Computing Pathways to Systems Biology: Key Contributions of Computational Methods in Pathway Identification

TL;DR

This paper reviews the significant computational methods developed over the past decade for reconstructing biological pathways, emphasizing their role in understanding cellular mechanisms and diseases like cancer.

Contribution

It provides a comprehensive roadmap of key computational contributions to pathway identification within systems biology over the last decade.

Findings

Computational methods have significantly advanced pathway reconstruction.

These methods have enhanced understanding of cellular mechanisms.

They have contributed to insights into systems biology diseases such as cancer.

Abstract

Understanding large molecular networks consisting of entities such as genes, proteins or RNAs that interact in complex ways to drive the cellular machinery has been an active focus of systems biology. Computational approaches have played a key role in systems biology by complementing theoretical and experimental approaches. Here we roadmap some key contributions of computational methods developed over the last decade in the reconstruction of biological pathways. We position these contributions in a 'systems biology perspective' to reemphasize their roles in unraveling cellular mechanisms and to understand 'systems biology diseases' including cancer.