Systems Biology and Regulatory Genomics: Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA; December 2-4, 2005, Revised Selected Papers

Weihui Wu, Yongling Song, Shouguang Jin (auth.), Eleazar Eskin, Trey Ideker, Ben Raphael, Christopher Workman (eds.)3540482938, 9783540482932

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.

The 21 revised full papers presented were carefully reviewed and selected for inclusion in the book. The papers address a broad variety of topics in systems biology and regulatory genomics including inference of gene regulatory and protein signaling networks, model prediction of drug mechanism, pathway mapping and evolution in protein interaction networks, multi-scale methods which bridge abstract and detailed models, systematic design of genome-scale experiments, modeling and recognition of regulatory elements, identification and modeling of cis-regulatory regions, modeling the structure and function of the regulatory region, and comparative genomics of regulation.

---

Table of contents :
Front Matter….Pages –
An Interactive Map of Regulatory Networks of Pseudomonas aeruginosa Genome….Pages 1-10
The Pathalyzer: A Tool for Analysis of Signal Transduction Pathways….Pages 11-22
Decomposition of Overlapping Protein Complexes: A Graph Theoretical Method for Analyzing Static and Dynamic Protein Associations….Pages 23-38
Comparison of Protein-Protein Interaction Confidence Assignment Schemes….Pages 39-50
Characterization of the Effects of TF Binding Site Variations on Gene Expression Towards Predicting the Functional Outcomes of Regulatory SNPs….Pages 51-61
Comparative Systems Biology of the Sporulation Initiation Network in Prokaryotes….Pages 62-69
Improvement of Computing Times in Boolean Networks Using Chi-square Tests….Pages 70-79
Build a Dictionary, Learn a Grammar, Decipher Stegoscripts, and Discover Genomic Regulatory Elements….Pages 80-94
Causal Inference of Regulator-Target Pairs by Gene Mapping of Expression Phenotypes….Pages 95-106
Examination of the tRNA Adaptation Index as a Predictor of Protein Expression Levels….Pages 107-118
Improved Duplication Models for Proteome Network Evolution….Pages 119-137
Application of Expectation Maximization Clustering to Transcription Factor Binding Positions for cDNA Microarray Analysis….Pages 138-149
Combinatorial Genetic Regulatory Network Analysis Tools for High Throughput Transcriptomic Data….Pages 150-165
Topological Robustness of the Protein-Protein Interaction Networks….Pages 166-177
A Bayesian Approach for Integrating Transcription Regulation and Gene Expression: Application to Saccharomyces Cerevisiae Cell Cycle Data….Pages 178-187
Probabilistic in Silico Prediction of Protein-Peptide Interactions….Pages 188-197
Improved Pattern-Driven Algorithms for Motif Finding in DNA Sequences….Pages 198-211
Annotation of Promoter Regions in Microbial Genomes Based on DNA Structural and Sequence Properties….Pages 212-224
An Interaction-Dependent Model for Transcription Factor Binding….Pages 225-234
Computational Characterization and Identification of Core Promoters of MicroRNA Genes in C. elegans , H. sapiens and A. thaliana ….Pages 235-248
A Comprehensive Kinetic Model of the Exocytotic Process: Evaluation of the Reaction Mechanism….Pages 249-257
Back Matter….Pages –