BACKGROUND: One of the major concerns of the biomedical community is the increasing prevalence of antimicrobial resistant microorganisms. Recent findings show that the diversification of colony morphology may be indicative of the expression of virule...
Quorum sensing peptides (QSPs) are the signaling molecules used by the Gram-positive bacteria in orchestrating cell-to-cell communication. In spite of their enormous importance in signaling process, their detailed bioinformatics analysis is lacking. ...
In this study we use a machine learning software (Ichnaea) to generate predictive models for water samples with different concentrations of fecal contamination (point source, moderate and low). We applied several MST methods (host-specific Bacteroide...
MOTIVATION: Advances in bacterial promoter predictors based on machine learning have greatly improved identification metrics. However, existing models overlooked the impact of negative datasets, previously identified in GC-content discrepancies betwe...
MOTIVATION: Identifying bacteriophages (phages) within metagenomic sequences is essential for understanding microbial community dynamics. Transformer-based foundation models have been successfully employed to address various biological challenges. Ho...
MOTIVATION: Plasmids play an essential role in horizontal gene transfer, aiding their host bacteria in acquiring beneficial traits like antibiotic and metal resistance. There exist some plasmids that can transfer, replicate, or persist in multiple or...
Diabetes mellitus is a complex metabolic disorder and one of the fastest-growing global public health concerns. The gut microbiota is implicated in the pathophysiology of various diseases, including diabetes. This study utilized 16S rRNA metagenomic ...
Antimicrobial peptides (AMPs) face stability and toxicity challenges in clinical use. Stapled modification enhances their stability and effectiveness, but its application in peptide design is rarely reported. This study built ten prediction models fo...
The prediction of the plasmid host range is crucial for investigating the dissemination of plasmids and the transfer of resistance and virulence genes mediated by plasmids. Several machine learning-based tools have been developed to predict plasmid h...
The emergence of drug-resistant bacteria, often referred to as "superbugs," poses a profound and escalating challenge to global health systems, surpassing the capabilities of traditional antibiotic discovery methods. As resistance mechanisms evolve r...