A network model for gene regulation

Computers and Chemical Engineering

Volumn 31, Issue 8, 2007, Pages 950-961

  Gupta, Rishi R ^a   Achenie, Luke E K ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Boolean algebra; Gene regulation; Microarray; Network; Time series

Indexed keywords

BOOLEAN ALGEBRA; DATABASE SYSTEMS; MATHEMATICAL MODELS; MICROARRAYS; RATS; TIME SERIES ANALYSIS;

BIOLOGICAL PROCESSES; GENE REGULATION; GENE REGULATORY NETWORKS;

GENE EXPRESSION;

BOOLEAN ALGEBRA; DATABASE SYSTEMS; GENE EXPRESSION; MATHEMATICAL MODELS; MICROARRAYS; RATS; TIME SERIES ANALYSIS;

EID: 34248212152     PISSN: 00981354     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compchemeng.2006.08.008     Document Type: Article

References (48)

1. Anon, 2006 http://www.biocarta.com
2. Anon, 2006, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed
3. Bittner M., Meltzer P., Chen Y., Jiang Y., Seftor E., Hendrix M., et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406 (2000) 536-540
4. Brownstein M.J., Trent J.M., and Boguski M.S. In: Patterson M., and Handel M. (Eds). Functional genomics, trends guide to bioinformatics (1998), Elsevier, Oxford 27-29
5. Collado-Vides J. Integrative representations of the regulation of gene expression. In: Collado-Vides J., Mag-asanik B., and Smith T.F. (Eds). Integrative approaches to molecular biology (1996), MIT Press, Cambridge, MA 179-203
6. Chu S., DeRisi J., Eisen M., Mulholland J., Botstein D., Brown P.O., et al. The transcriptional program of sporulation ion budding yeast. Science 282 (1998) 699-705
7. Hasty J., Isaacs F., Dolnik M., McMillen D., and Collins J.J. Designer gene networks: Towards fundamental cellular control. CHAOS 11 1 (2001) 207-220
8. Das A. How the phage lambda N gene product suppresses transcription termination: Communication of RNA polymerase with regulatory proteins mediated by signals in nascent RNA. Journal of Bacteriology 174 (1992) 6711-6716
9. D'haeseleer P., Wen X., Fuhrman S., and Somogyi R. Linear modeling of mRNA expression levels during CNS development and injury. Pacific Symposium on Biocomputing '99 (1999), World Scientific Publishing Co. 41-52
10. D'haeseleer, P. (2000). Reconstructing Gene Networks from Large Scale Gene Expression Data. Ph.D. dissertation, University of New Mexico.
11. D'haeseleer P., Liang S., and Somogyi R. Genetic network inference: From co-expression clustering to reverse engineering. Bioinformatics 16 8 (2000) 707-726
12. Echols H., Court D., and Green L. Genetics 83 (1976) 5-10
13. Dodd I.B., Shearwin K.E., and Egan J.B. Revisited gene regulation in bacteriophage λ. Current Opinion in Genetics and Development 15 (2005) 145-152
14. DeRisi J.L., Iyer V.R., and Brown P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278 5338 (1997) 680-686
15. Eisen M.B., Spellman P.T., Brown P.O., and Botstein D. Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America 95 (1998) 14863-14868
16. Fields S., Kohara Y., and Lockhart D.J. Functional genomics. Proceedings of the National Academy of Sciences of the United States of America 96 (1999) 8825-8826
17. Garg S., Hansen M.F., Rowe D.W., and Achenie L.E.K. An adaptive strategy for single and multi cluster gene assignment. Biotechnology Program 19 (2003) 1142-1148
18. Gross C.A. In: Neidhardt F.C., Curtiss III R., Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W.S., Riley M., Schaechter M., and Umbarger H.E. (Eds). Escherichia coli and Salmonella: Cellular and molecular biology (1996), ASM Press, Washington, DC 1389-1399
19. Gupta, R. R., Achenie, L. E. K., Rowe, D. W. & Kalajcik, I. (2006). Computational and statistical analysis of microarray data of fac sorted calvarial osteoblast differentiation, in preparation.
20. Herskowitz I., and Hagen D. The lysis-lysogeny decision of phage lambda: Explicit programming and responsiveness. Annual Review of Genetics 14 (1980) 399-445
21. Iyer V.R., Eisen M.B., Ross D.T., Schuler G., Moore T., Lee J.C.F., et al. The transcriptional program in the response of human fibroblasts to serum. Science 283 (1999) 83-87
22. Kalajzic I., Staal A., Yang W., Wu Y., Johnson S.E., Feyen J.H.M., et al. Gene expression profile of osteoprogenitor lineage cells at defined stages of differentiation. Journal of Biological Chemistry 280 26 (2004) 24618-24626
23. Kanehisa M., and Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28 1 (2000) 27-30
24. Kaufman S.A. Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology 22 (1969) 437-467
25. Kiehl, Thomas R., Mattheyses, Robert M., Simmons, and Melvin K. Hybrid simulation of cellular behavior. Bioinformatics 20 (2004) 316-322
26. Kourilsky P. Molecular Genetics and Genomics 122 (1973) 183-195
27. Kobiler O., Rokney A., Friedman N., Court D.L., Stavans J., and Oppenheim A.O. Quantitative kinetic analysis of the bacteriophage λ genetic network. PNAS 102 12 (2005) 4470-4475 March 22
28. Lander E.S. The new genomics: Global views of biology. Science 274 (1996) 536-539
29. Loomis W.F., and Sternberg P.W. Genetic networks. Science 269 (1995) 649
30. Marnellos G., and Mjolsness E. Pacific Symposium on Biocomputing 5 (1998) 30-41
31. Marnellos G., Deblandre G.A., Mjolsness E., and Kintner C. Pacific Symposium on Biocomputing 12 (2000) 329-340
32. McAdams H.H., and Arkin A. It's a noisy business! Genetic regulation at the nanomolar scale. Trends in Genetics 15 2 (1999) 65-69
33. McAdams H.H., and Shapiro L. Circuit simulation of genetic networks. Science 269 (1995) 650-656
34. Narberhaus F. Negative regulation of bacterial heat shock genes. Molecular Microbiology 31 (1999) 1-8
35. Newton M.A., Noueiry A., Sarkar D., and Ahlquist P. Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics 5 (2004) 155-176
36. Nowak R. Entering the postgenome era. Science 270 (1995) 368-371
37. Palsson B.O. What lies beyond bioinformatics?. Nature Biotechnology 15 (1997) 3-4
38. Ptashne M. Genetic switch: Phage λ and higher organisms, blackwell science. 2nd ed. (1992), Malden MA and Cell Press, Cambridge, UK
39. Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9 (1998) 3273-3297
40. Staden R. Graphic methods to determine the function of nucleic acid sequences. Nucleic Acids Research 12 (1984) 521-538
41. Strohman R.C. The coming Kuhnian revolution in biology. Nature Biotechnolgy 15 (1997) 194-200
42. Thieffry D. From global expression data to gene networks. BioEssays 21 11 (1999) 895-899
43. Tian T., and Burrage K. Bistability and switching in the lysis/lysogeny genetic regulatory network of bacteriophage λ. Journal of Theoretical Biology 227 (2004) 229-237
44. Tusher V.G., Tibshirani R., and Chu G. Proceedings of the National Academy of Sciences of the United States of America 98 (2001) 5116-5121
45. Vohradsky J. FASEB J. 15 (2001) 846-854
46. Wen X., Fuhrman S., Michaels G.S., Carr D.B., Smith S., Barker J.L., et al. Large-scale temporal gene expression mapping of central nervous system development. Proceedings of the National Academy of Sciences of the United States of America 95 1 (1998) 334-339 Jan 6
47. Yura T., and Nakahigashi K. Regulation of the heat-shock response. Current Opinion in Microbiology 2 (1999) 159-165
48. Yura T., Nagai H., and Mori H. Regulation of the heat-shock response in bacteria. Annual Review of Microbiology 47 (1993) 321-350