Algorithmic Perspectives of Network Transitive Reduction Problems and their Applications to Synthesis and Analysis of Biological Networks

Biology

Marek Karpinski¹  Bhaskar DasGupta²  Satabdi Aditya² 

[1] Department of Computer Science, University of Bonn, Bonn 53113, Germany;Department of Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA;

关键词: transitive reduction;    minimum equivalent digraph;    network synthesis;    disease networks;    combinatorial algorithms;   

DOI  :  10.3390/biology3010001

来源: DOAJ

【 摘 要 】

In this survey paper, we will present a number of core algorithmic questions concerning several transitive reduction problems on network that have applications in network synthesis and analysis involving cellular processes. Our starting point will be the so-called minimum equivalent digraph problem, a classic computational problem in combinatorial algorithms. We will subsequently consider a few non-trivial extensions or generalizations of this problem motivated by applications in systems biology. We will then discuss the applications of these algorithmic methodologies in the context of three major biological research questions: synthesizing and simplifying signal transduction networks, analyzing disease networks, and measuring redundancy of biological networks.

【 授权许可】

Unknown