Modeling gene regulatory networks with piecewise linear differential equations

Date

2007-09-16

Author

Gebert, J.
Radde, N.
Weber, Gerhard Wilhelm

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

159
views

0
downloads

Microarray chips generate large amounts of data about a cell's state. In our work we want to analyze these data in order to describe the regulation processes within a cell. Therefore, we build a model which is capable of capturing the most relevant regulating interactions and present an approach how to calculate the parameters for the model from time-series data. This approach uses the discrete approximation method of least squares to solve a data fitting modeling problem. Furthermore, we analyze the features of our proposed system, i.e., which kinds of dynamical behaviors the system is able to show.

Subject Keywords

Management Science and Operations Research, Modelling and Simulation, Information Systems and Management

URI

https://hdl.handle.net/11511/56789

Journal

EUROPEAN JOURNAL OF OPERATIONAL RESEARCH

DOI

https://doi.org/10.1016/j.ejor.2005.11.044

Collections

Graduate School of Applied Mathematics, Article

Suggestions

OpenMETU
Core

A conic quadratic formulation for a class of convex congestion functions in network flow problems Gürel, Sinan (Elsevier BV, 2011-06-01) In this paper we consider a multicommodity network flow problem with flow routing and discrete capacity expansion decisions. The problem involves trading off congestion and capacity assignment (or expansion) costs. In particular, we consider congestion costs involving convex, increasing power functions of flows on the arcs. We first observe that under certain conditions the congestion cost can be formulated as a convex function of the capacity level and the flow. Then, we show that the problem can be effici...
A multicriteria sorting approach based on data envelopment analysis for R&D project selection problem Karasakal, Esra (Elsevier BV, 2017-12-01) In this paper, multiple criteria sorting methods based on data envelopment analysis (DEA) are developed to evaluate research and development (R&D) projects. The weight intervals of the criteria are obtained from Interval Analytic Hierarchy Process and employed as the assurance region constraints of models. Based on data envelopment analysis, two threshold estimation models, and five assignment models are developed for sorting. In addition to sorting, these models also provide ranking of the projects. The de...
Manufacturing lead time estimation using data mining Ozturk, Atakan; Kayaligil, Sinan; Özdemirel, Nur Evin (Elsevier BV, 2006-09-01) We explore use of data mining for lead time estimation in make-to-order manufacturing. The regression tree approach is chosen as the specific data mining method. Training and test data are generated from variations of a job shop simulation model. Starting with a large set of job and shop attributes, a reasonably small subset is selected based on their contribution to estimation performance. Data mining with the selected attributes is compared with linear regression and three other lead time estimation metho...
Modeling of various biological networks via LCMARS AYYILDIZ DEMİRCİ, EZGİ; Purutçuoğlu Gazi, Vilda (Elsevier BV, 2018-09-01) In system biology, the interactions between components such as genes, proteins, can be represented by a network. To understand the molecular mechanism of complex biological systems, construction of their networks plays a crucial role. However, estimation of these biological networks is a challenging problem because of their high dimensional and sparse structures. Several statistical methods are proposed to overcome this issue. The Conic Multivariate Adaptive Regression Splines (CMARS) is one of the recent n...
A metamodeling methodology involving both qualitative and quantitative input factors Tunali, S; Batmaz, I (Elsevier BV, 2003-10-16) This paper suggests a methodology for developing a simulation metamodel involving both quantitative and qualitative factors. The methodology mainly deals with various strategic issues involved in metamodel estimation, analysis, comparison, and validation. To illustrate how to apply the methodology, a regression metamodel is developed for a client-server computer system. In particular, we studied how the response time is affected by the quantum interval, the buffer size. and the total number of terminals whe...

Citation Formats

J. Gebert, N. Radde, and G. W. Weber, “Modeling gene regulatory networks with piecewise linear differential equations,” EUROPEAN JOURNAL OF OPERATIONAL RESEARCH, pp. 1148–1165, 2007, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/56789.