Keywords and Synonyms
High-performance computational biology
Problem Definition
In the 50 years since the discovery of the structure of DNA, and with new techniques for sequencing the entire genome of organisms, biology is rapidly moving towards a data-intensive, computational science. Many of the newly faced challenges require high-performance computing, either due to the massive-parallelism required by the problem, or the difficult optimization problems that are often combinatoric and NP-hard. Unlike the traditional uses of supercomputers for regular, numerical computing, many problems in biology are irregular in structure, significantly more challenging to parallelize, and integer-based using abstract data structures.
Biologists are in search of biomolecular sequence data, for its comparison with other genomes, and because its structure determines function and leads to the understanding of biochemical pathways, disease prevention and cure, and the mechanisms of life itself....
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Recommended Reading
Bader, D.A., Moret, B.M.E., Warnow, T., Wyman, S.K., Yan, M.: High-performance algorithm engineering for gene-order phylogenies. In: DIMACS Workshop on Whole Genome Comparison, Rutgers University, Piscataway, NJ (2001)
Bader, D.A., Moret, B.M.E., Vawter, L.: Industrial applications of high-performance computing for phylogeny reconstruction. In: Siegel, H.J. (ed.) Proc. SPIE Commercial Applications for High-Performance Computing, vol. 4528, pp. 159–168, Denver, CO (2001)
Bader, D.A., Moret, B.M.E., Yan, M.: A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. J. Comp. Biol. 8(5), 483–491 (2001)
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Moret, B.M.E., Bader, D.A., Warnow, T., Wyman, S.K., Yan, M.: GRAPPA: a highperformance computational tool for phylogeny reconstruction from gene-order data. In: Proc. Botany, Albuquerque, August 2001
Moret, B.M.E., Bader, D.A., Warnow, T.: High-performance algorithm engineering for computational phylogenetics. J. Supercomp. 22, 99–111 (2002) Special issue on the best papers from ICCS'01
Moret, B.M.E., Wyman, S., Bader, D.A., Warnow, T., Yan, M.: A new implementation and detailed study of breakpoint analysis. In: Proc. 6th Pacific Symp. Biocomputing (PSB 2001), pp. 583–594, Hawaii, January 2001
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© 2008 Springer-Verlag
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Bader, D.A. (2008). Engineering Algorithms for Computational Biology. In: Kao, MY. (eds) Encyclopedia of Algorithms. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-30162-4_124
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DOI: https://doi.org/10.1007/978-0-387-30162-4_124
Publisher Name: Springer, Boston, MA
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