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Biology 2014, 3(1), 1-21; doi:10.3390/biology3010001
Review

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

1
, 1,*  and 2
Received: 19 July 2013; in revised form: 11 November 2013 / Accepted: 9 December 2013 / Published: 19 December 2013
(This article belongs to the Special Issue Developments in Bioinformatic Algorithms)
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Abstract: 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.
Keywords: transitive reduction; minimum equivalent digraph; network synthesis; disease networks; combinatorial algorithms transitive reduction; minimum equivalent digraph; network synthesis; disease networks; combinatorial algorithms
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Aditya, S.; DasGupta, B.; Karpinski, M. Algorithmic Perspectives of Network Transitive Reduction Problems and their Applications to Synthesis and Analysis of Biological Networks. Biology 2014, 3, 1-21.

AMA Style

Aditya S, DasGupta B, Karpinski M. Algorithmic Perspectives of Network Transitive Reduction Problems and their Applications to Synthesis and Analysis of Biological Networks. Biology. 2014; 3(1):1-21.

Chicago/Turabian Style

Aditya, Satabdi; DasGupta, Bhaskar; Karpinski, Marek. 2014. "Algorithmic Perspectives of Network Transitive Reduction Problems and their Applications to Synthesis and Analysis of Biological Networks." Biology 3, no. 1: 1-21.



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