Welcome to the Butler lab at the Conway Institute<\/a> at University College Dublin<\/a>. The lab is interested in fungal genomics, including the analysis of both pathogenic fungi and yeast with potential biotechnological applications. We have carried out large population studies of\u00a0Candida parapsilosis<\/em>\u00a0and\u00a0Candida tropicalis,\u00a0<\/em>including\u00a0investigating mechanisms associated with drug resistance.<\/em>\u00a0We identified the regulatory pathways controlling the growth of biofilms of\u00a0Candida parapsilosis\u00a0<\/em>on medical devices; investigated the response of pathogenic yeast to hypoxia; and characterised the origin of\u00a0Candida orthopsilosis<\/em>. We developed methods for generating gene knockouts in\u00a0Candida parapsilosis<\/em>, including the application of CRISPR, and we constructed a set of individual knockouts that were used to study regulation of sulphur metabolism. We use a number of comparative genomics approaches to study \u00a0evolution of the\u00a0Candida<\/em>\u00a0clade, including genomic sequencing (Illumina and minION) and RNA-seq. We\u00a0developed a genome browser (the\u00a0Candida Gene Order Browser)<\/a> to enable analysis of\u00a0Candida<\/em>\u00a0genomes. We also carry out detailed evolutionary analysis, including characterising the evolution and function of centromeres in\u00a0Candida<\/em>\u00a0species.<\/p>\n\n\n We participated in the SFI Research Centre for Training Genomics and Data Science<\/a> and the\u00a0OPATHY<\/a>\u00a0International Training Network, \u201cFrom Omics to Patient: Improving Diagnostics of Pathogenic Yeasts\u201d. See the OPATHY video about the beast in yeast (pathogenic\u00a0Candida<\/em>)\u00a0on YouTube,\u00a0here<\/a>. We also collaborate with Prof Tobias H\u00f6hl and Dr Bing Zhai the Memorial Sloan Kettering Cancer Center in New York, leading to a characterisation of gut to bloodstream transition of fungal isolates. The lab works closely with\u00a0Ken Wolfe\u2019s<\/a>\u00a0group at UCD.<\/p>\n\n\n\n We welcome both molecular and computational biologists.<\/p>\n\n\n\n Wild yeast project<\/a>: as part of undergraduate research at UCD, we designed two modules where students isolate, identify and then sequence the genomes of yeast from soil. As part of this project, we identified the first European isolates of Saccharomyces eubayanus<\/em>, a parent of the lager yeast, Saccharomyces pastorianus<\/em>. This led to a new fields of research. We have now isolated S. eubayanus<\/em> from all across Ireland. We have started a collection of wild yeasts from the Irish environment, whcih we propose to greatly expand starting in 2025. In addition, we will identify centromeres and develop cloning and editing systems for yeasts with biotechnological applications.<\/p>\n\n\n\n Follow the links at the top (or bottom) of the page to the Wild Yeast Project, people etc.<\/p>\n\n\n\n Geraldine Butler biography at UCD is available here<\/a>.<\/p>\n\n\n\n Tools<\/strong><\/p>\n\n\n\n The Candida Gene Order Browser: http:\/\/cgob.ucd.ie<\/a><\/p>\n\n\n\n Genomics Core Facility<\/strong><\/p>\n\n\n\n I am currently the director of the Genomics Core Facility<\/a> at the Conway Institute. Pease contact if you are interested in using the sequencing facilities.<\/p>\n\n\n\n Publications<\/strong><\/p>\n\n\n\n![\"DNA](\"http:\/\/butler.ucd.ie\/wp-content\/uploads\/2022\/11\/DNA_Botanis-282x300.jpg\")