Titlebook: Research in Computational Molecular Biology; 13th Annual Internat Serafim Batzoglou Conference proceedings 2009 Springer-Verlag Berlin Heid

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Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology, scales to high-dimensional models and is exact if the given model is affine. We demonstrate our method on a model of the acute inflammatory response to bacterial infection, and identify initial conditions consistent with 3 biologically relevant outcomes.

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Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification,ed on tandem Mass Spectrometry (MS/MS) data. The disadvantage is that MS/MS data only sequences a limited number of peptides and leaves many more peptides uncovered..Peptide Mass Fingerprinting (PMF) has been widely used to identify single purified proteins from single-stage MS data. Unfortunately,

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Boosting Protein Threading Accuracy,ombining sequence and structure features to measure the quality of a sequence-template alignment so that a dynamic programming algorithm can be used to optimize the scoring function. However, a linear scoring function cannot fully exploit interdependency among features and thus, limits alignment acc

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Cross Species Expression Analysis of Innate Immune Response,n activate different sets of genes. Microarray studies of human and mouse cells infected with various pathogens identified hundreds of differentially expressed genes. However, combining these datasets to identify common and unique response patterns remained a challenge. We developed methods based on

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