Bioinformatics

Structure, Function and Applications

Editors:

ISBN: 978-1-60327-428-9 (Print) 978-1-60327-429-6 (Online)

Table of contents (25 protocols)

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  1. Front Matter

    Pages i-xiv

  2. Structures

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      Pages 3-31

      UNAFold

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      Pages 33-85

      Protein Structure Prediction

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      Pages 87-104

      An Introduction to Protein Contact Prediction

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      Pages 105-122

      Analysis of Mass Spectrometry Data in Proteomics

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      Pages 123-146

      The Classification of Protein Domains

  3. Inferring Function

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      Pages 149-168

      Inferring Function from Homology

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      Pages 169-180

      The Rosetta Stone Method

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      Pages 181-199

      Inferring Functional Relationships from Conservation of Gene Order

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      Pages 201-216

      Phylogenetic Profiling

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      Pages 217-231

      Phylogenetic Shadowing

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      Pages 233-244

      Prediction of Regulatory Elements

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      Pages 245-255

      Expression and Microarrays

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      Pages 257-265

      Identifying Components of Complexes

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      Pages 267-278

      Integrating Functional Genomics Data

  4. Applications and Disease

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      Pages 281-296

      Computational Diagnostics with Gene Expression Profiles

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      Pages 297-326

      Analysis of Quantitative Trait Loci

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      Pages 327-347

      Molecular Similarity Concepts and Search Calculations

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      Pages 349-362

      Optimization of the MAD Algorithm for Virtual Screening

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      Pages 363-377

      Combinatorial Optimization Models for Finding Genetic Signatures from Gene Expression Datasets

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      Pages 379-392

      Genetic Signatures for a Rodent Model of Parkinson's Disease Using Combinatorial Optimization Methods

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