Model-Reduction by Simultaneous Determination of Network Topology and Parameters: Application to Modules in Biochemical Networks
Mano R. Maurya, San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, MC 0505, La Jolla, CA 92093-0505, Scott J. Bornheimer, Departments of Chemistry & Biochemistry and Cellular & Molecular Medicine, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, Venkat Venkatasubramanian, School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, IN 47907 and Shankar Subramaniam, San Diego Supercomputer Center, Department of Bioengineering, Department of Chemistry & Biochemistry, University of California San Diego, 9500 Giman Drive, La Jolla, CA 92093-0505 |
Biological Network Design Principles: Discovery through Optimization
Bambang Adiwijaya, Biological Engineering Division, MIT, 32 Vassar St #32-210, Cambridge, MA 02139, Paul I. Barton, Chemical Engineering, MIT, 77 Mass Ave, 66-464, Cambridge, MA 02139 and Bruce Tidor, Biological Engineering, Electrical Engineering and Computer Science, MIT, 32 Vassar St #32-211, Cambridge, MA 02139 |
Understanding the Ultrasensitive Responses of Tricyclic Cascade Networks
Theodore R. Rieger, Northwestern University, 2145 Sheridan Rd., E136, Evanston, IL 60208 and Vassily Hatzimanikatis, Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Room E136, Evanston, IL 60208-3120 |
Inferring Transcription Factor Activities with a Probabilistic Framework of Hidden Markov Model
Zheng Li1, Stephen M. Shaw1, Matthew J. Yedwabnick1 and Christina Chan2, (1)Department of Chemical Engineering and Material Science, Michigan State University, 2527 Engineering Building, East Lansing, MI 48824, (2)Michigan State University, 2527 Engineering Building, East Lansing, MI 48824 |
Isochron-Based Phase Sensitivity Analysis of Oscillatory Biological Systems
Rudiyanto Gunawan, University of California Santa Barbara, University of California Santa Barbara, Santa Barbara, CA 93106-5080 and Francis J. Doyle III, Department of Chemical Engineering, University of California Santa Barbara, University of California Santa Barbara, Santa Barbara, CA 93106-5080 |
Markov Chain Modeling of Pyelonephritis-Associated Pili Expression in Uropathogenic Escherichia Coli
Laura R. Jarboe, Baiyu Zhou, David Beckwith and James C. Liao, Department of Chemical Engineering, UCLA, 5805 Boelter Hall, 420 Westwood Pl, Los Angeles, CA 90095 |