Table of Contents

Analysis of Combinatorial Gene Regulation with Thermodynamic Models.- RNA Secondary Structure Prediction and Gene Regulation by Small RNAs.- Some Critical Data Quality Control Issues of Oligoarrays.- Stochastic-Process Approach to Nonequilibrium Thermodynamics and Biological Signal Transduction.- Granger Causality: Theory and Applications.- Transcription Factor Binding Site Identification by Phylogenetic Footprinting.- Learning Network from High-Dimensional Array Data.- Computational Methods for Predicting Domain–Domain Interactions.- Irreversible Stochastic Processes, Coupled Diffusions and Systems Biochemistry.- Probability Modeling and Statistical Inference in Periodic Cancer Screening.- On Construction of the Smallest One-sided Confidence Intervals and Its Application in Identifying the Minimum Effective Dose.- Group Variable Selection Methods and Their Applications in Analysis of Genomic Data.- Modeling Protein-Signaling Networks with Granger Causality Test.- DNA Copy Number Profiling in Normal and Tumor Genomes.- Spatial Disease Surveillance: Methods and Applications.- From QTL Mapping to eQTL Analysis.- An Evaluation of Gene Module Concepts in the Interpretation of Gene Expression Data.- Readout of Spike Waves in a Microcolumn.- False Positive Control for Genome-Wide ChIP-Chip Tiling Arrays.

Reviews

From the reviews:“This mosaic of reviews and research precisely reflects the dynamic field of computational and systems biology. All of the major organizational levels of life are represented … . Each chapter has a brief introduction to a biological subject, a review of the main mathematical and statistical models for that particular topic, and a description of the main applications and conclusions. There are an abundant number of references for each chapter. … This compilation … is likely to inspire generations of students, researchers, and readers.” (Adrian Pasculescu, ACM Computing Reviews, January, 2011)