Reconstruction of the genetic regulatory dynamics of the rat spinal cord development: Local Invariants approach

Journal of Biomedical Informatics

Volumn 35, Issue 5-6, 2002, Pages 343-351

  Fofanov, Yuriy ^a   Pettitt, B Montgomery ^a,b  

^a University of Houston   (United States)

^b University of Houston   (United States)

Author keywords

Gene expression; Genetic regulatory networks; Local Invariants; Reverse engineering

Indexed keywords

ACCURACY; ARTICLE; DATA BASE; DYNAMICS; EXPERIMENT; GENE; GENE EXPRESSION; GENETIC REGULATION; MATHEMATICS; MODEL; NONHUMAN; ORGANOGENESIS; PRIORITY JOURNAL; RAT; SPINAL CORD;

EID: 0043126917     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1532-0464(03)00035-2     Document Type: Article

References (24)

1. Reis B.Y., Butte A.S., Kohane I.S. Extracting knowledge from dynamics in gene expression. J. Biomed. Inform. 34:2001;15-27.
2. Roberts C.J., Nelson B., Marton M.J.et al. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science. 287:2000;873-880.
3. Endy D., Brent R. Modeling cellular behavior. Nature. 409:2001;391-395.
4. Chen T., He H.L., Church G.M. Modeling gene expression with differential equations. Pac. Symp. Biocomput. 4:1999;29-40.
5. Erb R.S., Michaels G.S. Sensitivity of biological models to errors in parameter estimates. Pac. Symp. Biocomput. 4:1999;53-64.
6. Weaver D.C., Workman C.T., Stormo G.D. Modeling regulatory networks with weight matrices. Pac. Symp. Biocomput. 4:1999;112-123.
7. Wahde M., Hertz J. Modeling genetic regulatory dynamics in neural development. J. Comput. Biol. 8(4):2001;429-442.
8. D'haeseleer P., Liang S., Somogyi R. Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics. 16(8):2000;707-726.
9. Rzhetsky A., Gomez S.M. Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics. 17(10):2001;988-996.
10. Voit E.O., Radivoyevitch T. Biochemical systems analysis of genome-wide expression data. Bioinformatics. 16(11):2000;1023-1037.
11. Wen X., Fuhrman S., Michaels G.S.et al. Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl. Acad. Sci. USA. 95:1998;334-339.
12. Press W.H., Teukolsky S.A., Vetterling W.T., Flannery B.P. Numeric recipes in C. 2nd ed. 1992;Cambridge University Press, Cambridge.
13. Wang X., Chosh S., Guo S. Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Res. 29(15):2001;e75-5.
14. Belosludtsev Y, Iverson B, Lemeshko S, et al. DNA microarrays based on noncovalent oligonucleotide attachment and hybridization in two dimensions. Anal Biochem 2001. Available from: http://www.idealibrary.com.
15. Ramdas L., Coombes K.R., Baggerly K.et al. Sources of nonlinearity in cDNA microarray expression measurements. Genome Biol. 2(11):2001;471-477.
16. Fofanov Y, Polinger V. Modeling temporal dynamics of gene expression with differential equations. Is the problem solvable? In: 12th International Genome Sequencing and Analysis Conference, Miami Beach, FL; 2000.
17. Fofanov Y, Polinger V. Causal relationships in genetic networks: a new generation of tools for gene expression Analysis. In: 4th Annual Conference on Computational Genomics, Baltimore, MD; 2000.
18. Fofanov Y, Polinger V. Causal relationships in genetic networks: a new approach for expression profile analysis. Technical Report #UH-CS-01-01. Available from: http://www.cs.uh.edu/~fofanov/r1.pdf.
19. Fofanov Y., Divnov S., Naumov A. Evolution-type modeling in the search of regularities based upon experimental results in physics. Problems Random Search. 11:1986;156-178. Zintane, Riga [in Russian].
20. Fofanov Y., Katsyuba O., Divnov S., Naumov A. An algorithm of structure identification of non-linear functional dependence. Avtometria. 6:1988;52-58. [in Russian].
21. Alon U., Barkai N., Notterman D.A.et al. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA. 96:1999;6745-6750.
22. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA. 95:1998;14863-14868.
23. Chomsky N. On certain formal properties of grammars. Inf. Contr. 2(2):1959;137-167.
24. Sebesta R.W. Concepts of programming languages. 4th ed. 1999;Addison-Wesley, Reading, MA.