1. An Overview of the Computational Analyses and Discovery of Transcription Factor Binding Sites Istvan Ladunga 2. Components and Mechanisms of Regulation of Gene Expression Alper Yilmaz and Erich Grotewold 3. Regulatory Regions in DNA: Promoters, Enhancers, Silencers, and Insulators Jean-Jack M. Riethoven 4. Three-Dimensional Structures of DNA-Bound Transcriptional Regulators Tripti Shrivastava and Tahir H. Tahirov 5. Identification of Promoter Regions and Regulatory Sites Victor V. Solovyev, Ilham A. Shahmuradov, and Asaf A. Salamov 6. Motif Discovery Using Expectation Maximization and Gibbs' Sampling Gary D. Stormo 7. Probabilistic Approaches to Transcription Factor Binding Site Prediction Stefan Posch, Jan Grau, Andre Gohr, Jens Keilwagen, and Ivo Grosse 8. The Motif Tool Assessment Platform (MTAP) for Sequence-Based Transcription Factor Binding Site Prediction Tools Daniel Quest and Hesham Ali 9. Computational Analysis of ChIP-seq Data Hongkai Ji 10. Probabilistic Peak Calling and Controlling False Discovery Rate Estimations in Transcription Factor Binding Site Mapping from ChIP-seq Shuo Jiao, Cheryl P. Bailey, Shunpu Zhang, and Istvan Ladunga 11. Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors Kenzie D. MacIsaac and Ernest Fraenkel 12. Inferring Protein-DNA Interaction Parameters from SELEX Experiments Marko Djordjevic 13. Kernel-Based Identification of Regulatory Modules Sebastian J. Schultheiss 14. Identification of Transcription Factor Binding Sites Derived from Transposable Element Sequences Using ChIP-seq Andrew B. Conley and I. King Jordan 15. Target Gene Identification via Nuclear Receptor Binding Site Prediction Gabor Varga 16. Computing Chromosome Conformation James Fraser, Mathieu Rousseau, Mathieu Blanchette, and Josee Dostie 17. Large-Scale Identification and Analysis of C-Proteins Valery Sorokin, Konstantin Severinov, and Mikhail S. Gelfand 18. Evolution of cis-RegulatorySequences in Drosophila Xin He and Saurabh Sinha 19. Regulating the Regulators: Modulators of Transcription Factor Activity Logan Everett, Matthew Hansen, and Sridhar Hannenhalli 20. Annotating the Regulatory Genome Stephen B. Montgomery, Katayoon Kasaian, Steven J.M. Jones, and Obi L. Griffith 21. Computational Identification of Plant Transcription Factors and the Construction of the PlantTFDB Database Kun He, An-Yuan Guo, Ge Gao, Qi-Hui Zhu, Xiao-Chuan Liu, He Zhang, Xin Chen, Xiaocheng Gu, and Jingchu Luo 22. Practical Computational Methods for Regulatory Genomics: A cisGRN-Lexicon and cisGRN-Browser for Gene Regulatory Networks Sorin Istrail, Ryan Tarpine, Kyle Schutter, and Derek Aguiar 23. Reconstructing Transcriptional Regulatory Networks Using Three-Way Mutual Information and Bayesian Networks Weijun Luo and Peter J. Woolf 24. Computational Methods for Analyzing Dynamic Regulatory Networks Anthony Gitter, Yong Lu, and Ziv Bar-Joseph