Imperial College London


Faculty of MedicineSchool of Public Health

Honorary Lecturer







Norfolk PlaceSt Mary's Campus





The development of high-throughput/next-generation sequencing technologies has provided an unprecedented opportunity to study the evolution and molecular epidemiology of eukaryotic pathogens. My research uses these technologies to describe and characterize new patterns of genomic, transcriptomic and epigenomic variation between and within populations of microbial pathogens and to link these to disease processes. I aim to continue to develop new approaches to study the evolution of infectious diseases with the goal of identifying new phenotypic determinants, and ultimately alleviating disease.


Farrer RA, Martel A, Verbrugghe E, Abouelleil A, Ducatelle R, Longcore JE,  James  TY,  Pasmans  F,  Fisher  MC,  Cuomo  CA.  Evolutionary innovations underpin niche-specific infection strategies across emerging pathogenic fungi. Nat. Commun. 8:14742 (2017)

Chen Y, Farrer RA, Giamberardino C, Sakthikumar S, Jones A, Yang T, Tenor J, Wagih O, Van Wyk M, Govender NP, Mitchell TG, Litvintseva AP, Cuomo  CA, Perfect JR. Microevolution of Serial  Clinical  Isolates  of Cryptococcus neoformans var. grubii and C. gattii. mBio 8(2):e00166-17 (2017).

Issi L, Farrer RA, Pastor K, Landry B, Delorey T, Bell G, Cuomo CA, Thompson D, Rao R. Members of the Zinc Cluster Factor family mediate pathogenicity in Candida albicans. Genetics 205:559-576 (2017).

Farrer RA, Voelz K, Henk DA, Johnston SA, Larner H, Fisher MC, May RC, Cuomo CA. Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii. Phil. Trans. R. Soc. B. 371(1709):20160021 (2016).

Muñoz JF, Farrer RA, Desjardins CA, Gallo JE, Sykes S, Sakthikumar S, Misas E, Whiston EA, Bagagli E, Soarez CM, Teixeira MDM, Taylor JW, McEwen JG, Clay OK, Cuomo CA. Genome diversity, recombination and virulence between the major lineages of Paracoccidioides. mSphere 1(5):e00213-16 (2016).

Leach MD, Farrer RA, Tan K, Miao Z, Walker LA, Cuomo CA, Wheeler RT, Brown  AJP, Wong KH, Cowen LE. Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans. Nat. Commun. 7:11704 (2016).

Farrer RA, Desjardins CA, Sakthikumar S, Gujja S, Saif S, Zeng Q, Chen Y, Voelz K, Heitman J, May RC, Fisher MC, Cuomo CA. Genome evolution and innovation across the four major lineages of Cryptococcus gattii. mBIO 6(5):e00868-15 (2015).

Schmidt SM, Lukasiewicz J, Farrer RA, Dam PV, Bertoldo C, Rep M. Comparative genomics of Fusarium oxysporum f.sp. melonis reveals the secreted protein recognized by the Fom-2 resistance gene in melon. New Phytol. 209(1):307-18 (2015).

Martel A, Blooi M, Adriaensen C, Van Rooij P, Beukema W, Fisher MC, Farrer RA, Schmidt BR, Tobler U, Goka K, Lips KR, Muletz C, Zamudio KR, Bosch J, Lötters S, Wombwell E, Garner TW, Cunningham AA, Spitzen-van der Sluijs A, Salvidio S, Ducatelle R, Nishikawa K, Nguyen TT, Kolby JE, Van Bocxlaer I, Bossuyt F, Pasmans F. Recent introduction of a chytrid fungus endangers Western Palearctic salamanders. Science 346(6209):630-631 (2014).

Voelz K, Ma H, Phadke S, Byrnes EJ, Zhu P, Mueller O, Farrer RA, Henk DA, Lewit Y, Hsueh YP, Fisher MC, Idnurm A, Heitman J, May RC. Transmission of hypervirulence traits via sexual reproduction within and between lineages of the human fungal pathogen Cryptococcus gattii. PLoS Genet. 9(9):e1003771 (2013).

Farrer RA, Henk DA, Garner TWJ, Balloux F, Woodhams DC, Fisher MC. Chromosomal copy number variation, selection and uneven rates of recombination reveal cryptic genome diversity linked to pathogenicity. PLoS Genetics 9(9):e1003771 (2013).

Farrer RA, Henk DA, MacLean D, Studholme DJ, Fisher MC. Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects. Sci Rep. 3:1512 (2013).

Cooke DE, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, Grünwald NJ, Hein I, MacLean D, McNicol JW, Randall E, Oliva RF, Pel MA, Shaw DS, Squires JN, Taylor MC, Vleeshouwers VG, Birch PR, Lees AK, Kamoun S. Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen. PLoS Pathog. 8(10):e1002940 (2012).

Farrer RA, Weinert LA, Bielby J, Garner TW, Balloux F, Clare F, Bosch J, Cunningham AA, Weldon C, du Preez LH, Anderson L, Pond SL, Shahar-Golan R, Henk DA, Fisher MC. Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. Proc. Natl. Acad. Sci. U.S.A. 108(46):18732-6 (2011).

Raffaele S, Farrer RA, Cano LM, Studholme DJ, MacLean D, Thines M, Jiang RH, Zody MC, Kunjeti SG, Donofrio NM, Meyers BC, Nusbaum C, Kamoun S. Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science. 330(6010):1540-3 (2010).

Farrer RA, Kemen E, Jones JD, Studholme DJ. De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol Lett. 291(1):103-11 (2009).


Fisher MC and Farrer RA. Outbreaks and the Emergence of Novel Fungal Infections: Lessons from the Panzootic of Amphibian Chytridiomycosis. J. Invasive Fungal Infect. 5:73-81 (2011).

Schornack S, Huitema E, Cano LM, Bozkurt TO, Oliva R, Van Damme M, Schwizer S, Raffaele S, Chaparro-Garcia A, Farrer R, Segretin ME, Bos J, Haas BJ, Zody MC, Nusbaum C, Win J, Thines M, Kamoun S. Ten things to know about oomycete effectors. Mol Plant Pathol. 10(6):795-803 (2009).

Book chapters

MC Fisher, J Stajich, RA Farrer, Emergence of the chytrid fungus Batrachochytrium dendrobatidis and global amphibian declines in Evolution of Virulence in Eukaryotic Microbes. Eds Heitman J, Sibley D and Howlett B (2012).



Farrer RA, Borman AM, Inkster T, et al., 2021, Genomic epidemiology of a Cryptococcus neoformans case cluster in Glasgow, Scotland, 2018, Microbial Genomics, Vol:7, ISSN:2057-5858

Farrer RA, Chang M, Davis MJ, et al., 2019, A new lineage of cryptococcus gattii (VGV) discovered in the Central Zambezian Miombo Woodlands, Mbio, Vol:10, ISSN:2150-7511, Pages:1-19

Farrer RA, 2019, Batrachochytrium salamandrivorans, Trends in Microbiology, Vol:27, ISSN:0966-842X, Pages:892-893

Ratti MF, Farrer RA, Cano LM, et al., 2019, Evaluation of High-Resolution Melting for Rapid Differentiation of Phytophthora Hybrids and Their Parental Species, Plant Disease, Vol:103, ISSN:0191-2917, Pages:2295-2304

van Dorp L, Wang Q, Shaw LP, et al., 2019, Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains, Microbial Genomics, Vol:5, ISSN:2057-5858

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