Computational Biology of Transcription Factor Binding

An Overview of the Computational Analyses and Discovery of Transcription Factor Binding Sites.- Components and Mechanisms of Regulation of Gene Expression.- Regulatory Regions in DNA: Promoters, Enhancers, Silencers, and Insulators.- Three-Dimensional Structures of DNA-Bound Transcriptional Regulators.- Identification of Promoter Regions and Regulatory Sites.- Motif Discovery Using Expectation Maximization and Gibbs’ Sampling.- Probabilistic Approaches to Transcription Factor Binding Site Prediction.- The Motif Tool Assessment Platform (MTAP) for Sequence-Based Transcription Factor Binding Site Prediction Tools.- Computational Analysis of ChIP-seq Data.- Probabilistic Peak Calling and Controlling False Discovery Rate Estimations in Transcription Factor Binding Site Mapping from ChIP-seq.- Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors.- Inferring Protein–DNA Interaction Parameters from SELEX Experiments.- Kernel-Based Identification of Regulatory Modules.- Identification of Transcription Factor Binding Sites Derived from Transposable Element Sequences Using ChIP-seq.- Target Gene Identification via Nuclear Receptor Binding Site Prediction.- Computing Chromosome Conformation.- Large-Scale Identification and Analysis of C-Proteins.- Evolution of cis-Regulatory Sequences in Drosophila.- Regulating the Regulators: Modulators of Transcription Factor Activity.- Annotating the Regulatory Genome.- Computational Identification of Plant Transcription Factors and the Construction of the PlantTFDB Database.- Practical Computational Methods for Regulatory Genomics: A cisGRN-Lexicon and cisGRN-Browser for Gene Regulatory Networks.- Reconstructing Transcriptional Regulatory Networks Using Three-Way Mutual Information and Bayesian Networks.-Computational Methods for Analyzing Dynamic Regulatory Networks.