Genetic network identification using convex programming

IET Systems Biology

Volumn 3, Issue 3, 2009, Pages 155-166

  Julius, A ^a   Zavlanos, M ^a   Boyd, S ^b   Pappas, G J ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APRIORI; ARTIFICIAL NETWORKS; BIOLOGICAL PROCESS; CONVEX PROGRAMMING; DROSOPHILA MELANOGASTER; EQUILIBRIUM STATE; EXPERIMENTAL DATA; EXPRESSION LEVELS; GENE REGULATORY NETWORKS; GENETIC NETWORKS; HARD PROBLEMS; IDENTIFICATION ALGORITHMS; INTERACTION PATTERN; LARGE-SCALE NETWORK; NETWORK STRUCTURES; NOVEL ALGORITHM; REGULATORY NETWORK; SMALL PERTURBATIONS; SUB-NETWORK; SYSTEMS BIOLOGY;

ESCHERICHIA COLI; GENE ENCODING; GENETIC PROGRAMMING;

TRANSCRIPTION;

MESSENGER RNA;

ANALYTIC METHOD; ARTICLE; CYTOLOGY; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENE INTERACTION; GENE REGULATORY NETWORK; GENETIC CODE; MICROARRAY ANALYSIS; MOLECULAR BIOLOGY; MOLECULAR MODEL; QUALITATIVE ANALYSIS; TRANSCRIPTION REGULATION; TRANSLATION REGULATION;

ALGORITHMS; ANIMALS; BODY PATTERNING; COMPUTER SIMULATION; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ROC CURVE; SOS RESPONSE (GENETICS); SYSTEMS BIOLOGY;

DROSOPHILA MELANOGASTER; ESCHERICHIA COLI;

EID: 66249091244     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb.2008.0130     Document Type: Article

References (26)

1. Bonneau, R., Reiss,AD.J., and Shannon, P.: Et al. 'The inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo', Genome Biol., 2006, 7, p. R36
2. Hayete, BN, Gardner, T.S., and Collins, J.J.: 'Size matters: network inference tackles the genome scale', Mole. Syst. Biol., 2007, 3, article no. 77
3. Geier, F., Timmer, J., and Fleck, C.: 'Reconstructing gene-regulatory networks from time-series, knockout data and prior knowledge', BMC Syst. Biol., 2007, 1, (11), article no. 11
4. Faith, J.J., Hayete, B., and Thaden, J.T.: Et al. 'Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles', PLoS Biol., 2007, 5, (1), p. e8
5. Bansal, M., Belcastro, V., Ambesi-Impiombato, A., and di Bernardo, D.: 'How to infer gene networks from expression profiles', Mole. Syst. Biol., 2007, 3, article no. 78
6. Gardner, T.S., di Bernardo, D., Lorenz, D., and Collins, J.J.: 'Inferring genetic networks and identifying compound mode of action via expression profiling', Science, 2003, 301, p. 102-105 0036-8075
7. Tegner, J., Yeung, M.K.S., Hasty, J., and Collins, J.J.: 'Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling', Proc. Natl. Acad. Sci., 2003, 100, (10), p. 5944-5949
8. Sontag, E., Kiyatkin, A., and Kholodenko, B.N.: 'Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data', Bioinformatics, 2004, 20, (12), p. 1877-1886
9. Bansal, M., Della Gatta, G., and di Bernardo, D.: 'Inference of gene regulatory networks and compound mode of action from time course gene expression profiles', Bioinformatics, 2006, 22, (7), p. 815-822
10. Hoffman, A.J., and McCormick, S.T.: 'A fast algorithm that makes matrices optimally sparse', Pulleybank, W.R., Progress in combinatorial optimization (Academic Press 1984), p. 185-196
11. Yeung, M.K.S., Tegner, J., and Collins, J.J.: 'Reverse engineering gene networks using singular value decomposition and robust regression', Proc. Natl. Acad. Sci., 2002, 99, (9), p. 6163-6168
12. Thomas, R., Mehrotra, S., Papoutsakis, E.T., and Hatzimanikatis, V.: 'A model-based optimization frame- work for the inference on gene regulatory networks from DNA array data', Bioinformatics, 2004, 20, (17), p. 3221-3235
13. Andrec, M., Kholodenko, B.N., Levy, R.M., and Sontag, E.: 'Inference of signaling and gene regulatory networks by steady-state perturbation experiments: Structure and accuracy', J. Theor. Biol., 2005, 232, (3), p. 427-441
14. Boyd, S., and Vandenberghe, L.: 'Convex optimization', (Cambridge University Press 2004), Available online at www.stanford.edu/boyd/ cvxbook/
15. 1-norm norm methods for convex cardinality problems', (Stanford University 2007), Available online at www.stanford.edu/class/ee364b/, Lecture Notes for EE364b
16. Lobo, M.S., Fazel, M., and Boyd, S.: 'Portfolio optimization with linear and fixed transaction costs', Ann. Oper. Res., 2007, 152, (1), p. 376-394
17. Hassibi, A., How, J., and Boyd, S.: 'Low-authority controller design via convex optimization', AIAA J. Guid. Control Dyn., 1999, 22, (6), p. 862-872
18. Li, F., and Yang, Y.: 'Recovering genetic regulatory networks from micro-array data and location analysis data', Genome Inf., 2004, 15, (2), p. 131-140
19. Han, S., Yoon, Y., and Cho, K.H.: 'Inferring biomolecular interaction networks based on convex optimization', Comput. Biol. Chem., 2007, 31, (5-6), p. 347-354 1476-9271
20. Guo, Y., and Schuurmans, D.: 'Learning gene regulatory networks via globally regularized risk mini- mization', Comparative genomics, (Springer Verlag, Berlin 2007), p. 83-95
21. Papachristodoulou, A., and Recht, B.: 'Determining Interconnections in chemical reaction networks', Proc. American Control Conf., New York, USA 2007, p. 4872-4877
22. Cosentino, C., Curatola, W., Montefusco, F., Bansal, M., di Bernardo, D., and Amato, F.: 'Linear matrix inequalities approach to reconstruction of biological networks', IET. Syst. Biol., 2007, 1, (3), p. 164-173 10.1049/iet-syb:20060054
23. Boyd, S., and Grant, M.C.: 'cvx - MATLAB software for disciplined convex programming', 2005, http://www.stanford.edu/~boyd/cvx/
24. Lusetti, S.L., Voloshin, O.N., Inman, R.B., Camerini-Otero, R.D., and Cox, M.M.: 'The DinI Protein Stabilizes RecA Protein Filaments', J. Biol. Chem., 2004, 279, (29), p. 30037-30046
25. De Muth, J.E.: 'Basic statistics and pharmaceutical statistical applications', 2nd (Chapman & Hall/CRC 2006)
26. Gardner, T.S., Cantor, C.R., and Collins, J.J.: 'Construction of a genetic toggle switch in Escherichia coli', Nature, 2000, 403, p. 339-342 0028-0836