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

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Department of Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA
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Department of Computer Science, University of Bonn, Bonn 53113, Germany
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Author to whom correspondence should be addressed.
Biology 2014, 3(1), 1-21; https://doi.org/10.3390/biology3010001
Received: 19 July 2013 / Revised: 11 November 2013 / Accepted: 9 December 2013 / Published: 19 December 2013
(This article belongs to the Special Issue Developments in Bioinformatic Algorithms)
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. View Full-Text
Keywords: transitive reduction; minimum equivalent digraph; network synthesis; disease networks; combinatorial algorithms transitive reduction; minimum equivalent digraph; network synthesis; disease networks; combinatorial algorithms
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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.

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