Inferring gene regulatory networks from expression data with prior knowledge by linear programming

2010 International Conference on Machine Learning and Cybernetics, ICMLC 2010

Volumn 6, Issue , 2010, Pages 3067-3072

  Liu, Zhi Ping ^a   Zhang, Xiang Sun ^b   Chen, Luonan ^a  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Gene expression; Gene regulatory network inference; Linear programming; Prior knowledge; Sparsity

Indexed keywords

EID: 78149322306     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICMLC.2010.5580748     Document Type: Conference Paper

References (23)

1. Akutsu T., Miyano S., Kuhara S., "Inferring qualitative relations in genetic networks and metabolic pathways", Bioinformatics, vol 16, pp. 727-734, 2000.
2. Chen L., Aihara K., "Stability and bifurcation analysis of differential difference-algebraic equations", IEEE Trans. Circuits Syst. I, vol 48, pp. 308-326, 2001.
3. Chen L., Aihara K., "Stability of genetic regulatory networks with time delay", IEEE Trans. Circuits Syst. I, vol 49, pp. 602-608, 2002.
4. Hartemink A.J., "Reverse engineering gene regulatory networks", Nat. Biotechnol., vol 23, pp. 554-555, 2005.
5. Jong H.D., "Modeling and simulation of genetic regulatory systems: a literature review", J. Comput. BioI., vol 9, pp. 67-103, 2002.
6. Gardner T.S., Faith J., "Reverse-engineering transcription control networks", Phys. Life Rev., vol 2, pp. 65-88, 2005.
7. Hickman G.J., Hodgman T.C., "Inference of gene regulatory networks using boolean-network inference methods", J. Bioinform. Comput. BioI., vol 7, pp. 1013-1029, 2009.
8. Husmeier D., "Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks", Bioinformatics, vol 19, pp. 2271-2282, 2003.
9. Beal M.J., Falciani F., Ghahramani Z., Rangel C., Wild D.L., "A Bayesian approach to reconstructing genetic regulatory networks with hidden factors", Bioinformatics, vol 21, pp. 349-356, 2005.
10. Bansal M., Balcastro V, Ambesi-Impiombato A., di Bernardo D., "How to infer gene networks from expression profiles", Mol. Syst. BioI., vol 3, 122, 2007.
11. Chen T., He, H.L., Church G.M., "Modeling gene expression with differential equations", Pac. Symp. Biocomput., vol 4, pp. 29-40, 1999.
12. Yeung M.K.S., Tegner J., Collins J.J, "Reverse engineering gene networks using singular value decomposition and robust regression", Proc. Natl. Acad. Sci. USA, vol 99, pp. 6163-6168, 2002.
13. Tegner J., Yeung M.K.S., Hasty J., Collins J.J., "Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling", Proc. Natl Acad. Sci. USA, vol 100, pp. 5944-5949, 2003.
14. Wang Y, Joshi T., Zhang X.S., Xu D., Chen L., "Inferring gene regulatory networks from multiple microarray datasets", Bioinformatics, vol 22, pp. 2413-2420, 2006.
15. D'Haeseleer P., Wen X., Fuhrman S., Somogyi R., "Linear modeling of mRNA expression levels during cns development", Pac. Symp. Biocomput., vol 4, pp. 41-52, 1999.
16. Marbach D., Prill R.J., Schaffter T., Mattiussi C., Floreano D., Stolovitzky G., "Revealing strengths and weaknesses of methods for gene network inference, " Proc. Natl. Acad. Sci. USA, vol 107, pp. 6286-6291, 2010.
17. Basso K., Margolin A., Stolovitzky G., "Reverse engineering of regulatory networks in human B cells", Nat. Genet., vol 37, pp. 382-390, 2005.
18. Hughes T.R., Marton M.J., Jones A.R., et aI., "Functional discovery via a compendium of expression profiles", Cell, vol 102, pp. 109-126, 2000.
19. Levine M., Davidson E.H., "Gene regulatory networks for development", Proc. Natl. Acad. Sci. USA, vol 102, pp. 4936-4942, 2005.
20. Marbach D., Schaffter T., Mattiussi C., Floreano D., "Generating realistic in silico gene networks for performance assessment of reverse engineering methods", J. Comput. BioI., vol 16, pp. 229-239, 2009.
21. Thomas R., Mehrotra S., Papoutsakis E.T., Hatzimanikatis V, "A model-based optimization framework for the inference on gene regulatory networks from DNA array data", Bioinformatics, vol 20, pp. 3221-3235, 2004.
22. Nachman I., Regev A., Friedman N., "Inferring quantitative models of regulatory networks from expression data", Bioinformatics, vol 20 (Suppl. 1), pp. i248-i256, 2004.
23. Wang R.S., Wang Y, Zhang X.S., Chen L., "Inferring transcriptional regulatory networks from high-throughput data", Bioinformatics, vol 23, pp. 3056-3064, 2007.