Combinatorial models and algorithms in bioinformatics

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My future research plans call for a continued focus on problems in bioinformatics and computational biology. Besides the theoretical values, results of the proposed research can have significant practical importance. The inverse protein folding problem and in particular hand-in-glove designs have significant relevance for understanding protein interactions and our solutions can help to target new protein designs for disease using in-silico techniques. Our algorithms for haplotyping have drawn the attention of biologists and we believe there is significant potential to help to narrow their search for disease markers. The complexity and algorithmic results on RNA pathway problems help in understanding RNA function in biological settings and in design of programmed molecular systems. Several practical questions we have considered in these various domains have an interdisciplinary character, and they are leasing us to explore exciting connections to fundamental problems in other areas.