DNA Microarray References


Reviews 

Schena M Genome analysis with gene expression microarrays. Bioessays 18:427-431, 1996.

Kozian DH, Kirschbaum BJ Comparative gene-expression analysis. Trends in Biotechnology 17:73-78, 1999.

Watson A, Mazumder A, Stewart M, Balasubramanian S Technology for microarray analysis of gene expression. Current Opinion in Biotechnology 9:609-614, 1998



Oligonucleotide Chips  

McGall, G., Labadie, J. Brock, P., Wallraff, G., Nguyen, T., and Hinsberg, W. Light-Directed Synthesis of High-Density Oligonucleotide Arrays Using Semiconductor Photoresists. Proc.Natl. Acad. Sci. U.S.A. 93:13555-13560,1996.

Lipshutz, R.J., Fodor, S.P.A., Gingeras, T.R., and Lockhart, D.J. High Density Synthetic Oligonucleotide Arrays. Nature Genetics. 21:20-24, 1999.

Singh-Gasson S, Green RD, Yue YJ, Nelson C, Blattner F, Sussman MR, Cerrina F, Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nature Biotechnology 17:974-978, 1999.



Bioelectronic Chips  

Cheng, J., Sheldon, E.L., Wu, L., Uribe, A., Gerrue, L.O., Carrino, J., Heller, M., and O'Connell, J. Electric field controlled preparation and hybridization analysis of DNA/RNA from E. coli on microfabricated bioelectronic chips. Nature Biotechnology, 16: 541-546, 1998.

Gilles, P., Wu, D., Foster, C., Dillon, P., and Chanock, S. Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips. Nature Biotechnology, 17: 365-370, 1999.

Cheng J, Sheldon EL, Wu L, Uribe A, Gerrue LO, Carrino J, Heller MJ, O'Connell JP, Nanotechnology,Miniaturization, Dielectrophoresis, Electroniclysis. Preparation and hybridization analysis of DNA/RNA from E-coli on microfabricated bioelectronic chips. Nature Biotechnology 16:541-546, 1998.



Microarrays and Macroarrays 

Brown PO, Botstein D. Exploring the new world of the genome with DNA microarrays. Nature Genetics 21:33-37,1999. This citation provides the rationale for data-driven research as opposed to hypothesis-driven research.

Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. Expression profiling using cDNA microarrays. Nature Genetics 21:10-14,1999.

Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470, 1995.

Zhao N, Hashida H, Takahashi N, Misumi Y, Sakaki Y High-density cDNA filter analysis: a novel approach for large-scale, quantitative analysis of gene expression. Gene 156:207-213, 1995.


Bioinformatics

Bassett DE, Eisen MB, Boguski MS Gene expression informatics - it's all in your mine. Nature Genetics 21:51-55,1999.

Bowtell DDL Options available - from start to finish - for obtaining expression data by microarray. Nature Genetics 21:25-32, 1999.

Ermolaeva O, Rastogi M, Pruitt KD, Schuler GD, Bittner ML, Chen Y, Simon R, Meltzer P, Trent JM, Boguski MS. Data management and analysis for gene expression arrays. Nature Genetics 20:19-23, 1998.

Hilsenbeck SG, Friedrichs WE, Schiff R, O'Connell P, Hansen RK, Osborne CK, Fuqua SAW Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. Journal of the National Cancer Institute 91:453-459, 1999.

Wittes J, Friedman HP Searching for evidence of altered gene expression: a comment on statistical analysis of microarray data. Journal of the National Cancer Institute 91:400-401, 1999.

Bittner M, Meltzer P, Trent J Data analysis and integration: of steps and arrows. Nature Genetics 22:213-215, 1999.

Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proceedings of the National Academy of Sciences of the United States of America 96:2907-2912, 1999.

Toronen P, Kolehmainen M, Wong C, Castren E, Analysis of gene expression data using self-organizing maps. FEBS Letters 451:142-146, 1999.



Applications 

Weinstein JN, Myers TG, O'Connor PM, Friend SH, Fornace AJ, Jr., Kohn, KW, Fojo T, Bates SE, Rubinstein LV, Anderson NL, Buolamwini JK, van, Osdol WW, Monks AP, Scudiero DA, Sausville EA, Zaharevitz DW, Bunow, B, Viswanadhan VN, Johnson GS, Wittes RE, Paull KD. An information-intensive approach to the molecular pharmacology of cancer. Science 275:343-349, 1997.

Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proceedings of the National Academy of Sciences of the United States of America 93:10614-10619, 1996.

DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen, Y, Su YA, Trent JM (1996) Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nature Genetics 14:457-460, 1996.

Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I The transcriptional program of sporulation in budding yeast. Science 282:699-705, 1998.



Technology 

Southern E, Mir K, Shchepinov M Molecular interactions on microarrays. Nature Genetics 21:5-9, 1999.

Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G Making and reading microarrays. Nature Genetics 21:15-19, 1999.

Baldwin D, Crane V, Rice D A comparison of gel-based, nylon filter and microarray techniques to detect differential RNA expression in plants. Current Opinion in Plant Biology 2:96-103, 1999.

Mir KU, Southern EM. Determining the influence of structure on hybridization using oligonucleotide arrays. Nature Biotechnology 17:788-792, 1999.

Bertucci F, Bernard K, Loriod B, Chang YC, Granjeaud S, Birnbaum D, Nguyen C, Peck K, Jordan BR Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples. Human Molecular Genetics 8:1715-1722, 1999.