Stephen R Doyle

UKRI Future Leaders Fellow, Group Leader @ Wellcome Sanger Institute

Overview

I am a molecular and computational biologist focused on understanding the evolutionary biology of parasitic worms that infect humans and animals. I lead a multidisciplinary research group where we use population-wide to single-cell resolution genomic approaches to understand the genetic mechanisms and phenotypic traits underpinning parasite adaptation and persistence. Using a combination of in vivo models and parasites sampled from endemic countries around the world, we measure and analyse helminth diversity across space and time, build genomic resources to support global parasitology communities, and develop genetic approaches to diagnose and surveil helminths, with the ultimate aim to inform the sustainable and effective control of helminths to improve human and animal health.

Employment

2020 - now Group Leader, UKRI Future Leaders Fellow / Career Development Fellow
Wellcome Sanger Institute, UK
Project: “The generation and maintenance of genetic novelty in parasitic helminths”

2015 - 2020 Postdoctoral Fellow
Parasite Genomics Group, Wellcome Sanger Institute, UK
Project: “Building Upon the Genome: using Haemonchus contortus genomic resources to develop novel interventions to control endemic GI parasites”

2012 - 2015 Early Career Development Fellow
Department of Genetics / Dept. Animal, Plant, and Soil Sciences, La Trobe University, Australia
Project: “Population genomics of ivermectin drug response in the human parasitic nematode, Onchocerca volvulus”

2011 Postdoctoral Fellow
Department of Genetics, La Trobe University, Australia
Project: “Development of markers for ivermectin resistance monitoring in Onchocerca volvulus”

Education

2006 - 2010 PhD
Department of Genetics, La Trobe University, Australia
Thesis title: “Development of genetic strategies for the investigation and treatment of mitochondrial DNA disorders”
Advisors: Dr Chee Kai Chan / Assoc. Prof. Warwick Grant

2005 Honours
Department of Genetics, La Trobe University, Australia
Thesis title: “Targeted non-viral gene delivery: Intracellular trafficking of polyethylenimine-peptide bio-conjugates”; First class honours awarded Advisor: Dr Chee Kai Chan

2001 - 2004 Bachelor of Medical Science
La Trobe University, Australia

Publications

Total: 70 publications; 14 first author; 11 senior author
Since 2019 (last 5 yrs): 35 publications; 3 first author; 10 senior author

2024

• Buddenborg SK, DOYLE SR (2024) Entering the spatial age of parasite genomics. Trends in Parasitology
• Buddenborg SK, Morrison A, Fletcher AC, Kieninger MR, Ng BL, Maitland K, McIntyre J, Hart E, Bartley D, Duque-Correa MA, DOYLE SR (2024) Optimisation of single-nuclei isolation and RNA sequencing of parasitic nematodes. BioRxiv
• Papaiakovou M, Waeschenbach A, Ajibola O, Ajjampur SSR, Anderson RM, Bailey R, Chung JB, Cambra Pelleja M, Caro NR, Chaima D, Cimino RO, Cools P, Cossa A, Dunn J, Galagan S, Gandasegui J, Grau Pujol B, Houlder E, Ibikounle M, Jenkins TP, Kalua K, Kjetland EF, Krolewiecki AJ, Levecke B, Luty AJF, MacDonald A, Mandomando I, Manuel M, Martinez-Valladares M, Mejia R, Mekonnen Z, Messa Jr A, Mpairwe H, Muchisse O, Munoz J, Mwinzi P, Novela V, Odiere MR, Sacoor C, Walson JL, Williams SA, McManus SW, Littlewood DTJ, Cantacessi C, DOYLE SR (2024) Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets. BioRxiv
• Gandasegui J, Grau-Pujol B, Novela V, Muchisse O, Cambra-Pellejà M, Cossa A, Jamine JC, Sacoor C, Brienen EAT, Catala-Moll F, van Lieshout L, Martínez-Valladares M, Paredes R, Muñoz J, DOYLE SR Deep-amplicon sequencing of the complete beta-tubulin gene in Trichuris trichiura before and after albendazole treatment. International Journal for Parasitology: Drugs and Drug Resistance
• McIntyre J, Morrison A, Maitland K, Berger D, Price DRG, Dougan S, Grigoriadis D, Tracey A, Holroyd N, Bull K, Rose Vineer H, Glover MJ, Morgan ER, Nisbet AJ, McNeilly T, Bartley Y, Sargison N, Bartley D, Berriman M, Cotton J, Devaney E, Laing R, DOYLE SR (2024) Chromosomal genome assembly resolves drug resistance loci in the parasitic nematode Teladorsagia circumcincta. Accepted PLoS Pathogens
• Goulding D, Tolley C, Mkandawire TT, DOYLE SR, Hart E, Airs PM, Grencis RK, Berriman M, Duque-Correa MA (2024) Hatching of whipworm eggs induced by bacterial contact is serine-protease dependent. BioRxiv
• Berger DJ, Park S-K, Crellen T, Vianney TJ, Kabatereine NB, Cotton JA, Sanya R, Elliot A, Tukahebwa EM, Adriko M, Standley CJ, Gouvras A, Kinunghi S, Haas H, Rabone M, Emery A, Lamberton PHL, Webster BL, Allan F, Buddenborg S, Berriman M, Marchant JS, DOYLE SR, Webster JP (2024) Extensive transmission and variation in a functional receptor for praziquantel resistance in endemic Schistosoma mansoni. BioRxiv
• Power RI, DOYLE SR, Šlapeta J. (2024) Whole genome amplification and sequencing of individual Dirofilaria immitis microfilariae. Experimental Parasitology
• Brann T, Beltramini A, Chaparro C, Berriman M, DOYLE SR, Protasio A. (2024) Subtelomeric plasticity contributes to gene family expansion in the human parasitic flatworm Schistosoma mansoni. BMC Genomics
• Gandasegui J, Power RI, Curry E, Lau DC-W, O’Neill CM, Wolstenholme A, Prichard R, Šlapeta J, DOYLE SR (2024) Genome structure and population genomics of the canine heartworm Dirofilaria immitis. International Journal for Parasitology
• Antonopoulos A, Charvet CL, Maitland K, DOYLE SR, Neveu C, Laing R. (2024) Functional validation of novel levamisole resistance marker S168T in Haemonchus contortus. International Journal for Parasitology: Drugs and Drug Resistance
• Antonopoulos A, Higgins O, DOYLE SR, Bartley D, Morrison A, Shalaby MM, Reboud J, Devaney E, Smith TJ, Laing R, Busin V (2024) Real-time single-base specific detection of the Haemonchus contortus S168T variant associated with levamisole resistance using loop-primer endonuclease cleavage loop-mediated isothermal amplification. Molecular and Cellular Probes
• Crawford KE, Hedtke SM, DOYLE SR, Kuesel AC, Armoo S, Osei-Atweneboana MY, Grant WN (2024) Genome-based tools for onchocerciasis elimination: Utility of the mitochondrial genome for delineating Onchocerca volvulus transmission zones. International Journal for Parasitology.

2023

• Buddenborg SK, Lu Z, Sankaranarayanan G, DOYLE SR, Berriman M. The stage-and sex-specific transcriptome of the human parasite Schistosoma mansoni. Scientific Data. Data exploration tool of Schisto lifecycle
• Roura A, DOYLE SR, Castro-Bugallo A, Gonzalez AF, Strugnell JM. Trophic ecology of Octopus vulgaris paralarvae along the Iberian Canary current eastern boundary upwelling system. Scientific Reports.
• Attenborough T, Rawlinson KA, Diaz Soria CL, Ambridge K, Sankaranarayanan G, Graham J, DOYLE SR, Rinaldi G, Berriman M (2023) A single-cell atlas of the free-living miracidium larva of Schistosoma mansoni. BioRxiv.
• Papaiakovou M, Fraija-Fernández N, James K, Briscoe AG, Hall A, Jenkins TP, Dunn J, Levecke B, Mekonnen Z, Cools P, DOYLE SR, Cantacessi C, Littlewood DTJ (2023) Evaluation of genome skimming to detect and characterise human and livestock helminths. International Journal for Parasitology. Cover art selected for this issue.

2022

• DOYLE SR, Laing R, Bartley D, Morrison A, Holroyd N, Maitland K, Antonopoulos A, Chaudhry U, Flis I, Howell S, McIntyre J, Gilleard JS, Tait A, Mable BK, Kaplan R, Sargison N, Britton C, Berriman M, Devaney E, Cotton J (2022) Genomic landscape of drug response reveals novel mediators of anthelmintic resistance. Cell Reports.
• Sargison N, Chambers A, Chaudhry U, Júnior LC, DOYLE SR, Ehimiyein A, Evans M, Jennings A, Kelly R, Sargison F, Sinclair M, Zahid O 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. Int. J Parasitol
• DOYLE SR (2022) Improving helminth genome resources in the post-genomic era. Trends in Parasitology. Cover art selected for this issue.
• DOYLE SR, Soe MJ, Nejsum P, Betson M, Cooper PJ, Peng L, Zhu XQ, Sanchez A, Matamoros G, Fontecha Sandoval GA, Cutillas C, Tchuente LAT, Mekonnen Z, Ame SM, Namwanje H, Levecke B, Berriman M, Fredensborg BL, Kapel CMO (2022) Population genomics of ancient and modern Trichuris trichiura. Nature Communications
• Gandasegui J, Onwuchekwa C, Krolewiecki AJ, DOYLE SR, Pullan RL, Enbiale W, Kepha S, Hatherell HA, van Lieshout L, Cambra-Pellejà M, Escola V, Muñoz J (2022) Ivermectin and albendazole coadministration: opportunities for strongyloidiasis control. The Lancet Infectious Diseases
• Laing R, DOYLE SR, McIntyre J, Maitland K, Morrison A, Bartley DJ, Kaplan R, Chaudhry U, Sargison N, Tait A, Cotton JA, Britton C, Devaney E (2021) Transcriptomic analyses implicate neuronal plasticity and chloride homeostasis in ivermectin resistance and recovery in a parasitic nematode. PLoS Pathogens
• Krolewiecki A, Enbiale W, Gandasegui J, van Lieshout L, Kepha S, Messa Junior A, Bengtson M, Gelaye W, Escola V, Martinez-Valladares M, Cambra-Pellejà M, Algorta J, Martí-Soler H, Fleitas P, Ballester MR, DOYLE SR, Williams NA, Legarda A, Mandomando I, Mwandawiro C, Muñoz J (2022) 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.[version 1; peer review: awaiting peer review]. Gates Open Research
• Antonopoulos A, DOYLE SR, Bartley DJ, Morrison A, Kaplan R, Howell S, Neveu C, Busin V, Devaney E, Laing R (2022) Allele specific PCR for a major marker of levamisole resistance in Haemonchus contortus. Int. J Parasitol-DDR
• Papaiakovou M, Littlewood TJ, DOYLE SR, Gasser R, Cantacessi C (2022) Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics–metabolomics. Parasites & Vectors
• Cotton J, DOYLE SR (2022) A genetic TRP down the channel to praziquantel resistance. Trends in Parasitology
• Vianney JV, Berger D, DOYLE SR, Sankaranarayanan G, Serubanja J, Nakawungu PK, Besigye F, Sanya R, Holroyd N, Allan F, Webb E, Elliott A, Berriman M, Cotton J (2022) Genome-wide analysis of Schistosoma mansoni reveals population structure and praziquantel drug selection pressure within Ugandan hot-spot communities. PLoS NTD
• Baltrusis P, DOYLE SR, Halvarsson P, Hoglund J (2022) Genome-wide analysis of response to ivermectin treatment by a Swedish field population of Haemonchus contortus. Int. J Parasitol-DDR
• Morrison AA, Chaudhry U, Andrews L, Melville L, DOYLE SR, Sargison ND, Bartley DJ (2022) Phenotypic and genotypic analysis of benzimidazole resistance in reciprocal genetic crosses of Haemonchus contortus. Int. J Parasitol-DDR

2021

• McCann K, Grant W, DOYLE SR (2021) The genome sequence of the Australian filarial nematode, Cercopithifilaria johnstoni. Wellcome Open Research.
• Buddenborg SK, Tracey A, Berger DJ, Lu Z, DOYLE SR, Fu B, Yang F, Reid AJ, Rodgers FH, Rinaldi G, Sankaranarayanan G, Bohme U, Holroyd N, Berriman M (2021) Assembled chromosomes of the blood fluke Schistosoma mansoni provide insight into the evolution of its ZW sex-determination system. bioRxiv.
• McLay TGB, Ladiges PY, DOYLE SR, Bayly MJ. (2021) Phylogeographic patterns of the sclerophyllous Australian grass tree (Xanthorrhoea Sm. Asphodelaceae) revealed using targeted amplicon sequencing. Australian Systematic Botany 34, 206-225

2020

• Kotze AC, Gilleard JS, DOYLE SR, Prichard RK. (2020) Challenges and opportunities for the adoption of molecular diagnostics for anthelmintic resistance. Int. J Parasitol-DDR
• DOYLE SR, Tracey A, Laing R, Holroyd N, Bartley D, Bazant W, Beasley H, Beech R, Britton C, Brooks K, Chaudhry U, Maitland K, Martinelli A, Noonan JD, Paulini M, Quail MA, Redman E, Rodgers FH, Sallé G, Shabbir MZ, Sankaranarayanan G, Wit J, Howe KL, Sargison N, Devaney E, Berriman M, Gilleard JS, Cotton JA. (2020) Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm. Communications Biology. Behind the Paper
• Diaz Soria CL, Lee J, Chong T, Coghlan A, Tracey A, Young M, Andrews T, Hall C, Ng BL, Rawlinson K, DOYLE SR, Leonard S, Lu Z, Bennett H, Rinaldi G, Newmark PA, Berriman M. (2020) Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni. Nature Communications.
• Durrant C, Thiele EA, Holroyd N, DOYLE SR, Sallé G, Tracey A, Sankaranaranayan G, Lotkowska M, Bennett HM, Huckvale T, Abdellah Z, Tchindebet O, Wossen M, Logora MSY, Coulibaly CO, Weiss AJ, Schulte-Hostedde A, Foster J, Cleveland CA, Yabsley MJ, Ruiz-Tiben E, Berriman M, Eberhard M, Cotton JA. (2020) Population genomic evidence that human and animal infections in Africa come from the same populations of Dracunculus medinensis. PLoS NTD.
• Olson PD, Tracey A, Bailie A, James K, Rodgers FH, DOYLE SR, Buddenborg S, Holroyd N, Berriman M. (2020) Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection. BMC Biology.

2019

• Parisi K, DOYLE SR, Lee E, Lowe R, Weerden NVD, Anderson M, Bleackley M. (2019) Screening the Saccharomyces cerevisiae non-essential gene deletion library reveals diverse mechanisms of action for antifungal plant defensins. Antimicrobial Agents and Chemotherapy.
• Sallé G, DOYLE SR, Cortet J, Cabaret J, Berriman M, Holroyd N, Cotton JA (2019) The global diversity of Haemonchus contortus is shaped by human intervention and climate. Nature Communications. Nat Micro Blog
• Rezansoff AM, Laing R, Martinelli A, Redman E, Bartley D, Holroyd N, Devaney E, DOYLE SR, Sargison ND, Cotton JA, Gilleard JS. (2019) The confounding effects of high genetic diversity on the determination and interpretation of differential gene expression analysis in the parasitic nematode Haemonchus contortus. Int. J Parasitol
• DOYLE SR, Sankaranarayan G, Allan F, Berger D, Castro PDJ, Collins JB, Crellen T, Duque-Correa MA, Ellis P, Jaleta TG, Laing R, Maitland K, McCarthy C, Moundai T, Softley B, Thiele E, Ouakou PT, Tushabe JV, Webster JP, Weiss AJ, Lok J, Devaney E, Kaplan RM, Cotton JA, Berriman M, Holroyd N. (2019) Evaluation of DNA extraction methods on individual helminth egg and larval stages for whole genome sequencing. Frontiers in Genetics.
• Hodgkinson JE, Kaplan RM, Kenyon F, Morgan ER, Park AW, Paterson S, Babayan SA, Beesley NJ, Britton C, Chaudray U, DOYLE SR, Ezenwa VO, Fenton A, Howell SB, Laing R, Mable BK, Matthews L, McIntyre J, Milne CE, Morrison TA, Prentice JC, Sargison ND, Williams DJL, Wolstenholme AJ, Devaney E. (2019) Refugia and anthelmintic resistance: concepts and challenges. Int. J Parasitol-DDR.
• DOYLE SR, Cotton JA. (2019) Genome-wide approaches to investigate anthelmintic resistance. Trends in Parasitology
• DOYLE SR, Illingworth CJR, Laing R, Bartley DJ, Redman E, Martinelli A, Holroyd N, Morrison AA, Rezansoff A, Tracey A, Devaney E, Berriman M, Sargison N, Cotton JA, Gilleard JS. (2019) Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus. BMC Genomics.
• Amor MD, DOYLE SR, Norman MD, Roura A, Hall NE, Robinson AJ, Leite TS, Strugnell JM. (2019) Genome-wide sequencing uncovers cryptic diversity and mito-nuclear discordance in the Octopus vulgaris species complex. BioRxiv

2018

• Armoo S, DOYLE SR, Hedtke SM, Adjami GA, Boakye DA, Kuesel AC, Osei-Atwnenboana MY, Grant WN. (2018) Reduced variation in Wolbachia density of larval stages in comparison with adults of Onchocerca volvulus: implications for clinical outcome of infection? BioRxiv.
• International Helminth Genomes Consortium. (2018) Comparative genomics of the major parasitic worms. Nature Genetics.
• Woodings LN, Murphy NP, DOYLE SR, Hall N, Robinson A, Liggins, G, Green BS, Strugnell JM. (2018) Outlier SNPs detect weak regional structure against a background of genetic homogeneity in the Eastern Rock Lobster, Sagmariasus verreauxi. Marine Biology.
• Kanzaki N, Tsai IJ, Tanaka R, Hunt VL, Tsuyama K, Liu D, Maeda Y, Woodruff G, Namai S, Kumagai R, Tracey A, Holroyd N, DOYLE SR, Murase K, Kitazume H, Billah MM, Ke HM, Wang J, Berriman M, Sternberg P, Sugimoto A, Kikuchi T. (2018) Biology and genome of a newly discovered sibling species of Caenorhabditis elegans. Nature Communications.
• DOYLE SR, Laing R, Bartley DJ, Britton C, Chaudhry U, Gilleard JS, Holroyd N, Mable BK, Maitland K, Morrison AA, Tait A, Tracey A, Berriman M, Devaney E, Cotton JA, Sargison ND. (2018) A genome resequencing-based genetic map reveals the recombination landscape of an outbred parasitic nematode in the presence of polyploidy and polyandry. Genome Biology and Evolution.

2017

• DOYLE SR, Bourguinat C, Nana-Djeunga HC, Kengne-Ouafo JA, Pion SDS, Bopda J, Kamgno J, Wanji S, Che H, Kuesel AC, Walker M, Basanez M-G, Boakye DA, Osei-Atweneboana MY, Boussinesq M, Prichard RK, Grant WN. (2017) Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals genetic drift and soft selective sweeps contribute to loss of drug sensitivity. PLoS NTD.
• Juma AR, Sahota A, Grommen SVH, O’Connor AE, Merriner DJ, Hu J, Hall NE, DOYLE SR, Damdimopoulos AE, Damdimopoulou PE, Barriga D, Hart AH, Van De Ven WJM, O’Bryan MK, De Groef B. (2017) PLAG1 deficiency impairs spermatogenesis in mice. Scientific Reports.
• Choi YJ, Bisset SA, DOYLE SR, Hallsworth-Pepin K, Martin J, Grant WN, Mitreva M. (2017) Genomic introgression mapping of field-derived multiple-anthelmintic resistance in the nematode parasite Teladorsagia circumcincta. PLoS Genet.
• Roura A, DOYLE SR, Nande M, Strugnell JS. (2017) You are what you eat: a genomic analysis of the gut microbiome of captive and wild Octopus vulgaris paralarvae and their zooplankton prey. Front. Physiol.
• Armoo SK, DOYLE SR, Osei-Atweneboana MY, Grant WN. (2017). Significant heterogeneity in Wolbachia copy number within and between populations of Onchocerca volvulus. Parasites and Vectors.

2016

• Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, DOYLE SR, Dunn M, Dunning Hotopp JC, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, Ribeiro J, Rogers MB, Stanley E, Swapna LS, Tsai IJ, Unnasch T, Voronin D, Parkinson J, Nutman TB, Ghedin E, Berriman M, Lustigman S. (2016) The genome of Onchocerca volvulus, the agent of River Blindness. Nature Microbiology.
• Villacorta-Rath C, Ilyushkina I, Strugnell JM, Green BS, Murphy NP, DOYLE SR, Hall NE, Robinson AJ, Bell, JJ. (2016) Outlier SNPs enable food traceability of the southern rock lobster, Jasus edwardsii. Marine Biology.
• DOYLE SR, Armoo S, Osei-Atweneboana MY, Renz A, Grant WN. (2016) 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. Parasites & Vectors.
• Mehta B, Daniel R, Phillips C, DOYLE SR, Elvidge G, Mcnevin D. (2016) Massively parallel sequencing of customised forensically informative SNP panels on the MiSeq. Electophoresis.
• Dyson ZA, Brown TL, Farrar B, DOYLE SR, Tucci J, Seviour RJ, Petrovski S, (2016). Locating and activating molecular ‘time bombs’: Induction of Mycolata prophages. PLoS One.
• Wong NC, Pope BJ, Candiloro I, Korbie D., Trau M, Wong SQ, Mikeska T, Van Denderen BJW, Thompson EW, Eggers S, DOYLE SR, Dobrovic A. (2016) MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing. BMC Bioinformatics.

2015

• Wong NC, Pope BJ, Candiloro I, Korbie D, Trau M, Wong SQ, Mikeska T, Van Denderen BJW, Thompson EW, Eggers S, DOYLE SR, Dobrovic A (2015) Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat. GigaScience.
• DOYLE SR, Griffiths IS, Murphy NP, Strugnell JM (2015) Low-coverage MiSeq next generation sequencing reveals the mitochondrial genome of the Eastern Rock Lobster, Sagmariasus verreauxi. Mitochondrial DNA.

2013

• DOYLE SR, Kasinadhuni NRP, Chan CK, Grant WN (2013) Evidence of evolutionary constraints on the sequence composition of mitochondrial matrix targeting sequences. PLoS One.

2011

• DOYLE SR, Chan CK, and Grant WN (2011) Enhanced annealing of mismatched oligonucleotides using a novel melting curve assay allows efficient in vitro discrimination and restriction of a single nucleotide polymorphism. BMC Biotechnology.
• Chan CK, Hart AH, Lister AN, DOYLE SR (2011) [Learning styles of 3rd year genetics students and their affection and perception of effectiveness of a range of instructional modes]. ACSME Proceedings 2011 Teaching for Diversity Challenges and Strategies.

2008

• DOYLE SR and Chan CK (2008) Mitochondrial gene therapy an evaluation of strategies for the treatment of mitochondrial DNA disorders. Hum Gene Ther. Figure 2 was selected as the cover artwork for the print issue.

2007

• DOYLE SR and Chan CK, (2007). Differential intracellular distribution of DNA complexed with polyethylenimine PEI and PEI-polyarginine PTD influences exogenous gene expression within live COS-7 cells. Genet Vaccines Ther.

Research Support

Total: ~£5.5 M GBP

2023

• EDCTP . Role: Co-Investigator. Amount: €3,553,000 (€369,000 to SRD/WSI).
  Title: “STOP 2030: Towards the interruption of transmission of soil-transmitted helminths: Promoting implementation of research results of a fixed-dose combination of co-formulated ivermectin and albendazole”.
• Sanger Excellence Fellowship. To support postdoctoral fellow, Mona Suleiman, for 3 yrs. Role: Principal Investigator.
  Title: “Experimental evolution in the parasitic worm Strongyloides to map ivermectin drug resistance in the lab and field”

2020

• UKRI Future Leaders Fellowship. Role: Principal Investigator. Amount: £1.3 M GBP / 4 yrs
  Title: “The generation and maintenance of genetic novelty in parasitic helminths”.

2014

• WHO/TDR Research on the Vulnerability of Preventative Chemotherapy of Helminth Infections to Emergence of Drug Resistance (three proposals; Grant and Doyle in collaboration with Osei-Atweneboana, M (Ghana), and Adjami, A (Burkina Faso)). Role: Co-Investigator.
  • CARIRS-markers: “Development of diagnostic genetic markers to detect sub-optimal response to ivermectin treatment” (Amount: $438,000 USD; Doyle lead writer)
  • CARIRS-mission: “Developing molecular tools to define Onchocerca volvulus transmission zones and estimate transmission risks between zones” (Amount: $224,000 USD)
  • TDResist: “A population genetic model for the selection and transmission of ivermectin sub-optimal response genotypes” (Amount: $87,000 USD)
• Burroughs Wellcome Collaborative Research Travel Award. Role: Principal Investigator. Amount: $3,350 AUD
• La Trobe University Understanding Disease RFA Grant. Role: Co-Investigator. Amount: $28,399 AUD
  Title: “Genetic tools to define epidemiological endpoints for onchocerciasis elimination in sub-Saharan Africa”.

2013

• Bill and Melinda Gates Grand Challenges, Explorations. Role: Co-Investigator. Amount: $100,000 USD
  Title: “A small animal model to bridge the gap between in vitro assay and human testing for drug development in onchocerciasis”
• La Trobe University Securing Food, Water and the Environment RFA grant. Role: Co-Investgator. Amount: $81,500 AUD
  Title: “Biodiversity and the evolution of host range of Cercopithfilaria spp., filarial parasites of small native mammals”
• WHO/TDR Research Capacity Strengthening and Knowledge Management Grant. Role: Co-Investgator. Amount: $50,000 USD
  Title: “Transfer of high resolution melt genotyping technology form Australia to Ghana, Cameroon and the WHO/Multi-disease Surveillance Center”.

2012

• Illumina MiSeq Grant. Role: Principal Investigator. Amount: $230,000 AUD
  “Investigating drug resistance in the nematode Onchocerca volvulus using a genotype-by-sequencing method”

2011

• La Trobe University eResearch Grant. Role: Co-Investigator. Amount: $50,000 AUD
  “Establishment of an analysis pipeline for next generation sequencing (NGS) data”
• La Trobe University Faculty Early Career Research Grant. Role: Principal Investigator. Amount: $3,500 AUD
  Doyle, SR: “Recombination-mediated stable transgenesis of Caenorhabditis elegans”

Mentorship (current lab, direct/indirect mentorship)

Current lab

Postdoctoral Research Associates
Sarah Buddenborg (2022-current)
Mona Suleiman (2023-current) (Sanger Excellence Fellow)
Javier Gandasegui (2024-current)

PhD candidates - direct supervision/mentorship
Marina Papaiakovou, Univerisity of Cambridge (co-supervisor with Cinzia Cantacessi) - (2022-2025)
Benedict Karani, University of Glasgow (co-supervisor with James Cotton, Roz Laing, Jennifer McIntyre, Fiona Kenyon) - (2023-2027)

Other - indirect supervision/mentorship
Jennifer McIntyre (Postdoctoral Research Associate, University of Glasgow) (2020-ongoing)
Shannan Summers (PhD candidate, London School of Hygeine and Tropical Medicine / Natural History Museum, London) - (2023-ongoing)
Rose Powers (PhD candidate, University of Sydney, Australia) (2023-ongoing)

Previous mentorship

PhD candidates - indirect supervision
Duncan Berger (Wellcome Sanger Institute)
Julia Rivero (Universidad de Sevilla, Spain) (2022) - 3 month stay at Sanger
Kirsty McCann (La Trobe Univerisity, Australia) (2015-2021)
Neha Sirwani (La Trobe University) (2013-2020)
Sam Armoo (La Trobe University, Australia) (2012-2017)

Masters candidates
Javier Gandasegui (Cardiff Univerity) (2021) - Master’s thesis summer project

Presentations

Departmental/Invited Talks

2024

• 24th Drug Design & Development Seminar (DDDS), Würzburg, Germany
• Moredun Research Institute, Edinburgh, UK
• University of Bath, Bath, UK
• Natural History Museum, London, UK
• French National Institute for Agriculture, Food, and Environment (INRAE), Toulouse, France
• Simposio internacional de Genómica, Peru (online)

2023

• ZAPworms, USA (virtual)
• NTD Day, York Biomedical Institute, UK
• Nematode Functional Genomics meeting, University of Glasgow, UK

2022

• British Association for Veterinary Parasitology (virtual)
• Molecular Helminthology: An Integrated Approach

2021

• Helminth Bioinformatics, Accra, Ghana (virtual)
• Berlin Parasitology Seminar series (virtual)
• Barcelona Institute for Global Health (virtual)

2020

• Department of Infectious Diseases, University of Georgia, USA (virtual)
• Host-Parasite Interactions Seminar Series, University of Calgary, Canada (virtual)

2019

• London School of Hygiene & Tropical Medicine, London, UK
• Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Scotland, UK
• Consortium for Anthelmintic and Susceptibility (CARS), Madison, USA

2018

• Genetic diversity of NTD Pathogens, Natural History Museum, London, UK

2017

• Innovative tools for NTD research: Exploiting genomics, RVC, London, UK.
• DIDE Seminar Series, Imperial College London, UK
• La Trobe University, Melbourne, Australia

2012

• Institute of Parasitology, McGill University, Montreal, Canada

2011

• Thomson Reuters System Biology Seminar Series Winter 2011, La Trobe University
• VLSCI NGS Informatics Retreat, Brighton, Australia

Conference talks / posters

2024

• UK Strongyloides Meeting, Bath, UK (talk)

2023

• Parasitic Helminths: New Perspectives in Biology and Infection, Hydra, Greece (talk)

2022

• British Association for Veterinary Parasitology (Invited Panel Member for ECR Careers session)

2021

• Molecular Helminthology: An Integrated Approach (Invited plenary speaker)
• World Association for the Advancement of Veterinary Parasitology (WAAVP) (talk)
• 5th Parasitic Nematode Workshop: Bridging the Divide (Invited plenary speaker) (virtual)

2019

• World Association for the Advancement of Veterinary Parasitology (WAAVP), Madison, USA (talk & poster)

2018

• Ecology, Evolution and Genomics of C. elegans and other Nematodes. Wellcome Sanger Institute, Cambridgeshire, UK.
• Meiosis and Beyond workshop, Earlham Institute, Norwich, UK (talk)

2017

• British Society for Parasitology, Dundee, Scotland.

2016

• INRA Parasitology Conference. Tours, France (Invited keynote speaker)
• British Society for Parasitology, Imperial College London, UK (poster)

2014

• Anthelmintics: From Discovery to Resistance: San Francisco, USA (talk & poster)
• Australian Society for Parasitology Conference, Canberra, Australia (talk)
• Molecular and Cellular Biology of Helminth Parasites VIII, Hydra, Greece (talk)

2012

• Australian Society for Parasitology Conference, Tasmania, Australia (talk & poster)
• Genetics Society of AustralAsia, Melbourne, Australia (poster)

2009

• 6th Annual Australian QPCR Meeting; Melbourne, Australia

2008

• 4th Australasian Gene Therapy Society Meeting, Melbourne, Australia

Outreach / media

2024

• Promotional - Bringing innovation to intestinal worm treatment - STOP2030 project

2022

• Promotional - Resistance genes mapped for drugs to treat parasitic worms
• Promotional - First genetic map of one of humans oldest parasites

2021

• Podcast - Two Brad for You - In Conversation 21 - Sharing Genomes and More with Stephen Doyle
• Promotional - Meet some of our Postdocs working at Wellcome Sanger Institute

2020

• Promotional - Puzzles and Parasites
• Promotional - Sanger researcher backed through flagship fellowship

Professional Associations and Contributions

Associate Editor

2023 - ongoing

• International Journal for Parasitology

2021 - 2023

• Parasites and Vectors (Parasite genetics, genomics and proteomics section)

Review Editor

2021 - ongoing

• Editorial Board of Neglected Tropical Diseases (speciality section of Frontiers in Tropical Diseases)

Journal Referee

Bioinformatics, Bioinformatics Advances, BMC Biotechnology, Frontiers Tropical Diseases, Genes, Genome Biology and Evolution, Genomics, GigaScience, International Journal of Parasitology, International Journal of Parasitology Drugs and Drug Resistance, Mitochondrial DNA Part B: Resources, Molecular Ecology Resources, Nature Communications, Nucleic Acid Research, Parasitology International, Parasites & Vectors, Parasitology Research, Pathogens, PLoS Neglected Tropical Diseases, PLoS One, PLoS Pathogens, Scientific Reports, Trends in Parasitology.

Grant Referee

Isaac Newton Trust, ZonMw (The Netherlands organisation for health research and development), BBSRC, NERC, MRC, UKRI

PhD thesis Referee

2024

• University of Liverpool, UK

2023

• University of Calgary, Canada
• James Cook University, Australia

Teaching Experience

Undergraduate

Practical Demonstrator: supervising groups of 16-25 students, direct face-to-face contact

Head Practical Demonstrator: delivery of pre-lab lectures and tutorials, supervision of 80-150 students and management of sessional demonstrators

Practical design/writing: development of new, and, updating of existing practical material, redevelopment of practical manuals and assessment guidelines.

3rd year Genetics Practical Unit Coordination: administration the 3rd year practical course, supervising up to 80 students, delivery of practical material including lectures and tutorials.

Postgraduate

Course Lead Instructor, High-Resolution Melt Genotyping and Populations Genetics for NTDs, Noguchi Memorial Institute for Medical Research, Accra, Ghana (2014)

Course Instructor, Working with Pathogen Genomes, Wellcome Trust Advanced Courses: Hinxton (Jan 2016), Ho Chi Minh City, Vietnam (November 2017), Cape Town, South Africa (2018), Montevideo, Uruguay (2018; lead instructor), Hinxton, UK (2019), Asia (online 2021), Latin America (online 2022).

Course Instructor, Helminth Bioinformatics, Wellcome Trust Advanced Courses: Accra, Ghana (2019), Asia (online 2021; lead instructor), Thailand (2023; lead instructor)

Course Instructor, Pathogen Genomics MSc, The London School of Hygiene & Tropical Medicine, London, UK: April/May 2018, 2019, April 2020, 2021 (remote online teaching), April 2022, 2023.