Jump to main content
Jump to site search
SCHEDULED MAINTENANCE Close the message box

Maintenance work is planned for Monday 16 August 2021 from 07:00 to 23:59 (BST).

Website performance may be temporarily affected and you may not be able to access some PDFs or images. If this does happen, refreshing your web browser should resolve the issue. We apologise for any inconvenience this might cause and thank you for your patience.


Issue 9, 2017

A comparative review of computational methods for pathway perturbation analysis: dynamical and topological perspectives

Author affiliations

Abstract

Stem cells offer great promise within the field of regenerative medicine but despite encouraging results, the large scale use of stem cells for therapeutic applications still faces challenges when it comes to controlling signaling pathway responses with respect to environmental perturbations. This step is critical for the elaboration of stable and reproducible differentiation protocols, and computational modeling can be helpful to overcome these difficulties. This article is a comparative review of the mechanism-based methods used for hypothesis-driven approaches and data-driven methods which are two types of computational approaches commonly used for analysing the dynamics of pathways involved in stem cell regulation. We firstly review works based on kinetic modelling. We emphasize the relationships between the dynamics of these pathways and their topological features, and illustrative examples are described to show how the analysis of these relationships can contribute to a more detailed and formal understanding of the signaling dynamics. This discussion is followed by a review of the recent data-driven pathway analysis methods. Based on a simplified description of the pathways, these methods are able to handle high dimensionality data, and topological features of the pathways taken into account in the latest methods improve both accuracy and predictive power. Nevertheless, progress is still needed to clarify the biological meaning of the topological decompositions used by these methods.

Graphical abstract: A comparative review of computational methods for pathway perturbation analysis: dynamical and topological perspectives

Supplementary files

Article information


Submitted
20 Mar 2017
Accepted
15 Jun 2017
First published
17 Jul 2017

Mol. BioSyst., 2017,13, 1692-1704
Article type
Review Article

A comparative review of computational methods for pathway perturbation analysis: dynamical and topological perspectives

Q. Vanhaelen, A. M. Aliper and A. Zhavoronkov, Mol. BioSyst., 2017, 13, 1692 DOI: 10.1039/C7MB00170C

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.


Search articles by author

Spotlight

Advertisements