ArticleGenome biology2007
DarkHorse: a method for genome-wide prediction of horizontal gene transfer.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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Who cites it
100 citing papers in PubMed.
- Ancestral hydrocarbon metabolism enables PET degradation by a natural bacterial consortium.mSystems · 2026Article
- Kente: A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Molecular and physiological acclimation to low light and iron scarcity in a globally abundant oceanic pelagophyte.Nature communications · 2026Article
- What impact do new homologs have on detecting interdomain horizontal gene transfer in eukaryotes? A reassessment of Katz (2015).Biology open · 2026Article
- A machine learning framework for interpreting phylogenetic tree patterns in interkingdom horizontal gene transfer.Frontiers in bioinformatics · 2026Article
- Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae.Nature communications · 2025Article
- Pan-genome analysis reveals genomic variations during enoki mushroom domestication, with emphasis on genetic signatures of cap color and stipe length.Journal of advanced research · 2025Article
- A survey of computational approaches for characterizing microbial interactions in microbial mats.Genome biology · 2025Review
- Systematic characterization of horizontally transferred biosynthetic gene clusters in the human gut microbiota using HTBGC-Finder.iMetaOmics · 2025Article
- Current state and future prospects of Horizontal Gene Transfer detection.NAR genomics and bioinformatics · 2025Review
- Rampant Interkingdom Horizontal Gene Transfer in Pezizomycotina? An Updated Inspection of Anomalous Phylogenies.International journal of molecular sciences · 2025Article
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- Profiling lateral gene transfer events in the human microbiome using WAAFLE.Nature microbiology · 2025Article
- Database Bias in the Detection of Interdomain Horizontal Gene Transfer Events in Pezizomycotina.Biology · 2024Article
- Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron.The ISME journal · 2024Article
- Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton.Nature communications · 2023Article
- A complete theoretical framework for inferring horizontal gene transfers using partial order sets.PloS one · 2023Article
- Leveraging comparative genomics to uncover alien genes in bacterial genomes.Microbial genomics · 2023Article
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40 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accuracy and efficiency. The method is also useful for retrospective assessments of horizontal transfer prediction reliability, recognizing orthologous sequences that may have been previously overlooked or unavailable. These features are demonstrated in bacterial, archaeal, and eukaryotic examples.
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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.