Bookedited by Istvan Ladunga.
Contents:
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 plant TFDB 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