Cecilia Deng

Long read sequencing in real-world applications

As a powerful technology with the ability to generate reads tens of thousands to million bases long, third generation of single-molecule long-read (SMLR) sequencing has gained popularity in various genomic research area. Its applications include but are not limited to telomere-to-telomere genome assembly, full-length transcriptome profiling, large structural variation detection, single-cell methylomes, targeted sequencing, and microbiome studies. In this talk, I will compare Oxford Nanopore Technologies and PacBio long reads, and 10X Genomics linked-reads technology, and discuss the fast-changing bioinformatics tools suitable for SMLR analysis, and potential pitfalls in horticultural data processing.

Cecilia Deng

Senior Scientist, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited

Cecilia Deng is a Bioinformatician and senior scientist at the New Zealand Institute for Plant and Food Research Limited (PFR), a New Zealand Government-owned Crown Research Institute (CRI). She is involved in ‘Genomics Aotearoa’, a new Ministry for Business Innovation and Employment (MBIE) SSIF (Strategic Science investment Fund) collaborative platform for genomics and bioinformatics research in New Zealand. Cecilia specialises in database development, sequencing data analysis and workflow management, with an emphasis on reproducible research. Cecilia has contributed to bioinformatics analysis in fruit crops (apple, pear, peach, blueberry and citrus), fish and fungal pathogen genomics projects. Cecilia has worked extensively in genome assembly, structure variation detection, high-throughput large scale genotyping, transcriptome profiling, and multi-omics integration. Her research interests include bioinformatics pipeline construction, plant-pathogen interactions, molecular markers discovery and their applications. Cecilia is a member of the Myrtle Rust research consortium, which won The Bio-Protection Research Centre Science Award 2020 in the Biosecurity Awards: Project “Ngā taonga – Safeguarding the mauri of myrtles and dependent ecosystems”.