Systems Biology and Regulatory Genomics

Zusammenfassung

This book constitutes the thoroughly refereed post-proceedings of two joint RECOMB 2005 satellite events: the First Annual Workshop on Systems Biology, RSB 2005 and the Second Annual Workshop on Regulatory Genomics, RRG 2005, held in San Diego, CA, USA in December 2005. It contains 21 revised full papers that address a broad variety of topics in systems biology and regulatory genomics.

Inhalt
An Interactive Map of Regulatory Networks of Pseudomonas aeruginosa Genome.- The Pathalyzer: A Tool for Analysis of Signal Transduction Pathways.- Decomposition of Overlapping Protein Complexes: A Graph Theoretical Method for Analyzing Static and Dynamic Protein Associations.- Comparison of Protein-Protein Interaction Confidence Assignment Schemes.- Characterization of the Effects of TF Binding Site Variations on Gene Expression Towards Predicting the Functional Outcomes of Regulatory SNPs.- Comparative Systems Biology of the Sporulation Initiation Network in Prokaryotes.- Improvement of Computing Times in Boolean Networks Using Chi-square Tests.- Build a Dictionary, Learn a Grammar, Decipher Stegoscripts, and Discover Genomic Regulatory Elements.- Causal Inference of Regulator-Target Pairs by Gene Mapping of Expression Phenotypes.- Examination of the tRNA Adaptation Index as a Predictor of Protein Expression Levels.- Improved Duplication Models for Proteome Network Evolution.- Application of Expectation Maximization Clustering to Transcription Factor Binding Positions for cDNA Microarray Analysis.- Combinatorial Genetic Regulatory Network Analysis Tools for High Throughput Transcriptomic Data.- Topological Robustness of the Protein-Protein Interaction Networks.- A Bayesian Approach for Integrating Transcription Regulation and Gene Expression: Application to Saccharomyces Cerevisiae Cell Cycle Data.- Probabilistic in Silico Prediction of Protein-Peptide Interactions.- Improved Pattern-Driven Algorithms for Motif Finding in DNA Sequences.- Annotation of Promoter Regions in Microbial Genomes Based on DNA Structural and Sequence Properties.- An Interaction-Dependent Model for Transcription Factor Binding.- Computational Characterization and Identification of Core Promotersof MicroRNA Genes in C. elegans, H. sapiens and A. thaliana.- A Comprehensive Kinetic Model of the Exocytotic Process: Evaluation of the Reaction Mechanism.