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AGN Simulation and Validation Model

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5167))

Abstract

An important question in computational biology is how genes are regulated and interact through gene networks. Some methods for the identification of gene networks from temporal data were proposed. An important open problem regards how to validate such resulting networks. This work presents an approach to validate such algorithms, considering three main aspects: (1) AGN model generation and simulation; (2) gene network identification; (3) validation of identified network.

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References

  1. Shmulevich, I., Dougherty, E.R.: Genomic Signal Processing, 1st edn. Princeton University Press, New Jersey (2007)

    MATH  Google Scholar 

  2. Barrera, J., Cesar Jr., R.M., Martins Jr., D.C., et al.: Constructing probabilistic genetic networks of Plasmodium falciparum from dynamical expression signals of the intraerythrocytic development cycle. In: Methods of Microarray Data Analysis V. Springer, Heidelberg (2006)

    Google Scholar 

  3. Liang, S., Fuhrman, S., Somogyi, R.: Reveal: a general reverse engineering algorithm for inference of genetic network architectures, pp. 18–29 (1998)

    Google Scholar 

  4. Shmulevich, I., et al.: Probabilistic boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18(2), 261–274 (2002)

    Article  MathSciNet  Google Scholar 

  5. Mendes, P., Sha, W., Ye, K.: Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics 19(Suppl. 2), 122ii–129 (2003)

    Google Scholar 

  6. Albert, R., Barabási, A.L.: Statistical mechanics of complex networks. Rev. Mod. Phys. 74(1), 47–97 (2002)

    Article  Google Scholar 

  7. Newman, M.E.J.: The structure and function of complex networks. SIAM Review 45(2), 167–256 (2003)

    Article  MATH  MathSciNet  Google Scholar 

  8. da F. Costa, L., Rodrigues, F.A., et al.: Characterization of complex networks: a survey of measurements. Advances in Physics 56(1), 167–242 (2007)

    Article  Google Scholar 

  9. Pudil, P., Novovičová, J., Kittler, J.: Floating search methods in feature selection. Pattern Recogn. Lett. 15(11), 1119–1125 (1994)

    Article  Google Scholar 

  10. da F. Costa, L., et al.: Predicting the connectivity of primate cortical networks from topological and spatial node properties. BMC Systems Biology 1, 1–16 (2007)

    Article  Google Scholar 

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Authors

Editor information

Ana L. C. Bazzan Mark Craven Natália F. Martins

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© 2008 Springer-Verlag Berlin Heidelberg

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Lopes, F.M., Cesar, R.M., da F. Costa, L. (2008). AGN Simulation and Validation Model. In: Bazzan, A.L.C., Craven, M., Martins, N.F. (eds) Advances in Bioinformatics and Computational Biology. BSB 2008. Lecture Notes in Computer Science(), vol 5167. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85557-6_17

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  • DOI: https://doi.org/10.1007/978-3-540-85557-6_17

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-85556-9

  • Online ISBN: 978-3-540-85557-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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