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Computational biology of transcription factor binding

Author: Istvan Ladunga
Publisher: New York, NY : Humana Press, 2010.
Series: Springer protocols (Series); Methods in molecular biology (Clifton, N.J.), v. 674.
Edition/Format:   eBook : Document : EnglishView all editions and formats
Summary:
Through great experimental difficulty, we've witnessed rapid, crucial developments at the intersection of computational biology, experimental technology, and statistics through which the vital process of transcriptional regulation can be further examined. In Computational Biology of Transcription Factor Binding, experts in the field examine the basic principles and provide detailed guidance for the computational  Read more...
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Genre/Form: Electronic books
Additional Physical Format: Print version:
Computational biology of transcription factor binding.
New York, NY : Humana Press, 2010
(OCoLC)665172551
Material Type: Document, Internet resource
Document Type: Internet Resource, Computer File
All Authors / Contributors: Istvan Ladunga
ISBN: 9781607618546 1607618540
OCLC Number: 670209749
Language Note: English.
Description: 1 online resource (xi, 454 pages) : illustrations.
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.
Series Title: Springer protocols (Series); Methods in molecular biology (Clifton, N.J.), v. 674.
Responsibility: edited by Istvan Ladunga.

Abstract:

Authoritative and easy to use, this volume examines the computational analysis of the biological interpretations of transcription factor binding. Cutting-edge protocols for computer biologists are  Read more...

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From the reviews:"Gives us an overview of transcription and its regulation. ... The methods are very up-to-date and clearly presented by authors ... . The use of tools for predicting transcription Read more...

 
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