Systematic component selection for gene-network refinement

Bioinformatics

Volumn 22, Issue 21, 2006, Pages 2674-2680

  Radde, Nicole ^a   Gebert, Jutta ^a   Forst, Christian V ^b  

^a UNIVERSITY OF COLOGNE   (Germany)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENE; CELL INTERACTION; CONTROLLED STUDY; DNA REPAIR; GENE CONTROL; GENE EXPRESSION PROFILING; GENE FUNCTION; GENETIC PARAMETERS; GENETIC SELECTION; MATHEMATICAL MODEL; METHODOLOGY; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROCESS MODEL; SIMULATION; STATISTICAL MODEL; STATISTICAL PARAMETERS;

MYCOBACTERIUM TUBERCULOSIS;

EID: 33750425792     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl440     Document Type: Article

References (21)

1. Bansal,M. et al. (2006) Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics, 22, 815-822.
2. Boshoff,H. et al. (2004) The transcriptional response of Mycobacterium tuberculosis to inhbitors of metabolism: Novel insights into drug mechanisms of action. Biol. Chem., 279, 40174-40184.
3. Breiman,L. (1993) Hinging hyperplanes for regression, classifictaion and function Approximation. IEEE Trans. Inform. Theory, 39, 999-1013.
4. Cabusora,L. et al. (2005) Differential network expression during drug and stress response. Bioinformatics, 21, 2898-2905.
5. Friedman,N. et al. (2000) Using Bayesian networks to analyze expression data. J. Comp. Biol., 7, 601-620.
6. Glass,L. and Kauffman,S.A. (1973) The logical analysis of continuous, non-linear biochemical control networks. J. Theor. Biol., 39, 103-129.
7. de Jong,H. and Page,M. (2000) Qualitative simulation of large and complex genetic regulatory Systems. In Horn,W. (ed.), In Proceedings of the ECAI 2000, IOS Press, pp. 191-195.
8. de Jong,H. (2002) Modeling and simulation of genetic regulatory systems: a literature review. J. Comp. Biol., 9, 67-103.
9. Djordjevic,M. et al. (2003) A biophysical approach to transcription factor binding site discovery. Genome Res., 13, 2381-2390.
10. Dullaghan,E.M. et al. (2002) The role of multiple SOS boxes upstream of the Mycobacterium tuberculosis lexA gene - identification of a novel DNA-damage-inducible gene. Microbiology, 148, 3609-3615.
11. Gebert,J. et al. (2006) Modeling gene regulatory networks with piecewise linear differential equations, accepted for publication in: EJOR Chall. of Cont. Opt. in Theory and Applications, in press.
12. Gerland,U. et al. (2002) Physical constraints and functional characteristics of transcription factor-dna interaction. Proc. Natl. Acad. Sci. USA, 99, 12015-12020.
13. Gustafsson,M. et al. (2005) Constructing and analyzing a large-scale gene-to-gene regulatory network - Lasso-constrained inference and biological validation. IEEE/ACM Trans. Comput. Biol. Bioinform., 2, 254-261.
14. Hershberger,J. et al. (2003) Finding the k-shortest simple paths: A new algorithm and its implementation. In proceedings of the 5th Workshop on Algorithm Engineering and Experiments, ALENEX 2003, Baltimore, USA, 26-36.
15. Jacob,F. and Monod,J. (1961) Genetic regulatory machanisms in the synthesis of proteins. J. Mol. Biol., 3, 318-356.
16. Jiménez,V.M. and Marzal,A. (1999) Computing the k-shortest paths: A new algorithm and an experimental comparison. In Lecture Notes in Computer Science 1668, 15-29, 3rd International Workshop on Algorithm Engineering (WAE 99) July 19-21, 1999, London, UK.
17. Luenberger,D.G. (1973) Introduction to Linear and Nonlinear Programming. Addison Wessley, Massachusetts.
18. Mizrahi,V. and Anderson,S.J. (1998) DNA repair in Mycobacterium tuberculosis. What have we learnt from the genome sequence? Mol. Microbiol., 29, 1331-1339.
19. Rand,L. et al. (2003) The majority of inducible DNA repair genes in Mycobacterium tuberculosis are induced independently of Rec A. Mol. Microbiol., 50, 1031-1042.
20. Walker,G.C. (1996) The SOS response of Escherichia coli. In Neidhardt,F.C. (ed.), Escherichia coli and Salmonella. Washington: ASM Press, pp. 1400-1416.
21. Yagil,G. and Yagil,E. (1971) On the relation between effector concentration and the rate of induced enzyme synthesis. Biophys. J., 11, 11-27.