Mapping the Genotype–Phenotype Relationship in Cellular Signaling Networks: Building Bridges Over the Unknown - Systems Biology: Networks, Models, and Applications - page 162

REFERENCES
1. Der, S. D., A. Zhou, B. R. Williams, et al. Identification of genes differentially

regulated by interferon alpha, beta, or gamma using oligonucleotide
arrays. Proceedings of the National Academy of Sciences USA , 95(26):15623-8,
1998.

2. Orlando, V. Mapping chromosomal proteins in vivo by formaldehyde-

crosslinked-chromatin immunoprecipitation. Trends in Biochemical Sciences ,
25(3):99-104, 2000.

3. Orlando, V., H. Strutt and R. Paro. Analysis of chromatin structure by in

vivo formaldehyde cross-linking. Methods , 11(2):205-14, 1997.

4. Buck, M. J. and J. D. Lieb. ChIP-chip: considerations for the design, analy-

sis, and application of genome-wide chromatin immunoprecipitation
experiments. Genomics , 83(3):349-60, 2004.

5. Dunn, K. L., P. S. Espino, B. Drobic, et al. The Ras-MAPK signal transduc-

tion pathway, cancer and chromatin remodeling. International Journal of
Biochemistry and Cell Biology , 83(1):1-14, 2005.

6. Kirmizis, A. and P. J. Farnham. Genomic approaches that aid in the identi-

fication of transcription factor target genes. Experimental Biology and
Medicine , 229(8):705-21, 2004.

7. Hanlon, S. E. and J. D. Lieb. Progress and challenges in profiling the

dynamics of chromatin and transcription factor binding with DNA
microarrays. Current Opinion in Genetic Development , 14(6):697-705, 2004.

8. Banerjee, N. and M. Q. Zhang. Identifying cooperativity among transcrip-

tion factors controlling the cell cycle in yeast. Nucleic Acids Research ,
31(23):7024-31, 2003.

9. Patterson, S. D. and R. H. Aebersold. Proteomics: the first decade and

beyond. Nature Genetics , 33(Suppl):311-23, 2003.

10. Chittur, S. V. DNA microarrays: tools for the 21st century. Combinatorial

Chemistry and High Throughput Screening , 7(6):531-7, 2004.

11. DeRisi, J. L., V. R. Iyer and P. O. Brown. Exploring the metabolic and

genetic control of gene expression on a genomic scale. Science ,
278(5338):680-6, 1997.

12. Nagaraj, V. H., R. A. O'Flanagan, A. R. Bruning, et al. Combined analysis

of expression data and transcription factor binding sites in the yeast
genome. BMC Genomics , 5(1):59, 2004.

13. Alizadeh, A. A., M. B. Eisen, R. E. Davis, et al. Distinct types of diffuse

large B-cell lymphoma identified by gene expression profiling. Nature ,
403(6769):503-11, 2000.

14. Schena, M., D. Shalon, R. W. Davis, et al. Quantitative monitoring of gene

expression patterns with a complementary DNA microarray. Science ,
270(5235):467-70, 1995.

15. Pease, A. C., D. Solas, E. J. Sullivan, et al. Light-generated oligonucleotide

arrays for rapid DNA sequence analysis. Proceedings of the National
Academy of Sciences USA , 91(11):5022-6, 1994.

16. Venter, J. C., M. D. Adams, G. G. Sutton, et al. Shotgun sequencing of the

human genome. Science , 280(5369):1540-2, 1998.

17. Bernal, A., U. Ear and N. Kyrpides. Genomes OnLine Database (GOLD): a

monitor of genome projects world-wide. Nucleic Acids Research ,
29(1):126-7, 2001.