Opportunities for Combinatorial Optimization in Computational Biology
Harvey J. Greenberg, William E. Hart, Giuseppe Lancia
INFORMS Journal on Computing · 2004 · Volume 16 · Issue 3
Abstract
This is a survey designed for mathematical programming people who do not know molecular biology and want to learn the kinds of combinatorial optimization problems that arise. After a brief introduction to the biology, we present optimization models pertaining to sequencing, evolutionary explanations, structure prediction, and recognition. Additional biology is given in the context of the problems, including some motivation for disease diagnosis and drug discovery. Open problems are cited with an extensive bibliography, and we offer a guide to getting started in this exciting frontier.
Keywords
computational biology, combinatorial optimization, global optimization, integer programming, minimum energy, bioinformatics, molecular structure prediction, protein folding, protein alignment, rearrangements, assembly, sequence alignment, SNP, sorting by reversals
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