Computational biology of transcription factor binding
By: edited by Istvan Ladunga
Series: Methods in molecular biology -- 674; Springer protocols; Methods in molecular biology (Clifton, N.J.) -- v. 674.; Springer protocols
Publisher: Humana Press
Published: 2010
Place of publication: New York, NY
Language: eng
Number of pages: 454
ISBN-13: 9781607618539; 9781607618546
Subjects: Computational Biology; Computational biology; Transcription Factors; Protein Binding; Laboratory Manuals; Transcription factors; Methods
Notes: Includes bibliographical references and index.
Table of contents: title: An overview of the computational analyses and discovery of transcription factor binding sites / Istvan Ladunga; title: Components and mechanisms of regulation of gene expression / Alper Yilmaz; title: Regulatory regions in DNA : promoters, enhancers, silencers, and insulators / Jean-Jack M. Riethoven; title: Three-dimensional structures of DNA-bound transcriptional regulators / Tripti Shrivastava and Tahir H. Tahirov; title: Identification of promoter regions and regulatory sites / Victor V. Solovyev, Ilham A. Shahmuradov, and Asaf A. Salamov; title: Motif discovery using expectation maximization and Gibbs' sampling / Gary D. Stormo; title: Probabilistic approaches to transcription factor binding site prediction / Stefan Posch ... [et al.]; title: The motif tool assessment platform (MTAP) for sequence-based transcription factor binding site prediction tools / Daniel Quest and Hesham Ali; title: Computational analysis of ChIP-seq data / Hongkai Ji; title: Probabilistic peak calling and controlling false discovery rate estimations in transcription factor binding site mapping from ChIP-seq / Shuo Jiao ... [et al.]; title: Sequence analysis of chromatin immunoprecipitation data for transcription factors / Kenzie D. MacIsaac and Ernest Fraenkel; title: Inferring protein-DNA interaction parameters from SELEX experiments / Marko Djordjevic; title: Kernel-based identification of regulatory modules / Sebastian J. Schultheiss; title: Identification of transcription factor binding sites derived from transposable element sequences using ChIP-seq / Andrew B. Conley and I. King Jordan; title: Target gene identification via nuclear receptor binding site prediction / Gabor Varga; title: Computing chromosome conformation / James Fraser ... [et al.]; title: Large-scale identification and analysis of C-proteins / Valery Sorokin, Konstantin Severinov, and Mikhail S. Gelfand; title: Evolution of cis-regulatory sequences in Drosophila / Xin He and Saurabh Sinha; title: Regulating the regulators : modulators of transcription factor activity / Logan Everett, Matthew Hansen, and Sridhar Hannenhalli; title: Annotating the regulatory genome / Stephen B. Montgomery ... [et al.]; title: Computational identification of plant transcription factors and the construction of the plantTFDB database / Kun He ... [et al.]; title: Practical computational methods for regulatory genomics : a cisGRN-lexicon and cisGRN-browser for gene regulatory networks / Sorin Istrail ... [et al.]; title: Reconstructing transcriptional regulatory networks using three-way mutual information and Bayesian networks/ Weijun Luo and Peter J. Woolf; title: Computational methods for analyzing dynamic regulatory networks / Anthony Gitter, Yong Lu, and Ziv Bar-Joseph.