probe-Capture Metagenomics in sepsis patients: A multicentre and prospective study.Clinical and translational medicine · 2025Article
- OLTA: Optimizing bait seLection for TArgeted sequencing.Bioinformatics (Oxford, England) · 2025Article
- Enriching the future of public health microbiology with hybridization bait capture.Clinical microbiology reviews · 2024Review
- Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater.Environmental science & technology · 2024Review
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- Deqformer: high-definition and scalable deep learning probe design method.Briefings in bioinformatics · 2024Article
- AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data.GigaScience · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
13 authors at 2 institutions in 1 country.
Funding
Abstract
The compounding challenges of low signal, high background, and uncertain targets plague many metagenomic sequencing efforts. One solution has been DNA capture, wherein probes are designed to hybridize with target sequences, enriching them in relation to their background. However, balancing probe depth with breadth of capture is challenging for diverse targets. To find this balance, we have developed the HUBDesign pipeline, which makes use of sequence homology to design probes at multiple taxonomic levels. This creates an efficient probe set capable of simultaneously and specifically capturing known and related sequences. We validated HUBDesign by generating probe sets targeting the breadth of coronavirus diversity, as well as a suite of bacterial pathogens often underlying sepsis. In separate experiments demonstrating significant, simultaneous enrichment, we captured SARS-CoV-2 and HCoV-NL63 in a human RNA background and seven bacterial strains in human blood. HUBDesign (https://github.com/zacherydickson/HUBDesign) has broad applicability wherever there are multiple organisms of interest.
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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.