Computational Biology of Transcription Factor Binding

Chapter 1 An Overview of the Computational Analyses and Discovery of Transcription Factor Binding Sites

Chapter 2 Components and mechanisms of regulation of gene expression.

Chapter 3 Regulatory Regions in DNA: Promoters, Enhancers, Silencers, and Insulators

Chapter 4 Three-Dimensional Structures of DNA-Bound Transcriptional Regulators

Chapter 5 Computational Biology of Transcription Factor Binding

Chapter 6 Motif Discovery Using Expectation Maximization and Gibbs’ Sampling

Chapter 7 Probabilistic Approaches to Transcription Factor Binding Site Prediction

Chapter 8 The Motif Tool Assessment Platform (MTAP) for Sequence-Based Transcription Factor Binding Site Prediction Tools

Chapter 9 Computational Analysis of ChIP-seq Data

Chapter 10 Probabilistic Peak Calling and Controlling False Discovery Rate Estimations in Transcription Factor Binding Site Mapping from ChIP-seq

Chapter 11 Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors

Chapter 12 Inferring Protein–DNA Interaction Parameters from SELEX Experiments

Chapter 13 Kernel-Based Identification of Regulatory Modules

Chapter 14 Identification of Transcription Factor Binding Sites Derived from Transposable Element Sequences Using ChIP-seq

Chapter 15 Target Gene Identification via Nuclear Receptor Binding Site Prediction

Chapter 16 Computing Chromosome Conformation

Chapter 17 Large-Scale Identification and Analysis of C-Proteins

Chapter 18 Evolution of cis -Regulatory Sequences in Drosophila

Chapter 19 Regulating the Regulators: Modulators of Transcription Factor Activity

Chapter 20 Annotating the Regulatory Genome

Chapter 21 Computational Identification of Plant Transcription Factors and the Construction of the PlantTFDB Database

Chapter 22 Practical Computational Methods for Regulatory Genomics: A cis GRN-Lexicon and cis GRN-Browser for Gene Regulatory Networks

Chapter 23 Reconstructing Transcriptional Regulatory Networks Using Three-Way Mutual Information and Bayesian Networks

Chapter 24 Computational Biology of Transcription Factor Binding