Systems Biology and Regulatory Genomics [electronic resource] : Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA; December 2-4, 2005, Revised Selected Papers / edited by Eleazar Eskin, Trey Ideker, Ben Raphael, Christopher Workman.

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 Promoters of MicroRNA Genes in C. elegans, H. sapiens and A. thaliana -- A Comprehensive Kinetic Model of the Exocytotic Process: Evaluation of the Reaction Mechanism.

It has become increasingly evident that the use of large-scale experimental data and the application of principles from systems biology are gaining widespread acceptance in mainstream biology.Systems biologyinvolvesthe use of global cellular measurements, i.e., genomic,proteomic,and metabolomic,to constructcomputationalmodelsof cel- lar processes and disease. These approaches involve an integration of experimental and computationaltechniquesand may include: 1) developingmodels of cellular processes, 2) measuring the response to perturbations of model components, and 3) iteratively formulating and testing new hypotheses for unexpected observations. A research area that is particularly importantto systems biologyis the study of gene regulatorynetworks.Althoughgenomesequencingeffortshavebeentremendouslys- cessful, much is unknown aboutthe regulationof these sequenced genomes. Automatic methods for helping decipher the regulatory mechanism are crucial for understa- ing the regulatory network as a whole. However, many new challenges are presented when analyzing complete genomes. These challenges include motif discovery in large genomes,leveraginginformationfrommultiplegenomes,detectionofweak signals and incorporatingdifferenttypes of genomicdata such as protein localization data and gene expression. Novel methodology will be particularly relevant given the hypothesis that theobservedphenotypicdifferencesbetweenorganismswithverysimilar genomesmay be due to variations in the gene regulation. The amount of research in both of these areas has exploded in recent years, as w- nessed by the number of research presentations at meetings such as RECOMB, ISMB, PSB, the Biopathways Consortium, and ICSB. The jointly held RECOMB Satellite on Systems Biology and the RECOMB Satellite on Regulatory Genomics provide a forum for addressing these challenges.