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A compressed sensing framework for identifying differentially expressed isoforms and transcriptomic aberrations in cancer samples

2012 Bioinformatics and Computational Biology Competition
Agriculture and Agri Food
Fisheries and Aquaculture
Genome Centre(s):
Genome British Columbia
Project Leader(s):
Cenk Sahinalp (Simon Fraser University), Colin Collins (University of British Columbia and Vancouver Prostate Centre)
Fiscal Year Project Launched: 
Project Description: 

New technology provides fast and accurate ways to analyze RNAs (which act as messengers carrying instructions from DNA) that code protein in a tissue. While there are many potential RNA products in a gene, it is believed that it is only necessary to identify and quantify a small number of RNA products in order to get information about a sample’s RNA content.

Drs. Cenk Sahinalp and Colin Collins are using a computing technique called compressed sensing to find the smallest possible number of RNA products from each gene. Their approach will also help pinpoint the essential differences between samples of RNA products from the same gene. Sahinalp and Collins will also use compressed sensing to identify tissues from prostate cancer patients that develop into more aggressive forms of the disease.