Error-Control and Constrained Coding Solutions for DNA Microarrays and Aptamer Array Designs

SPEAKER: Professor Olgica Milenkovic, University of Colorado, BoulderABSTRACT: DNA microarrays and aptamer arrays are two classes of systems used for analyzing the dynamical activity of cells in terms of their RNA and protein fingerprints. These macromolecule arrays provide valuable information for disease diagnostics and monitoring, as well as for the development and testing of genetic drugs and therapeutic RNA antibodies. In the past, substantial efforts were made to increase the quality of the manufacturing process and to improve the reliability of microarrays and aptamer arrays. Nevertheless, there still exist many issues that have to be resolved in order to ensure proper functionality of these arrays in the presence of failures and dropout events occurring during and after the production process.In the first part of the talk, we focus on several problems related to DNA microarrays. We briefly introduce gene regulatory networks and the process of reverse engineering regulatory networks in terms of DNA microarray data. We then proceed to describe how classical error-control coding techniques can be used to increase the accuracy of data generated by DNA arrays subjected to spot failures. We propose an integrated framework for analyzing quality control and error-correction in DNA microarrays generated by photolitographic VLSIPS (Very Large Scale Immobilized Polymer Synthesis) methods. In this context, the issues of base scheduling, mask design and border-length minimization, construction of quality control arrays and good probe multiplexing strategies are addressed. The presented analysis is based on combining and extending results regarding balanced error-correcting codes and superimposed codes.In the second part of the talk, we briefly describe aptamers and the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) process used for identifying and isolating RNA aptamers. We then proceed to describe a generalization of the paradigm of constrained coding and its application to structured selection and generation of RNA aptamers. The proposed approach is based on viewing (folded) RNA aptamers as words of regular and context-free grammars which include bio-chemical constraints in their production rules. The grammar based approach to constrained coding allows for counting the number of aptamer structures and for generating such structures in terms of well known combinatorial techniques.The material to be presented in the talk is self-contained and it is assumed that the audience does not have a background in molecular biology.BIO: Olgica Milenkovic received her MS degree in mathematics and PhD in electrical engineering from the University of Michigan, Ann Arbor, in 2001 and 2002, respectively. In August 2002, she joined the University of Colorado, Boulder, where she is an Assistant Professor in the Department of Electrical and Computer Engineering. In the summer of 2005, she was a Discrete Mathematics and Theoretical Computer Science (DIMACS) Visitor at Bell Labs, Lucent Technologies. She is currently a Visiting Professor at the Center for Information Theory and Applications at the University of California, San Diego. Her research interests include error-control and constrained coding, analysis of algorithms, combinatorics, probability theory, and bioinformatics.Host: Prof. Keith Chugg, chugg@usc.edu

Location: James H. Zumberge Hall Of Science (ZHS) - 163

Audiences: Everyone Is Invited

Contact: Mayumi Thrasher