The shuffle index and evaluation of models of signal transduction pathways

Proceedings of the Annual Southeast Conference

Volumn 2007, Issue , 2007, Pages 250-255

  Allen, Edward E ^a   Diao, Liyang ^a   Fetrow, Jacquelyn S ^b   John, David J ^a   Loeser, Richard F ^c   Poole, Leslie B ^d  

^a WAKE FOREST UNIVERSITY   (United States)

^b Departments of Computer Science and Physics

^c Section of Molecular Medicine   (United States)

^d WAKE FOREST SCHOOL OF MEDICINE   (United States)

Author keywords

Biological network modeling; Computational algebra; Computational biology; Game theory; Shuffle index

Indexed keywords

BIOLOGICAL NETWORK MODELING; COMPUTATIONAL ALGEBRA; COMPUTATIONAL BIOLOGY; SHUFFLE INDEX;

ALGEBRA; COMPUTATIONAL METHODS; DATA REDUCTION; GAME THEORY; PROTEINS; TIME SERIES ANALYSIS;

ALGORITHMS;

EID: 34248362847     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1233341.1233386     Document Type: Conference Paper

References (15)

1. E. E. Allen, J. S. Fetrow, L. W. Daniel, S. J. Thomas, and D. J. John. Algebraic dependency models of protein signal transduction networks from time-series data. Journal of Theoretical Biology, 238(2):317-330, January 2006.
2. E. E. Allen, J. S. Fetrow, D. J. John, and S. J. Thomas. Heuristics for dependency conjectures in proteomic signaling pathways. In Proceedings of the 43rd Annual Association for Computing Machinery Southeast Conference, pages 75-79, 2005.
3. E. E. Allen, A. Pecorella, J. Fetrow, D. J. John, and W. Turkett. Reconstructing networks using co-temporal functions. In M. Silaghi, editor, Proceedings of the 44th Annual Association for Computing Machinery Southeast Conference, pages 417-422, Melbourne, Florida, March 2006. ACM, ACM Press.
4. R. Baserga, A. H. an M. Rubini, M. Prisco, and B. Valentinis. The igf-i receptor in cell growth. Biochem Biophys Acta., 1332(3):105-125, June 1997.
5. A. A. Butler, S. Yakar, I. H. Gewolb, M. Karas, Y. Okubo, and D. LeRoith. Insulin-like growth factor-i receptor signal transduction: at the interface between physiology and cell biology. Comp Biochem Physio B Biochem Mol Bio., 121(1):19-26, September 1998.
6. I. P. Goulden and D. M. Jackson. Combinatorial Enumeration. Wiley Interscience, second edition, 1983.
7. H. Kitano. Computational cellular dynamics: a network-physics integral. Nature Reviews Molecular Cell Biology, 7:163, March 2006.
8. R. Laubenbacher and B. Stigler. A computational algebra approach to the reverse engineering of gene regulatory networks. Journal of Theoretical Biology, 229(4):523-537, August 2004.
9. R. F. Loeser, G. Shanker, C. S. Carlson, J. F. Gardin, B. Shelton, and W. E. Sonntag. Reduction in the chondrocyte response to insulin-like growth factor 1 in aging and osteoarthritis: studies in a non-human primate model of naturally occurring disease. Arthritis Rheum, 43:2110-2120, 2000.
10. H. Messai, Y. Duchossoy, A. Khatib, A. Panasyuk, and D. R. Mitrovic. Articular chondrocytes from aging rats respond poorly to insulin-like growth factor-1: an altered signaling pathway. Mech, Ageing Dev., 115:21-37, 2000.
11. K. Sachs, O. Perez, D. Pe'er, D. A. Lauffenburger, and G. P. Nolan. Causal protein-signaling networks derived from multiparameter single-cell data. Science, 308:523-529, April 2005.
12. A. Shanmuganathan, S. V. Avery, S. A. Willetts, and J. E. Houghton. Copper-induced oxidative stress in Saccharomyces cerevisiae targets enzymes of the glycolytic pathway. FEBS Letters, 556:253-259, December 2004.
13. R. J. Spillman. Classical and Contemporary Cryptology. Pearson Prentice Hall, second edition, 2005.
14. B. G. Starkman, J. D. Cravero, M. Delcarlo, and R. F. Loeser. Igf-i stimulation of proteoglycan synthesis by chondrocytes requires activation of the pi 3-kinase pathway but not erk mapk. Biochem J., 389(3):723-729, august 2005.
15. D. Ventura and T. M. T. An empirical comparison of discretization methods. Proceedings of the Tenth International Symposium on Computer and Information Sciences, pages 443-450, 1995.