Selected references

  

Our microarray project with Arabidopsis

Reymond P and Farmer EE. Jasmonate and salicylate as global signals for defense gene expression. Curr Op Plant Biol 1: 404-411 (1998).

Reymond P., Weber H., Damond M. and Farmer E.E. Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis. Plant Cell 12: 707-719 (2000).

Reymond P. DNA microarrays and plant defence. Plant Physiol Biochem 39: 313-321 (2001). Special issue: Plant genomics.

Stintzi A., Weber H., Reymond P., Browse J. and Farmer E.E.. Plant defense in the absence of jasmonic acid: The role of cyclopentenones PNAS 98: 12837-12842 (2001).

Alméras E., Stolz S., Vollenweider S., Reymond P., Mène-Saffrané L., and Farmer, E.E., Reactive electrophile species activate defense gene expression in Arabidopsis. Plant J. 34, 205-216 (2003).

Weber H., Chételat A., Reymond P. and Farmer E.E. (2004) Selective and powerful stress gene expression in Arabidopsis in response to malondialdehyde. Plant J. 37:877-888.

 

General

Castellino A. When the chips are down. Genome Research 7: 943-946 (1997)

Hoheisel J. Oligomer-chip technology. Trends in Biotechnology 15: 465-469 (1997)

Marshall A., Hodgson J. DNA chips: An array of possibilities. Nature Biotechnology 16: 27-31 (1998).

Johnston M. Gene chips: Array of hope for understanding gene regulation. Current Biology 8: R171-R174 (1998).

 

Description of the technology

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

Shalon D, Smith SJ, Brown PO. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Research 6: 639-645 (1996).

Schena M. Genome analysis with gene expression microarrays. BioEssays. 18: 427-431 (1996).

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).

Graves DJ poweful tools for genetic analysis come of age. Trends in Biotechnology 17: 127-134 (1999).

 

Several papers on microarrays: nature genetics supplement-volume 21-January 1999

 

Applications

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

Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. USA 93: 10614-10619 (1996).

DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686 (1997).

Heller RA, Schena M, Chai A, Shalon D, Bedilion T, Gilmore J, Woolley DE, Davis RW. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci USA 94: 2150-2155 (1997).

Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci USA 94: 13057-13062 (1997).

Trent JM, Bittner M, Zhang J, Wiltshire R, Ray M, Su Y, Gracia E, Meltzer P, DeRisi J, Penland L, Brown P. Use of microgenomic technology for analysis of alterations in DNA copy number and gene expression in malignant melanoma. Clinical and Experimental Immunology 107 Suppl 1: 33-40 (1997).

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).

Ruan Y, Gilmore J, Conner T. Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. The Plant Journal 15: 821-833 (1998).

Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell ccycle-regulated genes of the yeast Saccharomyces cerevisiae by microaray hybridization. Molecular Biology of the Cell 9: 3273-3297 (1998).

Iyer VR, Eisen M, Ross DT, Schuler G, Moore T, Lee JCF, Trent JM, Staudt LM, Hudson J, Boguski MS, Lashkari D, Shalon D, Botstein D, Brown PO. The transcriptional program in the response of human fibroblasts to serum. Science 283: 83-87 (1999).

 

Up-to-date list of papers on microarrays:

http://linkage.rockefeller.edu/wli/microarray/