Analyzing and designing small RNA-mediated gene regulation
Pål Sætrom
Dept. of Computer and Information Science and Dept. of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway

Small non-coding RNAs such as microRNAs (miRNAs) and short interfering RNAs (siRNAs) can regulate many genes by base pairing to sites in mRNAs. For miRNAs, these regulatory targets determine the miRNAs' function, but for siRNAs, most of these regulatory targets represent unwanted side-effects that obfuscate experimental results. Understanding how miRNAs recognize targets is therefore important both for predicting miRNA function and for analyzing siRNA effects. We have developed methods that assess miRNA's overall regulatory effects and have used these to design robust siRNAs.