staphylococcus-aureus

StaphScope is a comprehensive bioinformatics tool for Staphylococcus aureus genomic analysis including MLST typing, spa typing, SCCmec analysis, antimicrobial resistance detection, virulence factors, plasmid profiling, and lineage prediction from whole genome sequencing data. Designed specifically for MRSA research

Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.

The AMRnet dashboard aims to make high-quality, robust and reliable genome-derived AMR surveillance data accessible to a wide audience

Application of Machine Learning with MALDI-TOF MS for Rapid Differentiation between Methicillin-susceptible and Methicillin-resistant Staphylococcus aureus

SCAPE - StaphyloCoccus Aureus Pangenome Exploration

QUT Capstone Project featuring a vanilla javascript project designed to display genome information from a PostgreSQL database in a user friendly way. Allows genomes to be tagged in groups and generates simple aggregate statistics.

A machine learning pipeline to classify bacterial species (Staphylococcus, Pseudomonas) from Surface-Enhanced Raman Spectroscopy (SERS) data using Python, Scikit-learn, and a Random Forest model.

Raw data and code for the Genomic Analysis of Singles and Pools (GASP) project - https://doi.org/10.1099/mgen.0.001111

Three Nigella sativa alkaloids (indazoles nigellidine, nigellicine; isoquinoline nigellimine) vs S. aureus FtsZ (PDB 3VOA): ADMET screening; docking with Vina, AutoDock4, GNINA, DiffDock-L (redock RMSD 0.307 Å); 4I55 tubulin counter-screen; 100 ns MD; MM-GBSA −13.28 ± 0.97 kcal/mol (SD). Computational predictions only.

Curated genomic database of Staphylococcus aureus virulence factors, including enterotoxins, adhesins, and immune evasion genes. These determinants enable host colonisation, immune evasion, and tissue damage, forming the basis of pathogenic potential.

Curated genomic database of Staphylococcal Pathogenicity Islands (SaPIs), mobile genetic elements in Staphylococcus aureus that contribute to virulence through carriage of enterotoxin and other virulence-associated genes.

In this study, I present a deep learning framework that utilizes raw MALDI-TOF-MS proteomic profiles as the input data source, trained strictly against high-fidelity labels derived from WGS ground truth, facilitating the detection of certain clonal complex and genes of Staphylococcus aureus.

Curated genomic database of Staphylococcus plasmids, mobile genetic elements that contribute to bacterial adaptation and pathogenicity through horizontal gene transfer. These elements may carry virulence factors, including enterotoxins, as well as antimicrobial resistance genes and other adaptive traits.

Staphylococcus aureus bakteriyofaj izolatlarinin assembly ve karakterizasyon ciktilari (metaviralSPAdes, CheckV, BACPHLIP, vContact2)

A bioinformatics pipeline for RNA-Seq analysis of Staphylococcus aureus persisters under antibiotic stress, based on Peyrusson et al. (2020). Built with Nextflow and Docker for reproducibility.

Curated genomic database of Staphylococcus aureus enterotoxin genes and variants, supporting detection of toxigenic potential in food safety and public health genomics.

Curve Growth modeling-IPASS project

This repository introduces the codes applied to the nasal microbial community of the latest available curated GEMs of D. pigrum and S. aureus.

ML pipeline and biomarker stability analysis for MALDI-TOF AMR prediction