Implementing arithmetic and other analytic operations by transcriptional regulation

PLoS Computational Biology

Volumn 4, Issue 5, 2008, Pages

  Cory, Sean M ^a   Perkins, Theodore J ^b  

^a MCGILL UNIVERSITY   (Canada)

^b MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; TRANSCRIPTION; TRANSCRIPTION FACTORS;

ACCURACY AND PRECISION; ARITHMETIC OPERATIONS; BIOLOGICAL NETWORKS; CHEMICAL KINETIC MODEL; COMPUTATIONAL DEVICES; EXPRESSION LEVELS; SIMPLE++; TIME VARYING SIGNAL; TRANSCRIPTIONAL REGULATION; TUNABLES;

MACHINERY;

TRANSCRIPTION FACTOR;

ACCURACY; ARITHMETIC; ARTICLE; CHEMICAL REACTION KINETICS; GENE EXPRESSION; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MATHEMATICAL PARAMETERS; SIMULATION; STATISTICAL SIGNIFICANCE; TRANSCRIPTION REGULATION;

ALGORITHMS; COMPUTER SIMULATION; COMPUTERS, MOLECULAR; GENE EXPRESSION REGULATION; MATHEMATICS; MODELS, GENETIC; SIGNAL PROCESSING, COMPUTER-ASSISTED; TRANSCRIPTION FACTORS; TRANSCRIPTIONAL ACTIVATION;

EID: 44949100280     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000064     Document Type: Article

References (55)

1. Arkin AP (2000) Signal processing in biochemical reaction networks. In: Walleczek J, ed. Self-Organized Biological Dynamics and Nonlinear Control Cambridge University Press.
2. Regev A, Shapiro E (2002) Cells as computation. Nature 419: 343.
3. Guet CC, Elowitz MB, Hsing W, Leibler S (2002) Combinatorial synthesis of genetic networks. Science 296: 1466-1479.
4. Setty Y, Mayo AE, Surette MG, Alon U (2003) Detailed map of a cis-regulatory input function. Proc Natl Acad Sci U S A 100: 7702-7707.
5. Mayo AE, Setty Y, Shavit S, Zaslaver A, Alon U (2006) Plasticity of the cis-regulatory input function of a gene. PLoS Biol 4: e45.
6. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, et al. (2002) Molecular biology of the cell, fourth edition Garland Publishing.
7. Glass L, Kauffman SA (1973) The logical analysis of continuous, non-linear biochemical control networks. J Theor Biol 39: 103-129.
8. Hjelmfelt A, Weinberger ED, Ross J (1991) Chemical implementation of neural networks and Turing machines. Proc Natl Acad Sci U S A 88: 10983-10987.
9. Arkin A, Ross J (1994) Computational functions in biochemical reaction networks. Biophys J 67: 560-578.
10. Buchler NE, Gerland U, Hwa T (2003) On schemes of combinatorial transcription logic. Proc Natl Acad Sci U S A 100: 5136-5141.
11. Sauro HM (2004) The computational versatility of proteomic signaling networks. Current Proteomics 1: 67-81.
12. Hjelmfelt A, Weinberger ED, Ross J (1992) Chemical implementation of finitestate machines. Proc Natl Acad Sci U S A 89: 383-387.
13. Magnasco MO (1997) Chemical kinetics is Turing universal. Phys Rev Lett 78: 1190-1193.
14. Ben-Hur A, Siegelmann HT (2004) Computation in gene networks. Chaos 14: 145-151.
15. Bodnar J (1997) Programming the Drosophila embryo. J Theor Biol 188: 391-445.
16. Sanchez L, van Helden J, Thieffry D (1997) Establishment of the dorso-ventral pattern during embryonic development of Drosophila melanogaster: a logical analysis. J Theor Biol 189: 377-389.
17. Mendoza L, Alvarez-Buylla ER (1998) Dynamics of the genetic regulatory network for Arabidopsis thaliana flower morphogenesis. J Theor Biol 193: 307-319.
18. Mendoza L, Thieffry D, Alvarez-Buylla ER (1999) Genetic control of flower morphogenesis in arabidopsis thaliana: a logical analysis. Bioinformatics 14: 593-696.
19. Sanchez L, Thieffry D (2001) A logical analysis of the gap gene system. J Theor Biol 211: 115-141.
20. Albert R, Othmer HG (2003) The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J Theor Biol 223: 1-18.
21. Sanchez L, Thieffry D (2003) Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module. J Theor Biol 224: 517-537.
22. Faure A, Naldi A, Chaouiya C, Thieffry D (2006) Dynamical analysis of a generic boolean model for the control of the mammalian cell cycle. Bioinformatics 22: e124-e131.
23. Gonzalez A, Chaouiya C, Thieffry D (2006) Dynamical analysis of the regulatory network defining the dorsal-ventral boundary of the drosophila wing imaginal disc. Genetics 174: 1625-1634.
24. Wolpert L (1968) The french flag problem. In: Waddington CH, ed. Towards a Theoretical Biology. Chicago: Aldine Publishing Company. pp 125-133.
25. Glass L (1975) Combinatorial and topological methods in nonlinear chemical kinetics. J Chem Phys 63: 1325-1335.
26. Ghosh R, Tomlin CJ (2001) Lateral inhibition through delta-noth signaling: A piecewise affine hybrid model. In: Benedetto MDD, Sangiovanni-Vincentelli A, eds. Lectures Notes in Computer Science 2034. pp 232-246.
27. de Jong H, Geiselmann J, Batt G, Hernandez C, Page M (2004) Qualitative simulation of the initiation of sporulation in Bacillus subtilis. Bull Math Biol 66: 261-300.
28. Ropers D, de Jong H, Page M, Schneider D, Geiselmann J (2006) Qualitative simulation of the carbon starvation response in Escherichia coli. BioSystems 84: 124-152.
29. Perkins TJ, Jaeger J, Reinitz J, Glass L (2006) Reverse engineering the gap gene network of Drosophila melanogaster. PLoS Comput Biol 2: e51.
30. Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342.
31. Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403: 335-338.
32. Yuh CH, Bolouri H, Davidson EH (1998) Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 279: 1896-1902.
33. Hjelmfelt A, Ross J (1992) Chemical implementation and thermodynamics of collective neural networks. Proc Natl Acad Sci U S A 89: 388-391.
34. Deckard A, Sauro HM (2004) Preliminary studies on the in silico evolution of biochemical networks. Chembiochem 5: 1423-1431.
35. Barkai N, Leibler S (1997) Robustness in simple biochemical networks. Nature 387: 913-917.
36. Alon U, Surette MG, Barkai N, Leibler S (1999) Robustness in bacterial chemotaxis. Nature 397: 168-171.
37. Rao CV, Wolf DM, Arkin AP (2002) Control, exploitation and tolerance of intracellular noise. Nature 420: 231-237.
38. Houchmandzadeh B, Wieschaus E, Leibler S (2002) Establishment of developmental precision and proportions in the early Drosophila embryo. Nature 415: 798-802.
39. Eldar A, Dorfman R, Weiss D, Ashe H, Shilo BZ, et al. (2002) Robustness of the BMP morphogen gradient in Drosophila embryonic patterning. Nature 419: 304-308.
40. Von Dassow G, Meir E, Munro EM, Odell GM (2000) The segment polarity network is a robust developmental module. Nature 406: 188-192.
41. Samoilov M, Arkin A, Ross J (2002) Signal processing by simple chemical systems. J Phys Chem A 106: 10205-10221.
42. Tkacik G Jr, CGC, Bialek W (2007) Information flow and optimization in transcriptional control. ArXiv: 0705.0313v1.
43. Libby E, Perkins TJ, Swain PS (2007) Noisy information processing through transcriptional regulation. Proc Natl Acad Sci U S A 104: 7151-7156.
44. Thattai M, van Oudenaarden A (2001) Intrinsic noise in gene regulatory networks. Proc Natl Acad Sci U S A 98: 8614-8619.
45. Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340-2361.
46. Swain PS, Elowitz MB, Siggia ED (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci U S A 99: 12795-12800.
47. Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8: 450-461.
48. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
49. Shen-Orr S, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31: 64-68.
50. Mangan S, Alon U (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 100: 11980-11985.
51. Mangan S, Itzkovitz S, Zaslaver A, Alon U (2006) The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J Mol Biol 356: 1073-1081.
52. Ko CH, Takahashi JS (2006) Molecular components of the mammalian circadian clock. Hum Mol Genet 15: R271-R277.
53. Andrews BW, Yi TM, Iglesias PA (2006) Optimal noise filtering in the chemotactic response of Escherichia coli. PLoS Comput Biol 2: e154.
54. Bachmair A, Finley D, Varshavsky A (1986) In vivo half-life of a protein is a function of its amino-terminal residue. Science 234: 179-186.
55. Belle A, Tanay A, Bitincka L, Shamir R, O'Shea EK (2006) Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci U S A 103: 13004-13009.