This 1.5-day workshop will include a short introduction to next-generation sequencing theory and an introduction to Galaxy. The hands-on component of the workshop will cover the concepts of de novo assembly and initial annotation of a genome from short-read NGS data.
Polyploid and long read technologies
Join us to meet researchers from Plant and Food Research (PFR) in New Zealand and discuss “Polyploid and long read technologies”.
When: Wednesday 9 May from 2pm to 3pm
Where: QBP Multimedia Room (Bld 80 Room 3.141), The University of Queensland, St Lucia
Dr Susan Thomson is the Programme Leader for Genome Analysis within the Molecular & Digital Breeding science group at Plant & Food Research LTD, New Zealand. Susan has a diverse background with origins in human molecular and cellular biology with a focus on drug-resistant cancer cells and programmed cell death. Susan moved to plant research at PFR as a member of the international consortium responsible for generating the potato genome sequence. Involvement in both wet bench and bioinformatic aspects of the sequence project lead to Susan joining the Bioinformatics team, of which she is now a senior member. Susan has been a leader in polyploid variant analysis and transposable element analysis including transposition detection, her key interests include developing pipelines for local haplotyping of polyploids and the use of emerging long read technology for genomics, transcriptomics and structural variant detection. Susan also has interests in data management, curation and visualisation and their use for advancing genomics within breeding programmes.
Amali Thrimawithana is a Bioinformatician at the New Zealand Institute for Plant and Food Research Limited since 2011, after graduating with a Masters of Bioinformatics from University of Auckland. She has been involved in research projects focusing on fungal pathogens, insect pests and plants where she has undertaken bioinformatics analysis including de novo assembly and annotation of genomes and transcriptomes, differential expression analysis as well as comparative genomics. Her current major areas of interest focus on understanding insect pests of important horticultural crops, genome exploration of native New Zealand plant species, RNASeq, visualisation and metagenomics. She is also a certified software carpentry instructor and has interest in reproducible research and training.
Cecilia Deng is a senior Bioinformatician at the New Zealand Institute for Plant and Food Research Limited (PFR). Coming from computer science and engineering background, Cecilia is specialized in database development, big data (genomics, transcriptomics and metabolomics) analysing, integration and management. She has led the bioinformatics analysis in fruit crops (apple, pear, peach and citrus) and pipfruit pathogen genomics projects. She is involved in ‘Genomics Aotearoa’, a new MBIE SSIF collaborative platform for genomics and bioinformatics research in New Zealand. Cecilia has worked extensively in genome assembly, large & small structure variation detection, high-throughput large scale genotyping, transcriptome profiling and differential expression test. Her research interests include bioinformatics pipeline construction, plant-pathogen interactions, molecular markers discovery and their applications.