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Gene Regulation and Systems Biology

Synopsis: An open access, peer reviewed electronic journal that covers regulation of genes and proteins they encode and the broader field of systems biology.


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About this journal

ISSN: 1177-6250


Aims and scope:

Gene Regulation and Systems Biology is concerned with the regulation of genes and the proteins they encode and the relationship between gene regulation and the wider field of systems biology.

The regulation of genes and the proteins they encode is at the core of systems biology. Understanding the role of gene regulation in the context of the entire system as it relates to disease processes will aid therapeutic development. Therefore, combining our knowledge of gene expression and promoter control, improving gene and protein networks, and determining the role of signal transduction will enhance our ability to treat complex diseases.

Systems biology is concerned with the integration of different levels of information to understand how complex biological systems function. By studying the relationships and interactions between various parts of a biological system (including gene and protein networks involved in cell signaling) it may be possible to create an understandable model of the whole system. Mathematical, analytic, and particularly computer simulation and heuristics are used as research methods.

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Submissions, excluding editorials, letters to the editor and dedications, will be peer reviewed by two reviewers.  Reviewers are required to provide fair, balanced and constructive reports.  

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Application of Petri Nets in Bone Remodeling

Authors: Lingxi Li and Hiroki Yokota
Publication Date: 06 Jul 2009
Gene Regulation and Systems Biology 2009:3 105-114

Lingxi Li1 and Hiroki Yokota2

1Departments of Electrical and Computer Engineering and 2Biomedical Engineering Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202.

Abstract

Understanding a mechanism of bone remodeling is a challenging task for both life scientists and model builders, since this highly interactive and nonlinear process can seldom be grasped by simple intuition. A set of ordinary differential equations (ODEs) have been built for simulating bone formation as well as bone resorption. Although solving ODEs numerically can provide useful predictions for dynamical behaviors in a continuous time frame, an actual bone remodeling process in living tissues is driven by discrete events of molecular and cellular interactions. Thus, an event-driven tool such as Petri nets (PNs), which may dynamically and graphically mimic individual molecular collisions or cellular interactions, seems to augment the existing ODE-based systems analysis. Here, we applied PNs to expand the ODE-based approach and examined discrete, dynamical behaviors of key regulatory molecules and bone cells. PNs have been used in many engineering areas, but their application to biological systems needs to be explored. Our PN model was based on 8 ODEs that described an osteoprotegerin linked molecular pathway consisting of 4 types of bone cells. The models allowed us to conduct both qualitative and quantitative evaluations and evaluate homeostatic equilibrium states. The results support that application of PN models assists understanding of an event-driven bone remodeling mechanism using PN-specific procedures such as places, transitions, and firings.

Categories: Systems biology


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