ArticleNucleic acids research2020
Seeker: alignment-free identification of bacteriophage genomes by deep learning.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers, 3 of them syntheses that pooled it.
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Who cites it
77 citing papers in PubMed, 3 syntheses or guidelines pooled it, 132 citations in OpenAlex.
- Precision phage therapy in the AI/ML era: a systematic review of discovery-to-clinical translation evidence.Frontiers in microbiology · 2026Pooled it
- Bioinformatics Tools and Approaches for Virus Discovery in Genomic Data: A Systematic Review.Viruses · 2025Pooled it
- Antimicrobial resistance crisis: could artificial intelligence be the solution?Military Medical Research · 2024Pooled it
- Innovative Applications of Artificial Intelligence in Bacteriophage Research: A New Chapter in Future Medicine.Microorganisms · 2026Review
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Review
- Bacteriophages in gut metagenomes: from analysis to application.Virology journal · 2026Review
- HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.GigaScience · 2026Article
- Viral communities from long-term anaerobic alkane-oxidizing enrichment cultures encode predicted cell surface adhesion functions.The ISME journal · 2026Article
- Microbial dysbiosis in cholangiocarcinoma.Frontiers in microbiology · 2026Review
- Advances in deep learning for antimicrobial research.Frontiers in microbiology · 2026Review
- Phage therapy againstFrontiers in microbiology · 2026Review
- Host-virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier.Microbial genomics · 2025Article
- Prophage Activation: An In Silico Platform for Identifying Prophage Regulatory Elements to Inform Phage Engineering Against Drug-Resistant Bacteria.Life (Basel, Switzerland) · 2025Article
- Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world.Briefings in bioinformatics · 2025Review
- The effect of taxonomic, host-dependent features and sample bias on virus host prediction using machine learning and short sequence k-mers.Scientific reports · 2025Article
- Soil microbial responses to multiple global change factors as assessed by metagenomics.Nature communications · 2025Article
- The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut.PLoS computational biology · 2025Article
- A review of neural networks for metagenomic binning.Briefings in bioinformatics · 2025Review
- PharaCon: a new framework for identifying bacteriophages via conditional representation learning.Bioinformatics (Oxford, England) · 2025Article
17 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in metagenomic sequencing have enabled discovery of diverse, distinct microbes and viruses. Bacteriophages, the most abundant biological entity on Earth, evolve rapidly, and therefore, detection of unknown bacteriophages in sequence datasets is a challenge. Most of the existing detection methods rely on sequence similarity to known bacteriophage sequences, impeding the identification and characterization of distinct, highly divergent bacteriophage families. Here we present Seeker, a deep-learning tool for alignment-free identification of phage sequences. Seeker allows rapid detection of phages in sequence datasets and differentiation of phage sequences from bacterial ones, even when those phages exhibit little sequence similarity to established phage families. We comprehensively validate Seeker's ability to identify previously unidentified phages, and employ this method to detect unknown phages, some of which are highly divergent from the known phage families. We provide a web portal (seeker.pythonanywhere.com) and a user-friendly Python package (github.com/gussow/seeker) allowing researchers to easily apply Seeker in metagenomic studies, for the detection of diverse unknown bacteriophages.
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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.