This study presents a dual investigation of Salmonella enterica subspecies I, focusing on serovar prediction and core genome characteristics. We utilized two large genomic datasets (panX and NCBI Pathogen Detection) to test machine learning methods f...
BACKGROUND: Heteroresistance (HR) is a significant type of antibiotic resistance observed for several bacterial species and antibiotic classes where a susceptible main population contains small subpopulations of resistant cells. Mathematical models, ...
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...
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...
Journal of microbiology and biotechnology
40147921
Group A (GAS) is a major pathogen with diverse clinical outcomes linked to its genetic variability, making accurate phenotype prediction essential. While previous studies have identified many GAS-associated genetic factors, translating these finding...
Listeria monocytogenes is a potentially severe disease-causing bacteria mainly transmitted through food. This pathogen is of great concern for public health and the food industry in particular. Many countries have implemented thorough regulations, an...
() antibiotic resistance poses a global health threat. Accurate identification of antibiotic resistant strains is essential for the control of infection. In the present study, our goal is to leverage the whole-genome data of to develop practical an...
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
40113053
Despite current surveillance and sanitation strategies, foodborne pathogens continue to threaten the food industry and public health. Whole genome sequencing (WGS) has reached an unprecedented resolution to analyse and compare pathogenic bacterial is...
Selenoproteins are a special group of proteins with major roles in cellular antioxidant defense. They contain the 21st amino acid selenocysteine (Sec) in the active sites, which is encoded by an in-frame UGA codon. Compared to eukaryotes, identificat...
Biosynthetic gene clusters (BGCs), key in synthesizing microbial secondary metabolites, are mostly hidden in microbial genomes and metagenomes. To unearth this vast potential, we present BGC-Prophet, a transformer-based language model for BGC predict...