Volume 5, Issue 2 (2025)

Medicinal-plant pathway discovery increasingly combines genome assemblies, gene-expression profiles, metabolite measurements, spatial information, and functional assays, yet the presence of multiple data layers does not itself resolve which gene produces, modifies, transports, or regulates a given metabolite. This article develops an original, evidence-bounded multi-omics architecture for gene–metabolite assignment in specialized metabolism. The analysis separates candidate nomination from biolo

Microbial genome mining routinely identifies far more biosynthetic gene clusters (BGCs) than can be experimentally characterized, creating a prioritization problem rather than a simple detection problem. Sequence novelty is frequently treated as the principal triage signal, yet sequence divergence does not guarantee production, structural novelty, ecological relevance, or practical chemical access. This article develops an original computational prioritization model that integrates four non-equi

Untargeted plant LC–MS/MS routinely produces far more reproducible spectral features than can be assigned to authenticated molecular structures. The resulting gap between detection and identification is increasingly filled by spectral-library search, molecular networking, formula inference, class prediction, candidate ranking, predicted spectra, retention modeling, and de novo structure generation. These tools expand chemical coverage, but their outputs are often reported at a level of structura

Poor aqueous solubility frequently lowers the apparent developability of phytochemical candidates, yet that judgment is often made before formulation has revealed whether the limitation is intrinsic, state-dependent, or technologically tractable. This article develops an original formulation-aware developability model in which candidate quality is treated as conditional on material state, gastrointestinal dissolution behavior, exposure-relevant solution state, and the suitability of the selected

Pharmacognosy frequently moves across materials and levels of inference: a botanical extract produces a phenotype, chemical analysis detects candidate constituents, an isolated compound shows activity, and computational or experimental work nominates a molecular target. These observations are scientifically valuable but do not represent equivalent claims. Mechanistic overstatement arises when evidence supporting one level is silently transferred to another—for example, when extract activity is a

Transferring plant biosynthetic genes into a microbial chassis can reproduce enzyme inventories without reproducing the cellular conditions that made the pathway functional in its native organism. This distinction becomes increasingly consequential as heterologous routes incorporate membrane-associated enzymes, redox-intensive reactions, spatially separated intermediates, toxic metabolites, competing precursor demands, and products that require active removal. This article develops an original p

Industrial fermentation routes are commonly ranked from laboratory performance, yet scale-up changes the physical environment, the temporal exposure history of cells, and the economic consequences of upstream choices. This article develops an original, evidence-bounded bioprocess decision model for assessing when a route that appears superior at small scale may become less attractive after scale-dependent biological, engineering, and recovery constraints are considered. The analysis separates ab

Endophytic fungi can harbor extensive biosynthetic capacity, yet natural-product discovery commonly interrogates them after removal from the host and transfer to simplified culture. This creates a central uncertainty: chemistry observed ex planta may represent only one state within a larger, interaction-dependent chemical repertoire. This integrative review synthesized ecological, metabolomic, genomic, regulatory, co-culture, and pathway-activation evidence relevant to endophyte chemical express