Greenbaum et al 23 Molecular Cell Biology 19(3): 1720-30. Harry, J. L., M. R. Wilkins, et al. (2000). Proteomics: Capacity versus utility. Electrophoreisis 21(6): 1071-1081. Hatzimanikatis, V., L. H. Choe, et al. (1999). Proteomics: theoretical and experimental considerations. Biotechnol Prog 15(3): 312-8. Haynes, P.A. and Yates, J.R. (2000) Proteome profiling-pitfalls and progress. Yeast 17: 81-87. Hegyi, H. and M. Gerstein (1999). The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J Mol Biol 288(1): 147-64. Holstege, F. C., E. G. Jennings, et al. (1998). Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95(5): 717-728. Ishii M., S.Hashimoto, et al. (2000). Direct Comparison of GeneChip and SAGE on the Quantitative Accuracy in Transcript Profiling Analysis. Genomics 68(2):136-143. Ito, T., K. Tashiro, et al. (2000). Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci 97(3): 1143-1147. Jackson, R. J. and M. Wickens (1997). Translational controls impinging on the 5'-untranslated region and initiation factor proteins. Curr Opin Genet Dev 7(2): 233-41. Jacobs Anderson, J. S. and R. Parker (2000). Computational identification of cis-acting elements affecting post- transcriptional control of gene expression in Saccharomyces cerevisiae. Nucleic Acids Res 28(7): 1604-17. Jaeger, J. A., D. H. Turner, et al. (1990). Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol 183: 281-306. Jansen, R. and M. Gerstein (2000). Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins. Nucleic Acids Res 28(6): 1481-8. Jelinsky, S. A. and L. D. Samson (1999). Global response of Saccharomyces cerevisiae to an alkylating agent. Proc Natl Acad Sci U S A 96(4): 1486-91. Jones, D. T. (1998). Do transmembrane protein superfolds exist? FEBS Lett 423(3): 281-5. Jones, D. T. (1999). GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 287(4): 797-815. Kidd, D et al. (2001) Profiling serine hydrolase activities in complex proteomes. Biochemistry 40(13):4005-4015. Klaff, P., D. Riesner, et al. (1996). RNA structure and the regulation of gene expression. Plant Mol Biol 32(1-2): 89-106. Klose, J. (1975). Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26(3): 231-43. Krogh, A. et al (2001).Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305(3):567-580.   Lin, J. and M. Gerstein (2000). Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res 10(6): 808- 18. Lindahl, L. and A. Hinnebusch (1992). Diversity of mechanisms in the regulation of translation in prokaryotes and lower eukaryotes. Curr Opin Genet Dev 2(5): 720-6. Lipshutz, R. F. S., Gingeras TR, Lockhart DJ (1999). High density synthetic oligonucleotide arrays. Nature Genetics 21(1): 20-24.