Titlebook: Bioinformatics Research and Applications; 5th International Sy Ion Măndoiu,Giri Narasimhan,Yanqing Zhang Conference proceedings 2009 Spring

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Using Gene Expression Modeling to Determine Biological Relevance of Putative Regulatory Networks,te regulatory networks by three methods using Bayesian network approach from an oxidative stress gene expression time course experiments. We show that better networks, identified by percentage of interactions between genes sharing at least one GO-Slim Biological Process terms, do indeed generate more predictive EMN’s.

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An Experimental Analysis of Consensus Tree Algorithms for Large-Scale Tree Collections,es on 128 to 1,024 taxa. Experimental results show that our HashCS approach is up to 100 times faster than MrBayes and up to 9 times faster than PAUP*. Fast consensus algorithms such as HashCS can be used in a variety of ways, such as in real-time to detect whether a phylogenetic search has converged.

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Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots, ever be made in the matrix M (that is normally used by TAG parsing algorithms). Our algorithm for ESLTAGs parsing takes .(. min {.,. .}) time and .( min {.,. .}) space. We show that these algorithms perform better in practice than the algorithms of Uemura, et al. [19].

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