Computational Biology of Transcription Factor Binding

1. Front Matter

   Pages i-xi

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2. An Overview of the Computational Analyses and Discovery of Transcription Factor Binding Sites

   • Istvan Ladunga

   Pages 1-22

3. Components and Mechanisms of Regulation of Gene Expression

   • Alper Yilmaz, Erich Grotewold

   Pages 23-32

4. Regulatory Regions in DNA: Promoters, Enhancers, Silencers, and Insulators

   • Jean-Jack M. Riethoven

   Pages 33-42

5. Three-Dimensional Structures of DNA-Bound Transcriptional Regulators

   • Tripti Shrivastava, Tahir H. Tahirov

   Pages 43-55

6. Identification of Promoter Regions and Regulatory Sites

   • Victor V. Solovyev, Ilham A. Shahmuradov, Asaf A. Salamov

   Pages 57-83

7. Motif Discovery Using Expectation Maximization and Gibbs’ Sampling

   • Gary D. Stormo

   Pages 85-95

8. Probabilistic Approaches to Transcription Factor Binding Site Prediction

   • Stefan Posch, Jan Grau, André Gohr, Jens Keilwagen, Ivo Grosse

   Pages 97-119

9. The Motif Tool Assessment Platform (MTAP) for Sequence-Based Transcription Factor Binding Site Prediction Tools

   • Daniel Quest, Hesham Ali

   Pages 121-141

10. Computational Analysis of ChIP-seq Data

    • Hongkai Ji

    Pages 143-159

11. Probabilistic Peak Calling and Controlling False Discovery Rate Estimations in Transcription Factor Binding Site Mapping from ChIP-seq

    • Shuo Jiao, Cheryl P. Bailey, Shunpu Zhang, Istvan Ladunga

    Pages 161-177

12. Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors

    • Kenzie D. MacIsaac, Ernest Fraenkel

    Pages 179-193

13. Inferring Protein–DNA Interaction Parameters from SELEX Experiments

    • Marko Djordjevic

    Pages 195-211

14. Kernel-Based Identification of Regulatory Modules

    • Sebastian J. Schultheiss

    Pages 213-223

15. Identification of Transcription Factor Binding Sites Derived from Transposable Element Sequences Using ChIP-seq

    • Andrew B. Conley, I. King Jordan

    Pages 225-240

16. Target Gene Identification via Nuclear Receptor Binding Site Prediction

    • Gabor Varga

    Pages 241-249

17. Computing Chromosome Conformation

    • James Fraser, Mathieu Rousseau, Mathieu Blanchette, Josée Dostie

    Pages 251-268

18. Large-Scale Identification and Analysis of C-Proteins

    • Valery Sorokin, Konstantin Severinov, Mikhail S. Gelfand

    Pages 269-282

19. Evolution of cis-Regulatory Sequences in Drosophila

    • Xin He, Saurabh Sinha

    Pages 283-296

20. Regulating the Regulators: Modulators of Transcription Factor Activity

    • Logan Everett, Matthew Hansen, Sridhar Hannenhalli

    Pages 297-312

Transcriptional regulation controls the basic processes of life. Its complex, dynamic, and hierarchical networks control the momentary availability of messenger RNAs for protein synthesis. Transcriptional regulation is key to cell division, development, tissue differen- ation, and cancer as discussed in Chapters 1 and 2. We have witnessed rapid, major developments at the intersection of computational biology, experimental technology, and statistics. A decade ago, researches were struggling with notoriously challenging predictions of isolated binding sites from low-throughput experiments. Now we can accurately predict cis-regulatory modules, conserved cl- ters of binding sites (Chapters 13 and 15), partly based on high-throughput ch- matin immunoprecipitation experiments in which tens of millions of DNA segments are sequenced by massively parallel, next-generation sequencers (ChIP-seq, Chapters 9, 10, and 11). These spectacular developments have allowed for the genome-wide mappings of tens of thousands of transcription factor binding sites in yeast, bacteria, mammals, insects, worms, and plants. Please also note the no less spectacular failures in many laboratories around the world.

• Annotation
• ChIP-seq
• Genome browsers
• Motif discovery tools
• Promoter
• Statistics
• Transcriptional regulation
• cis-Regulatory modules
• gene expression
• genes
• genome
• molecular biology
• sequence analysis
• transcription

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 factors binding sites is also very carefully presented in a text that is accessible for beginners … . In summary, this book presents an important tool for entering the growing field of bioinformatics and its use for the study of transcription. … If we cannot read all books ever written, this one is a good choice.” (Carla Columbano Oliveira, Brazilian Journal of Pharmaceutical Sciences, Vol. 47 (2), Summer, 2011)

• , Department of Statistics, University of Nebraska-Lincoln, Lincoln, USA

  Istvan Ladunga

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