PhD Position Available – Analyzing alternative splicing events in human transcriptome sequencing data


Dr Qiongyi Zhao

Dr Kostya Shakhbazov

A/Prof Naomi Wray

Project Description

Alternative splicing (AS) is a regulated process during gene expression that results in a single gene locus transcribing to multiple isoforms. It is well known that alternative splicing occurs as a normal phenomenon in eukaryotes, and alternative pre-mRNA splicing affects the majority of human genes and plays important roles in development and disease. However, the methodology for accurate identification of AS events based on high throughput sequencing data is not yet well developed. Current publically available tools/packages like “DEXSeq” and “cufflinks” only focus on differential usage of exons in known isoforms or just provide partial results for AS events. Thus, it is essential to develop new analytical methods or tools to accurately identify AS events and facilitate the RNA-Seq community to study AS events.

The PhD project will involve developing a user-friendly tool to identify AS events based on RNA-Seq data sets and analysing AS events in human transcriptome sequencing data. Analyses may focus on AS events in disease vs control (for example Motor Neurone Disease or Schizophrenia) or in male vs. female. Development of a user-friendly tool is essential and important for the RNA-Seq community.

The PhD student will be based within the QBI bioinformatics core that supports all sequencing projects undertaken on the in-house Illumina HiSeq. The student will be exposed to a range of ongoing projects and will learn skills in computational approaches/pipelines to integrate and analyze large-scale NGS data sets including genomics, expression, transcriptomics, epigenomics and proteomics data sets for scientific discovery and validation. A small sequencing project designed by the student could also be part of the project.

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