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Open AccessSelected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)
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Open AccessCharacterizing building blocks of resource constrained biological networks
Identification of motifs–recurrent and statistically significant patterns–in biological networks is the key to understand the design principles, and to infer governing mechanisms of biological systems. This, h...
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Open AccessShortest path counting in probabilistic biological networks
Biological regulatory networks, representing the interactions between genes and their products, control almost every biological activity in the cell. Shortest path search is critical to apprehend the structure...
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Open AccessProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies
Identifying motifs in biological networks is essential in uncovering key functions served by these networks. Finding non-overlap** motif instances is however a computationally challenging task. The fact that...
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Open AccessSelected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)
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Article
Open AccessSelected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)
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Open AccessIdentification of large disjoint motifs in biological networks
Biological networks provide great potential to understand how cells function. Network motifs, frequent topological patterns, are key structures through which biological networks operate. Finding motifs in biol...
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Open AccessSignal reachability facilitates characterization of probabilistic signaling networks
Studying biological networks is of extreme importance in understanding cellular functions. These networks model interactions between molecules in each cell. A large volume of research has been done to uncover ...
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Open AccessIndexing a protein-protein interaction network expedites network alignment
Network query problem aligns a small query network with an arbitrarily large target network. The complexity of this problem grows exponentially with the number of nodes in the query network if confidence in th...
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Open AccessHierarchical decomposition of dynamically evolving regulatory networks
Gene regulatory networks describe the interplay between genes and their products. These networks control almost every biological activity in the cell through interactions. The hierarchy of genes in these netwo...
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Open AccessA scalable method for identifying frequent subtrees in sets of large phylogenetic trees
We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 t...
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Open AccessHIDEN: Hierarchical decomposition of regulatory networks
Transcription factors regulate numerous cellular processes by controlling the rate of production of each gene. The regulatory relations are modeled using transcriptional regulatory networks. Recent studies hav...
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Open AccessMetabolic network alignment in large scale by network compression
Metabolic network alignment is a system scale comparative analysis that discovers important similarities and differences across different metabolisms and organisms. Although the problem of aligning metabolic n...