Umer Naveed Chaudhry

The paper presents a bioinformatic pipeline for assembling Ascaris mtDNA from low-coverage whole-genome data, revealing a novel clade (Clade D) in human samples from Ethiopia.

The paper develops and validates a multilocus sequence typing scheme for Fasciola hepatica using next-generation sequencing to study population genetic structure across UK cattle and sheep populations.

This study analyzes genetic structure in Fasciola hepatica populations across UK ruminants using mt-ND1 and mt-COX1 loci, finding limited genetic structure and high gene flow.

This paper develops a qPCR assay and tremabiome deep amplicon sequencing method to improve fluke species identification in livestock, finding high co-infection rates and improved sensitivity compared to traditional methods.

This study identifies genomic signatures of benzimidazole drug resistance in Haemonchus contortus using field populations with defined treatment histories, showing the isotype-1 β-tubulin gene as the primary resistance locus.

The paper creates a graph genome incorporating global cattle diversity, showing it includes more sequence and improves mapping and variant calling.

The paper maps resistance loci for three anthelmintic classes in a parasitic nematode, identifies novel alleles for benzimidazoles and levamisole, and implicates cky-1 in ivermectin resistance.

This paper identifies gene expression changes associated with ivermectin resistance in parasitic nematodes through genetic crosses and RNA-seq, revealing upregulation of specific genes linked to neuronal plasticity and chloride homeostasis.

The paper uses genetic modeling to analyze the evolutionary origins of dihydrofolate reductase mutations in Plasmodium vivax, finding single and multiple origins for different mutations.

The paper presents a high-quality, chromosome-scale genome assembly of Haemonchus contortus using long-read sequencing, revealing genetic diversity and transcriptional regulation.

The paper compares the genetic diversity of Theileria annulata in cattle and water buffalo in Pakistan, finding higher diversity in cattle-derived populations.

The paper characterizes Fasciola gigantica in Punjab, Pakistan, identifying genetic differences and potential dispersal routes among neighboring countries in the Indian subcontinent.

The paper confirms the presence of Dicrocoelium dendriticum in the Himalaya ranges of Pakistan using genetic analysis of flukes collected from the Chitral valley.

The paper introduces a metabarcoded DNA sequencing method for detecting Plasmodium species in human malaria patients, showing improved diagnostic performance compared to an immunochromatographic assay.

The paper analyzes genetic diversity and multiplicity of infection in Fasciola gigantica isolates from Pakistani livestock using mt-ND-1 locus sequencing.

The paper develops a high-throughput method to determine anthelmintic resistance allele frequencies in gastrointestinal nematodes using Illumina Mi-seq sequencing.

The paper identifies the F200Y mutation as a common benzimidazole resistance mutation in Haemonchus contortus and H. placei in buffalo and cattle, showing multiple emergence events in H. contortus and a single emergence in H. placei.

This paper constructs a genetic map of Haemonchus contortus using whole-genome resequencing, revealing recombination patterns and reproductive traits like polyandry and polyploidy.