Nabil-Fareed Alikhan

amr.watch provides an interactive platform to analyze and visualize AMR trends from global WGS data, enabling ongoing situational awareness for research and policy.

vaccines.watch is an interactive platform that uses global genome data to monitor vaccine targets and interventions, enabling analysis of vaccine target diversity and genomic landscape gaps.

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

The paper analyzes whole genome sequences of invasive Salmonella isolates in The Gambia to study changes in serovar distribution and virulence factors over time.

This study characterizes the genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in rural Gambia, identifying novel sequence types and antimicrobial resistance genes.

This study analyzes genomic diversity and antimicrobial resistance in Escherichia coli isolates from non-human primates in the Gambia, identifying novel sequence types and potential human pathogen exchange.

CoronaHiT is a method for high-throughput SARS-CoV-2 genome sequencing that improves coverage and throughput compared to existing protocols.

This study constructs a phylogenetic tree of 131 S. Typhimurium strains to reveal population structure and adaptation to domesticated and wild animal hosts.

Galru rapidly predicts Mycobacterium tuberculosis spoligotypes from uncorrected long reads with performance comparable to short read methods.

GrapeTree visualizes genomic relationships among 100,000 bacterial pathogens using a minimum spanning tree algorithm and interactive layouts.

SPARSE improves taxonomic classification of metagenomic reads by reducing false positives and enhancing sensitivity for low-abundance species detection.

This study compares six MLST software tools using real and simulated data, evaluating their accuracy, performance on outbreak datasets, contamination impact, and computational requirements.