Jody Emile Phelan

Focal inbreeding and clonal transmission of Plasmodium vivax in pre-elimination Vietnam

This study analyzes genomic diversity of Plasmodium vivax in Vietnam, finding decreasing infection complexity, increasing clonal inbreeding, and stable drug resistance allele frequencies over a 10-year period.

A novel tool for designing targeted gene amplicons and an optimised set of primers for high-throughput sequencing in tuberculosis genomic studies

TOAST optimises amplicon design for tuberculosis genomic studies, enabling high-throughput sequencing of drug resistance mutations across multiple platforms.

hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling

hAMRonization standardizes AMR gene detection outputs from multiple tools into a unified format for easier analysis and integration.

fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing

fastlin rapidly and accurately types Mycobacterium tuberculosis complex lineages from sequencing data, detecting mixed-lineage strains and estimating proportions.

Towards environmental detection, quantification, and molecular characterization of Anopheles stephensi and Aedes aegypti from larval breeding sites

This study validates the use of environmental DNA (eDNA) for detecting and characterizing Anopheles stephensi and Aedes aegypti mosquitoes from larval breeding sites using multiplex TaqMan assays and amplicon-sequencing panels.

Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia

The paper characterizes genomic diversity and antimicrobial resistance in non-typhoidal Salmonella from The Gambia, identifying multidrug-resistant strains and their epidemiological implications.

GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning

GenTB predicts tuberculosis drug resistance from genomic data using machine learning, achieving higher sensitivity than existing tools with slightly lower specificity.

An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets

The paper develops an online immuno-analytics tool to analyze SARS-CoV-2 genetic and immunological data, identifying mutation trends and potential diagnostic targets.

A Novel Multiplex qPCR Assay for Detection of Plasmodium falciparum with Histidine-rich Protein 2 and 3 (pfhrp2 and pfhrp3) Deletions in Polyclonal Infections

This paper develops a multiplex qPCR assay to detect Plasmodium falciparum and identify pfhrp2 and pfhrp3 deletions in field samples with high sensitivity and specificity.

Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world

The paper analyzes global SARS-CoV-2 whole genome sequences to identify strain diversification and selective pressures, finding two major clades and potential mutations affecting diagnostics and vaccine efficacy.

Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity

The paper analyzes Ct genomic diversity and identifies SNPs associated with ocular localization and disease severity in a West African trachoma-endemic population.