ArticleBMC genomics2020
Detecting horizontal gene transfer: a probabilistic approach.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 29 citations in OpenAlex.
- Horizontal gene transfer in Saccharomyces cerevisiae and other Saccharomycotina yeasts: a review.World journal of microbiology & biotechnology · 2026Review
- A machine learning framework for interpreting phylogenetic tree patterns in interkingdom horizontal gene transfer.Frontiers in bioinformatics · 2026Article
- Leveraging FracMinHash Containment for GenomicbioRxiv : the preprint server for biology · 2025Article
- Mechanisms, detection, and impact of horizontal gene transfer in plant functional evolution.The Plant cell · 2025Review
- Article
- Current state and future prospects of Horizontal Gene Transfer detection.NAR genomics and bioinformatics · 2025Review
- An Overview of the Recent Advances in Antimicrobial Resistance.Microorganisms · 2024Review
- Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis.Microbiology spectrum · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Origins and Evolution of NovelbioRxiv : the preprint server for biology · 2023Article
- Unraveling virulence determinants in extended-spectrum beta-lactamase-producing Escherichia coli from East Africa using whole-genome sequencing.BMC infectious diseases · 2023Article
- Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation.BMC genomics · 2023Article
- A Review of the Host Plant Location and Recognition Mechanisms of Asian Longhorn Beetle.Insects · 2023Review
- HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method.Nucleic acids research · 2023Article
- Possible effect of mutations on serological detection of Borrelia burgdorferi sensu stricto ospC major groups: An in-silico study.PloS one · 2023Article
- A complete theoretical framework for inferring horizontal gene transfers using partial order sets.PloS one · 2023Article
- An Approximate Bayesian Computation Approach for Modeling Genome Rearrangements.Molecular biology and evolution · 2022Article
- Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022Review
- Indirect identification of horizontal gene transfer.Journal of mathematical biology · 2021Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHorizontal gene transfer (HGT) is the event of a DNA sequence being transferred between species not by inheritance. HGT is a crucial factor in prokaryotic evolution and is a significant source for genomic novelty resulting in antibiotic resistance or the outbreak of virulent strains. Detection of HGT and the mechanisms responsible and enabling it, is hence of prime importance.Existing algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from its recipient genome. Closely related species pose an even greater challenge as most genes are very similar and therefore, the phylogenetic signal is weak anyhow. Notwithstanding, the importance of detecting HGT between such organisms is extremely high for the role of HGT in the emergence of new highly virulent strains.
resultsIn a recent work we devised a novel technique that relies on loss of synteny around a gene as a witness for HGT. We used a novel heuristic for synteny measurement, SI (Syntent Index), and the technique was tested on both simulated and real data and was found to provide a greater sensitivity than other HGT techniques. This synteny-based approach suffers low specificity, in particular more closely related species. Here we devise an adaptive approach to cope with this by varying the criteria according to species distance. The new approach is doubly adaptive as it also considers the lengths of the genes being transferred. In particular, we use Chernoff bound to decree HGT both in simulations and real bacterial genomes taken from EggNog database.
conclusionsHere we show empirically that this approach is more conservative than the previous χ
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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.