ArticleBioinformatics (Oxford, England)2023
HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 23 citations in OpenAlex.
- Plasmidomics: studying plasmids as ecological entities beyond their hosts.Microbial genomics · 2026Review
- Biofilm-forming traits enrich the plasmid diversity and functional potential in particle-attached bacteria in coastal ecosystems.Microbiology spectrum · 2026Article
- MNBC-ME categorizes viral and plasmid sequences within metagenomes and identifies putative species or plasmid host.BMC bioinformatics · 2026Article
- PlasmidGPT: A generative framework for plasmid analysis and generation.Science advances · 2026Article
- Urban greenspaces harbour distinct plasmid communities enriched in heavy metal resistance and competitive traits in arid soils.Microbiology (Reading, England) · 2026Article
- A Cautionary Case for Host Assignment Based on Broad Environmental blaEnvironmental microbiology reports · 2026Article
- Origin of replication discovery for environmentally isolatediScience · 2026Article
- Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.Environmental science and ecotechnology · 2026Article
- A novel self-transmissible mega plasmid from extensively drug-resistantCurrent research in microbial sciences · 2026Article
- ProFiT-SPEci-FISH: a novel approach for linking plasmids to hosts in complex microbial communities at the single-cell level.Microbiome · 2025Article
- Microbiome Single Cell Atlases Generated with a Commercial Instrument.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- MOSTPLAS: a self-correction multi-label learning model for plasmid host range prediction.Bioinformatics (Oxford, England) · 2025Article
- Predicting the bacterial host range of plasmid genomes using the language model-based one-class support vector machine algorithm.Microbial genomics · 2025Article
- HFTC: a hierarchical fungal taxonomic classification model for ITS sequences using low-dimensional embedding features.Frontiers in genetics · 2025Article
- MetaCompare 2.0: differential ranking of ecological and human health resistome risks.FEMS microbiology ecology · 2024Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationAs prevalent extrachromosomal replicons in many bacteria, plasmids play an essential role in their hosts' evolution and adaptation. The host range of a plasmid refers to the taxonomic range of bacteria in which it can replicate and thrive. Understanding host ranges of plasmids sheds light on studying the roles of plasmids in bacterial evolution and adaptation. Metagenomic sequencing has become a major means to obtain new plasmids and derive their hosts. However, host prediction for assembled plasmid contigs still needs to tackle several challenges: different sequence compositions and copy numbers between plasmids and the hosts, high diversity in plasmids, and limited plasmid annotations. Existing tools have not yet achieved an ideal tradeoff between sensitivity and precision on metagenomic assembled contigs.
resultsIn this work, we construct a hierarchical classification tool named HOTSPOT, whose backbone is a phylogenetic tree of the bacterial hosts from phylum to species. By incorporating the state-of-the-art language model, Transformer, in each node's taxon classifier, the top-down tree search achieves an accurate host taxonomy prediction for the input plasmid contigs. We rigorously tested HOTSPOT on multiple datasets, including RefSeq complete plasmids, artificial contigs, simulated metagenomic data, mock metagenomic data, the Hi-C dataset, and the CAMI2 marine dataset. All experiments show that HOTSPOT outperforms other popular methods. AVAILABILITY AND IMPLEMENTATION: The source code of HOTSPOT is available via: https://github.com/Orin-beep/HOTSPOT.
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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.