Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

Making whole bacterial genome sequencing data analysis easy

HydrAMP: a deep generative model for antimicrobial peptide discovery

Code for the paper "Antimicrobial resistance prediction in clinical isolates through machine learning on MALDI-TOF mass spectra"

AMR/VF LGT focused bacterial genomics analysis workflow

Harmonization of AMR predictor tool outputs

An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences

A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.

Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow

PhyloTrace is a GUI platform for bacterial monitoring offering a toolkit of analyses like hashed cgMLST typing and Antimicrobial Resistance Screening.

PRAWNS: A fast and scalable bioinformatics tool that generates an efficient pan-genome representation of closely related whole genomes to provide a concise list of genomic features

Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants

Implementation of the pipeline described in the work "Artificial intelligence model to predict resistances in Gram-negative bloodstream infections" by Bonazzetti et al., npj Digit. Med. 8, 319 (2025)

Data and code repository for study aiming to understand ESBL carriage in Blantyre, Malawi

Antimicrobial Resistance Test Interpretation Engine

MTB++ a software developed to predict antimicrobial resistance to 13 antibiotics and 3 families of antimicrobials.

Here is my participation to the 2024 edition of the HackBio Internship (AMR in cancer track).

An interactive and user-friendly web application to explore the hospital microbiome and genetic makeup

LLM-powered classification of phage protein functions to identify strong lytic candidates against Klebsiella, using transfer learning and biological embeddings.