Head, Bioinformatics and Cancer Genomics Laboratory

Prof Shi received his PhD in Computer Science from Harbin Institute of Technology, Harbin, China in 2000. After postdoctoral training at Tsinghua University, Beijing, China, he moved to Australia to take up a research fellow position at Deakin University in 2003. In 2006, he made a career transition to bioinformatics and joined the Bioinformatics Division at the Walter and Eliza Hall Institute. He was appointed as a Laboratory Head at the Walter and Eliza Hall Institute in 2016. In 2020, he was recruited to the Olivia Newton-John Cancer Research Institute to establish and lead the bioinformatics program.

Professor Shi has developed bioinformatics methods that have been widely adopted in the field. He is internationally recognized as an expert in developing methods for quantifying RNA-seq gene expression data. He has a career citation of >32,000. He was a Web of Science Highly Cited Researcher in both 2020 and 2018 (Clarivate Analytics), being recognized as one of the most cited researchers in the world.

Professor’s Shi’s research focuses on developing cutting-edge bioinformatics tools for the mapping and quantification of single-cell and bulk RNA-seq data, detection of alternative splicing of genes, discovery of structural variants and gene fusions in cancer genome, chromatin accessibility analysis, transcription factor binding analysis and machine learning method for predicting patient outcome.

His lab has developed the Rsubread/Subread toolbox that includes Subread/Subjunc aligner, featureCounts quantification program, cellCounts single-cell RNA-seq quantification program and other bioinformatics tools. Rsubread/Subread can be accessed via Bioconductor, SourceForge and GitHub.

He also has a strong interest in using genomics data to understand the molecular mechanisms underlying the development of cancer and immune diseases. He collaborates widely with many labs and groups at the ONJCRI and other institutes.