Computational biology and high-performance computing

ABSTRACT

Understanding evolution and the basic structure and function of proteins are two grand challenge problems in biology that can be solved only through the use of high-performance computing.

REFERENCES

• 1: Bader, D., Moret, B., and Yan, M. A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. J. Comput. Biol. 8, 5 (Oct. 2001), 483--491.
• 2: Dunker, A., Ensign, L., Arnold, G., and Roberts, L. Proposed molten globule intermediates in fd phage penetration and assembly. FEBS Lett. 292, 1--2 (Nov. 1991), 275--278.
• 3: Farris, J. The logical basis of phylogenetic analysis. In Advances in Cladistics, N. Platnick and V. Funk, Eds. Columbia University Press, New York, 1983, 1--36.
• 4: Felsenstein, J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17, 6 (Sept. 1981), 368--376.
• 5: Sridhar Hannenhalli , Pavel Pevzner, Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals, Proceedings of the twenty-seventh annual ACM symposium on Theory of computing, p.178-189, May 29-June 01, 1995, Las Vegas, Nevada, United States [doi>10.1145/225058.225112]
• 6: F. Allen , G. Almasi , W. Andreoni , D. Beece , B. J. Berne , A. Bright , J. Brunheroto , C. Cascaval , J. Castanos , P. Coteus , P. Crumley , A. Curioni , M. Denneau , W. Donath , M. Eleftheriou , B. Fitch , B. Fleischer , C. J. Georgiou , R. Germain , M. Giampapa , D. Gresh , M. Gupta , R. Haring , H. Ho , P. Hochschild , S. Hummel , T. Jonas , D. Lieber , G. Martyna , K. Maturu , J. Moreira , D. Newns , M. Newton , R. Philhower , T. Picunko , J. Pitera , M. Pitman , R. Rand , A. Royyuru , V. Salapura , A. Sanomiya , R. Shah , Y. Sham , S. Singh , M. Snir , F. Suits , R. Swetz , W. C. Swope , N. Vishnumurthy , T. J. C. Ward , H. Warren , R. Zhou, Blue Gene: a vision for protein science using a petaflop supercomputer, IBM Systems Journal, v.40 n.2, p.310-327, February 2001
• 7: Bernard M. E. Moret , David A. Bader , Tandy Warnow, High-Performance Algorithm Engineering for Computational Phylogenetics, The Journal of Supercomputing, v.22 n.1, p.99-111, May 2002 [doi>10.1023/A:1014362705613]
• 8: Moret, B., Wyman, S., Bader, D., Warnow, T., and Yan, M. A new implementation and detailed study of breakpoint analysis. In Proceedings of the Sixth Pacific Symposium on Biocomputing 2001 (Big Island, HI, Jan. 3--7, 2001). World Scientific Publishing Co., Inc., Hackensack, NJ, 2001, 583--594.
• 9: Saitou, N. and Nei, M. The neighbor-joining method: A new method for reconstruction of phylogenetic trees. Molec. Biol. Evol. 4, 4 (July 1987), 406--425.
• 10: Sankoff, D. and Blanchette, M. Multiple genome rearrangement and breakpoint phylogeny. J. Comput. Biol. 5, 3 (Fall 1998), 555--570.
• 11: Schena, M., Shalon, D., Davis, R., and Borown, P. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 5235 (Oct. 20, 1995), 456--460.
• 12: Venter, J. et al. The sequence of the human genome. Science 291, 5507 (Feb. 16, 2001), 1304--1351.

INDEX TERMS

Primary Classification:
  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES

Additional Classification:
  C. Computer Systems Organization
  C.2 COMPUTER-COMMUNICATION NETWORKS

  H. Information Systems
  H.5 INFORMATION INTERFACES AND PRESENTATION (I.7)
      H.5.1 Multimedia Information Systems

  I. Computing Methodologies
  I.6 SIMULATION AND MODELING
      I.6.0 General
      I.6.1 Simulation Theory
      I.6.2 Simulation Languages
      I.6.3 Applications
      I.6.7 Simulation Support Systems
      I.6.8 Types of Simulation