Biological sequence analysis and genomic variant discovery

Biological sequence analysis and genomic variant discovery

Project details

Next-generation and third-generation sequencing technologies are being used worldwide as an important tool to elucidate the molecular mechanisms underpinning biological processes. However, the massive volume of data generated from these technologies continues to pose significant challenges for bioinformaticians.

We are interested in developing novel methods for mapping long and short reads generated from these sequencing technologies to a reference genome to find the true origin of biological sequences (Liao et al., Nucleic Acids Research, 2013,41(10):e108). We would also like to develop efficient and accurate method to detect genomic mutations in the cancer genome. These mutations include insertion, deletion, duplication, inversion and translocation.

Prospective students are expected to have a good computing background (eg. computer science, mathematics, statistics, physics, etc.). One or two projects are available.

 

About our research group

Our research focuses on developing highly efficient bioinformatics methods for analysis of high-throughput genomic data, including NGS data and microarray data. We recently developed a paradigm-shifting algorithm called “seed-and-vote” for read mapping (Liao, Nucleic Acids Research, 2013,41(10):e108), which forms the foundation for our further methodology development for biological sequence alignment and genomic variant discovery. We are also interested in developing algorithms for calling absolutely expressed genes and for quantifying expression levels of different isoforms of genes, using RNA-seq data.

We have established close collaborations with immunologists and cancer researchers in the Institute and we apply the new methods we develop to our collaborative projects to facilitate biological discoveries. 

Researchers:

Dr Wei Shi

Profile photo of Dr Wei Shi
Dr
Wei
Shi
Laboratory Head

Project Type:

Melanie Bahlo

Talking to Einstein A Go Go as we celebrate the Australian Society for Medical Research (ASMR) 'Medical Research Week'.