Discovering functions and revealing mechanisms at molecular level from biological networks

Abstract

With the increasingly accumulated data from high-throughput technologies, study on biomolecular networks has become one of key focuses in systems biology and bioinformatics. In particular, various types of molecular networks (e.g., protein-protein interaction (PPI) network; gene regulatory network (GRN); metabolic network (MN); gene coexpression network (GCEN)) have been extensively investigated, and those studies demonstrate great potentials to discover basic functions and to reveal essential mechanisms for various biological phenomena, by understanding biological systems not at individual component level but at a system-wide level. Recent studies on networks have created very prolific researches on many aspects of living organisms. In this paper, we aim to review the recent developments on topics related to molecular networks in a comprehensive manner, with the special emphasis on the computational aspect. The contents of the survey cover global topological properties and local structural characteristics, network motifs, network comparison and query, detection of functional modules and network motifs, function prediction from network analysis, inferring molecular networks from biological data as well as representative databases and software tools.

Exploring the constrained maximum edge-weight connected graph problem

“…• Step-3: Apply the Balas additive method [11] to the sorted edges with the connectivity test embedded. For step 3 we use a variant of the Balas additive method [11] , which is an enumeration scheme for solving 0-1 integer programming problem.…”

“…Such systems include the Internet, social and friendship networks, food webs, biomolecular networks, and citation networks. Due to the popularity of network application in real world, the study of networks has attracted many scientists from various fields such as mathematics, physics, computer science and sociology [10,11] .…”

Mathematical Model and Algorithm for Link Community Detection in Bipartite Networks

“…Since some nodes or links may have the same function in complex system. One of the most important topics in the area of networks is the community detection, which is a universal problem in many disciplines such as sociology, computer science and biology [5]- [7].…”

The Interactions of the Largest Subunit of RNA Polymerase II with Other Cellular Proteins: a Bioinformatic Approach

“…Based on these experimental studies, several bioinformatic tools have been developed to comprehensively analyze protein interaction networks of different cellular proteins. Here, we have used the Cytoscape software (Zhang et al, 2007) and Biogrid/ Biomart database to identify the interactions of the largest subunit of RNA Polymerase II (RNAPII), Rpb1, with other proteins in yeast. Such analysis has revealed a large number of primary interactions of Rpb1p with many proteins involved in the regulation of transcription, chromatin structure, DNA repair, and other cellular events as discussed below.…”