Research output: Contribution to Journal/Magazine › Journal article › peer-review
Research output: Contribution to Journal/Magazine › Journal article › peer-review
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TY - JOUR
T1 - A mathematical program to refine gene regulatory networks
AU - Lulli, Guglielmo
AU - Romauch, Martin
PY - 2009/5/28
Y1 - 2009/5/28
N2 - In this paper, we propose a methodology for making sense of large, multiple time-series data sets arising in expression analysis. Specifically, we present a mathematical model to release a reduced and coherent regulatory system given a putative regulatory network. We give two equivalent formulations of the problem and prove that the problem is NP-complete. For solving large scale instances we implemented an Ant Colony Optimization procedure. A computational analysis on randomly generated test instances validates the proposed algorithm and the computations on real data concerning Saccharomyces cerevisiae show the practicability of the proposed methodology.
AB - In this paper, we propose a methodology for making sense of large, multiple time-series data sets arising in expression analysis. Specifically, we present a mathematical model to release a reduced and coherent regulatory system given a putative regulatory network. We give two equivalent formulations of the problem and prove that the problem is NP-complete. For solving large scale instances we implemented an Ant Colony Optimization procedure. A computational analysis on randomly generated test instances validates the proposed algorithm and the computations on real data concerning Saccharomyces cerevisiae show the practicability of the proposed methodology.
KW - Ant colony optimization
KW - Gene regulatory networks
KW - Mathematical programming
KW - Reverse engineering
U2 - 10.1016/j.dam.2008.06.044
DO - 10.1016/j.dam.2008.06.044
M3 - Journal article
AN - SCOPUS:67349151303
VL - 157
SP - 2469
EP - 2482
JO - Discrete Applied Mathematics
JF - Discrete Applied Mathematics
SN - 0166-218X
IS - 10
ER -