ArticlePLoS computational biology2023
A fast machine-learning-guided primer design pipeline for selective whole genome amplification.
Article in PLoS computational biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 21 citations in OpenAlex.
- Low-Abundance and FragmentaryBiomolecules · 2026Article
- Review
- Recent advances in isothermal amplification techniques for detection of animal diseases.Frontiers in veterinary science · 2026Review
- Simultaneous population genomics of hosts and their parasites with selective whole genome amplification.Parasites & vectors · 2025Article
- Protease andAnimals : an open access journal from MDPI · 2025Article
- The Evolution of Nucleic Acid-Based Diagnosis Methods from the (pre-)CRISPR to CRISPR era and the Associated Machine/Deep Learning Approaches in Relevant RNA Design.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Beyond the genome: the role of functional markers in contemporary plant breeding.Frontiers in plant science · 2025Review
- AI in SERS sensing moving from discriminative to generative.Npj biosensing · 2025Review
- Progress in the application of isothermal amplification technology in the diagnosis of infectious diseases.Frontiers in microbiology · 2025Review
- Advances in nucleic acid probe-based detection of gene point mutations: a review.Frontiers in chemistry · 2025Review
- A Novel and Rapid Selective Viral Genome Amplification and Sequencing Method for African Swine Fever Virus.Viruses · 2024Article
- A novel isothermal whole genome sequencing approach for Monkeypox Virus.Scientific reports · 2024Article
- primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other.Journal of open source software · 2024Article
- Turning the needle into the haystack: Culture-independent amplification of complex microbial genomes directly from their native environment.PLoS pathogens · 2024Review
- Time series-based hybrid ensemble learning model with multivariate multidimensional feature coding for DNA methylation prediction.BMC genomics · 2023Article
- Article
- Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies.PLoS pathogens · 2023Article
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
Abstract
Addressing many of the major outstanding questions in the fields of microbial evolution and pathogenesis will require analyses of populations of microbial genomes. Although population genomic studies provide the analytical resolution to investigate evolutionary and mechanistic processes at fine spatial and temporal scales-precisely the scales at which these processes occur-microbial population genomic research is currently hindered by the practicalities of obtaining sufficient quantities of the relatively pure microbial genomic DNA necessary for next-generation sequencing. Here we present swga2.0, an optimized and parallelized pipeline to design selective whole genome amplification (SWGA) primer sets. Unlike previous methods, swga2.0 incorporates active and machine learning methods to evaluate the amplification efficacy of individual primers and primer sets. Additionally, swga2.0 optimizes primer set search and evaluation strategies, including parallelization at each stage of the pipeline, to dramatically decrease program runtime. Here we describe the swga2.0 pipeline, including the empirical data used to identify primer and primer set characteristics, that improve amplification performance. Additionally, we evaluate the novel swga2.0 pipeline by designing primer sets that successfully amplify Prevotella melaninogenica, an important component of the lung microbiome in cystic fibrosis patients, from samples dominated by human DNA.
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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.