ArticleToxins2015
HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes.
Article in Toxins, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
25 citing papers in PubMed, 41 citations in OpenAlex.
- A machine learning framework for interpreting phylogenetic tree patterns in interkingdom horizontal gene transfer.Frontiers in bioinformatics · 2026Article
- The effects of Pseudomonas strains isolated from Achnatherum inebrians on plant growth: A genomic perspective.Environmental microbiology reports · 2024Article
- Database Bias in the Detection of Interdomain Horizontal Gene Transfer Events in Pezizomycotina.Biology · 2024Article
- HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer.Briefings in bioinformatics · 2023Article
- A complete theoretical framework for inferring horizontal gene transfers using partial order sets.PloS one · 2023Article
- Article
- hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.International journal of molecular sciences · 2022Article
- Application of Gene Knockout and Heterologous Expression Strategy in Fungal Secondary Metabolites Biosynthesis.Marine drugs · 2022Review
- Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022Review
- Growth ofJournal of fungi (Basel, Switzerland) · 2022Review
- Medium levels of transcription and replication related chromosomal instability are associated with poor clinical outcome.Scientific reports · 2021Article
- Article
- Transcription Factors in the FungusJournal of fungi (Basel, Switzerland) · 2021Article
- Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity.Journal of fungi (Basel, Switzerland) · 2021Article
- Genome Sequence and Adaptation Analysis of the Human and Rice Pathogenic StrainPathogens (Basel, Switzerland) · 2021Article
- Fungal evolution: cellular, genomic and metabolic complexity.Biological reviews of the Cambridge Philosophical Society · 2020Article
- Article
- Evolution of the extracytoplasmic function σ factor protein family.NAR genomics and bioinformatics · 2020Article
- Understanding the Genetic Code.Journal of bacteriology · 2019Review
- Secondary Metabolite Dereplication and Phylogenetic Analysis Identify Various Emerging Mycotoxins and Reveal the High Intra-Species Diversity inFrontiers in microbiology · 2019Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
Abstract
Horizontal gene transfer (HGT) is a fast-track mechanism that allows genetically unrelated organisms to exchange genes for rapid environmental adaptation. We developed a new phyletic distribution-based software, HGT-Finder, which implements a novel bioinformatics algorithm to calculate a horizontal transfer index and a probability value for each query gene. Applying this new tool to the Aspergillus fumigatus, Aspergillus flavus, and Aspergillus nidulans genomes, we found 273, 542, and 715 transferred genes (HTGs), respectively. HTGs have shorter length, higher guanine-cytosine (GC) content, and relaxed selection pressure. Metabolic process and secondary metabolism functions are significantly enriched in HTGs. Gene clustering analysis showed that 61%, 41% and 74% of HTGs in the three genomes form physically linked gene clusters (HTGCs). Overlapping manually curated, secondary metabolite gene clusters (SMGCs) with HTGCs found that 9 of the 33 A. fumigatus SMGCs and 31 of the 65 A. nidulans SMGCs share genes with HTGCs, and that HTGs are significantly enriched in SMGCs. Our genome-wide analysis thus presented very strong evidence to support the hypothesis that HGT has played a very critical role in the evolution of SMGCs. The program is freely available at http://cys.bios.niu.edu/HGTFinder/ HGTFinder.tar.gz.
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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.