Titlebook: Research in Computational Molecular Biology; 14th Annual Internat Bonnie Berger Conference proceedings 2010 Springer-Verlag Berlin Heidelbe

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A New Algorithm for Improving the Resolution of Cryo-EM Density Maps,l instrumentation and computational power have spawned numerous cryo-EM studies of large biomolecular complexes resulting in the reconstruction of three-dimensional density maps at intermediate and low resolution. In this resolution range, identification and interpretation of structural elements and

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Towards Automated Structure-Based NMR Resonance Assignment,model that can start from a complete or partial assignment, generate multiple assignments, and model not only the assignment of spins to residues, but also pairwise dependencies consisting of pairs of spins to pairs of residues. It is still a challenge for automated resonance assignment systems to p

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Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra,ase represent a recently emerged alternative approach to peptide identification. However, the sizes of the Spectral Dictionaries quickly grow with the peptide length making their generation impractical for long peptides. We introduce Gapped Spectral Dictionaries (all plausible . interpretations with

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interpose

Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression,ethod. An E-MAP allows the construction of a large, weighted network of both aggravating and alleviating genetic interactions between genes. By clustering genes into modules and establishing relationships between those modules, we can discover compensatory pathways. We introduce a general framework

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Simultaneous Identification of Causal Genes and Dys-Regulated Pathways in Complex Diseases,s in many cancers exist, other combinations of genomic perturbations potentially lead to the same disease, dysregulating important pathways of the cellular system. In this study, we developed novel computational methods to identify dysregulated pathways and their direct causes in individual patients

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Incremental Signaling Pathway Modeling by Data Integration,ften an inherently . process, with new pathway players and interactions continuously being discovered and additional experimental data being generated. Here we focus on the problem of performing model parameter estimation incrementally by integrating new experimental data into an existing model. A p

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