Biological sequence analysis and genomic variant discovery (Masters option available)

Biological sequence analysis and genomic variant discovery (Masters option available)

Details of project

Next-generation sequencing (NGS) technologies are increasingly used in laboratories and clinics worldwide to facilitate better understanding and diagnosis of diseases. The massive volume of data from these technologies continues to pose significant challenges for bioinformaticians.

We are interested in developing novel methods for mapping both long and short NGS reads (and other biological sequences) 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 more accurate methods for detecting genomic variants (eg. insertions, deletions, translocations etc.) in cancer genomes using NGS data.

Prospective students are expected to have a computer science background and/or have strong programming skills. One or two projects are available for PhD or Masters study.

 

 

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: