• 1413 Citations
20092019
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Research Output 2009 2019

  • 1413 Citations
  • 29 Article
  • 2 Chapter (peer-reviewed)
2019

Batrachochytrium salamandrivorans

Farrer, R. A., 22 May 2019, In : Trends in Microbiology. 2 p.

Research output: Contribution to journalArticle

Evaluation of high resolution melting for rapid differentiation of Phytophthora hybrids and their parental species

Ratti, M. F., Farrer, R. A., Cano, L. M., Faedda, R. & Goss, E., 5 Apr 2019, In : Plant Disease.

Research output: Contribution to journalArticle

Phytophthora
melting
pathogens
wild plants
Solanaceae
3 Downloads (Pure)

Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains

van Dorp, L., Wang, Q., Shaw, L. P., Acman, M., Brynildsrud, O. B., Eldholm, V., Wang, R., Gao, H., Yin, Y., Chen, H., Ding, C., Farrer, R. A., Didelot, X., Balloux, F. & Wang, H., 2019, In : Microbial Genomics. 5, 11 p.

Research output: Contribution to journalArticle

Open Access
File
Carbapenems
Klebsiella pneumoniae
Disease Outbreaks
Plasmids
Genome
2018
1 Citation (Scopus)

Author Correction - Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris

Rhodes, J., Abdolrasouli, A., Farrer, R. A., Cuomo, C. A., Aanensen, D. M., Armstrong-James, D., Fisher, M. C. & Schelenz, S., 31 May 2018, In : Emerging Microbes and Infections. 7, 1, p. 104

Research output: Contribution to journalArticle

Candida
Disease Outbreaks
Epidemiology
Infection
5 Citations (Scopus)
3 Downloads (Pure)

Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi

Fisher, M. C., Ghosh, P., Shelton, J. M. G., Bates, K., Brookes, L., Wierzbicki, C., Rosa, G. M., Farrer, R. A., Aanensen, D. M., Alvarado-Rybak, M., Bataille, A., Berger, L., Böll, S., Bosch, J., Clare, F. C., A Courtois, E., Crottini, A., Cunningham, A. A., Doherty-Bone, T. M., Gebresenbet, F. & 36 othersGower, D. J., Höglund, J., James, T. Y., Jenkinson, T. S., Kosch, T. A., Lambertini, C., Laurila, A., Lin, C-F., Loyau, A., Martel, A., Meurling, S., Miaud, C., Minting, P., Ndriantsoa, S., O'Hanlon, S. J., Pasmans, F., Rakotonanahary, T., Rabemananjara, F. C. E., Ribeiro, L. P., Schmeller, D. S., Schmidt, B. R., Skerratt, L., Smith, F., Soto-Azat, C., Tessa, G., Toledo, L. F., Valenzuela-Sánchez, A., Verster, R., Vörös, J., Waldman, B., Webb, R. J., Weldon, C., Wombwell, E., Zamudio, K. R., Longcore, J. E. & Garner, T. W. J., 17 May 2018, In : Scientific Reports. 8, 7772.

Research output: Contribution to journalArticle

Open Access
File
Amphibians
Fungi
Toes
Population
Larva
29 Citations (Scopus)
3 Downloads (Pure)

Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris

Rhodes, J., Abdolrasouli, A., Farrer, R. A., Cuomo, C. A., Aanensen, D. M., Armstrong-James, D., Fisher, M. C. & Schelenz, S., 29 Mar 2018, In : Emerging Microbes and Infections. 7, 43.

Research output: Contribution to journalArticle

Open Access
File
Candida
Disease Outbreaks
Epidemiology
Nanopores
Genome
10 Citations (Scopus)
4 Downloads (Pure)

Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen

Ene, I. V., Farrer, R. A., Hirakawa, M. P., Agwamba, K., Cuomo, C. A. & Bennett, R. J., 11 Sep 2018, In : PNAS. 115, 37, p. E8688-E8697

Research output: Contribution to journalArticle

Open Access
File
Diploidy
Candida albicans
Loss of Heterozygosity
Genome
Mutation Rate
3 Citations (Scopus)
3 Downloads (Pure)

MARDy: Mycology Antifungal Resistance Database

Nash, A., Sewell, T., Farrer, R. A., Abdolrasouli, A., Shelton, J. M. G., Fisher, M. C. & Rhodes, J., 15 Sep 2018, In : Bioinformatics. 34, 18, p. 3233-3234 2 p.

Research output: Contribution to journalArticle

Open Access
File
Mycology
Fungal Drug Resistance
Fungi
Drug Resistance
Genes
45 Citations (Scopus)

Recent Asian origin of chytrid fungi causing global amphibian declines

O'Hanlon, S. J., Rieux, A., Farrer, R. A., Rosa, G. M., Waldman, B., Bataille, A., Kosch, T. A., Murray, K. A., Brankovics, B., Fumagalli, M., Martin, M. D., Wales, N., Alvarado-Rybak, M., Bates, K. A., Berger, L., Böll, S., Brookes, L., Clare, F., Courtois, E. A., Cunningham, A. A. & 38 othersDoherty-Bone, T. M., Ghosh, P., Gower, D. J., Hintz, W. E., Höglund, J., Jenkinson, T. S., Lin, C-F., Laurila, A., Loyau, A., Martel, A., Meurling, S., Miaud, C., Minting, P., Pasmans, F., Schmeller, D. S., Schmidt, B. R., Shelton, J. M. G., Skerratt, L. F., Smith, F., Soto-Azat, C., Spagnoletti, M., Tessa, G., Toledo, L. F., Valenzuela-Sánchez, A., Verster, R., Vörös, J., Webb, R. J., Wierzbicki, C., Wombwell, E., Zamudio, K. R., Aanensen, D. M., James, T. Y., Gilbert, M. T. P., Weldon, C., Bosch, J., Balloux, F., Garner, T. W. J. & Fisher, M. C., 11 May 2018, In : Science. 360, 6389, p. 621-627 7 p.

Research output: Contribution to journalArticle

Chytridiomycota
Amphibians
Fungi
Far East
Biodiversity
5 Downloads (Pure)

Transcriptional Heterogeneity of Cryptococcus gattii VGII Compared with Non-VGII Lineages Underpins Key Pathogenicity Pathways

Farrer, R. A., Ford, C. B., Rhodes, J., Delorey, T., May, R. C., Fisher, M. C., Cloutman-Green, E., Balloux, F. & Cuomo, C. A., 24 Oct 2018, In : mSphere. 3, 5, e00445-18.

Research output: Contribution to journalArticle

Open Access
File
Cryptococcus gattii
Virulence
Capsules
Genes
Macrophages
2017
4 Citations (Scopus)

Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens

Farrer, R. A. & Fisher, M. C., 2017, Fungal Phylogenetics and Phylogenomics. Townsend, J. P. & Wang, Z. (eds.). Elsevier, p. 73-140 68 p. (Advances in Genetics; vol. 100).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Epigenomics
Fungi
Plant Diseases
Animal Diseases
Mycoses
18 Citations (Scopus)
3 Downloads (Pure)

Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi

Farrer, R. A., Martel, A., Verbrugghe, E., Abouelleil, A., Ducatelle, R., Longcore, J. E., James, T. Y., Pasmans, F., Fisher, M. C. & Cuomo, C. A., 21 Mar 2017, In : Nature Communications. 8, 11 p., 14742.

Research output: Contribution to journalArticle

Open Access
File
fungi
infectious diseases
Fungi
emerging
Genes
14 Citations (Scopus)
3 Downloads (Pure)

Microevolution of Serial Clinical Isolates of Cryptococcus neoformans var. grubii and C. gattii

Chen, Y., Farrer, R. A., Giamberardino, C., Sakthikumar, S., Jones, A., Yang, T., Tenor, J. L., Wagih, O., Van Wyk, M., Govender, N. P., Mitchell, T. G., Litvintseva, A. P., Cuomo, C. A. & Perfect, J. R., Mar 2017, In : mBio. 8, 2, 18 p., e00166-17.

Research output: Contribution to journalArticle

Open Access
File
Cryptococcus neoformans
Cryptococcus
Fluconazole
Recurrence
Virulence
3 Citations (Scopus)
4 Downloads (Pure)

Synima: a Synteny imaging tool for annotated genome assemblies

Farrer, R. A., 21 Nov 2017, In : BioMed Central Bioinformatics. 18, 1, 4 p., 507.

Research output: Contribution to journalArticle

Open Access
File
Synteny
Genome
Genes
Imaging
Imaging techniques
7 Citations (Scopus)

Zinc Cluster Transcription Factors Alter Virulence in Candida albicans

Issi, L., Farrer, R. A., Pastor, K., Landry, B., Delorey, T., Bell, G. W., Thompson, D. A., Cuomo, C. A. & Rao, R. P., Feb 2017, In : Genetics. 205, 2, p. 559-576 18 p.

Research output: Contribution to journalArticle

Candida albicans
Virulence
Zinc
Transcription Factors
Reactive Oxygen Species
2016
22 Citations (Scopus)

Comparative genomics of Fusarium oxysporum f. sp. melonis reveals the secreted protein recognized by the Fom-2 resistance gene in melon

Schmidt, S. M., Lukasiewicz, J., Farrer, R., Dam, P., Bertoldo, C. & Rep, M., Jan 2016, In : New Phytologist. 209, 1, p. 307-318 12 p.

Research output: Contribution to journalArticle

Fusarium oxysporum f. sp. melonis
Cucurbitaceae
Fusarium
Genomics
melons
26 Citations (Scopus)
4 Downloads (Pure)

Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides

Muñoz, J. F., Farrer, R. A., Desjardins, C. A., Gallo, J. E., Sykes, S., Sakthikumar, S., Misas, E., Whiston, E. A., Bagagli, E., Soares, C. M. A., Teixeira, M. D. M., Taylor, J. W., Clay, O. K., McEwen, J. G. & Cuomo, C. A., 6 Oct 2016, In : mSphere. 1, 5, 18 p., e00213-16.

Research output: Contribution to journalArticle

Open Access
File
Paracoccidioides
Genetic Recombination
Virulence
Genome
Peptide Hydrolases
28 Citations (Scopus)
7 Downloads (Pure)

Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans

Leach, M. D., Farrer, R. A., Tan, K., Miao, Z., Walker, L. A., Cuomo, C. A., Wheeler, R. T., Brown, A. J. P., Wong, K. H. & Cowen, L. E., 26 May 2016, In : Nature Communications. 7, 11704.

Research output: Contribution to journalArticle

Open Access
File
chromatin
Chromatin Assembly and Disassembly
Candida
Candida albicans
Chromatin
10 Citations (Scopus)
4 Downloads (Pure)

Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii

Farrer, R. A., Voelz, K., Henk, D. A., Johnston, S. A., Fisher, M. C., May, R. C. & Cuomo, C. A., 5 Dec 2016, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 371, 1709, 11 p., 20160021.

Research output: Contribution to journalArticle

Open Access
File
Cryptococcus gattii
Metagenomics
virulence
Fungi
Virulence
2015
41 Citations (Scopus)
4 Downloads (Pure)

Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii

Farrer, R. A., Desjardins, C. A., Sakthikumar, S., Gujja, S., Saif, S., Zeng, Q., Chen, Y., Voelz, K., Heitman, J., May, R. C., Fisher, M. C. & Cuomo, C. A., 1 Sep 2015, In : mBio. 6, 5, 12 p., e00868-15.

Research output: Contribution to journalArticle

Open Access
File
Cryptococcus gattii
Genome
Virulence
Genes
Cryptococcus
2014
195 Citations (Scopus)

Recent introduction of a chytrid fungus endangers Western Palearctic salamanders

Martel, A., Blooi, M., Adriaensen, C., Van Rooij, P., Beukema, W., Fisher, M. C., Farrer, R. A., Schmidt, B. R., Tobler, U., Goka, K., Lips, K. R., Muletz, C., Zamudio, K. R., Bosch, J., Lötters, S., Wombwell, E., Garner, T. W. J., Cunningham, A. A., Spitzen-van der Sluijs, A., Salvidio, S. & 7 othersDucatelle, R., Nishikawa, K., Nguyen, T. T., Kolby, J. E., Van Bocxlaer, I., Bossuyt, F. & Pasmans, F., 31 Oct 2014, In : Science. 346, 6209, p. 630-631 2 p.

Research output: Contribution to journalArticle

Urodela
Amphibians
Fungi
Biodiversity
Emerging Communicable Diseases
2013
57 Citations (Scopus)
4 Downloads (Pure)

Chromosomal copy number variation, selection and uneven rates of recombination reveal cryptic genome diversity linked to pathogenicity

Farrer, R. A., Henk, D. A., Garner, T. W. J., Balloux, F., Woodhams, D. C. & Fisher, M. C., 15 Aug 2013, In : PLoS Genetics. 9, 8, 13 p., e1003703.

Research output: Contribution to journalArticle

Open Access
File
Chytridiomycota
pathogenicity
Genetic Recombination
recombination
Virulence
29 Citations (Scopus)
4 Downloads (Pure)

Transmission of Hypervirulence traits via sexual reproduction within and between lineages of the human fungal pathogen cryptococcus gattii

Voelz, K., Ma, H., Phadke, S., Byrnes, E. J., Zhu, P., Mueller, O., Farrer, R. A., Henk, D. A., Lewit, Y., Hsueh, Y-P., Fisher, M. C., Idnurm, A., Heitman, J. & May, R. C., 5 Sep 2013, In : PLoS Genetics. 9, 9, 18 p., e1003771.

Research output: Contribution to journalArticle

Open Access
File
Cryptococcus gattii
sexual reproduction
virulence
Disease Outbreaks
Reproduction
21 Citations (Scopus)
5 Downloads (Pure)

Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects

Farrer, R. A., Henk, D. A., MacLean, D., Studholme, D. J. & Fisher, M. C., 21 Mar 2013, In : Scientific Reports. 3, 6 p., 1512.

Research output: Contribution to journalArticle

Open Access
File
Benchmarking
Single Nucleotide Polymorphism
Sequence Alignment
Fungal Genome
Metagenomics
2012
1 Citation (Scopus)

Emergence of the Chytrid Fungus Batrachochytrium Dendrobatidis and Global Amphibian Declines

Fisher, M. C., Stajich, J. E. & Farrer, R., Aug 2012, Evolution of Virulence in Eukaryotic Microbes. Sibley, L. D., Howlett, B. J. & Heitman, J. (eds.). Wiley-Blackwell , p. 461-472 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

189 Citations (Scopus)
4 Downloads (Pure)

Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen

Cooke, D. E. L., Cano, L. M., Raffaele, S., Bain, R. A., Cooke, L. R., Etherington, G. J., Deahl, K. L., Farrer, R. A., Gilroy, E. M., Goss, E. M., Grünwald, N. J., Hein, I., MacLean, D., McNicol, J. W., Randall, E., Oliva, R. F., Pel, M. A., Shaw, D. S., Squires, J. N., Taylor, M. C. & 4 othersVleeshouwers, V. G. A. A., Birch, P. R. J., Lees, A. K. & Kamoun, S., 4 Oct 2012, In : PLoS Pathogens. 8, 10, 14 p., e1002940.

Research output: Contribution to journalArticle

Open Access
File
Solanum tuberosum
Starvation
varespladib methyl
Genome
Phytophthora infestans
2011
261 Citations (Scopus)

Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage

Farrer, R. A., Weinert, L. A., Bielby, J., Garner, T. W. J., Balloux, F., Clare, F., Bosch, J., Cunningham, A. A., Weldon, C., du Preez, L. H., Anderson, L., Pond, S. L. K., Shahar-Golan, R., Henk, D. A. & Fisher, M. C., 15 Nov 2011, In : PNAS. 108, 46, p. 18732-18736 5 p.

Research output: Contribution to journalArticle

Chytridiomycota
Amphibians
Biodiversity
Genetic Recombination
Central America
3 Citations (Scopus)
Chytridiomycota
Mycoses
Amphibians
Disease Outbreaks
Virulence
2010
218 Citations (Scopus)

Genome evolution following host jumps in the Irish potato famine pathogen lineage

Raffaele, S., Farrer, R. A., Cano, L. M., Studholme, D. J., MacLean, D., Thines, M., Jiang, R. H. Y., Zody, M. C., Kunjeti, S. G., Donofrio, N. M., Meyers, B. C., Nusbaum, C. & Kamoun, S., 10 Dec 2010, In : Science. 330, 6010, p. 1540-1543 4 p.

Research output: Contribution to journalArticle

Solanum tuberosum
Starvation
Genome
Phytophthora infestans
Genes
2009
71 Citations (Scopus)

De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads

Farrer, R. A., Kemen, E., Jones, J. D. G. & Studholme, D. J., 1 Feb 2009, In : FEMS Microbiology Letters. 291, 1, p. 103-111 9 p.

Research output: Contribution to journalArticle

Pseudomonas syringae
Nucleotides
Genome
Untranslated RNA
Proteomics
102 Citations (Scopus)

Ten things to know about oomycete effectors

Schornack, S., Huitema, E., Cano, L. M., Bozkurt, T. O., Oliva, R., Van Damme, M., Schwizer, S., Raffaele, S., Chaparro-Garcia, A., Farrer, R., Segretin, M. E., Bos, J., Haas, B. J., Zody, M. C., Nusbaum, C., Win, J., Thines, M. & Kamoun, S., 1 Nov 2009, In : Molecular Plant Pathology. 10, 6, p. 795-803 9 p.

Research output: Contribution to journalArticle

Oomycetes
Genetic Research
trafficking
historical perspective
pathology