Table of Contents *

• Articulation of hybrid (i.e. digital and analog) systems view in the context of transcriptional regulation processes and circuits.
• The development of ideas from entropy-based processes which maximize information contents/communication among components of a system in order to achieve global goals. These ideas view the biological processes in the context of stochastic dynamics governed by probability densities and distributions.
• Development of learning optimization approaches that incorporates on-line adaptation, without knowledge of the end results or explicit final goals or targets. This approach uses local information only to achieve global organization within the context of gene transcriptional regulation.
• Software decomposed into components, which elevates the granularity of programming. Plug-in compatible components enables large scale reuse that is necessary for a BIO-SPICE platform.

1. Keller, S.A., Mao, Y.M., Struffi, P., Margulies, C….and D. N. Arnosti "dCtBP dependent and independent repression activities of the Drosophila Knirps protein" (2000) Mol. Cell. Biol. 20: 7247-7258.
2. Hewitt, G.F., Strunk, B.S., Priputin, T., Wang, X.-D., Amey, R., Pabst, B.A., Kosman, D., Reinitz, J., and Arnosti, D.N. "Transcriptional repression by the Drosophila Giant protein: cis element positioning provides an alternative means of interpreting an effector gradient". Development, 126, 1201-1210.
3. Arnosti, D.N., Barolo, S., Levine., M, and Small, S. (1996) "The eve stripe 2 enhancer employs multiple modes of transcriptional synergy". Development 122, 205-214.
4. Arnosti, D.N., S. Gray, S. Barolo, J. Zhou and M. Levine (1996) "The gap protein knirps mediates both quenching and direct repression in the Drosophila embryo". EMBO J. 15, 3659-3666.
5. Small, S., Arnosti, D.N. and Levine, M. (1993) "Spacing ensures autonomous expression of different stripe enhancers in the even-skipped promoter". Development 119, 767-772.
6. M. Kulkarni and D.N. Arnosti, unpublished observations.
7. Mao, Y., Keller, S., Foley, K., Margulies, C., and Arnosti, D.N. A functional repression domain of the Knirps gap protein. (manuscript in preparation for Mol. Cell Biol.
8. Hewitt, G.F., Strunk, B.S., Priputin, T., Wang, X.-D., Amey, r., Pabst, B.A., Kosman, D., Reinitz, J., and Arnosti, D.N. Transcriptional repression by the Drosophila Giant protein: cis element positioning provides an alternative means of interpreting an effector gradient. Development, 126, 1201-1210.
9. Arnosti, D.N., Barolo, S., Levine., M, and Small, S. (1996) The eve stripe 2 enhancer employs multiple modes of transcriptional synergy. Development 122, 205-214.
10. Arnosti, D.N., S. Gray, S. Barolo, J. Zhou and M. Levine (1996) The gap protein knirps mediates both quenching and direct repression in the Drosophila embryo. EMBO J. 15, 3659-3666.
11. Small, S., Arnosti, D.N. and Levine, M. (1993) Spacing ensures autonomous expression of different stripe enhancers in the even-skipped promoter. Development 119, 767-772.
12. F.L. Lewis and V.L.Syrmos. " Optimal Control " John Wiley & Sons, INC. NY, 1995.
13. H.K.Khalil. " Nonlinear Control Systems. " Prentice Hall, INC. NJ, 1996
14. N.K.Bose and P.Liang. " Neural Network Fundamentals with graphs, algorithms, and applications. " McGraw-Hill, INC. 1996
15. S. Haykin. " Neural Networks : A Comprehensive Foundation. " Prentice Hall, INC. NJ, 1999
16. J.Birk and M.Zeitz. " Extended Luenberger Observer for Non-Linear Multivariable Systems. " INT.J.Control. Vol. 47, No.6, 1988. Pages 1823-1836
17. S.Raghavan and J.K.Hedrick. " Observer Design for a Class of Nonlinear Systems. " INT.J.Control. Vol. 59, No.2, 1994. Pages 515-528
18. M.Alamir."Optimization Based Nonlinear Observer revisited." INT.J.Control. Vol. 72, No. 13, 1999. Pages. 1204-1217
19. G.Zimmer. "State Observation by on-line Minimization. ".INT.J.Control. Vol. 60, No. 4 Pages 595-606
20. F.M.Salam and H.J.Oh. " Design of a Temporal Learning Chip for Signal Generation and Classification. " Journal on Analog Integrated Circuits and Signal Processing. Kluwer Academic Publishers, No. 18, 1999. Pages 229-242.
21. F.M.Salam. "On-Chip Temporal Learning for Recurrent Networks: Theory, Design, Implementation, and Tests. " In the book, Learning in Silicon, Kluwer Publishers Editors.
22. T. W. Lee, A.J. Bell, and R. Lambert, "Blind separation of delayed and convolved sources", NIPS, 1996, MIT press, Vol.9, pp758-764.
23. H. Yang and S. Amari: "Adaptive on-line learning algorithms for blind separation: Maximum entropy and minimal mutual information". Neural Comput., 9:1457–1482,1997.
24. S. Amari, S. Douglas, A. Cichocki, and H. Yang: "Multichannel blind deconvolution and equalization using the natural gradient." In Proc. IEEE Workshop on Signal Processing Adv. in Wireless Communications, pages 101–104, Paris, France, April 1997.
25. L. Zhang and A. Cichocki: "Blind separation/deconvolution of sources using canonical stable state-space models, Proceeding of the 1998 international Symposium on Nonlinear Theory and its Applications (NOLTA'98), Crans-Montana, Sept, 14-17, 1998, pp. 927-930.
26. F. M. A. Salam. "An adaptive network for blind separation of independent signals." International Symposium on Circuits and Systems, 1:431-1434, May 1993.
27. Ammar B. A. Gharbi and Fathi Salam: "Separation of Mixed Signals in Dynamic Environments: Formulation and some Implementation."; Appeared in IEEE Proc. of 37th Midwest Symposium on circuits and Systems'94, vol. 1, pp. 587-599, Lafayette, LA, USA.
28. Ammar B. A. Gharbi and Fathi Salam: "Implementation and Experimental Results of a Chip for the Separation of Mixed and Filtered Signals."; Appeared in the Journal of Circuits, Systems and Computers, vol.6, no.2, pp.115-139, April 1996.
29. A. B. Gharbi and F. M. Salam. "Implementation and experimental results of a chip for the separation of mixed and filtered signals."; Journal of Circuits, Systems and Computers, 6(2):115-139, April 1996.
30. G. Erten, F. M. Salam; "Real Time Separation of Audio Signals Using Digital Signal Processors"; Proceedings of the 40th Midwest Symposium on Circuits and Systems, 1997, Volume: 2, 1998 Page(s): 1237 –1240
31. Ammar B. A. Gharbi and Fathi Salam: "Algorithms for Blind Signal Separation and Recovery in Static and Dynamic Environments." Appeared in IEEE Proc. ISCAS'97, June 9-12, Hong Kong.
32. http://www.egr.msu.edu/annweb
33. Baeuerle, P.A. and Baltimore, D. 1996. NF-k B: Ten Years After. Cell 87, 13-20.
34. Blackwood, E.M., and Kadonaga, J.T. 1998. Going the distance: a current view of enhancer action. Science 281, 60-63.
35. Kroos, L., Zhang, B., Ichikawa, I., and Yu, Y.-T. N. 1999. Control of s factor activity during Bacillus subtilis sporulation. Mol. Microb. 31, 1285-1294.
36. Elowitz, M.B. and Liebler, S. 2000. A synthetic oscillatory network of transcirptional regulators. Nature 403, 335-338.
37. Gardner, T.S., Canto, C.R., and Collins, J.J., 2000. Construction of a genetic toggle switch in Escherichia coli . Nature 403, 339-342.
38. A. Nerode and W. Kohn, "An Autonomous Systems Control Theory: An Overview," The Proceedings of the IEEE Symposium on Computer-Aided Control System Design, Napa, CA, March 1992.
39. W. Bencze and G. Franklin, "A Separation Principle for Hybrid Control System Design," IEEE Control System Magazine, April 1995
40. B. McCarragher and H. Asada, "A Discrete Event Approach to the Control of Robotic Assembly Tasks," The Proceedings of ICRA’p3, Atlanta, GA, May 1993
41. Panos J. Antsaklis, James A. Stiver and Michael Lemmon, "Hybrid System Modeling and Autonomous Control Systems," in Hybrid Systems, R. Grossman, A. Nevode, A. Ravn, and H. Rischel, Eds, pp. 361-392, New York: Springer, 1993
42. M. S. Branicky, V. S. Borkar, S. K. Mitter, "A unified Framework for Hybrid Control: Model and Optimal Control Theory," IEEE Transactions on Automatic Control, vol 43, No. 1, January 1998
43. Recent Trends in the Stability Analysis of Hybrid Dynamical Systems, Anthony N. Michel, IEEE Transactions on Circuits and Systems – I: Fundamental theory, Vol 45, No. 1, January, 1999
44. Hui Ye, A. N. Michel, and Ling Hou, "Stability Theory for Hybrid Dynamical Systems," IEEE Transactions on Automatic Control, vol. 43, No. 4, pp. 461-474, April 1998
45. Michael S. Branicky, "Multiple Lyapunov Functions and Other Analysis Tools for Switched and Hybrid Systems," IEEE Transactions on Automatic Control, vol. 43, No. 4, pp. 475-485, April 1998
46. Jindong Tan and Ning Xi, "Singularityless Task Level Robot Motion Control --- A Hybrid System Approach," submitted to IEEE Transactions on Robotics and Automation
47. Spong, M.W., "Applications of Switching Control in Robot Locomotion," IEEE Conference on Decision and Control, Tampa, Fl., Dec. 16-18, 1998.
48. Bishop, B.E., and Spong, M.W., Control of Redundant Manipulators Using Logic-Based Switching, IEEE Conference on Decision and Control, Tampa, Fl., Dec. 16-18, 1998.
49. Austin D.J., McCarragher B.J., "Model-adaptive hybrid dynamic control for robotic assembly tasks," International Journal of Robotics Research, 18 (10): 998-1012 Oct 1999
50. Hespanha JP, Liberzon D, Morse AS, "Logic-based switching control of a nonholonomic system with parametric modeling uncertainty," Systems and Control letters, 38 (3): 167-177 OCT 26 1999
51. Xi N, Tarn TJ, Bejczy AK, "Intelligent planning and control for multirobot coordination: An event-based approach," IEEE Transaction on Robotics and Automation 12 (3): 439-452 JUN 1996
52. Jindong Tan and Ning Xi, "Hybrid System Design for Singularityless Task Level Robot Controllers," The proceedings of ICRA 2000, San Francisco, April 2000, pp. 3007-3012
53. Dubey RV, McGhee S, Chan TF, "Probability-based weighting of performance criteria for redundant manipulators," Journal of Intelligent and Robotic Systems, 19 (1): 89-103 MAY 1997