Stephen R. Doyle

Group Leader
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stephen.doyleobfuscate@sanger.ac.uk

Stephen is a molecular and computational biologist with broad interests in understanding genetic change over time.

Stephen is currently a UKRI Future Leaders Fellow (Group Leader) in the Parasites and Microbes Programme at the Wellcome Sanger Institute in the UK. His Fellowship, which started in September 2020, is supported by UKRI and The Wellcome Trust.

Prior to this, Stephen was a Senior Postdoctoral Fellow from 2015-2020 in the Parasite Genomics group led by Matt Berriman at the Sanger Institute. During this time, Stephen focused on developing genetic resources to understand anthelmintic resistance in two economically important pathogens of small ruminants, Haemonchus contortus and Teladorsagia circumcincta. This work led to the assembly of a chromosome-scale genome for H. contortus and identification of QTL and causal loci for benzimidazole, levamisole and ivermectin resistance.

Stephen’s first postdoctoral postion was in the Nematode Functional Genomics group led by Warwick Grant at La Trobe University in Melbourne, Australia. Here, Stephen focused on the genetic analysis of sub-optimal responses by Onchocerca volvulus to ivermectin. This work led to the first genome-wide comparative analysis between “good” and “poor” responders in Ghana and Cameroon, revealing multiple but distinct genetic signatures of selection differentiating response types.

Stephen received his PhD in Genetics at La Trobe University in 2011.

CV

Papers

Genome structure and population genomics of the canine heartworm Dirofilaria immitis

Trophic ecology of Octopus vulgaris paralarvae along the Iberian Canary current eastern boundary upwelling system

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

A single-cell atlas of the free-living miracidium larva of Schistosoma mansoni

Evaluation of genome skimming to detect and characterise human and livestock helminths

Faecal egg counts and nemabiome metabarcoding highlight the genomic complexity of equine cyathostomin communities and provide insight into their dynamics in a Scottish native pony herd

Genomic landscape of drug response reveals mediators of anthelmintic resistance

Improving helminth genome resources in the post-genomic era

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

Allele specific PCR for a major marker of levamisole resistance in Haemonchus contortus

Ivermectin and albendazole coadministration: opportunities for strongyloidiasis control

Population genomics of ancient and modern Trichuris trichiura

Transcriptomic analyses implicate neuronal plasticity and chloride homeostasis in ivermectin resistance and response to treatment in a parasitic nematode

An adaptive phase II/III safety and efficacy randomized controlled trial of single day or three-day fixed-dose albendazole-ivermectin co-formulation versus albendazole for the treatment of Trichuris trichiura and other STH infections. ALIVE trial protocol

Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics–metabolomics

A genetic TRP down the channel to praziquantel resistance

Genome-wide analysis of response to ivermectin treatment by a Swedish field population of Haemonchus contortus

Phenotypic and genotypic analysis of benzimidazole resistance in reciprocal genetic crosses of Haemonchus contortus

The genome sequence of the Australian filarial nematode, Cercopithifilaria johnstoni

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

Phylogeographic patterns of the Australian grass trees (Xanthorrhoea Asphodelaceae) shown using targeted amplicon sequencing

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

Challenges and opportunities for the adoption of molecular diagnostics for anthelmintic resistance

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

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

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

Screening the Saccharomyces cerevisiae nonessential gene Deletion library reveals diverse mechanisms of action for antifungal plant defensins

The global diversity of Haemonchus contortus is shaped by human intervention and climate

The confounding effects of high genetic diversity on the determination and interpretation of differential gene expression analysis in the parasitic nematode Haemonchus contortus

Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing

Utility of the Onchocerca volvulus mitochondrial genome for delineation of parasite transmission zones

Refugia and anthelmintic resistance: Concepts and challenges

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

Genome-wide sequencing uncovers cryptic diversity and mito-nuclear discordance in the Octopus vulgaris species complex

Genome-wide approaches to Investigate anthelmintic resistance

Outlier SNPs detect weak regional structure against a background of genetic homogeneity in the Eastern Rock Lobster, Sagmariasus verreauxi

Reduced variation in Wolbachia density of larval stages in comparison with adults of Onchocerca volvulus: implications for clinical outcome of infection?

Biology and genome of a newly discovered sibling species of Caenorhabditis elegans

A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry

Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals genetic drift and soft selective sweeps contribute to loss of drug sensitivity

PLAG1 deficiency impairs spermatogenesis and sperm motility in mice

Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta

You Are What You Eat: A Genomic Analysis of the Gut Microbiome of Captive and Wild Octopus vulgaris Paralarvae and Their Zooplankton Prey

Significant heterogeneity in Wolbachia copy number within and between populations of Onchocerca volvulus

The genome of Onchocerca volvulus, agent of river blindness

Outlier SNPs enable food traceability of the southern rock lobster, Jasus edwardsii

Discrimination between Onchocerca volvulus and O. ochengi filarial larvae in Simulium damnosum (s.l.) and their distribution throughout central Ghana using a versatile high-resolution speciation assay

Massively parallel sequencing of customised forensically informative SNP panels on the MiSeq

Locating and Activating Molecular ‘Time Bombs’: Induction of Mycolata Prophages

MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing

Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat

Low-coverage MiSeq next generation sequencing reveals the mitochondrial genome of the Eastern Rock Lobster, Sagmariasus verreauxi

Evidence of evolutionary constraints on the sequence composition of mitochondrial matrix targeting sequences

Enhanced annealing of mismatched oligonucleotides using a novel melting curve assay allows efficient in vitro discrimination and restriction of a single nucleotide polymorphism

Mitochondrial gene therapy an evaluation of strategies for the treatment of mitochondrial DNA disorders

Differential intracellular distribution of DNA complexed with polyethylenimine (PEI) and PEI-polyarginine PTD influences exogenous gene expression within live COS-7 cells

Posts

Reflections on 2022

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