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B. Vasic, V. Ravanmehr, A. R. Krishnan, "An Information Theoretic Approach to Constructing Robust Boolean Gene Regulatory Networks," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 1, pp. 5265, January/February, 2012.  
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@article{ 10.1109/TCBB.2011.61, author = {B. Vasic and V. Ravanmehr and A. R. Krishnan}, title = {An Information Theoretic Approach to Constructing Robust Boolean Gene Regulatory Networks}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {9}, number = {1}, issn = {15455963}, year = {2012}, pages = {5265}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.61}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  An Information Theoretic Approach to Constructing Robust Boolean Gene Regulatory Networks IS  1 SN  15455963 SP52 EP65 EPD  5265 A1  B. Vasic, A1  V. Ravanmehr, A1  A. R. Krishnan, PY  2012 KW  noise KW  Boolean functions KW  cellular biophysics KW  genetics KW  network topology KW  artificial gene regulatory networks KW  information theoretic approach KW  robust boolean gene regulatory networks KW  cell cycle KW  Boolean network model KW  gene expression levels KW  cellular noise KW  projective geometry codes KW  network topology KW  Boolean functions KW  attractor structure KW  Gene expression KW  Mathematical model KW  Proteins KW  Robustness KW  Noise KW  Boolean functions KW  Logic gates KW  error correction coding. KW  Gene regulatory networks KW  Boolean networks KW  cell cycle KW  error correction VL  9 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] A. Beyer, S. Bandyopadhyay, and T. Ideker, “Integrating Physical and Genetic Maps: From Genomes to Interaction Networks,” Nature Rev. Genetics, vol. 8, no. 9, pp. 699710, 2007.
[2] M. Kærn, W.J. Blake, and J.J. Collins, “The Engineering of Gene Regulatory Networks,” Ann. Review of Biomedical Eng., vol. 5, pp. 176206, Aug. 2003.
[3] B.P. Kramer, M. Fischer, and M. Fussenegger, “SemiSynthetic Mammalian Gene Regulatory Networks,” Metabolic Eng., vol. 7, no. 4, pp. 241250, 2005.
[4] H. Kobayashi, M. Kærn, M. Araki, K. Chung, T.S. Gardner, C.R. Cantor, and J.J. Collins, “Programmable Cells: Interfacing Natural and Engineered Gene Networks,” Proc. Nat'l Academy of Sciences USA, vol. 101, no. 22, pp. 84148419, 2004.
[5] D.A. Drubin, J.C. Way, and P.A. Silver, “Designing Biological Systems,” Genes and Development, vol. 21, no. 3, pp. 242254, 2007.
[6] N. Strelkowa and M. Barahona, “Switchable Genetic Oscillator Operating in QuasiStable Mode,” J. The Royal Soc. Interface, vol. 7, pp. 10711082, 2010.
[7] K. Nasmyth, “Evolution of the Cell Cycle,” Philosophical Trans.: Biological Sciences, vol. 349, pp. 271281, 1995.
[8] A. Murray and T. Hunt, The Cell Cycle. Oxford Univ. Press, 1993.
[9] F. Li, T. Long, Y. Lu, Q. Ouyang, and C. Tang, “The Yeast Cellcycle Network is Robustly Designed,” Proc. Nat'l Academy of Sciences USA, vol. 101, no. 14, pp. 47814786, 2004.
[10] K. Willadsen and J. Wiles, “Robustness and StateSpace Structure of Boolean Gene Regulatory Models,” J. Theoretical Biology, vol. 249, no. 4, pp. 749765, 2007.
[11] N.W. Trepode, H.A. Armelin, M. Bittner, J. Barrera, M.D. Gubitoso, and R.F. Hashimoto, “A Robust Structural pgn Model for Control of CellCycle Progression Stabilized by Negative Feedbacks,” EURASIP J. Bioinformatics and Systems Biology, vol. 2007, p. 8, 2007.
[12] W. Lee and J. Huang, “Robustness and Topology of the Yeast Cell Cycle Boolean Network,” FEBS Letters, vol. 583, no. 5, pp. 927932, 2009.
[13] E. Remy, P. Ruet, and D. Thieffry, “Graphic Requirements for Multistability and Attractive Cycles in a Boolean Dynamical Framework,” Advances in Applied Math., vol. 41, no. 3, pp. 335350, 2008.
[14] M. Davidich and S. Bornholdt, “The Transition from Differential Equations to Boolean Networks: A Case Study in Simplifying a Regulatory Network Model,” J. Theoretical Biology, vol. 255, no. 3, pp. 269277, 2008.
[15] K.C. Chen, A. CsikaszNagy, B. Gyorffy, J. Val, B. Novak, and J.J. Tyson, “Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle,” Molecular Biology Cell, vol. 11, no. 1, pp. 369391, 2000.
[16] D. Irons, “Logical Analysis of the Budding Yeast Cell Cycle,” J. Theoretical Biology, vol. 257, no. 4, pp. 543559, 2009.
[17] A. Faure and D. Thieffry, “Logical Modelling of Cell Cycle Control in Eukaryotes: A Comparative Study,” Molecular BioSystems, vol. 5, pp. 15691581, 2009.
[18] R. Pal, I. Ivanov, A. Datta, M.L. Bittner, and E.R. Dougherty, “Generating Boolean Networks with a Prescribed Attractor Structure,” Bioinformatics, vol. 21, no. 21, pp. 40214025, 2005.
[19] P. Smolen, D. Baxter, and J. Byrne, “Mathematical Modeling of Gene Networks,” Neuron, vol. 26, no. 3, pp. 567580, 2000.
[20] J. Hasty, D. McMillen, F. Isaacs, and J. Collins, “Computational Studies of Gene Regulatory Networks: In Numero Molecular Biology,” Nature Rev. Genetics, vol. 2, no. 4, pp. 268279, 2001.
[21] E. Dougherty, I. Shmulevich, and M. Bittner, “Genomic Signal Processing: The Salient Issues,” EURASIP J. Applied Signal Processing, pp. 146153, 2004.
[22] R. Jansen, H. Yu, D. Greenbaum, Y. Kluger, N. Krogan, S. Chung, A. Emili, M. Snyder, J. Greenblatt, and M. Gerstein, “A Bayesian Networks Approach for Predicting ProteinProtein Interactions from Genomic Data,” Science, vol. 302, no. 5644, pp. 449453, 2003.
[23] A. Aytuna, A. Gursoy, and O. Keskin, “Prediction of ProteinProtein Interactions by Combining Structure and Sequence Conservation in Protein Interfaces,” Bioinformatics, vol. 21, no. 12, pp. 28502855, 2005.
[24] A. Hartemink, D. Gifford, T. Jaakkola, and R. Young, “Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks,” Proc. Pacific Symp. Biocomputing, vol. 6, pp. 422433, 2001.
[25] C. Yeang and T. Jaakkola, “Modeling the Combinatorial Functions of Multiple Transcription Factors,” J. Computational Biology, vol. 13, no. 2, pp. 463480, 2006.
[26] N. Friedman, “Inferring Cellular Networks Using Probabilistic Graphical Models,” Science Signaling, vol. 303, no. 5659, pp. 799805, 2004.
[27] R. Albert and A. Barabási, “Statistical Mechanics of Complex Networks,” Rev. of Modern Physics, vol. 74, no. 1, pp. 4797, 2002.
[28] E. Koonin, Y. Wolf, and G. Karev, Power Laws, ScaleFree Networks and Genome Biology. Springer Verlag, 2006.
[29] L.A.N. Amaral, A. Scala, M. Barthelemy, and H.E. Stanley, “Classes of Smallworld Networks,” Proc. Nat'l Academy of Sciences USA, vol. 97, no. 21, pp. 1114911152, 2000.
[30] U. Bastolla and G. Parisi, “The Modular Structure of Kauffman Networks,” Physica D: Nonlinear Phenomena, vol. 115, nos. 3/4, pp. 219233, 1998.
[31] P. D'haeseleer, S. Liang, and R. Somogyi, “Genetic Network Inference: From CoExpression Clustering to Reverse Engineering,” Bioinformatics, vol. 16, no. 8, pp. 707726, 2000.
[32] S. Kauffman and S. Levin, “Towards a General Theory of Adaptive Walks on Rugged Landscapes$^\ast$ ,” J. Theoretical Biology, vol. 128, no. 1, pp. 1145, 1987.
[33] F. Kschischang, B. Frey, and H. Loeliger, “Factor Graphs and the SumProduct Algorithm,” IEEE Trans. Information Theory, vol. 47, no. 2, pp. 498519, Feb. 2001.
[34] R. Hermsen, S. Tans, P. ten Wolde, and V. Rhodius, “Transcriptional Regulation by Competing Transcription Factor Modules,” PLoS Computational Biology, vol. 2, p. e164, 2006.
[35] N. Buchler, U. Gerland, and T. Hwa, “On Schemes of Combinatorial Transcription Logic,” Proc. Nat'l Academy of Sciences USA, vol. 100, no. 9, pp. 51365141, 2003.
[36] C. Yuh, H. Bolouri, and E. Davidson, “Genomic Cisregulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene,” Science, vol. 279, no. 5358, pp. 18961902, 1998.
[37] J. von Neumann, “Probabilistic Logics and the Synthesis of Reliable Organisms from Unreliable Components,” Brain Theory: Reprint Volume, p. 110, World Scientific, 1988.
[38] Coding and Signal Processing for Magnetic Recording Systems, B. Vasic and E. Kurtas, eds. CRC Press, 2004.
[39] N. Pippenger, “Developments in ‘the Synthesis of Reliable Organisms from Unreliable Gates’,” Proc. Symposia in Pure Math., pp. 311324, 1990.
[40] S. Kauffman, The Origins of Order: Self Organization and Selection in Evolution. Oxford Univ. Press, 1993.
[41] A. Garg, K. Mohanram, A. Di Cara, G. De Micheli, and I. Xenarios, “Modeling Stochasticity and Robustness in Gene Regulatory Networks,” Bioinformatics, vol. 25, no. 12, pp. i101i109, 2009.
[42] D.T. Gillespie, “Exact Stochastic Simulation of Coupled Chemical Reactions,” The J. Physical Chemistry, vol. 81, no. 25, pp. 23402361, 1977.
[43] H.H. McAdams and A. Arkin, “It's a Noisy Business! Genetic Regulation at the Nanomolar Scale,” Trends in Genetics, vol. 15, no. 2, pp. 6569, 1999.
[44] J.M. Pedraza and A. Oudenaarden, “Noise in Gene Regulatory Networks,” Complex Systems Science in Biomedicine, E. MicheliTzanakou, T.S. Deisboeck, and J.Y. Kresh, eds., pp. 211226, Springer, 2006.
[45] E.R. AlvarezBuylla, A. Chaos, M. Aldana, M. Benitez, Y. CortesPoza, C. EspinosaSoto, D.A. Hartasanchez, R.B. Lotto, D. Malkin, G.J. Escalera Santos, and P. PadillaLongoria, “Floral Morphogenesis: Stochastic Explorations of a Gene Network Epigenetic Landscape,” PLoS ONE, vol. 3, no. 11, p. e3626, 2008.
[46] M.I. Davidich and S. Bornholdt, “Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast,” PLoS ONE, vol. 3, no. 2, p. e1672, http://dx.plos.org10.1371%2Fjournal. pone.0001672 , Feb. 2008.
[47] E. Fredkin and T. Toffoli, Conservative Logic, pp. 4781. SpringerVerlag, 2002.
[48] D. Harlan Wood and J. Chen, “Fredkin Gate Circuits via Recombination Enzymes,” Proc. IEEE Congress Evolutionary Computation, vol. 2, pp. 18961900, June 2004.
[49] H. Thapliyal and M.B. Srinivas, “An Extension to DNA Based Fredkin Gate Circuits: Design of Reversible Sequential Circuits Using Frekin Gates,” Proc. CoRR, vol. abs/cs/0603092, http://arxiv.org/abs/cs0603092, 2006.
[50] S. Kauffman, P. Carsten, B. Samuelsson, and C. Troein, “Genetic Networks with Canalyzing Boolean Rules are Always Stable,” Proc. Nat'l Academy of Sciences USA, vol. 101, no. 49, pp. 1710217107, http://www.pnas.org/cgi/doi/10.1073pnas.0407783101 , Dec. 2004.
[51] M. Terzer, M. Jovanovic, A. Choutko, O. Nikolayeva, A. Korn, D. Brockhoff, F. Zurcher, M. Freidmann, R. Schutze, E. Zitzler, J. Stelling, and S. Panke, “Design of a Biological Half Adder,” IET Synthetic Biology, vol. 1, no. 1.2, pp. 5358, June 2007.
[52] R. Weiss, G.E. Homsy, and T.F. KnightJr., “Toward in Vivo Digital Circuits,” Proc. DIMACS Workshop Evolution as Computation, vol. 349, pp. 271281, 1995.
[53] K. Mangla, D.L. Dill, and M.A. Horowitz, “Timing Robustness in the Budding and Fission Yeast Cell Cycles,” PLoS ONE, vol. 5, no. 2, p. e8906, http://www.plosone.org/articleinfo%3A doi%2F10.1371%2Fjournal.pone.0008%906 , Feb. 2010.
[54] S. Lin and D.J. CostelloJr., Error Control Coding: Fundamentals and Applications. PrenticeHall, 1983.
[55] R.M. Tanner, “A Recursive Approach to Low Complexity Codes,” IEEE Trans. Information Theory, vol. IT27, no. 5, pp. 533547, Sept. 1981.
[56] S.K. Chilappagari and B. Vasic, “Error Correction Capability of ColumnWeightThree LDPC Codes,” IEEE Trans. Information Theory, vol. 55, no. 5, pp. 20552061, May 2009.
[57] L. Rudolph, “A Class of Majority Logic Decodable Codes,” IEEE Trans. Information Theory, vol. IT13, no. 2, pp. 305307, Apr. 1967.
[58] A. Roguev, S. Bandyopadhyay, M. Zofall, K. Zhang, T. Fischer, S. Collins, H. Qu, M. Shales, H. Park, J. Hayles, K. Hoe, D. Kim, T. Ideker, S. Grewal, J. Weissman, and N. Krogan, “Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast,” Science, vol. 322, pp. 405410, 2008.
[59] S. Bandyopadhyay, M. Mehta, D. Kuo, M. Sung, R. Chuang, E. Jaehnig, B. Bodenmiller, K. Licon, W. Copeland, M. Shales, D. Fiedler, J. Dutkowski, A. Guenole, H. van Attikum, K. Shokat, R. Kolodner, W. Huh, R. Aebersold, M. Keogh, N. Krogan, and T. Ideker, “Rewiring of Genetic Networks in Response to DNA Damage,” Science, vol. 330, pp. 13851389, 2010.
[60] C. Harbison et al., “Transcriptional Regulatory Code of a Eukaryotic Genome,” Nature, vol. 431, no. 7004, pp. 99104, 2004.
[61] B. Vasic, S.K. Chilappagari, S. Sankaranarayanan, and R. Radhakrishnan, “Failures of the Gallager B Decoder: Analysis and Applications,” Proc. Second Information Theory and Applications Workshop, 2006.
[62] E.F. AssmusJr. and J.D. Key, Design and Their Codes. Cambridge Univ. Press, 1992.
[63] J. Colbourn and J.H. Dinitz, The Handbook of Combinatorial Designs. CRC Press, 1996.
[64] Y. Kou, S. Lin, and M.P.C. Fossorier, “LowDensity ParityCheck Codes Based on Finite Geometries: A Rediscovery and New Results,” IEEE Trans. Information Theory, vol. 47, no. 7, pp. 27112736, Nov. 2001.