Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.

ABSTRACT:

Motivation

Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters.

Results

In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parame

SUBMITTER: Henriques D 

PROVIDER: S-EPMC4565031 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature