Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 409650
Title Evaluation of design strategies for time course experiments in genetic networks: the XlnR regulon in Aspergillus niger
Author(s) Omony, J.; Mach-Aigner, A.R.; Graaff, L.H. de; Straten, G. van; Boxtel, A.J.B. van
Source In: Proceedings of the 9th International Conference on Computational Methods in Systems Biology, CMSB "11, Paris, France, 21-23 September 2011. - New York, NY, USA : ACM - ISBN 9781450308175 - p. 25 - 33.
Event New York, NY, USA : ACM - ISBN 9781450308175 CMSB "11, 9th International Conference on computational methods in systems biology, Paris, France, 2011-09-21/2011-09-23
Department(s) Systems and Control Group
Microbiological Laboratory
Publication type Contribution in proceedings
Publication year 2011
Abstract One of the challenges in the reconstruction of genetic network is to find experimental designs that maximize the information content in the data. In this work the information value of time course experiments (TCEs) is used to rank experimental designs. The study concerns the dynamic response of genes in the XlnR regulon of Aspergillus niger, whereby it was the goal to find the best moment to administer an extra pulse of inducing D-xylose. Low and high trigger concentrations are considered. The models that govern the regulation of the target genes in this regulon are used for simulation. Parameter sensitivity analysis, Fisher Information Matrix (FIM) and the E-modified criterion are used for the design performance assessment. The results show that the best time to give a second pulse of a low concentration trigger of D-xylose is when the D-xylose concentration from the first pulse is not yet completed reduced. Secondly, pulses with high trigger concentrations were simulated, parameter sensitivities computed, and the experimental designs evaluated. Overall, after the first pulse of 1 mM D-xylose, using a second pulse of 5 (or 10) mM D-xylose yields the best experimental design - leading to improved parameter estimates
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