Advisors: Anne Condon, Professor, Computer Science Department, UBC
Chris Thachuk, Graduate Student, Computer Science Department, UBC
Location: BETA (Bioinformatics, and Experimental and Theoretical Algorithmics) Lab, 2366 Main Mall, Point Grey Campus, UBC
Motivation:
The Human Genome Project has enabled a revolutionary step forward in understanding our genes and their function. A significant next challenge is to understand genome variation across individuals and its correlation with disease, as well as genomic mutations and rearrangements in cancerous cells. With the availability of a reference human genome sequence, current studies focus on resequencing, that is, inference of the genome of interest by alignment of millions of short reads, produced by sequencing the genome, to an available reference genome. While much work has been done on producing software capable of aligning reads to a reference, there is a growing need for software that can address the specific challenges associated with sequence data derived from cancerous tissue and from transcriptomes.
Project outline:
The goal of this project is to produce a high quality software package for next generation sequencing data alignment with a focus on the challenges of handling transcriptome derived data, as well as data from cancerous tissue. The project will explore the use of state-of-the-art text indexing techniques and string comparison algorithms, with a focus on producing high performance software.
The project will be undertaken in collaboration with researchers at the BC Cancer Research Centre and is suitable for either graduate students interested in a potential thesis topic or advanced undergraduate students interested in bioinformatics, algorithmic design, and software development in general.
Experience programming in C and/or C++ is must. Previous experience in software development projects and background in bioinformatics are also desirable but not required.
The position may be part-time (at least 10 hours per week) or full-time.
If interested, please e-mail a résumé, transcript, and short summary of any related work experience to Anne Condon. Hourly pay range for a third or fourth year undergraduate student is $17–19/hour, and for a MSc student is $25–28/hour, depending on experience.