Computational expansion of genetic networks

Bioinformatics

Volumn 17, Issue SUPPL. 1, 2001, Pages

  Tanay, Amos ^a   Shamir, Ron ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ERGOSTEROL; TRANSCRIPTION FACTOR;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; FUNGAL GENE; GENE EXPRESSION PROFILING; GENETIC PROCEDURES; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; SACCHAROMYCES CEREVISIAE; STATISTICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; ERGOSTEROL; GENE EXPRESSION PROFILING; GENES, FUNGAL; GENETIC TECHNIQUES; MODELS, GENETIC; SACCHAROMYCES CEREVISIAE; SOFTWARE; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 0037509648     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.suppl_1.S270     Document Type: Article

References (25)

1. Akutsu, T., Kuhara, S., Maruyama, O. & Miyano, S. (1998). Identification of gene regulatory networks by strategic gene disruptions and gene overexpressions. In Proceedings of the Annual ACM-SIAM Symposium on Discrete Mathematics (SODA 98). pp. 695-702.
2. Akutsu, T., Miyano, S. & Kuhara, S. (1999). Identification of genetic networks from a small number of gene expression patterns under the boolean network model. In Proceedings of the 1999 Pacific Symposioum in Biocomputing (PSB 99). pp. 17-28.
3. Akutsu, T., Miyano, S. & Kuhara, S. (2000). Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint functions. In Proceedings of the Fourth Annual International Conference on Computational Molecular Biology (RECOMB 00). pp. 8-14.
4. Arkin, A., Ross, J. & McAdams, H. (1998). Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda infected escherichia coli cells. Genetics, 149, 1275-1279.
5. Ball, C. et al. (2001). Saccharomyces genome database provides tools to survey gene expression and functional analysis data. Nucleic Acids Research, 29, 80-1.
6. Bammert, G. & Fostel, J. (2000). Genome-wide expression patterns in Saccharomyces cerevisiae: comparison of drug treatments and genetic alterations affecting biosynthesis of ergosterol. Antimicrobial Agents and Chemotherapy, 44, 1255-1265.
7. Chen, T., Filkov, V. & Skiena, S. S. (1999a). Identifying gene regulatory networks from experimental data. In Proceedings of the Third Annual International Conference on Computational Molecular Biology (RECOMB 99). pp. 94-103.
8. Chen, T., He, H. L. & Church, G. M. (1999b). Modeling gene expression with differential equations. In Proceedings of the 1999 Pacific Symposioum in Biocomputing (PSB 99). pp. 29-40.
9. Costanzo, M. et al. (2001). YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Research, 29, 75-9.
10. Daum, G., Lees, N., Bard, M. & Dickson, R. (1998). Biochemistry, cell biology and molecular biology of lipids of Saccharomyces cerevisiae. Yeast, 14,1471-1510.
11. DeRisi, J., Iyer, V. & Brown, P. (1997). Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680-686.
12. Dhaseleer, P., Liang, S. & Somogyi, R. (2000). Genetic network inference: from co-expression clustering to reverse engineering. Bioinfonnatics, 16, 707-726.
13. Dhaseleer, P., Wen, X., Fuhrman, S. & Somogyi, R. (1999). Linear modeling of mRNA expression levels during CNS development and injury. In Proceedings of the 1999 Pacific Symposioum in Biocomputing (PSB 99). pp. 41-52.
14. Eisen, M., Spellman, P., Brown, P. & Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Science USA, 95, 14863-14868.
15. Friedman, N., Linial, M., Nachman, I. & Pe'er, D. (2000). Using Bayesian networks to analyze expression data. In Proceedings of the Fourth Annual International Conference on Computational Molecular Biology (RECOMB 00). pp. 127-135.
16. Hughes, T. et al. (2000). Functional discovery via a compendium of expression profiles. Cell, 102, 109-26.
17. Ideker, T., Thorsson, V. & Karp, R. (2000). Discovery of regulatory interaction through perturbation: inference and experimental design. In Proceedings of the 2000 Pacific Symposioum in Biocomputing (PSB 00). pp. 305-316.
18. Karp, R. M., Stoughton, R. & Yeung, K. Y. (1999). Algorithms for choosing differential gene expression experiments. In Proceedings of the Third Annual International Conference on Computational Molecular Biology (RECOMB 99). pp. 208-217.
19. Kauffman, S. (1993). The Origins Of Order, Self Organization and Selection in Evoultion. Oxford University Press.
20. Liang, S., Fuhrman, S. & Somogoyi, R. (1998). REVEAL, a general reverse engineering algorithm for inference of genetic network architectures. In Proceedings of the 1998 Pacific Symposioum in Biocomputing (PSB 98). pp. 18-29.
21. Sharan, R. & Shamir, R. (2000). CLICK: a clustering algorithm with applications to gene expression analysis. In Proceedings of the Eighth Annual Conference on Intelligent Systems for Molecular Biology (ISMB 00). pp. 307-316.
22. Somogyi, R. & Sniegoski, C. (1996). Modeling the complexity of genetic networks, understanding multigene and pleiotropic regulation. Complexity, 1, 45-50.
23. Spellman, P. et al. (1998). Comprehensive identification of cell cycle regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell, 9, 3273-3297.
24. Tun, T. & Loper, J. (1992). Multiple regulatory elements control expression of the gene encoding the Saccharomyces cerevisiae Cytochrome P450, lanosterol 14a-demethylase (ERG 11). JBC, 267, 2046-56.
25. Zien, A., Kuffner, R., Zimmer, R. & Lengauer, T. (2000). Analysis of gene expression data with pathway scores. In Proceedings of the Eighth Annual Conference on Intelligent Systems for Molecular Biology (ISMB 00). pp. 407-417.