Visualization challenges for a new cyber-pharmaceutical computing paradigm

Proceedings - IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics

Volumn , Issue , 2001, Pages 7-18

  Turner, R J ^a   Chaturvedi, K ^a   Edwards, N J ^a   Fasulo, D ^a   Halpern, A L ^a   Huson, D H ^a   Kohlbacher, O ^a   Miller, J R ^a   Reinert, K ^a   Remington, K A ^a   Schwartz, R ^a   Walenz, B ^a   Yooseph, S ^a   Istrail, S ^a  

^a CELERA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84963563106     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/PVGS.2001.964398     Document Type: Conference Paper

References (27)

1. AEBERSOLD, R., AND GOODLETT, D. R. Mass spectrometry in proteomics. Chemical Reviews 101 (2001), 269-295.
2. ALTSCHUL, S. F., GISH, W., MILLER, W., MYERS, E. W., AND LIPMAN, D. J. Basic local alignment search tool. Journal of Molecular Biology 215 (1990), 403-410.
3. ALTSHULER, D., POLLARA, V. J., COWLES, C. R., VAN ETTEN, W. J., BALDWIN, J., LINTON, L., AND LANDER, E. S. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407 (2000), 513-519.
4. BERMAN, H., WESTBROOK, J., FENG, Z., GILLILAND, G., BHAT, T., WEISSIG, H., SHINDYALOV, I., AND BOURNE, P. The protein data bank. Nucleic Acids Research 28 (2000).
5. BRODER, S., AND VENTER, J. C. Sequencing the entire genomes of free-living organisms: the foundation of pharmacology in the new millennium. Annu. Rev. Pharamacol. Toxicol. 40 (2000), 97-132.
6. BRODER, S., AND VENTER, J. C. Sequencing the entire human genome: Towards a new cyberpharmaceutical paradigm. Journal of Commercial Biotechnology 6, 4 (2000), 270-283.
7. BURGE, C., AND KARLIN, S. Prediction of complete gene structures in human genomic DNA. Journal of Molecular Biology 268 (1997), 78-94.
8. COLLINS, F. S., PATRINOS, A., JORDAN, E., CHAKRAVARTI, A., GESTELAND, R., AND WALTERS, L. New goals for the U. S. human genome project: 1998-2003. Science 282 (1998), 682-289.
9. DERISI, J., IYER, V., AND BROWN, P. Exploring the metabolic and genetic control of gene expression on a genome scale. Science 278 (1997), 680-686.
10. FLEISCHMANN, R., ADAMS, M., WHITE, O., CLAYTON, R., KIRKNESS, E., KERLAVAGE, A., BULT, C., TOMB, J.-F., BOUGHERTY, B., MERRICK, J., MCKENNEY, K., SUTTON, G., FITZHUGH, W., FIELDS, C., JOCAYNE, J., SCOTT, J., SHIRLEY, R., LIU, L.-I., GLODEK, A., KELLEY, J., WEIDMAN, J., PHILLIPS, C., SPRIGGS, T., HEDBLOM, E., COTTON, M., UTTERBACK, T., HANNA, M., NGUYEN, D., SAUDEK, D., BRANDON, R., FINE, L., FRITCHMAN, J., FUHRMANN, J., GEOGHAGEN, N., GNEHM, C., MCDONALD, L., SMALL, K., FRASER, C., SMITH, H., AND VENTER, J. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269 (1995), 496-512.
11. FLOREA, L., HARTELL, G., ZHANG, Z., RUBIN, G. M., AND MILLER, W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Research 8 (1998), 967-974.
12. GOLUB, T., SLONIM, D., TAMAYO, P., HUARD, C., CAASENBEEK, J., COLLER, H., LOH, M., DOWNING, J., CALIGIURI, M., BLOOMFIELD, C., AND LANDER, E. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286 (1999), 531-537.
13. GUSSIO, R., PATTABIRAMAN, N., ZAHAREVITZ, D. W., KELLOGG, G. E., TOPOL, I. A., RICE, W. G., SCHAEFFER, C. A., ERICKSON, J. W., AND BURT, S. K. All-atom models for the non-nucleoside binding site of HIV-1 reverse transcriptase complexed with inhibitors: a 3D QSAR approach. J. Med. Chem. 39 (1996).
14. HUMPHREY, W., DALKE, A., AND SCHULTEN, K. VMD-visual molecular dynamics. J. Molecular Graphics 14 (1996).
15. HUSON, D. H., HALPERN, A. L., LAI, Z., REINERT, K., MYERS, E. W., AND SUTTON, G. G. Comparing assemblies using fragments and mate-pairs. To appear at: "Workshop on Algorithms in Bioinformatics" (WABI-01), 2001.
16. HUSON, D. H., REINERT, K., AND MYERS, E. W. The greedy path-merging algorithm for sequence assembly. In Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB-01) (2001), pp. 157-163.
17. INTERNATIONAL HUMAN GENOME SEQUENCING CONSORTIUM. Initial sequencing and analysis of the human genome. Nature 409, 6822 (2001), 860-921.
18. LOCKHART, D., DONG, H., BYRNE, M., FOLLETTIE, M., GALLO, M., CHEE, M., MITTMANN, M., WANG, C., KOBAYASHI, M., HORTON, H., AND BROWN, E. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14, 13 (1996), 1675-1680.
19. MULLIKIN, J. C., HUNT, S. E., COLE, C. G., MORTIMORE, B. J., RICE, C. M., BURTON, J., MATTHEWS, L. H., PAVITT, R., PLUMB, R. W., SIMS, S. K., AINSCOUGH, R. M., ATTWOOD, J., BAILEY, J. M., BARLOW, K., BRUSKIEWICH, R. M., BUTCHER, P. N., CARTER, N. P., CHEN, Y., CLEE, C. M., COGGILL, P. C., DAVIES, J., DAVIES, R. M., DAWSON, E., FRANCIS, M. D., JOY, A. A., LAMBLE, R. G., LANGFORD, C. F., MACARTHY, J., MAL, L. V., MORELAND, A., OVERTON-LARTY, E. K., ROSS, M. T., SMITH, L. C., STEWARD, C. A., SULSTON, J. E., TINSLEY, E. J., TURNEY, K. J., WILLEY, D. L., WILSON, G. D., MCMURRAY, A. A., DUNHAM, I., ROGERS, J., AND BENTLEY, D. R. An SNP map of human chromosome 22. Nature 407 (2000), 516-520.
20. MYERS, E. W., SUTTON, G. G., DELCHER, A. L., DEW, I. M., FASULO, D. P., FLANIGAN, M. J., KRAVITZ, S. A., MOBARRY, C. M., REINERT, K. H. J., REMINGTON, K. A., ANSON, E. L., BOLANOS, R. A., CHOU, H.-H., JORDAN, C. M., HALPERN, A. L., LONARDI, S., BEASLEY, E. M., BRANDON, R. C., CHEN, L., DUNN, P. J., LAI, Z., LIANG, Y, NUSSKERN, D. R., ZHAN, M., ZHANG, Q., ZHENG, X., RUBIN, G. M., ADAMS, M. D., AND VENTER, J. C. A whole-genome assembly of Drosophila. Science 287 (2000), 2196-2204.
21. RISCH, N. J. Searching for genetic determinants in the new millennium. Nature 405 (2000), 847-856.
22. SACHIDANANDAM, R., WEISSMAN, D., SCHMIDT, S. C., KAKOL, J. M., STEIN, L. D., MARTH, G., SHERRY, S., MULLIKIN, J. C., MORTIMORE, B. J., WILLEY, D. L., HUNT, S. E., COLE, C. G., COGGILL, P. C., RICE, C. M., NING, Z., ROGERS, J., BENTLEY, D. R., KWOK, P. Y., MARDIS, E. R., YEH, R. T., SCHULTZ, B., COOK, L., DAVENPORT, R., DANTE, M., FULTON, L., HILLIER, L., WATERSTON, R. H., MCPHERSO, N. J. D., GILMAN, B., SCHAFFNER, S., VAN ETTEN, W. J., REICH, D., HIGGINS, J., DALY, M. J., BLUMENSTIEL, B., BALDWIN, J., STANGE-THOMANN, N., ZODY, M. C., LINTON, F., LANDER, E. S., AND ATSHULER, D. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409 (2001), 928-933.
23. SCHENA, M., HELLER, R., THERIAULT, T., KONRAD, K., LACHENMEIER, E., AND DAVIS, R. Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol. 16 (1998), 301-306.
24. THE ARABIDOPSIS GENOME INITATIVE. Analysis of the genome sequence of the flowering plant arabidopsis thaliana. Nature 408 (2000), 796-815.
25. The C.ELEGANS SEQUENCING CONSORTIUM. Sequence and analysis of the genome of c. elegans. Science 282 (1998), 2012-2018.
26. VENTER, J. C., ADAMS, M. D., MYERS, E. W., ET AL. The sequence of the human genome. Science 291 (2001), 1145-1434.
27. WODICKA, L., DONG, H., MITTMANN, M., HO, M., AND LOCKHART, D. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 15 (1997), 1359-1367.