Taane Gregory Clark

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

The paper develops a rules-based classifier to predict ciprofloxacin resistance in Klebsiella pneumoniae from genotype data and demonstrates its global distribution association with quinolone consumption.

A Plasmodium falciparum Pangenome Resource to Drive Structural Variant Discovery and to assist Malaria Control

This paper introduces PfPan, a P. falciparum pangenome that improves structural variant detection and aids malaria control by identifying drug resistance and diagnostic evasion variants.

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.

Menaquinone depletion resensitises bedaquiline-resistant tuberculosis

This study identifies MenG inhibitors that restore bedaquiline susceptibility in resistant tuberculosis strains through menaquinone pathway disruption.

Gametocyte production and transmission fitness of African and Asian Plasmodium falciparum isolates with differential susceptibility to artemisinins

This study compares gametocyte production and transmission fitness of ART-sensitive and ART-resistant P. falciparum isolates across multiple mosquito species.

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.

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

This paper reclassifies SHV β-lactamase alleles in K. pneumoniae genomes based on mutations, improving genotype-phenotype understanding and updating the Kleborate tool.

A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission

MixInfect2 accurately detects mixed Mycobacterium tuberculosis infections and estimates strain proportions, improving upon previous methods.

Uncovering the genetic diversity in Aedes aegypti insecticide resistance genes through global comparative genomics

The paper analyzes genetic diversity in four insecticide resistance genes of Aedes aegypti across global populations to identify mutations and copy number variations associated with insecticide resistance.

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.

Getting close to nature - Plasmodium knowlesi reference genome sequences from contemporary clinical isolates

The paper develops a method to generate comprehensive genome sequences of Plasmodium knowlesi from clinical isolates and provides insights into the evolution of gene families associated with antigenic variation.

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.

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.