Statistical method for revealing form-function relations in biological networks

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 2, 2011, Pages 446-451

  Mugler, Andrew ^a,d   Grinshpun, Boris ^a   Franks, Riley ^b   Wiggins, Chris H ^a,c  

^a Columbia University ^*  (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^c Och Spine at New York Presbyterian Hospitals   (United States)

^d FOM INSTITUTE AMOLF   (Netherlands)

Author keywords

Dynamical systems; Form and function; Information theory; Systems biology

Indexed keywords

ANALYTIC METHOD; ARTICLE; AUTOREGULATION; BIOLOGICAL NETWORK; INFORMATION PROCESSING; MATHEMATICAL ANALYSIS; PREDICTION; PRIORITY JOURNAL; STATISTICAL ANALYSIS; SYSTEMS BIOLOGY; TRANSCRIPTION REGULATION;

ALGORITHMS; GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; MODELS, STATISTICAL; MODELS, THEORETICAL; SYSTEMS BIOLOGY; TRANSCRIPTION, GENETIC;

EID: 79551672951     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1008898108     Document Type: Article

References (33)

1. Thompson D (1917) On growth and form (Cambridge University Press, Cambridge, United Kingdom).
2. Sherrington SC (1906) The integrative action of the nervous system (Yale University Press, New Haven, CT).
3. Stricker J, et al. (2008) A fast, robust and tunable synthetic gene oscillator. Nature 456:516-519.
4. Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403:339-342.
5. Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403:335-338.
6. Cusick ME, Klitgord N, Vidal M, Hill DE (2005) Interactome: gateway into systems biology. Hum Mol Genet 2:R171-181.
7. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470.
8. Giot L, et al. (2003) A protein interaction map of Drosophila melanogaster. Science 302:1727-1736.
9. Guet CC, Elowitz MB, Hsing W, Leibler S (2002) Combinatorial synthesis of genetic networks. Science 296:1466-1470.
10. Basu S, Mehreja R, Thiberge S, Chen MT, Weiss R (2004) Spatiotemporal control of gene expression with pulse-generating networks. Proc Natl Acad Sci USA 101:6355-6360.
11. Mangan S, Zaslaver A, Alon U (2003) The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol 334:197-204.
12. Strogatz SH (2000) Nonlinear dynamics and chaos: With applications to physics, biology, chemistry, and engineering (Westview Press, Cambridge, MA).
13. Ziv E, Nemenman I, Wiggins CH (2007) Optimal signal processing in small stochastic biochemical networks. PLoS ONE 2:e1077.
14. Mugler A, Ziv E, Nemenman I, Wiggins CH (2008) Serially regulated biological networks fully realise a constrained set of functions. IET Syst Biol 2:313-322.
15. Mugler A, Ziv E, Nemenman I, Wiggins CH (2009) Quantifying evolvability in small biological networks. IET Syst Biol 3:379-387.
16. Tkačik G, Callan CG, Bialek W (2008) Information flow and optimization in transcriptional regulation. Proc Natl Acad Sci USA 105:12265-12270.
17. Mehta P, Goyal S, Long T, Bassler BL, Wingreen NS (2009) Information processing and signal integration in bacterial quorum sensing. Mol Syst Biol 5:325.
18. Walczak AM, Tkačik G, Bialek W (2010) Optimizing information flow in small genetic networks. II. Feed-forward interactions. Phys Rev E 81:41905.
19. Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340-2361.
20. Paulsson J (2004) Summing up the noise in gene networks. Nature 427:415-418.
21. Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 297:1183-1186.
22. Walczak AM, Mugler A, Wiggins CH (2009) A stochastic spectral analysis of transcriptional regulatory cascades. Proc Natl Acad Sci USA 106:6529-6534.
23. Mugler A, Walczak AM, Wiggins CH (2009) Spectral solutions to stochastic models of gene expression with bursts and regulation. Phys Rev E 80:041921.
24. Buchler NE, Gerland U, Hwa T (2003) On schemes of combinatorial transcription logic. Proc Natl Acad Sci USA 100:5136-5141.
25. Bintu L, et al. (2005) Transcriptional regulation by the numbers: models. Curr Opin Genet Dev 15:116-124.
26. Bintu L, et al. (2005) Transcriptional regulation by the numbers: applications. Curr Opin Genet Dev 15:125-135.
27. Kaplan S, Bren A, Zaslaver A, Dekel E, Alon U (2008) Diverse two-dimensional input functions control bacterial sugar genes. Mol Cell 29:786-792.
28. Cox RS, Surette MG, Elowitz MB (2007) Programming gene expression with combinatorial promoters. Mol Syst Biol 3:145.
29. 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.
30. Elf J, Ehrenberg M (2003) Fast evaluation of fluctuations in biochemical networks with the linear noise approximation. Genome Res 13:2475-2484.
31. van Kampen NG (1992) Stochastic processes in physics and chemistry (North-Holland, Amsterdam).
32. Borg I, Groenen PJF (2005) Modern multidimensional scaling: theory and applications (Springer-Verlag, New York, NY), 2nd ed.
33. Hermsen R, Ursem B, ten Wolde PR (2010) Combinatorial gene regulation using auto-regulation. PLoS Comput Biol 6:e1000813.