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Dr Rhys Farrer

Dr Rhys Farrer

Lecturer

 Geoffrey Pope 325

 

Geoffrey Pope Building, University of Exeter , Stocker Road, Exeter, EX4 4QD, UK

Overview

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 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 as a Lecturer in Bioinformatics. My current projects focus on the evolution of virulence across several fungal genera with a particular focus on Candida, Cryptococcus and several Chytridiomycota species.

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

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.

Publications

Key publications | Publications by category | Publications by year

Publications by category


Journal articles

Fisher MC, Ghosh P, Shelton JMG, Bates K, Brookes L, Wierzbicki C, Rosa GM, Farrer RA, Aanensen DM, Alvarado-Rybak M, et al (In Press). Development and worldwide use of a non-lethal and minimal population-level impact protocols for the isolation of chytrids from amphibians.  Abstract.
Muñoz JF, Gade L, Chow NA, Loparev VN, Juieng P, Berkow EL, Farrer RA, Litvintseva AP, Cuomo CA (In Press). Genomic basis of multidrug-resistance, mating, and virulence in Candida auris and related emerging species.  Abstract.
Leach MD, Farrer RA, Tan K, Miao Z, Walker LA, Cuomo CA, Wheeler RT, Brown AJP, Wong KH, Cowen LE, et al (In Press). Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans. Nature Communications, 7 Abstract.  Full text.
Farrer RA, Ford CB, Rhodes J, Delorey T, May RC, Fisher MC, Cloutman-Green E, Balloux F, Cuomo CA (In Press). Transcriptional heterogeneity of Cryptococcus gattii VGII compared with non-VGII lineages underpins key pathogenicity pathways.  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 Phytophthora Hybrids and Their Parental Species. PLANT DISEASE, 103(9), 2295-2304. Author URL.  Full text.
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 Klebsiella pneumoniae hospital outbreak strains. MICROBIAL GENOMICS, 5(4). Author URL.  Full text.
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.  Full text.
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 Candida auris. EMERGING MICROBES & INFECTIONS, 7 Author URL.  Full text.
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 Candida auris (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.  Full text.
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.  Full text.
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, 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 Cryptococcus neoformans var. grubii and C. gattii. MBIO, 8(2). Author URL.  Full text.
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 Candida albicans. GENETICS, 205(2), 559-576. Author URL.
Schmidt SM, Lukasiewicz J, Farrer R, van Dam P, Bertoldo C, Rep M (2016). Comparative genomics of Fusarium oxysporum f. sp melonis reveals the secreted protein recognized by the Fom-2 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.
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 Cryptococcus gattii. 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.  Full text.
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

Farrer RA, Fisher MC (2017). Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens. In  (Ed) FUNGAL PHYLOGENETICS AND PHYLOGENOMICS, 73-140.  Author URL.

Publications by year


In Press

Fisher MC, Ghosh P, Shelton JMG, Bates K, Brookes L, Wierzbicki C, Rosa GM, Farrer RA, Aanensen DM, Alvarado-Rybak M, et al (In Press). Development and worldwide use of a non-lethal and minimal population-level impact protocols for the isolation of chytrids from amphibians.  Abstract.
Muñoz JF, Gade L, Chow NA, Loparev VN, Juieng P, Berkow EL, Farrer RA, Litvintseva AP, Cuomo CA (In Press). Genomic basis of multidrug-resistance, mating, and virulence in Candida auris and related emerging species.  Abstract.
Leach MD, Farrer RA, Tan K, Miao Z, Walker LA, Cuomo CA, Wheeler RT, Brown AJP, Wong KH, Cowen LE, et al (In Press). Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans. Nature Communications, 7 Abstract.  Full text.
Farrer RA, Ford CB, Rhodes J, Delorey T, May RC, Fisher MC, Cloutman-Green E, Balloux F, Cuomo CA (In Press). Transcriptional heterogeneity of Cryptococcus gattii VGII compared with non-VGII lineages underpins key pathogenicity pathways.  Abstract.

2019

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 Phytophthora Hybrids and Their Parental Species. PLANT DISEASE, 103(9), 2295-2304. Author URL.  Full text.
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 Klebsiella pneumoniae hospital outbreak strains. MICROBIAL GENOMICS, 5(4). Author URL.  Full text.

2018

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.  Full text.
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 Candida auris. EMERGING MICROBES & INFECTIONS, 7 Author URL.  Full text.
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 Candida auris (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.  Full text.
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.  Full text.
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.

2017

Farrer R (2017). Candida auris gene annotations.  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.
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 Cryptococcus neoformans var. grubii and C. gattii. MBIO, 8(2). Author URL.  Full text.
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 Candida albicans. GENETICS, 205(2), 559-576. Author URL.

2016

Schmidt SM, Lukasiewicz J, Farrer R, van Dam P, Bertoldo C, Rep M (2016). Comparative genomics of Fusarium oxysporum f. sp melonis reveals the secreted protein recognized by the Fom-2 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.
Farrer R (2016). Homolaphlyctis polyrhiza Genome FASTA.  Abstract.
Farrer R (2016). Homolaphlyctis polyrhiza annotation CDS FASTA.  Abstract.
Farrer R (2016). Homolaphlyctis polyrhiza annotation GFF3.  Abstract.
Farrer R (2016). Homolaphlyctis polyrhiza annotation peptide FASTA.  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.

2015

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.

2014

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.

2013

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 Cryptococcus gattii. 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.  Full text.

2012

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.

2011

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.

2010

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.

2009

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.

Rhys_Farrer Details from cache as at 2019-11-20 06:03:55

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