References

From The Circuits and Biology Lab at UMN

Here are some papers that are of interest to our research group. (Please add to this list.)

Contents 1 Books 2 Websites 3 Synthetic/Computational Biology 4 Noisy/Probabilistic Logic 5 Feedback 6 SAT-Based Algorithms 7 Logic Synthesis

Books

• Uri Alon, "Introduction to Systems Biology"

Websites

• BioModels Database, http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=home

Synthetic/Computational Biology

• Uri Alon, "Network Motifs: Theory and Experimental Approaches."

• Katherine C. Chen, Laurence Calzone, Attila Csikasz-Nagy, Frederick R. Cross, Bela Novak, and John J. Tyson, "Integrative Analysis of Cell Cycle Control in Budding Yeast."

• Daniel T. Gillespie, "Stochastic Simulation of Chemical Kinetics."

• Albert Goldbetert and DanieL E. Koshland, "An Amplified Sensitivity Arising From Covalent Modification in Biological Systems."

• Leland H. Hartwell, John J. Hopfield, Stanislas Leibler and Andrew W. Murray, "From Molecular to Modular Cell Biology."

• Eric Libby, Theodore J. Perkins, and Peter S. Swain, "Noisy Information Processing Through Transcriptional Regulation."

• Tianhai Tian and Kevin Burrage, "Stochastic Models for Regulatory Networks of the Genetic Toggle Switch."

• John J. Tyson, Katherine C. Chen, and Bela Novak, "Sniffers, Buzzers, Toggles and Blinkers."

• Shatam Agarwal and Jaijeet Roychowdhury, "Efficient Multiscale Simulation of Circadian Rhythms using Automated Phase Macromodelling Techniques."

Noisy/Probabilistic Logic

• Itai Benjamin, Gil Kalai and Oded Schramm, "Noise Sensitivity of Boolean Functions and Applications to Percolation."
• Alex Brodsky and Nicholas Pippenger, "The Boolean Functions Computed by Random Boolean Formulas or How to Grow the Right Function."
• M. Kochen, "Extension of Moore-Shannon Model for Relay Circuits."
• Smita Krishnaswamy, George Viamontes, Igor Markov, and John Hayes, "Probabilistic Transfer Matrices in Symbolic Reliability Analysis of Logic Circuits."
• E. F. Moore and C. E. Shannon, "Reliable Circuits Using Less Reliable Relays."
• Nicholas Pippenger and Geng Lin, "Fault-Tolerant Circuit-Switching Networks."

Feedback

• Wolfgang Maass, Prashant Joshi, and Eduardo D. Sontag, "Computational Aspects of Feedback in Neural Circuits."
• Jie-Hong R. Jiang, Alan Mishchenko, and Robert k. Brayton, " On Breakable Cyclic Definitions."

SAT-Based Algorithms

• K.L. McMillan, "Interpolation and SAT-Based Model Checking"
• C.-C. Lee, J.-H. R. Jiang, C.-Y. Huang, and A. Mishchenko, "Scalable exploration of functional dependency by interpolation and incremental SAT solving"
• S. Chatterjee, A. Mishchenko, R. Brayton, and A. Kuehlmann, "On resolution proofs for combinational equivalence"

Logic Synthesis

• R. Brayton, R. Rudell, A. Sangiovanni-Vincentelli and A. Wang, "MIS: A Multiple-Level Logic Optimization System"
• R. Brayton, G. Hachtel and A. Sangiovanni-Vincentelli, "Multilevel Logic Synthesis"