Matthew Berriman

Expression of TRPMPZQ in excitable cells and sensory structures throughout the Schistosoma mansoni lifecycle

This study uses immunolocalization and single-cell RNAseq to show TRPMPZQ expression in excitable cells and sensory structures across Schistosoma mansoni life stages, with reduced expression in PZQ-resistant strains.

In vitro sexual dimorphism establishment in schistosomes

This paper refines an in vitro protocol for culturing schistosomes to achieve sexual dimorphism, showing that human serum promotes red blood cell digestion and sexual differentiation compared to fetal bovine serum.

Apollo 3: Multi-Species Genome Curation

Apollo 3 is a new manual genome annotation tool that integrates with JBrowse 2, enabling multi-genome editing and synteny visualization.

Canonical WNT signalling governs Echinococcus metacestode development

This study shows that canonical WNT signaling is essential for Echinococcus metacestode development, with its disruption causing anteriorization and loss of posterior structures.

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.

Recapitulating whipworm development in vitro using caecaloids

This study establishes an in vitro system using caecaloids to recapitulate whipworm development, showing that larvae develop anatomical features and growth patterns similar to in vivo conditions.

The histone code of love: epigenetics of maturation of gonads in the human blood fluke Schistosoma mansoni

This study analyzes histone modifications, chromatin accessibility, and transcription in Schistosoma mansoni gonads to uncover the histone code governing gene expression and reproductive development.

Host microbiome determines host specificity of the human whipworm, Trichuris trichiura

This study shows that the human whipworm's host specificity is driven by the host microbiome, using a humanized-microbiota mouse model and metagenomic analysis.

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.

Hatching of whipworm eggs induced by bacterial contact is serine-protease dependent

This study identifies serine proteases as key mediators of whipworm egg hatching induced by bacterial contact, revealing bacterial and larval enzyme interactions.

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

A single locus determines praziquantel response in Schistosoma mansoni

The paper reanalyzes a GWAS to show that a single locus on chromosome 3 determines praziquantel response in Schistosoma mansoni, rather than two loci.

Single cell transcriptomics of the human parasite Schistosoma mansoni first intra-molluscan stage reveals tentative tegumental and stem cell regulators.

The paper performs single-cell transcriptomics on the first intra-molluscan stage of Schistosoma mansoni to identify key cell type regulators and their biological processes.

The stage- and sex-specific transcriptome of the human parasite Schistosoma mansoni

This study provides a comprehensive transcriptomic analysis of Schistosoma mansoni across eight life stages, revealing sex-specific gene expression patterns and developmental transitions.

A manually curated annotation characterises genomic features of P. falciparum lncRNAs

The paper manually annotates and characterizes genomic features of long noncoding RNAs in Plasmodium falciparum using long-read RNA sequencing and curated data.

Population genomics of ancient and modern Trichuris trichiura

This study presents the first population genomics analysis of Trichuris trichiura using whole-genome sequencing of ancient and modern samples, revealing genetic structure and admixture patterns across human and primate hosts.

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.

Daily rhythms in the transcriptomes of the human parasite Schistosoma mansoni

This study identifies daily transcriptomic rhythms in Schistosoma mansoni, revealing rhythmic gene expression patterns and their potential relevance to parasite survival and drug targets.

Characterising genome architectures using Genome Decomposition Analysis

This paper introduces GDA, a tool for characterising genome architectures, and demonstrates its effectiveness on Apicomplexa parasites and scalability to large genomes.

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.

The transcriptome of Schistosoma mansoni developing eggs reveals key mediators in pathogenesis and life cycle propagation.

This study analyzes the transcriptome of Schistosoma mansoni developing eggs to identify genes involved in pathogenesis and life cycle progression.

Assembled chromosomes of the blood fluke Schistosoma mansoni provide insight into the evolution of its ZW sex-determination system

The paper assembles the chromosomes of Schistosoma mansoni, revealing insights into the evolution of its ZW sex-determination system through gene annotation and synteny analysis.

The parasitic nematode Strongyloides ratti exists as populations of long-lived asexual lineages.

This study uses single worm whole genome sequencing to show that Strongyloides ratti populations in the UK consist of long-lived asexual lineages with hyperdiverse parasitic genes.

Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni

This study creates a single-cell RNA sequencing atlas of the early intra-mammalian stage of Schistosoma mansoni, identifying gene expression profiles and validating cell markers.

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.

Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection

The paper presents the complete genome of Hymenolepis microstoma, revealing chromosome structures capped by centromeres that serve both segregation and protection roles.

Analysis of Plasmodium vivax schizont transcriptomes from field isolates reveals heterogeneity of expression of genes involved in host-parasite interactions

This study analyzes P. vivax schizont transcriptomes from field isolates, revealing gene expression heterogeneity and identifying genes involved in host-parasite interactions.