Book 2009

Bioinformatics for Systems Biology

Editors:

ISBN: 978-1-934115-02-2 (Print) 978-1-59745-440-7 (Online)

Table of contents (32 chapters)

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  1. Front Matter

    Pages i-xiii

  2. Life of a Cell and Its Analysis

    1. Front Matter

      Pages 1-1

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      Chapter

      Pages 3-31

      Structure and Function of the Nucleus and Cell Organelles

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      Chapter

      Pages 33-49

      Transcription and the Control of Gene Expression

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      Chapter

      Pages 51-66

      RNA Processing and Translation

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      Chapter

      Pages 67-87

      DNA Replication, Recombination, and Repair

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      Chapter

      Pages 89-104

      Cell Signaling

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      Chapter

      Pages 105-117

      Epigenetics of Spermiogenesis

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      Chapter

      Pages 119-136

      Genomic Tools for Analyzing Transcriptional Regulatory Networks

  3. Statistical Tools and Their Application

    1. Front Matter

      Pages 137-137

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      Chapter

      Pages 139-150

      Probability and Hypothesis Testing

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      Chapter

      Pages 151-162

      Stochastic Models for Biological Patterns

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      Chapter

      Pages 163-180

      Population Genetics

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      Chapter

      Pages 181-205

      Statistical Tools for Gene Expression Analysis and Systems Biology and Related Web Resources

  4. Transcriptome Analysis

    1. Front Matter

      Pages 207-207

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      Chapter

      Pages 209-225

      What Goes in is What Comes Out: How to Design and Implement a Successful Microarray Experiment

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      Chapter

      Pages 227-265

      Tools and Approaches for an End-to-End Expression Array Analysis

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      Chapter

      Pages 267-279

      Analysis of Alternative Splicing with Microarrays

  5. Structural and Functional Sequence Analysis

    1. Front Matter

      Pages 281-281

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      Chapter

      Pages 283-313

      An Introduction to Multiple Sequence Alignment — and the T-Coffee Shop. Beyond Just Aligning Sequences: How Good can you Make your Alignment, and so What?

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      Chapter

      Pages 315-337

      A Spectrum of Phylogenetic-Based Approaches for Predicting Protein Functional Sites

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      Chapter

      Pages 339-352

      The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection

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      Chapter

      Pages 353-366

      In Silico Discovery of DNA Regulatory Sites and Modules

  6. Literature Mining for Association and Meaning

    1. Front Matter

      Pages 367-367

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      Chapter

      Pages 369-383

      Mining the Research Literature in Systems Biology

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      Chapter

      Pages 385-399

      GoPubMed: Exploring PubMed with Ontological Background Knowledge

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