Using circuit structural analysis techniques for networks in systems biology

International Workshop on System Level Interconnect Prediction, SLIP

Volumn , Issue , 2009, Pages 37-44

  Reda, Sherief ^a  

^a Brown University   (United States)

Author keywords

Networks; Rent's rule; Systems biology

Indexed keywords

ARTIFICIAL NETWORKS; CELL FUNCTIONS; CELLULAR NETWORK; CIRCUIT ANALYSIS; CLASSICAL LOGIC; CLASSICAL METHODS; DEGREE SEQUENCE; DIGITAL LOGIC CIRCUIT; GENE TRANSCRIPTIONS; INFORMATION PROCESSING; METABOLIC ACTIVITY; NETWORKS AND SYSTEMS; PROCESS INFORMATION; REAL NETWORKS; RENT'S RULE; STRUCTURAL SIMILARITY; SYSTEMS BIOLOGY;

BIOINFORMATICS; BIOLOGY; CELLULAR NEURAL NETWORKS; DATA PROCESSING; DIGITAL INTEGRATED CIRCUITS; ELECTRIC NETWORK ANALYSIS; ELECTRIC POWER SYSTEM INTERCONNECTION; INFRARED DETECTORS; STRUCTURAL ANALYSIS; SWITCHING CIRCUITS; TECHNICAL PRESENTATIONS; TOPOLOGY; TRANSCRIPTION;

LOGIC CIRCUITS;

EID: 77950795108     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1572471.1572478     Document Type: Conference Paper

References (23)

1. U. Alon, An Introduction to Systems Biology: Design Priniciples of Biological Circuits. Chapman & Hall/CRC, 2007.
2. -, "mDraw: Network visualization Tool," http://www.weizmann.ac. il/mcb/UriAlon/.
3. S. Balachandran and D. Bhatia, "A Priori Wirelength and Interconnect Estimation Based on Circuit Characteristics," in Workshop on System Level Interconnect Prediction, 2003, pp. 77-84.
4. P. Bork, L. Jensen, C. von Mering, A. Ramani, and I. Lee, "Protein Interaction Networks from Yeast to Human," Current Opinion in Structural Biology, vol.19, pp. 292-299, 2004.
5. F. Brglez, D. Bryan, and K. Kozminski, "Combinational Profiles of Sequential Benchmark Circuits," in Proc. International Symposium on Circuits and Signals, 1989, pp. 1929-1934.
6. C. Chang, J. Cong, M. Romesis, and M. Xie, "Optimality and Scalability Study of Existing Placement Algorithms," IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol.23(4), pp. 537-549, 2004.
7. P. Christie and D. Stroobandt, "The Interpretation and Application of Rent's Rule," IEEE Transactions on VLSI Systems, vol.8(6), pp. 639-648, 2000.
8. J. Dambre, D. Stroobandt, and J. V. Campenhout, "Toward the Accurate Prediction of Placement Wirelength Distributions in VLSI Circuits," IEEE Transactions on VLSI Systems, vol.12(4), pp. 339-348, 2004.
9. W. E. Donath, "Statistical Properties of the Placement of a Graph," SIAM J. Appl. Math, vol.16(2), pp. 439-457, 1968.
10. -, "Placement and Average Interconnection Lengths of Computer and Systems," IEEE Trans. Circuits and Systems, vol.26), pp. 272-277, 1979.
11. P. Eichenberger et al., "The Program of Gene Transcription for a Single Differentiating Cell Type During Sporulation in Bacillus subtilis," PLoS Biol, vol.2, no.1664-1683, 2004.
12. C. Gkantsidis, M. Mihail, and E. Zegura, "The Markov Chain Simulation Method for Generating Connected Power Law Random," in Proc. of orkshop on Algorithm Engineering and Experiments (ALENEX), 2003, pp. 16-25.
13. L. Hagen, A. B. Kahng, F. J. Kurdahi, and C. Ramachandran, "On the Intrinsic Rent Parameter and Spectra-Based Partitioning Methodologies," IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol.13(1), pp. 27-37, 1994.
14. T. Hamada, C.-K. Cheng, and P. M. Chau, "A Wire Length Estimation Technique Utilizing Neighborhood Density Equations," in Proc. Design Automation Conference, 1992, pp. 57-61.
15. A. B. Kahng and S. Reda, "Intrinsic Shortest Path Length: A New, Accurate A Priori Wirelength Estimator," in Proc. International Conference on Computer Aided Design, 2005, pp. 173-180.
16. G. Karypis and V. Kumar, "Multilevel k-way Hhypergraph Partitioning," in Proc. Design Automation Conference, 1999, pp. 343-348.
17. B. Landman and R. Russo, "On a Pin versus Block Relationship for Partitions of Logical Graphs," IEEE Transactions on Computers, vol.20(C), pp. 793-813, 1971.
18. Q. Liu and M. Marek-Sadowska, "Pre-Layout Wire Length and Congestion Estimation," in Proc. Design Automation Conference, 2004, pp. 582-587.
19. R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon, "Network Motifs: Simple Building Blocks of Complex Networks," Science, vol.298, no.5594, pp. 824-827, 2002.
20. B. Palsson, Systems Biology: Properites of Reconstructed Networks. Cambridge University Press, 2006.
21. D. Stroobandt, A Priori Wire Length Estimates for Digital Design. Kluwer Academic Publishers, 2001.
22. F. Viger and M. Latapy, "Efficient and Simple Generation of Random Simple Connected Graphs with Prescribed Degree Sequence," in Proc. of Conference of Computing and Combinatoric (COCOON), ser. LNCS 3595, 2005, pp. 440-449.
23. X. Yang, E. Bozorgzadeh, and M. Sarrafzadeh, "Wirelength Estimation based on Rent Exponents of Partitioning and Placement," in Workshop on System Level Interconnect Prediction, 2001, pp. 25-31.