Systems Biology and Regulatory Genomics

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.