Modeling of DNA microarray data by using physical properties of hybridization

Proceedings of the National Academy of Sciences of the United States of America

Volumn 100, Issue 13, 2003, Pages 7575-7580

  Held, G A ^a   Grinstein, G ^a   Tu, Y ^a  

^a IBM T J WATSON RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CORRELATION ANALYSIS; DNA HYBRIDIZATION; DNA MICROARRAY; MOLECULAR MODEL; PRIORITY JOURNAL; VALIDATION PROCESS;

ALGORITHMS; BIOPHYSICS; DOSE-RESPONSE RELATIONSHIP, DRUG; HUMANS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; STATISTICS; THERMODYNAMICS;

EID: 0037934649     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0832500100     Document Type: Article

References (19)

1. Brown, P. O. & Botstein, D. (1999) Nat. Genet. 21, 33-37.
2. Lipshutz, R. J., Fodor, S. P. A., Gingeras, T. R. & Lockhart, D. J. (1999) Nat. Genet. 21, 20-24.
3. Lockhart, D. J., Dong, H. L., Byrne, M. C., Follettie, M. T., Gallo, M. V., Chee, M. S., Mittmann, M., Wang, C. W., Kobayashi, M., Horton, H. & Brown, E. L. (1996) Nat. Biotechnol. 14, 1675-1680.
4. Affymetrix (2001) Statistical Algorithms Reference Guide, Affymetrix Technical Note (Affymetrix, Santa Clara, CA).
5. Mount, D. W. (2001) Bioinformatics: Sequence and Genome Analysis (Cold Spring Harbor Lab. Press, Plainview, NY), pp. 519-523.
6. Li, C. & Wong, W. H. (2001) Proc. Natl. Acad. Sci. USA 98, 31-36.
7. Naef, F., Hacker, C. R., Patil, N. & Magnasco, M. (2002) Genome Biol. 3, research0018.1-0018.11.
8. Tu, Y., Stolovitzky, G. & Klein, U. (2002) Proc. Natl. Acad. Sci. USA 99, 14031-14036.
9. Affymetrix (2001) Array Design for the GeneChip Human Genome U133 Set, Affymetrix Technical Note (Affymetrix, Santa Clara, CA).
10. Affymetrix (2001) New Statistical Algorithms for Monitoring Gene Expression on GeneChip Probe Arrays, Affymetrix Technical Note (Affymetrix, Santa Clara, CA).
11. SantaLucia, J. (1998) Proc. Natl. Acad. Sci. USA 95, 1460-1465.
12. Forman, J. E., Walton, I. D., Stern, D., Rava, R. P. & Trulson, M. O. (1998) in Molecular Modeling of Nucleic Acids, eds. Leontis, N.B. & SantaLucia, J. (Am. Chem. Soc., Washington, DC), Vol. 682, pp. 206-228.
13. Peyret, N., Seneviratne, P. A., Allawi, H. T. & SantaLucia, J. (1999) Biochemistry 38, 3468-3477.
14. Hill, A. A., Brown, E. L., Whitley, M. Z., Tucker-Kellog, G., Hunter, C. P. & Slonim, D. K. (2001) Genome Biol. 2, research 0055.1-0055.13.
15. Hoffmann, R., Seidl, T. & Dugas, M. (2002) Genome Biol. 3, research0033.1-0033.11.
16. Dai, H. Y., Meyer, M., Stepaniants, S., Ziman, M. & Stoughton, R. (2002) Nucleic Acids Res. 30, e86.
17. Kepler, T. B., Crosby, L. & Morgan, K. T. (2002) Genome Biol. 3, research0037.1-0037.12.
18. Cantor, C. R. & Schimmel, P. R. (1980) Biophysical Chemistry Part III: The Behavior of Biological Macromolecules (Freeman, San Francisco).
19. Hekstra, D., Taussig, A. R., Magnasco, M. & Naef, F. (2003) Nucleic Acids Res. 31, 1962-1968.