Dr Wei Shi

Laboratory Head
Bioinformatics Division, Walter and Eliza Hall Institute, Australia
Phone: +61 3 9345 2848
Email: shi at wehi dot edu dot au

Research interests

My research focuses on developing fast and accurate computational methods for the analyses of large-scale genomic data, including next-generation sequencing data and microarray data. I am also interested in applying genomic techniques to understand the differentiation of lymphocytes in immune system at the molecular level.

Student projects

Projects for Ph.D, Master and Honour students are available. See links below for details. Internship is considered as well.

Click here for information about how to apply for a Ph.D in Walter and Eliza Hall Institute.


(1) Subread software package: a tool kit for processing next-gen sequencing data. It comprises a suite of programs for processing next-gen sequencing data including

  • Subread: a general-purpose read aligner which can align both genomic DNA-seq and RNA-seq reads. It can also be used to discover genomic mutations including short indels and structural variants.
  • Subjunc: a read aligner developed for aligning RNA-seq reads and for the detection of exon-exon junctions. Gene fusion events can be detected as well.
  • featureCounts: a software program developed for counting reads to genomic features such as genes, exons, promoters and genomic bins. This is currently the fastest read counting software in the field.
  • exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.

(2) Rsubread: a Bioconductor R package. This package provides Bioconductor users access to the Subread software package.

(3) neqc: a function for normalizing Illumina whole-genome expression BeadChip data. It is implemented in Bioconductor package limma.