Bio-mimetic evolutionary reverse engineering of genetic regulatory networks

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4447 LNCS, Issue , 2007, Pages 155-165

  Marbach, Daniel ^a   Mattiussi, Claudio ^a   Floreano, Dario ^a  

^a EPFL   (Switzerland)

Author keywords

Analog Genetic Encoding (AGE); Gene networks; Genetic algorithm; Reverse engineering; Steady state data; Systems biology

Indexed keywords

BIOMIMETICS; EVOLUTIONARY ALGORITHMS; GENE ENCODING; REVERSE ENGINEERING;

ANALOG GENETIC ENCODING (AGE); GENE NETWORKS; STEADY STATE DATA; SYSTEMS BIOLOGY;

GENETIC ENGINEERING;

EID: 38049088928     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-71783-6_15     Document Type: Conference Paper

References (18)

1. Gardner, T.S., di Bernardo, D., Lorenz, D., Collins, J.J.: Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301(5629) (2003) 102-5
2. D'Haeseleer, P., Wen, X., Fuhrman, S., Somogyi, R.: Linear modeling of mRNA expression levels during CNS development and injury. Pac Symp Biocomput (1999) 41-52
3. Brazhnik, P.: Inferring gene networks from steady-state response to single-gene perturbations. J Theor Biol 237(4) (2005) 427-440
4. Come, D., Pridgeon, C.: Investigating issues in the reconstructability of genetic regulatory networks. In: Congress on Evolutionary Computation. (2004)
5. Yeung, M.K.S., Tegnér, J., Collins, J.J.: Reverse engineering gene networks using singular value decomposition and robust regression. PNAS 99(9) (2002) 6163-8
6. Ljung, L.: System identification: Theory for the user. Prentice Hall, Upper Saddle River, NJ (1999)
7. Bäck, T., Fogel, D., Michalewicz, Z., eds.: Evolutionary Computation 1: Basic Algorithms and Operators. Institute of Physics, Bristol (2000)
8. Mattiussi, C.: Evolutionary synthesis of analog networks. PhD thesis, Ecole Polytechnique Fédérale de Lausanne, Lausanne (2005)
9. Mattiussi, C., Floreano, D.: Analog Genetic Encoding for the Evolution of Circuits and Networks. IEEE Transactions on Evolutionary Computation (2006, To appear)
10. Dürr, P., Mattiussi, C., Floreano, D.: Neuroevolution with Analog Genetic Encoding. In: Parallel Problem Solving from Nature - PPSN IX. Volume 4193 of LNCS. (2006) 671-680
11. Reinitz, J., Sharp, D.H.: Mechanism of eve stripe formation. Mech Dev 49(1-2) (1995) 133-58
12. Jaeger, J., Surkova, S., Blagov, M., Janssens, H., Kosman, D., Kozlov, K.N., Manu, Myasnikova, E., Vanario-Alonso, CE., Samsonova, M., Sharp, D.H., Reinitz, J.: Dynamic control of positional information in the early drosophila embryo. Nature 430(6997) (Jul 2004) 368-371
13. Wahde, M., Hertz, J., Andersson, M.: Reverse engineering of sparsely connected genetic regulatory networks. In: Proceedings of the 2nd Workshop of Biochemical Pathways and Genetic Networks. (2001)
14. Noman, N., Iba, H.: Inference of gene regulatory networks using S-system and differential evolution. In: GECCO'05. (2005)
15. Kimura, S., Ide, K., Kashihara, A., Kano, M., Hatakeyama, M., Masui, R., Nakagawa, N., Yokoyama, S., Kuramitsu, S., Konagaya, A.: Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinformatics 21(7) (2005) 1154-63
16. Kholodenko, B.N., Kiyatkin, A., Bruggeman, F.J., Sontag, E., Westerhoff, H.V., Hoek, J.B.: Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. PNAS 99(20) (2002) 12841-12846
17. de la Fuente, A., Brazhnik, P., Mendes, P.: Linking the genes: inferring quantitative gene networks from microarray data. Trends Genet 18(8) (Aug 2002) 395-398
18. Weaver, D.: Modeling regulatory networks with weight matrices. In: Pacific Symposium on Biocomputing. (1999)