"Bioinformatics Algorithm Design and Analysis, and Web-Service Development"

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Algorithm design and analysis plays a central role in computer science. Bioinformatics and computational omics are emerging interdisciplinary areas of study that require expertise from computational sciences and biological sciences. On one hand, biology has become a high-throughput science where its applications are desperate for advanced computing techniques to digest the huge volume of biological data to provide further insights leading to new biological discoveries. On the other hand, the practice of algorithm design and analysis on the computational problems formulated from biological applications helps improve our understandings of the nature of computation which can potentially trigger computational breakthroughs. The proposed interdisciplinary research has exactly this two-fold significance. The target applications in our proposed research are genomics applications based on single nucleotide polymorphism (SNP) genotype data, and proteomics and metabolomics applications based on mass spectral data. In the former, our main goal is to build the dense SNP haplotype map to provide finer and deterministic haplotype allelic information for reviving haplotype-based genome-wide linkage and association studies (GWAS); in the latter, we aim to design novel algorithms with proven performance, to automate the peptide and metabolite identification for the most effective use of mass spectral data. If successful, we will be able to confront the bottleneck of genotype-based GWAS, particularly to make contributions to the cattle genomic selection programs; we will be able to use the whole proteome profile for whole genome annotation to detect new genes not expected by current gene prediction tools; we will also be able to use the whole metabolome quantitative profiling to pinpoint effective biomarkers to assist disease diagnosis. Our research results, including curated data, analytical results, and designed algorithms, will be extended into web-services for the community. We have started several subtopics of the proposed research, and have foreseen a number of successes. The proposed research will also train highly qualified personnel for Canada's bioinformatics interdisciplinary research.