Optimizing static thermodynamic models of transcriptional regulation

Bioinformatics

Volumn 25, Issue 13, 2009, Pages 1640-1646

  Bauer, Denis C ^a   Bailey, Timothy L ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTION FACTOR;

ARTICLE; COMPUTER SIMULATION; EMBRYO; GENE EXPRESSION; GENE TARGETING; GENETIC ALGORITHM; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN DNA INTERACTION; QUANTITATIVE ANALYSIS; THERMODYNAMICS; TRANSCRIPTION REGULATION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; THERMODYNAMICS; TRANSCRIPTION, GENETIC;

EID: 67649230197     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp283     Document Type: Article

References (13)

1. Bauer,D.C. and Bailey,T.L. (2008a) Stream: Static Thermodynamic REgulAtory Model of transcription. Bioinformatics, 24, 2544-2545.
2. Bauer,D.C. and Bailey,T.L. (2008b) Studying the functional conservation of cisregulatory modules and their transcriptional output. BMC Bioinformatics, 9, 220.
3. Chu,K.-W. et al. (1999) Parallel simulated annealing by mixing of states. J. Comput. Phys., 148, 646-662.
4. Holland,J.H. (1975) Adaptation in Natural and Artificial Systems. University of Michigan Press.
5. Janssens,H. et al. (2006)Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat. Genet., 38, 1159-1165.
6. Lam,J.K.-C. (1988) An Efficient Simulated Annealing Schedule. PhD Thesis, New Haven, CT.
7. Manke,T. et al. (2008) Statistical modeling of transcription factor binding affinities predicts regulatory interactions. PLoS Comput. Biol., 4, e1000039.
8. Prentiss,M.C. et al. (2008) Protein structure prediction using basin-hopping. J. Chem. Phys., 128, 225106.
9. Reinitz,J. et al. (2003) Transcriptional control in Drosophila. Complexus, 1, 54-64.
10. Riedmiller,M. and Braun,H. (1994) Rprop - description and implementation details. Available at http://citeseer.ist.psu.edu/old/711503.html
11. Segal,E. et al. (2008). Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature, 451, 535-540.
12. Stormo,G.D. (1998) Information content and free energy in DNA-protein interactions. J. Theor. Biol., 195, 135-137.
13. Zinzen,R.P. and Papatsenko,D. (2007) Enhancer responses to similarly distributed antagonistic gradients in development. PLoS Comput. Biol. 3, e84.