Computational Biology of Transcription Factor Binding - Ladunga, Istvan; SpringerLink (Online service) (Totowa, NJ : Humana Press : Imprint: Humana, 2010)
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.
Keywords: Proteins .; Bioinformatics .; Computational biology .; Protein Science; Computer Appl. in Life Sciences