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Pattern-Based Biclustering with Constraints for Gene Expression Data Analysis

by Sara C. Madeira
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BicNET: Efficient Biclustering of Biological Networks to Unravel Non-Trivial Modules

by Rui Henriques, Sara C. Madeira
"... Abstract. The discovery of dense biclusters in biological networks re-ceived an increasing attention in recent years. However, despite the im-portance of understanding the cell behavior, dense biclusters can only identify modules where genes, proteins or metabolites are strongly con-nected. These mo ..."
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Abstract. The discovery of dense biclusters in biological networks re-ceived an increasing attention in recent years. However, despite the im-portance of understanding the cell behavior, dense biclusters can only identify modules where genes, proteins or metabolites are strongly con-nected. These modules are thus often associated with trivial, already known interactions or background processes not necessarily related with the studied conditions. Furthermore, despite the availability of bicluster-ing algorithms able to discover modules with more flexible coherency, their application over large-scale biological networks is hampered by efficiency bottlenecks. In this work, we propose BicNET (Biclustering NETworks), an algorithm to discover non-trivial yet coherent modules in weighted biological networks with heightened efficiency. First, we motivate the rel-evance of discovering network modules given by constant, symmetric and plaid biclustering models. Second, we propose a solution to discover these flexible modules without time and memory bottlenecks by seizing high ef-ficiency gains from the inherent structural sparsity of networks. Results from the analysis of protein and gene interaction networks support the relevance and efficiency of BicNET. 1
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