SysGen seminar – Alicia Oshlack – 29th July, 2016


Gene expression analysis using de novo assembled transcriptomes

Alicia Oshlack
Murdoch Children’s Research Institute
Associate Member – Centre for Systems Genomics

Friday 29th July
ESJ King Theatre, Medical Building, The University of Melbourne

Next generation sequencing has revolutionized transcriptomics, because it allows cDNA sequences to be read and expression quantification to be measured by a single, affordable assay, RNA-seq. The short read sequences commonly used to generate RNA-seq can be used for estimating expression levels, performing differential expression and reconstructing expressed transcripts. In particular, studies involving non-model organisms have benefited from the technology as no prior knowledge of the genes is needed in order to generate data. Instead, expressed transcripts can be built from the data using de novo assembly. In this talk I will discuss some of the commonly used strategies for the analysis of RNA-seq data. I will also present methods we have developed for the analysis of differential expression in non-model organisms and de novo assembled transcriptome data. I will finish the talk by presenting some unpublished work on concepts and tools for visualising, performing differential transcript usage and discovering novel variants in assembled transcriptomes from non-model organisms and cancer.


A/Prof Alicia Oshlack is the head of Bioinformatics at the Murdoch Childrens Research Institute and an NHMRC Career Development Fellow. She is most well known for her work on methods for the analysis of RNA-seq data. She proposed the first normalisation method, gene-set testing approach and published the first comprehensive review in the field in the leading journal Genome Biology. She has also made major advances in the areas of epigenetic analysis and clinical sequencing. She has a number of strong collaborations across a variety of areas related to development and disease including cancer, kidney development, sex determination and rare childhood diseases. She has received several major awards including the Australian Academy of Science Gani Medal for human genetics and the Lorne Genome Conference Millennium award.

Enquiries: Andrew Siebel (