ReviewBriefings in bioinformatics2018
Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites.
Review in Briefings in bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 1 of them a synthesis that pooled it.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
59 citing papers in PubMed, 1 synthesis or guideline pooled it, 124 citations in OpenAlex.
- BioprospectingFrontiers in fungal biology · 2021Pooled it
- Bacterial biosynthetic superclusters: emerging drivers of synergistic natural products against antimicrobial resistance.Essays in biochemistry · 2026Review
- Genome mining of Trp-anthranilic acid cyclic dipeptides in Aspergillus driven by analysis of NRPS adenylation domains.Archives of microbiology · 2026Article
- Draft Genome Sequence ofMicroorganisms · 2026Article
- Mining the Hidden Pharmacopeia: Fungal Endophytes, Natural Products, and the Rise of AI-Driven Drug Discovery.International journal of molecular sciences · 2026Review
- Screening the Antibiotic Activity of Cave Actinobacteria Against Multidrug-Resistant Strains ofInternational journal of microbiology · 2026Article
- Strategies to decipher silent biosynthetic gene clusters in actinomycetes.Archives of microbiology · 2025Review
- mCancer communications (London, England) · 2025Article
- Whole genome analysis of Stenotrophomonas geniculata MK2 and antagonism against Botrytis cinerea in strawberry.International microbiology : the official journal of the Spanish Society for Microbiology · 2025Article
- Revisiting Traditional Medicinal Plants: Integrating Multiomics, In Vitro Culture, and Elicitation to Unlock Bioactive Potential.Plants (Basel, Switzerland) · 2025Review
- Exploring the modern approaches to enhance fungal endophyte-derived bioactive secondary metabolites.3 Biotech · 2025Review
- Article
- Anticancer Ribosomally Synthesized and Post-Translationally Modified Peptides from Plants: Structures, Therapeutic Potential, and Future Directions.Current issues in molecular biology · 2024Review
- Unlocking the potential of bacterial endophytes from medicinal plants for drug discovery.Microbial biotechnology · 2024Review
- Genetic basis and selection of glyceollin elicitation in wild soybean.Frontiers in plant science · 2024Article
- Deep learning in microbiome analysis: a comprehensive review of neural network models.Frontiers in microbiology · 2024Review
- Bacterial cytochrome P450s: a bioinformatics odyssey of substrate discovery.Frontiers in microbiology · 2024Article
- Comparative genome analysis of the freshwater fungus Filosporella fistucella indicates potential for plant-litter degradation at cold temperatures.G3 (Bethesda, Md.) · 2023Article
- Present and future outlooks on environmental DNA-based methods for antibiotic discovery.Current opinion in microbiology · 2023Review
- Whole genome analysis of Bacillus amyloliquefaciens TA-1, a promising biocontrol agent against Cercospora arachidicola pathogen of early leaf spot in Arachis hypogaea L.BMC plant biology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Specialized metabolites (also called natural products or secondary metabolites) derived from bacteria, fungi, marine organisms and plants constitute an important source of antibiotics, anti-cancer agents, insecticides, immunosuppressants and herbicides. Many specialized metabolites in bacteria and fungi are biosynthesized via metabolic pathways whose enzymes are encoded by clustered genes on a chromosome. Metabolic gene clusters comprise a group of physically co-localized genes that together encode enzymes for the biosynthesis of a specific metabolite. Although metabolic gene clusters are generally not known to occur outside of microbes, several plant metabolic gene clusters have been discovered in recent years. The discovery of novel metabolic pathways is being enabled by the increasing availability of high-quality genome sequencing coupled with the development of powerful computational toolkits to identify metabolic gene clusters. To provide a comprehensive overview of various bioinformatics methods for detecting gene clusters, we compare and contrast key aspects of algorithmic logic behind several computational tools, including 'NP.searcher', 'ClustScan', 'CLUSEAN', 'antiSMASH', 'SMURF', 'MIDDAS-M', 'ClusterFinder', 'CASSIS/SMIPS' and 'C-Hunter' among others. We also review additional tools such as 'NRPSpredictor' and 'SBSPKS' that can infer substrate specificity for previously identified gene clusters. The continual development of bioinformatics methods to predict gene clusters will help shed light on how organisms assemble multi-step metabolic pathways for adaptation to various ecological niches.
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What OpenQuestion holds
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.