Gene regulatory network inference using out of equilibrium statistical mechanics

HFSP Journal

Volumn 2, Issue 4, 2008, Pages 183-188

  Benecke, Arndt ^a,b  

^a INSTITUT DES HAUTES ÉTUDES SCIENTIFIQUES   (France)

^b UNIV LILLE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

EID: 53249088665     PISSN: 19552068     EISSN: 1955205X     Source Type: Journal    
DOI: 10.2976/1.2957743     Document Type: Article

References (21)

1. Adams, D (1979). The Hitchhiker's guide to the galaxy, Pan Books, London.
2. Audit, B, Nicolay, S, Huvet, M, Touchon, M, D'aubenton-carafa, Y, Thermes, C, and Arneodo, A (2007). "DNA replication timing data corroborate in silico human replication origin predictions." Phys. Rev. Lett. 99, 248102.
3. Barrera, LO, and Ren, B, (2006). "The transcriptional regulatory code of eukaryotic cells-insights from genome-wide analysis of chromatin organization and transcription factor binding." Curr. Opin. Cell Biol. 18, 291-2980.
4. Benecke, A (2003). "Genomic plasticity and information processing by transcription coregulators." ComPlexUs 1, 65-76.
5. Benecke, A (2006). "Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs." Eur. Phys. J. E 19, 379-384.
6. Berg, J (2008a). "Dynamics of gene expression and the regulatory inference problem." Europhys. Lett. 82, 28010.
7. Berg, J (2008b). "Out-of-equilibrium dynamics of gene expression and the Jarzynski equality." Phys. Rev. Lett. 100, 188101.
8. Braunstein, A, and Zecchina, R (2006). "Learning by message passing in networks of discrete synapses." Phys. Rev. Lett. 96, 030201.
9. Castiglione, P, Falcioni, M, Lesne, A, and Vulpiani, A (2008). Chaos and coarse graining in statistical mechanics. Cambridge, UK, Cambridge University Press.
10. Cloonan, N et al. (2008). "Stem cell transcriptome profiling via massivescale mRNA sequencing." Nat. Methods 5, 613-619.
11. Jaynes, ET (1984). "Prior information and ambiguity in inverse problems." SIAM-AMS Proc. 14, 151-166.
12. Kaern, M, Elston, TC, Blake, WJ, and Collins, JJ (2005). "Stochasticity in gene expression: from theories to phenotypes." Nat. Rev. Genet. 6, 451-464.
13. Kurchan, J (1998). "Fluctuation theorem for stochastic dynamics." J. Phys. A 31, 3719-3729.
14. Lesne, A (2006). "The chromatin regulatory code: beyond an histone code." Eur. Phys. J. E 19, 375-377.
15. Lesne, A, and Benecke, A (2008). "Probability landscapes for integrative genomics." Theor. Biol. Med. Mod. 5, 9.
16. Maston, GA, Evans, SK, and Green, MR (2006). "Transcriptional regulatory elements in the human genome." Annu. Rev Genom. Hum. Genet. 7, 29-59.
17. McAdams, HH, and Arkin, A (1997). "Stochastic mechanisms in gene expression." Proc. Natl. Acad. Sci. U.S.A. 94, 814-819.
18. Metivier, R et al. (2008). "Cyclic DNA methylation of a transcriptionally active promoter." Nature (London) 452, 45-53.
19. Rajewsky, N, Vergassola, M, Gaul, U, and Siggia, ED (2002). "Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo." BMC Bioinf. 3, 30.
20. Ritort, F (2004). "Work fluctutions and transient violoations of the second law: perspectives in theory and experiment." Poincaré seminars. Dalibard, J, Duplantier, B, and Rivasseau, V (eds.) pp. 195-229, Birkhäuser, Basel, Switzerland.
21. Siggia, ED (2005). "Computational methods for transcriptional regulation." Curr. Opin. Genet. Dev. 15, 214-221.