Oligonucleotide Array Technology

Lipshutz, R. J, S. Fodor, T. Gingeras and D. Lockhart. (1999). High density synthetic ologonucleotide arrays. Nature Genetics, supplement, Vol 21: 20-24

Li, C. and Wong W.H. (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci., 98, 31-36.

Lockhart, D., H. Dong, M. Byrne, M. Follettie, M. Gallo, M. Chee, M. Mittmann, C. Wang, M. Kobayashi, H. Horton, and E. Brown. (1996). Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14: 1675-1680

Wodicka, L., H. Dong, M. Mittmann, M. Ho, and D. Lockhart. (1997). Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 15: 1359-1367

C-DNA Microarrays Technology

Chen Y, Dougherty E, Bittner M. Ratio-Based Decisions and the Quantitative Analysis of cDNA Micro-array Images. Journal of Biomedical Optics 2: 364 (1997).

Duggan D.J., Bittner M., Chen Y., Meltzer P., Trent J .M. Expression profiling using cDNA microarrays. Nat Genet 21(1 Suppl):10-4, 1999. Review.

Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett DE Jr, Hartwell LH, Brown PO, Friend SH [Rosetta/Stanford]. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med. 1998 Nov;4(11):1293-301

Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science1995 Oct 20;270(5235):467-70

Shalon D, Smith SJ, Brown PO. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 1996 Jul;6(7):639-45

Other Arrays: SNP, Genomic, Tissue, Proteins, etc.

Kononen J, Bubendorf L, Kallioniemi A, Barlund M, Schraml P, Leighton S, Torhorst J, Mihatsch MJ, Sauter G, Kallioniemi OP. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med 1998 Jul;4(7):844-847

G. MacBeath and S.L. Schreiber, Printing Proteins as Microarrays for High-Throughput Function Determination, Science 2000, September 8; 289(5485): p. 1760-1763.

Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Haab, B.B., Dunham M.J., and Brown, P.O. Genome Biology 2001 2(2): research0004.1-0004.13

Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO [Stanford] Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 1999 Sep;23(1):41-6

Wang DG, Fan JB, et al, Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 1998 May 15;280(5366):1077-82

Analysis methods (high-level):

Alon, U., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S., Mack, D., Levine, A. J. (1999). Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. U. S. A. 96: 6745-6750

Alter, O., et al. (2000), Singular value decomposition for genome-wide expression data processing and modeling. PNAS 97(18):10101-10106.

Eisen, M., P. Spellman, P. Brown, and D. Botstein. (1998). Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. 95: 14863-14868

Brown MPS, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M, Haussler D (2000) Knowledge-based analysis of microarray gene expression data by using support vector machines. PNAS, 97, 262-267.

Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander E, Golub T (1998) Interpreting patterns of gene expression with self-organizing maps: methods and applications to hematopoetic differentiation. PNAS, 96, 2907-2912.

For statistical methods see:

Gary Churchill: http://aretha.jax.org/jax-cgi/churchill/start/index.cgi

Art Owen: http://www-stat.stanford.edu/~owen/

Terry Speed: http://www.stat.berkeley.edu/users/terry/zarray/Html/index.html

Rob Tibshirani: http://www-stat.stanford.edu/~tibs/lab/index.html