Description

Book Synopsis
Presents algorithmic techniques for solving problems in bioinformatics, including applications that shed new light on molecular biology

This book introduces algorithmic techniques in bioinformatics, emphasizing their application to solving novel problems in post-genomic molecular biology. Beginning with a thought-provoking discussion on the role of algorithms in twenty-first-century bioinformatics education, Bioinformatics Algorithms covers:

  • General algorithmic techniques, including dynamic programming, graph-theoretical methods, hidden Markov models, the fast Fourier transform, seeding, and approximation algorithms

  • Algorithms and tools for genome and sequence analysis, including formal and approximate models for gene clusters, advanced algorithms for non-overlapping local alignments and genome tilings, multiplex PCR primer set selection, and sequence/network motif finding

  • Microarray design and analysis, including algorithms for

    Trade Review

    "This clear and approachable presentation makes the book appropriate for researchers, practioners, and graduate students." (Mathematical Reviews, Issue 2009b)

    "This volume will be a nice addition to the bioinformatician's bookshelf." (Quarterly Review of Biology, December 2008)



    Table of Contents

    Preface ix

    Contributors xi

    1 Educating Biologists in the 21st Century: Bioinformatics Scientists versus Bioinformatics Technicians 1
    Pavel Pevzner

    Part I Techniques 7

    2 Dynamic Programming Algorithms for Biological Sequence and Structure Comparison 9
    Yuzhen Ye and Haixu Tang

    3 Graph Theoretical Approaches to Delineate Dynamics of Biological Processes 29
    Teresa M. Przytycka and Elena Zotenko

    4 Advances in Hidden Markov Models for Sequence Annotation 55
    Broňa Brejová, Daniel G. Brown, and Tomáš Vinař

    5 Sorting- and FFT-Based Techniques in the Discovery of Biopatterns 93
    Sudha Balla, Sanguthevar Rajasekaran, and Jaime Davila

    6 A Survey of Seeding for Sequence Alignment 117
    Daniel G. Brown

    7 The Comparison of Phylogenetic Networks: Algorithms and Complexity 143
    Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, and Giancarlo Mauri

    Part II Genome and Sequence Analysis 175

    8 Formal Models of Gene Clusters 177
    Anne Bergeron, Cedric Chauve, and Yannick Gingras

    9 Integer Linear Programming Techniques for Discovering Approximate Gene Clusters 203
    Sven Rahmann and Gunnar W. Klau

    10 Efficient Combinatorial Algorithms for DNA Sequence Processing 223
    Bhaskar DasGupta and Ming-Yang Kao

    11 Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints 241
    K.M. Konwar, I.I. Măndoiu, A.C. Russell, and A.A. Shvartsman

    12 Recent Developments in Alignment and Motif Finding for Sequences and Networks 259
    Sing-Hoi Sze

    Part III Microarray Design and Data Analysis 277

    13 Algorithms for Oligonucleotide Microarray Layout 279
    Sérgio A. De Carvalho Jr. and Sven Rahmann

    14 Classification Accuracy Based Microarray Missing Value Imputation 303
    Yi Shi, Zhipeng Cai, and Guohui Lin

    15 Meta-Analysis of Microarray Data 329
    Saumyadipta Pyne, Steve Skiena, and Bruce Futcher

    Part IV Genetic Variation Analysis 353

    16 Phasing Genotypes Using a Hidden Markov Model 355
    P. Rastas, M. Koivisto, H. Mannila, and E. Ukkonen

    17 Analytical and Algorithmic Methods for Haplotype Frequency Inference: What Do They Tell Us? 373
    Steven Hecht Orzack, Daniel Gusfield, Lakshman Subrahmanyan, Laurent Essioux, and Sebastien Lissarrague

    18 Optimization Methods for Genotype Data Analysis in Epidemiological Studies 395
    Dumitru Brinza, Jingwu He, and Alexander Zelikovsky

    Part V Structural and Systems Biology 417

    19 Topological Indices in Combinatorial Chemistry 419
    Sergey Bereg

    20 Efficient Algorithms for Structural Recall in Databases 439
    Hao Wang, Patra Volarath, and Robert W. Harrison

    21 Computational Approaches to Predict Protein–Protein and Domain–Domain Interactions 465
    Raja Jothi and Teresa M. Przytycka

    Index 493

Bioinformatics Algorithms

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    Order before 4pm today for delivery by Fri 19 Jun 2026.

    A Hardback by I Mandoiu, Alexander Zelikovsky, Yi Pan


      View other formats and editions of Bioinformatics Algorithms by I Mandoiu

      Publisher: Wiley
      Publication Date: 28/03/2008
      ISBN13: 9780470097731, 978-0470097731
      ISBN10:

      Description

      Book Synopsis
      Presents algorithmic techniques for solving problems in bioinformatics, including applications that shed new light on molecular biology

      This book introduces algorithmic techniques in bioinformatics, emphasizing their application to solving novel problems in post-genomic molecular biology. Beginning with a thought-provoking discussion on the role of algorithms in twenty-first-century bioinformatics education, Bioinformatics Algorithms covers:

      • General algorithmic techniques, including dynamic programming, graph-theoretical methods, hidden Markov models, the fast Fourier transform, seeding, and approximation algorithms

      • Algorithms and tools for genome and sequence analysis, including formal and approximate models for gene clusters, advanced algorithms for non-overlapping local alignments and genome tilings, multiplex PCR primer set selection, and sequence/network motif finding

      • Microarray design and analysis, including algorithms for

        Trade Review

        "This clear and approachable presentation makes the book appropriate for researchers, practioners, and graduate students." (Mathematical Reviews, Issue 2009b)

        "This volume will be a nice addition to the bioinformatician's bookshelf." (Quarterly Review of Biology, December 2008)



        Table of Contents

        Preface ix

        Contributors xi

        1 Educating Biologists in the 21st Century: Bioinformatics Scientists versus Bioinformatics Technicians 1
        Pavel Pevzner

        Part I Techniques 7

        2 Dynamic Programming Algorithms for Biological Sequence and Structure Comparison 9
        Yuzhen Ye and Haixu Tang

        3 Graph Theoretical Approaches to Delineate Dynamics of Biological Processes 29
        Teresa M. Przytycka and Elena Zotenko

        4 Advances in Hidden Markov Models for Sequence Annotation 55
        Broňa Brejová, Daniel G. Brown, and Tomáš Vinař

        5 Sorting- and FFT-Based Techniques in the Discovery of Biopatterns 93
        Sudha Balla, Sanguthevar Rajasekaran, and Jaime Davila

        6 A Survey of Seeding for Sequence Alignment 117
        Daniel G. Brown

        7 The Comparison of Phylogenetic Networks: Algorithms and Complexity 143
        Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, and Giancarlo Mauri

        Part II Genome and Sequence Analysis 175

        8 Formal Models of Gene Clusters 177
        Anne Bergeron, Cedric Chauve, and Yannick Gingras

        9 Integer Linear Programming Techniques for Discovering Approximate Gene Clusters 203
        Sven Rahmann and Gunnar W. Klau

        10 Efficient Combinatorial Algorithms for DNA Sequence Processing 223
        Bhaskar DasGupta and Ming-Yang Kao

        11 Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints 241
        K.M. Konwar, I.I. Măndoiu, A.C. Russell, and A.A. Shvartsman

        12 Recent Developments in Alignment and Motif Finding for Sequences and Networks 259
        Sing-Hoi Sze

        Part III Microarray Design and Data Analysis 277

        13 Algorithms for Oligonucleotide Microarray Layout 279
        Sérgio A. De Carvalho Jr. and Sven Rahmann

        14 Classification Accuracy Based Microarray Missing Value Imputation 303
        Yi Shi, Zhipeng Cai, and Guohui Lin

        15 Meta-Analysis of Microarray Data 329
        Saumyadipta Pyne, Steve Skiena, and Bruce Futcher

        Part IV Genetic Variation Analysis 353

        16 Phasing Genotypes Using a Hidden Markov Model 355
        P. Rastas, M. Koivisto, H. Mannila, and E. Ukkonen

        17 Analytical and Algorithmic Methods for Haplotype Frequency Inference: What Do They Tell Us? 373
        Steven Hecht Orzack, Daniel Gusfield, Lakshman Subrahmanyan, Laurent Essioux, and Sebastien Lissarrague

        18 Optimization Methods for Genotype Data Analysis in Epidemiological Studies 395
        Dumitru Brinza, Jingwu He, and Alexander Zelikovsky

        Part V Structural and Systems Biology 417

        19 Topological Indices in Combinatorial Chemistry 419
        Sergey Bereg

        20 Efficient Algorithms for Structural Recall in Databases 439
        Hao Wang, Patra Volarath, and Robert W. Harrison

        21 Computational Approaches to Predict Protein–Protein and Domain–Domain Interactions 465
        Raja Jothi and Teresa M. Przytycka

        Index 493

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