Predictive Methods Using RNA Sequences

Francois Major, Computer Science, University of Montreal
Russ Altman, Medical Informatics, Stanford University

The importance of RNA informatics, as well as the number of individuals and industries involved in RNA research, are constantly increasing. On the other hand, the RNA informatics community has not followed the RNA biology communitee in this RNA science "booming", perhaps because of a lack in accessible RNA data. The goals of this tutorial are to present state-of-the-art RNA informatics by giving pointers to RNA data, by introducing the main computational tools applied to RNAs, by discussing the differences between RNAs and proteins, and by presenting the current and next challenges in RNA informatics. After formally defining the common abstractions of RNAs (from primary to quaternary structure), common computational tools for studying and analyzing RNA sequence and structure will be overviewed, including tools for maintaining RNA sequence and structure databases, for identifying structural and functional RNAs in the genome, for aligning RNA sequences, and for predicting secondary and tertiary structure.

Francois Major:
has been involved in RNA informatics since 1984. He has developed, in collaboration with his colleagues Cedergren and Gautheret, two highly employed computer programs: RNAMOT to search for RNA motifs in the genome, and MC-SYM to model RNA 3-D structures from low-resolution experimental data. He currently has over 30 publications in the field, and his laboratory, over the last five years, has embark upon projects that involve the identification of RNA patterns in messenger RNAs, automated motif searching and folding, RNA 3-D structure analysis tools, and RNA-drug docking. Over the last six years, he has taught at the University of Montreal Java and C++ programming, data structures and algorithms, artificial intelligence, and bioinformatics.

Russ Altman:
Russ Biagio Altman is associate professor of medicine (and computer science by courtesy) at Stanford University. His primary research interests are in the application of computing technology to basic molecular biological problems of relevance to medicine. He is currently developing techniques for collaborative scientific computation over the Internet, including novel user interfaces to biological data in the area of pharmacogenomics. Other work focuses on the analysis of functional microenvironments within macromolecules and the application of nonlinear optimization algorithms for determining the structure and function of biological macromolecules, particularly the bacterial ribosome. He is on the executive committee (as Molecular Science Thrust leader) for the National Partnership for Advanced Computational Infrastructure (NPACI), the NSF-sponsored program at the San Diego Supercomputer Center. Dr. Altman holds an M.D. from Stanford Medical School, a Ph.D. in medical information sciences from Stanford, and an A.B. from Harvard College. He has been the recipient of the U.S. Presidential Early Career Award for Scientists and Engineers, a National Science Foundation CAREER Award, and the Western Society of Clinical Investigation Annual Young Investigator Award. He is a fellow of the American College of Physicians and the American College of Medical Informatics.

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