Dr Rhys Farrer
Senior Lecturer
R.Farrer@exeter.ac.uk
Geoffrey Pope 325
Geoffrey Pope Building, University of Exeter , Stocker Road, Exeter, EX4 4QD, UK
Overview
My research uses several sequencing technologies to study the patterns of genomic, transcriptomic, and gene-regulatory variation between and within populations of microbial pathogens.
I am a Senior Lecturer in Bioinformatics and my current projects focus on the evolution of virulence across several fungal genera with a particular focus on Candida, Cryptococcus and Chytridiomycota species.
I received my PhD in Clinical Medicine in 2013 from Imperial College London. Between 2013-2017, I worked at the Broad Institute of MIT and Harvard as a Wellcome Trust Postdoctoral Fellow. In 2018 I worked at UCL in London before joining the MRC Center for Medical Mycology at first the University of Aberdeen and then the University of Exeter in August 2019.
Qualifications
2012 Ph.D. Clinical Medicine, Imperial College, London, UK
2008 M.Sc. Bioinformatics (Distinction), University of East Anglia, Norwich, UK
2007 B.Sc. (Hons) Cellular Biology, University of East Anglia, Norwich, UK
Research group links
Research
Research interests
My research uses high-throughput/next generation sequencing technologies to study the patterns of genomic, transcriptomic, and gene-regulatory variation between and within populations of microbial pathogens. I received my PhD in Clinical Medicine in 2013 from Imperial College London. Between 2013-2017, I worked at the Broad Institute of Harvard and MIT as a Wellcome Trust Postdoctoral Fellow. In 2018 I worked at UCL in London before more recently joining the University of Aberdeen as a Lecturer in Bioinformatics. My current projects include studying the evolution of virulence in various human pathogens, including Cryptococcus gattii.
Research grants
- 2022 National Centre for the Replacement Refinement
Establishment of the thermotolerant Arabian killifish as a model for infection studies - 2022 Wellcome Trust
Mechanistic insights into fungal pathogenicity and drug resistance using a novel lineage of Cryptococcus - 2018 Wellcome Trust
The genetics and epigenetics underpinning a broad spectrum of human fungal pathogens
Publications
Journal articles
Webster VL, Hemmings S, Pérez M, Fisher MC, Brown MJF, Farrer RA (2024). Revealing the genome of the microsporidian <i>Vairimorpha bombi</i>, a potential driver of bumble bee declines in North America. G3: Genes, Genomes, Genetics, 14(4). Abstract.
Li X, Muñoz JF, Gade L, Argimon S, Bougnoux M-E, Bowers JR, Chow NA, Cuesta I, Farrer RA, Maufrais C, et al (2023). Comparing genomic variant identification protocols for Candida auris. Microb Genom, 9(4). Abstract. Author URL.
Malavia-Jones D, Farrer RA, Stappers MHT, Edmondson MB, Borman AM, Johnson EM, Lipke PN, Gow NAR (2023). Strain and temperature dependent aggregation of Candida auris is attenuated by inhibition of surface amyloid proteins. The Cell Surface, 10, 100110-100110.
Wacker T, Helmstetter N, Wilson D, Fisher MC, Studholme DJ, Farrer RA (2023). Two-speed genome evolution drives pathogenicity in fungal pathogens of animals. Proceedings of the National Academy of Sciences, 120(2). Abstract.
Wacker T, Helmstetter N, Wilson D, Fisher MC, Studholme DJ, Farrer RA (2023). Two-speed genome evolution drives pathogenicity in fungal pathogens of animals (vol 120, e2212633120, 2023). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 120(28). Author URL.
Helmstetter N, Chybowska AD, Delaney C, Da Silva Dantas A, Gifford H, Wacker T, Munro C, Warris A, Jones B, Cuomo CA, et al (2022). Population genetics and microevolution of clinical Candida glabrata reveals recombinant sequence types and hyper-variation within mitochondrial genomes, virulence genes, and drug targets. Genetics, 221(1). Abstract. Author URL.
Chen H, Yin Y, van Dorp L, Shaw LP, Gao H, Acman M, Yuan J, Chen F, Sun S, Wang X, et al (2021). Drivers of methicillin-resistant Staphylococcus aureus (MRSA) lineage replacement in China. Genome Med, 13(1). Abstract. Author URL.
Farrer RA, Borman AM, Inkster T, Fisher MC, Johnson EM, Cuomo CA (2021). Genomic epidemiology of a Cryptococcus neoformans case cluster in Glasgow, Scotland, 2018. Microbial Genomics, 7(3). Abstract.
Farrer RA (2021). HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes. BMC Bioinformatics, 22(1). Abstract.
Chybowska AD, Childers DS, Farrer RA (2020). Nine Things Genomics can Tell Us About Candida auris. Frontiers in Genetics, 11 Abstract.
Farrer RA, Chang M, Davis MJ, van Dorp L, Yang D-H, Shea T, Sewell TR, Meyer W, Balloux F, Edwards HM, et al (2019). A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands. mBio, 10(6). Abstract.
Farrer RA (2019). Batrachochytrium salamandrivorans. Trends in Microbiology, 27(10), 892-893.
Ratti MF, Farrer RA, Cano LM, Faedda R, Goss EM (2019). Evaluation of High-Resolution Melting for Rapid Differentiation of <i>Phytophthora</i> Hybrids and Their Parental Species. PLANT DISEASE, 103(9), 2295-2304. Author URL.
van Dorp L, Wang Q, Shaw LP, Acman M, Brynildsrud OB, Eldholm V, Wang R, Gao H, Yin Y, Chen H, et al (2019). Rapid phenotypic evolution in multidrug-resistant <i>Klebsiella pneumoniae</i> hospital outbreak strains. MICROBIAL GENOMICS, 5(4). Author URL.
Fisher MC, Ghosh P, Shelton JMG, Bates K, Brookes L, Wierzbicki C, Rosa GM, Farrer RA, Aanensen DM, Alvarado-Rybak M, et al (2018). Development and worldwide use of a non-lethal and minimal population-level impact protocols for the isolation of chytrids from amphibians. Abstract.
Fisher MC, Ghosh P, Shelton JMG, Bates K, Brookes L, Wierzbicki C, Rosa GM, Farrer RA, Aanensen DM, Alvarado-Rybak M, et al (2018). Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi. SCIENTIFIC REPORTS, 8 Author URL.
Muñoz JF, Gade L, Chow NA, Loparev VN, Juieng P, Berkow EL, Farrer RA, Litvintseva AP, Cuomo CA (2018). Genomic basis of multidrug-resistance, mating, and virulence in<i>Candida auris</i>and related emerging species. Abstract.
Rhodes J, Abdolrasouli A, Farrer RA, Cuomo CA, Aanensen DM, Armstrong-James D, Fisher MC, Schelenz S (2018). Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen <i>Candida auris</i>. EMERGING MICROBES & INFECTIONS, 7 Author URL.
Rhodes J, Abdolrasouli A, Farrer RA, Cuomo CA, Aanensen DM, Armstrong-James D, Fisher MC, Schelenz S (2018). Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen <i>Candida auris</i> (vol 7, pg 43, 2018). EMERGING MICROBES & INFECTIONS, 7 Author URL.
Muñoz JF, Gade L, Chow NA, Loparev VN, Juieng P, Berkow EL, Farrer RA, Litvintseva AP, Cuomo CA (2018). Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species. Nat Commun, 9(1). Abstract. Author URL.
Ene LV, Farrer RA, Hirakawa MP, Agwamba K, Cuomo CA, Bennett RJ (2018). Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 115(37), E8688-E8697. Author URL.
Nash A, Sewell T, Farrer RA, Abdolrasouli A, Shelton JMG, Fisher MC, Rhodes J (2018). MARDy: Mycology Antifungal Resistance Database. BIOINFORMATICS, 34(18), 3233-3234. Author URL.
O'Hanlon SJ, Rieux A, Farrer RA, Rosa GM, Waldman B, Bataille A, Kosch TA, Murray KA, Brankovics B, Fumagalli M, et al (2018). Recent Asian origin of chytrid fungi causing global amphibian declines. Science, 360(6389), 621-627. Abstract. Author URL.
Farrer RA, Ford CB, Rhodes J, Delorey T, May RC, Fisher MC, Cloutman-Green E, Balloux F, Cuomo CA (2018). Transcriptional Heterogeneity of Cryptococcus gattii VGII Compared with Non-VGII Lineages Underpins Key Pathogenicity Pathways. mSphere, 3(5). Abstract. Author URL.
Farrer RA, Ford CB, Rhodes J, Delorey T, May RC, Fisher MC, Cloutman-Green E, Balloux F, Cuomo CA (2018). Transcriptional heterogeneity of<i>Cryptococcus gattii</i>VGII compared with non-VGII lineages underpins key pathogenicity pathways. Abstract.
Farrer RA, Martel A, Verbrugghe E, Abouelleil A, Ducatelle R, Longcore JE, James TY, Pasmans F, Fisher MC, Cuomo CA, et al (2017). Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi. Nat Commun, 8 Abstract. Author URL.
Chen Y, Farrer RA, Giamberardino C, Sakthikumar S, Jones A, Yang T, Tenor JL, Wagih O, Van Wyk M, Govender NP, et al (2017). Microevolution of Serial Clinical Isolates of <i>Cryptococcus neoformans</i> var. <i>grubii</i> and <i>C</i>. <i>gattii</i>. MBIO, 8(2). Author URL.
Farrer RA (2017). Synima: a Synteny imaging tool for annotated genome assemblies. BMC Bioinformatics, 18(1). Abstract. Author URL.
Issi L, Farrer RA, Pastor K, Landry B, Delorey T, Bell GW, Thompson DA, Cuomo CA, Rao RP (2017). Zinc Cluster Transcription Factors Alter Virulence in <i>Candida albicans</i>. GENETICS, 205(2), 559-576. Author URL.
Schmidt SM, Lukasiewicz J, Farrer R, van Dam P, Bertoldo C, Rep M (2016). Comparative genomics of <i>Fusarium oxysporum</i> f. sp <i>melonis</i> reveals the secreted protein recognized by the <i>Fom</i>-<i>2</i> resistance gene in melon. NEW PHYTOLOGIST, 209(1), 307-318. Author URL.
Muñoz JF, Farrer RA, Desjardins CA, Gallo JE, Sykes S, Sakthikumar S, Misas E, Whiston EA, Bagagli E, Soares CMA, et al (2016). Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides. mSphere, 1(5). Abstract. Author URL.
Leach MD, Farrer RA, Tan K, Miao Z, Walker LA, Cuomo CA, Wheeler RT, Brown AJP, Wong KH, Cowen LE, et al (2016). Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans. Nature Communications, 7 Abstract.
Farrer RA, Voelz K, Henk DA, Johnston SA, Fisher MC, May RC, Cuomo CA (2016). Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii. Philos Trans R Soc Lond B Biol Sci, 371(1709). Abstract. Author URL.
Farrer RA, Desjardins CA, Sakthikumar S, Gujja S, Saif S, Zeng Q, Chen Y, Voelz K, Heitman J, May RC, et al (2015). Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii. mBio, 6(5), e00868-e00815. Abstract. Author URL.
Martel A, Blooi M, Adriaensen C, Van Rooij P, Beukema W, Fisher MC, Farrer RA, Schmidt BR, Tobler U, Goka K, et al (2014). Recent introduction of a chytrid fungus endangers Western Palearctic salamanders. SCIENCE, 346(6209), 630-631. Author URL.
Farrer RA, Henk DA, Garner TWJ, Balloux F, Woodhams DC, Fisher MC (2013). Chromosomal Copy Number Variation, Selection and Uneven Rates of Recombination Reveal Cryptic Genome Diversity Linked to Pathogenicity. PLOS GENETICS, 9(8). Author URL.
Voelz K, Ma H, Phadke S, Byrnes EJ, Zhu P, Mueller O, Farrer RA, Henk DA, Lewit Y, Hsueh Y-P, et al (2013). Transmission of Hypervirulence Traits via Sexual Reproduction within and between Lineages of the Human Fungal Pathogen <i>Cryptococcus gattii</i>. PLOS GENETICS, 9(9). Author URL.
Farrer RA, Henk DA, MacLean D, Studholme DJ, Fisher MC (2013). Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects. Sci Rep, 3 Abstract. Author URL.
Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al (2012). Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen. PLOS PATHOGENS, 8(10). Author URL.
Farrer RA, Weinert LA, Bielby J, Garner TWJ, Balloux F, Clare F, Bosch J, Cunningham AA, Weldon C, du Preez LH, et al (2011). Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108(46), 18732-18736. Author URL.
Fisher MC, Farrer RA (2011). Outbreaks and the emergence of novel fungal infections: Lessons from the panzootic of amphibian chytridiomycosis. Journal of Invasive Fungal Infections, 5(3), 73-81. Abstract.
Raffaele S, Farrer RA, Cano LM, Studholme DJ, MacLean D, Thines M, Jiang RHY, Zody MC, Kunjeti SG, Donofrio NM, et al (2010). Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science, 330(6010), 1540-1543. Abstract. Author URL.
Farrer RA, Kemen E, Jones JDG, Studholme DJ (2009). De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol Lett, 291(1), 103-111. Abstract. Author URL.
Schornack S, Huitema E, Cano LM, Bozkurt TO, Oliva R, van Damme M, Schwizer S, Raffaele S, Chaparro-Garcia A, Farrer R, et al (2009). Ten things to know about oomycete effectors. MOLECULAR PLANT PATHOLOGY, 10(6), 795-803. Author URL.
Chapters
Coelho C, Farrer RA (2020). Pathogen and host genetics underpinning cryptococcal disease. In (Ed) Advances in Genetics, 1-66. Abstract.
Farrer RA, Fisher MC (2017). Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens. In (Ed) FUNGAL PHYLOGENETICS AND PHYLOGENOMICS, 73-140. Author URL.
Fisher MC, Stajich JE, Farrer RA (2013). Emergence of the Chytrid Fungus Batrachochytrium Dendrobatidis and Global Amphibian Declines. In (Ed) Evolution of Virulence in Eukaryotic Microbes, Wiley, 461-472.
Supervision / Group
Postdoctoral researchers
- Qinxi Ma
- Diana Tamayo
