James Anthony Cotton

TRPtracker: a community database for monitoring praziquantel sensitivity at TRPMPZQ variants

TRPtracker aggregates TRPMPZQ variants and their PZQ sensitivity data to monitor resistance and support schistosomiasis control strategies.

Different isolates of Leishmania aethiopica elicit distinct effector functions in primary human monocytes

This study shows that different Leishmania aethiopica isolates trigger distinct effector responses in human monocytes, with long-term cultured parasites eliciting different outcomes than recently isolated ones.

Chromosomal genome assembly resolves drug resistance loci in the parasitic nematode Teladorsagia circumcincta

The paper generates a chromosome-scale genome assembly for Teladorsagia circumcincta and identifies genetic loci associated with drug resistance to improve anthelmintic resistance diagnostics.

Evolutionary genomics of a zoonotic parasite across the Neotropical Realm

The paper analyzes the genomic diversity of Leishmania (Viannia) braziliensis across the Neotropical Realm, identifying two major parasite groups associated with different biomes and highlighting ecological and epidemiological differences.

Distinct neutrophil effector functions in response to different isolates of Leishmania aethiopica

The paper investigates how different Leishmania aethiopica isolates affect neutrophil effector functions in vitro, finding that long-term cultured isolates induce more ROS production and distinct neutrophil populations.

Extensive transmission and variation in a functional receptor for praziquantel resistance in endemic Schistosoma mansoni

The paper uses population genomics and functional genetics to identify praziquantel resistance variants in Schistosoma mansoni.

A single-cell atlas of the miracidium larva of the human blood fluke Schistosoma mansoni: cell types, developmental pathways and tissue architecture

Parasite genetic variation and systemic immune responses are not associated with different clinical presentations of cutaneous leishmaniasis caused by Leishmania aethiopica

This study investigates whether parasite genetic variation or immune responses differ among clinical presentations of cutaneous leishmaniasis caused by Leishmania aethiopica, finding no significant associations.

Genomic signatures of selection associated with benzimidazole drug treatments in Haemonchus contortus field populations

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.

Genome-wide analysis of Schistosoma mansoni reveals population structure and praziquantel drug selection pressure within Ugandan hot-spot communities

The paper analyzes whole-genome sequences of Schistosoma mansoni from Ugandan fishing communities to assess population structure and genetic changes associated with praziquantel treatment.

Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal new biological insights

The paper presents a new high-quality genome assembly and annotation for Cryptosporidium parvum IOWA, revealing structural and functional insights into its genome and evolutionary relationships with related species.

Genomic landscape of drug response reveals novel mediators of anthelmintic resistance

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.

Transcriptomic analyses implicate neuronal plasticity and chloride homeostasis in ivermectin resistance and recovery in a parasitic nematode

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.

Population genomic evidence that human and animal infections in Africa come from the same populations of Dracunculus medinensis

The paper uses genomic data from Guinea worm infections in humans and dogs to show they originate from the same population, indicating transmission between species and a population bottleneck.

Extensive genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm

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

Ecological divergence and hybridization of Neotropical Leishmania parasites

This study examines the evolutionary history and hybridization of Leishmania parasites using whole genome sequencing, revealing ecological divergence and genetic mosaic ancestry in hybrids.

Genomic analysis of natural intra-specific hybrids among Ethiopian isolates of Leishmania donovani

The paper analyzes whole-genome sequences of Leishmania donovani isolates from Ethiopia to investigate hybridization patterns and recombination in natural populations.

Global genome diversity of the Leishmania donovani complex

The paper presents a comprehensive genome-wide study of Leishmania donovani complex isolates, revealing genetic diversity and structural variation across species and geographical regions.

Evaluation of DNA extraction methods on individual helminth egg and larval stages for whole genome sequencing

The paper evaluates DNA extraction methods for whole genome sequencing of individual helminth eggs and larvae, showing successful sequencing for six of eight species tested.

The global diversity of the major parasitic nematode Haemonchus contortus is shaped by human intervention and climate

This study analyzes the global genetic diversity of Haemonchus contortus, revealing human-driven dispersal and climate adaptation mechanisms.

Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus

The paper identifies a single major QTL on chromosome V associated with ivermectin resistance in Haemonchus contortus through genome-wide analysis of genetic crosses.

Comparative genomics of the major parasitic worms

This paper compares genomes of 81 nematode and platyhelminth species to identify gene families related to parasitism and prioritize new drug targets.

Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus

This paper assembles and annotates reference genomes for Leishmania naiffi and Leishmania guyanensis, revealing genomic traits and evolutionary patterns in the Viannia subgenus.

Complete avian malaria parasite genomes reveal features associated with lineage specific evolution in birds and mammals

The paper reports the genome sequencing of two avian malaria parasites and identifies lineage-specific features associated with their evolution in birds and mammals.

Evolutionary analysis implicates RNA polymerase II pausing and chromatin structure in nematode piRNA biogenesis

The paper investigates piRNA biogenesis in nematodes, showing that piRNA upstream motifs are derived from snRNA promoter elements and that piRNA production depends on RNA polymerase II pausing and chromatin structure.

A genome resequencing-based genetic map reveals the recombination landscape of an outbred parasitic nematode in the presence of polyploidy and polyandry

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