Description

Book Synopsis

The first comprehensive overview of preprocessing, mining, and postprocessing of biological data

Molecular biology is undergoing exponential growth in both the volume and complexity of biological data?and knowledge discovery offers the capacity to automate complex search and data analysis tasks. This book presents a vast overview of the most recent developments on techniques and approaches in the field of biological knowledge discovery and data mining (KDD)?providing in-depth fundamental and technical field information on the most important topics encountered.

Written by top experts, Biological Knowledge Discovery Handbook: Preprocessing, Mining, and Postprocessing of Biological Data covers the three main phases of knowledge discovery (data preprocessing, data processing?also known as data mining?and data postprocessing) and analyzes both verification systems and discovery systems.

BIOLOGICAL DATA PREPROCESSING

  • Part A: Biological Data

    Trade Review

    “This book is a unique resource for practitioners and researchers in computer science, life science, and mathematics.” (Zentralblatt MATH, 1 June 2015)



    Table of Contents

    PREFACE xiii

    CONTRIBUTORS xv

    SECTION I BIOLOGICAL DATA PREPROCESSING

    PART A: BIOLOGICAL DATA MANAGEMENT

    1 GENOME AND TRANSCRIPTOME SEQUENCE DATABASES FOR DISCOVERY, STORAGE, AND REPRESENTATION OF ALTERNATIVE SPLICING EVENTS 5
    Bahar Taneri and Terry Gaasterland

    2 CLEANING, INTEGRATING, AND WAREHOUSING GENOMIC DATA FROM BIOMEDICAL RESOURCES 35
    Fouzia Moussouni and Laure Berti-Equille

    3 CLEANSING OF MASS SPECTROMETRY DATA FOR PROTEIN IDENTIFICATION AND QUANTIFICATION 59
    Penghao Wang and Albert Y. Zomaya

    4 FILTERING PROTEIN–PROTEIN INTERACTIONS BY INTEGRATION OF ONTOLOGY DATA 77
    Young-Rae Cho

    PART B: BIOLOGICAL DATA MODELING

    5 COMPLEXITY AND SYMMETRIES IN DNA SEQUENCES 95
    Carlo Cattani

    6 ONTOLOGY-DRIVEN FORMAL CONCEPTUAL DATA MODELING FOR BIOLOGICAL DATA ANALYSIS 129
    Catharina Maria Keet

    7 BIOLOGICAL DATA INTEGRATION USING NETWORK MODELS 155
    Gaurav Kumar and Shoba Ranganathan

    8 NETWORK MODELING OF STATISTICAL EPISTASIS 175
    Ting Hu and Jason H. Moore

    9 GRAPHICAL MODELS FOR PROTEIN FUNCTION AND STRUCTURE PREDICTION 191
    Mingjie Tang, Kean Ming Tan, Xin Lu Tan, Lee Sael, Meghana Chitale, Juan Esquivel-Rodrýguez, and Daisuke Kihara

    PART C: BIOLOGICAL FEATURE EXTRACTION

    10 ALGORITHMS AND DATA STRUCTURES FOR NEXT-GENERATION SEQUENCES 225
    Francesco Vezzi, Giuseppe Lancia, and Alberto Policriti

    11 ALGORITHMS FOR NEXT-GENERATION SEQUENCING DATA 251
    Costas S. Iliopoulos and Solon P. Pissis

    12 GENE REGULATORY NETWORK IDENTIFICATION WITH QUALITATIVE PROBABILISTIC NETWORKS 281
    Zina M. Ibrahim, Alioune Ngom, and Ahmed Y. Tawfik

    PART D: BIOLOGICAL FEATURE SELECTION

    13 COMPARING, RANKING, AND FILTERING MOTIFS WITH
    CHARACTER CLASSES: APPLICATION TO BIOLOGICAL SEQUENCES ANALYSIS 309
    Matteo Comin and Davide Verzotto

    14 STABILITY OF FEATURE SELECTION ALGORITHMS AND ENSEMBLE FEATURE SELECTION METHODS IN
    BIOINFORMATICS 333
    Pengyi Yang, Bing B. Zhou, Jean Yee-Hwa Yang, and Albert Y. Zomaya

    15 STATISTICAL SIGNIFICANCE ASSESSMENT FOR BIOLOGICAL FEATURE SELECTION: METHODS AND ISSUES 353
    Juntao Li, Kwok Pui Choi, Yudi Pawitan, and Radha Krishna Murthy Karuturi

    16 SURVEY OF NOVEL FEATURE SELECTION METHODS FOR CANCER CLASSIFICATION 379
    Oleg Okun

    17 INFORMATION-THEORETIC GENE SELECTION IN EXPRESSION DATA 399
    Patrick E. Meyer and Gianluca Bontempi

    18 FEATURE SELECTION AND CLASSIFICATION FOR GENE EXPRESSION DATA USING EVOLUTIONARY COMPUTATION 421
    Haider Banka, Suresh Dara, and Mourad Elloumi

    SECTION II BIOLOGICAL DATA MINING

    PART E: REGRESSION ANALYSIS OF BIOLOGICAL DATA

    19 BUILDING VALID REGRESSION MODELS FOR BIOLOGICAL DATA USING STATA AND R 445
    Charles Lindsey and Simon J. Sheather

    20 LOGISTIC REGRESSION IN GENOMEWIDE ASSOCIATION ANALYSIS 477
    Wentian Li and Yaning Yang

    21 SEMIPARAMETRIC REGRESSION METHODS IN LONGITUDINAL DATA: APPLICATIONS TO AIDS CLINICAL TRIAL DATA 501
    Yehua Li

    PART F: BIOLOGICAL DATA CLUSTERING

    22 THE THREE STEPS OF CLUSTERING IN THE POST-GENOMIC ERA 521
    Raffaele Giancarlo, Giosu´e Lo Bosco, Luca Pinello, and Filippo Utro

    23 CLUSTERING ALGORITHMS OF MICROARRAY DATA 557
    Haifa Ben Saber, Mourad Elloumi, and Mohamed Nadif

    24 SPREAD OF EVALUATION MEASURES FOR MICROARRAY CLUSTERING 569
    Giulia Bruno and Alessandro Fiori

    25 SURVEY ON BICLUSTERING OF GENE EXPRESSION DATA 591
    Adelaide Valente Freitas, Wassim Ayadi, Mourad Elloumi, Jose Luis Oliveira, and Jin-Kao Hao

    26 MULTIOBJECTIVE BICLUSTERING OF GENE EXPRESSION DATA WITH BIOINSPIRED ALGORITHMS 609
    Khedidja Seridi, Laetitia Jourdan, and El-Ghazali Talbi

    27 COCLUSTERING UNDER GENE ONTOLOGY DERIVED CONSTRAINTS FOR PATHWAY IDENTIFICATION 625
    Alessia Visconti, Francesca Cordero, Dino Ienco, and Ruggero G. Pensa

    PART G: BIOLOGICAL DATA CLASSIFICATION

    28 SURVEY ON FINGERPRINT CLASSIFICATION METHODS FOR BIOLOGICAL SEQUENCES 645
    Bhaskar DasGupta and Lakshmi Kaligounder

    29 MICROARRAY DATA ANALYSIS: FROM PREPARATION TO CLASSIFICATION 657
    Luciano Cascione, Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, and Alfredo Pulvirenti

    30 DIVERSIFIED CLASSIFIER FUSION TECHNIQUE FOR GENE EXPRESSION DATA 675
    Sashikala Mishra, Kailash Shaw, and Debahuti Mishra

    31 RNA CLASSIFICATION AND STRUCTURE PREDICTION: ALGORITHMS AND CASE STUDIES 685
    Ling Zhong, Junilda Spirollari, Jason T. L. Wang, and Dongrong Wen

    32 AB INITIO PROTEIN STRUCTURE PREDICTION: METHODS AND CHALLENGES 703
    Jad Abbass, Jean-Christophe Nebel, and Nashat Mansour

    33 OVERVIEW OF CLASSIFICATION METHODS TO
    SUPPORT HIV/AIDS CLINICAL DECISION MAKING 725
    Khairul A. Kasmiran, Ali Al Mazari, Albert Y. Zomaya, and Roger J. Garsia

    PART H: ASSOCIATION RULES LEARNING FROM BIOLOGICAL DATA

    34 MINING FREQUENT PATTERNS AND ASSOCIATION RULES FROM BIOLOGICAL DATA 737
    Ioannis Kavakiotis, George Tzanis, and Ioannis Vlahavas

    35 GALOIS CLOSURE BASED ASSOCIATION RULE MINING FROM BIOLOGICAL DATA 761
    Kartick Chandra Mondal and Nicolas Pasquier

    36 INFERENCE OF GENE REGULATORY NETWORKS BASED ON ASSOCIATION RULES 803
    Cristian Andres Gallo, Jessica Andrea Carballido, and Ignacio Ponzoni

    PART I: TEXT MINING AND APPLICATION TO BIOLOGICAL DATA

    37 CURRENT METHODOLOGIES FOR BIOMEDICAL NAMED ENTITY RECOGNITION 841
    David Campos, Sergio Matos, and José Luýs Oliveira

    38 AUTOMATED ANNOTATION OF SCIENTIFIC DOCUMENTS: INCREASING ACCESS TO BIOLOGICAL KNOWLEDGE 869
    Evangelos Pafilis, Heiko Horn, and Nigel P. Brown

    39 AUGMENTING BIOLOGICAL TEXT MINING WITH SYMBOLIC INFERENCE 901
    Jong C. Park and Hee-Jin Lee

    40 WEB CONTENT MINING FOR LEARNING GENERIC RELATIONS AND THEIR ASSOCIATIONS FROM TEXTUAL BIOLOGICAL DATA 919
    Muhammad Abulaish and Jahiruddin

    41 PROTEIN–PROTEIN RELATION EXTRACTION FROM BIOMEDICAL ABSTRACTS 943
    Syed Toufeeq Ahmed, Hasan Davulcu, Sukru Tikves, Radhika Nair, and Chintan Patel

    PART J: HIGH-PERFORMANCE COMPUTING FOR BIOLOGICAL DATA MINING

    42 ACCELERATING PAIRWISE ALIGNMENT ALGORITHMS BY USING GRAPHICS PROCESSOR UNITS 971
    Mourad Elloumi, Mohamed Al Sayed Issa, and Ahmed Mokaddem

    43 HIGH-PERFORMANCE COMPUTING IN HIGH-THROUGHPUT SEQUENCING 981
    Kamer Kaya, Ayat Hatem, Hatice Gulcin Ozer, Kun Huang, and Umit V. Catalyurek

    44 LARGE-SCALE CLUSTERING OF SHORT READS FOR METAGENOMICS ON GPUs 1003
    Thuy Diem Nguyen, Bertil Schmidt, Zejun Zheng, and Chee Keong Kwoh

    SECTION III BIOLOGICAL DATA POSTPROCESSING

    PART K: BIOLOGICAL KNOWLEDGE INTEGRATION AND VISUALIZATION

    45 INTEGRATION OF METABOLIC KNOWLEDGE FOR GENOME-SCALE METABOLIC RECONSTRUCTION 1027
    Ali Masoudi-Nejad, Ali Salehzadeh-Yazdi, Shiva Akbari-Birgani, and Yazdan Asgari

    46 INFERRING AND POSTPROCESSING HUGE PHYLOGENIES 1049
    Stephen A. Smith and Alexandros Stamatakis

    47 BIOLOGICAL KNOWLEDGE VISUALIZATION 1073
    Rodrigo Santamarýa

    48 VISUALIZATION OF BIOLOGICAL KNOWLEDGE BASED ON MULTIMODAL BIOLOGICAL DATA 1109
    Hendrik Rohn and Falk Schreiber

    INDEX 1127

Biological Knowledge Discovery Handbook

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    A Hardback by Mourad Elloumi, Albert Y. Zomaya, Yi Pan

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      Publisher: John Wiley & Sons Inc
      Publication Date: 31/01/2014
      ISBN13: 9781118132739, 978-1118132739
      ISBN10: 1118132734
      Also in:
      Database design and theory Biology, life sciences

      Description

      Book Synopsis

      The first comprehensive overview of preprocessing, mining, and postprocessing of biological data

      Molecular biology is undergoing exponential growth in both the volume and complexity of biological data?and knowledge discovery offers the capacity to automate complex search and data analysis tasks. This book presents a vast overview of the most recent developments on techniques and approaches in the field of biological knowledge discovery and data mining (KDD)?providing in-depth fundamental and technical field information on the most important topics encountered.

      Written by top experts, Biological Knowledge Discovery Handbook: Preprocessing, Mining, and Postprocessing of Biological Data covers the three main phases of knowledge discovery (data preprocessing, data processing?also known as data mining?and data postprocessing) and analyzes both verification systems and discovery systems.

      BIOLOGICAL DATA PREPROCESSING

      • Part A: Biological Data

        Trade Review

        “This book is a unique resource for practitioners and researchers in computer science, life science, and mathematics.” (Zentralblatt MATH, 1 June 2015)



        Table of Contents

        PREFACE xiii

        CONTRIBUTORS xv

        SECTION I BIOLOGICAL DATA PREPROCESSING

        PART A: BIOLOGICAL DATA MANAGEMENT

        1 GENOME AND TRANSCRIPTOME SEQUENCE DATABASES FOR DISCOVERY, STORAGE, AND REPRESENTATION OF ALTERNATIVE SPLICING EVENTS 5
        Bahar Taneri and Terry Gaasterland

        2 CLEANING, INTEGRATING, AND WAREHOUSING GENOMIC DATA FROM BIOMEDICAL RESOURCES 35
        Fouzia Moussouni and Laure Berti-Equille

        3 CLEANSING OF MASS SPECTROMETRY DATA FOR PROTEIN IDENTIFICATION AND QUANTIFICATION 59
        Penghao Wang and Albert Y. Zomaya

        4 FILTERING PROTEIN–PROTEIN INTERACTIONS BY INTEGRATION OF ONTOLOGY DATA 77
        Young-Rae Cho

        PART B: BIOLOGICAL DATA MODELING

        5 COMPLEXITY AND SYMMETRIES IN DNA SEQUENCES 95
        Carlo Cattani

        6 ONTOLOGY-DRIVEN FORMAL CONCEPTUAL DATA MODELING FOR BIOLOGICAL DATA ANALYSIS 129
        Catharina Maria Keet

        7 BIOLOGICAL DATA INTEGRATION USING NETWORK MODELS 155
        Gaurav Kumar and Shoba Ranganathan

        8 NETWORK MODELING OF STATISTICAL EPISTASIS 175
        Ting Hu and Jason H. Moore

        9 GRAPHICAL MODELS FOR PROTEIN FUNCTION AND STRUCTURE PREDICTION 191
        Mingjie Tang, Kean Ming Tan, Xin Lu Tan, Lee Sael, Meghana Chitale, Juan Esquivel-Rodrýguez, and Daisuke Kihara

        PART C: BIOLOGICAL FEATURE EXTRACTION

        10 ALGORITHMS AND DATA STRUCTURES FOR NEXT-GENERATION SEQUENCES 225
        Francesco Vezzi, Giuseppe Lancia, and Alberto Policriti

        11 ALGORITHMS FOR NEXT-GENERATION SEQUENCING DATA 251
        Costas S. Iliopoulos and Solon P. Pissis

        12 GENE REGULATORY NETWORK IDENTIFICATION WITH QUALITATIVE PROBABILISTIC NETWORKS 281
        Zina M. Ibrahim, Alioune Ngom, and Ahmed Y. Tawfik

        PART D: BIOLOGICAL FEATURE SELECTION

        13 COMPARING, RANKING, AND FILTERING MOTIFS WITH
        CHARACTER CLASSES: APPLICATION TO BIOLOGICAL SEQUENCES ANALYSIS 309
        Matteo Comin and Davide Verzotto

        14 STABILITY OF FEATURE SELECTION ALGORITHMS AND ENSEMBLE FEATURE SELECTION METHODS IN
        BIOINFORMATICS 333
        Pengyi Yang, Bing B. Zhou, Jean Yee-Hwa Yang, and Albert Y. Zomaya

        15 STATISTICAL SIGNIFICANCE ASSESSMENT FOR BIOLOGICAL FEATURE SELECTION: METHODS AND ISSUES 353
        Juntao Li, Kwok Pui Choi, Yudi Pawitan, and Radha Krishna Murthy Karuturi

        16 SURVEY OF NOVEL FEATURE SELECTION METHODS FOR CANCER CLASSIFICATION 379
        Oleg Okun

        17 INFORMATION-THEORETIC GENE SELECTION IN EXPRESSION DATA 399
        Patrick E. Meyer and Gianluca Bontempi

        18 FEATURE SELECTION AND CLASSIFICATION FOR GENE EXPRESSION DATA USING EVOLUTIONARY COMPUTATION 421
        Haider Banka, Suresh Dara, and Mourad Elloumi

        SECTION II BIOLOGICAL DATA MINING

        PART E: REGRESSION ANALYSIS OF BIOLOGICAL DATA

        19 BUILDING VALID REGRESSION MODELS FOR BIOLOGICAL DATA USING STATA AND R 445
        Charles Lindsey and Simon J. Sheather

        20 LOGISTIC REGRESSION IN GENOMEWIDE ASSOCIATION ANALYSIS 477
        Wentian Li and Yaning Yang

        21 SEMIPARAMETRIC REGRESSION METHODS IN LONGITUDINAL DATA: APPLICATIONS TO AIDS CLINICAL TRIAL DATA 501
        Yehua Li

        PART F: BIOLOGICAL DATA CLUSTERING

        22 THE THREE STEPS OF CLUSTERING IN THE POST-GENOMIC ERA 521
        Raffaele Giancarlo, Giosu´e Lo Bosco, Luca Pinello, and Filippo Utro

        23 CLUSTERING ALGORITHMS OF MICROARRAY DATA 557
        Haifa Ben Saber, Mourad Elloumi, and Mohamed Nadif

        24 SPREAD OF EVALUATION MEASURES FOR MICROARRAY CLUSTERING 569
        Giulia Bruno and Alessandro Fiori

        25 SURVEY ON BICLUSTERING OF GENE EXPRESSION DATA 591
        Adelaide Valente Freitas, Wassim Ayadi, Mourad Elloumi, Jose Luis Oliveira, and Jin-Kao Hao

        26 MULTIOBJECTIVE BICLUSTERING OF GENE EXPRESSION DATA WITH BIOINSPIRED ALGORITHMS 609
        Khedidja Seridi, Laetitia Jourdan, and El-Ghazali Talbi

        27 COCLUSTERING UNDER GENE ONTOLOGY DERIVED CONSTRAINTS FOR PATHWAY IDENTIFICATION 625
        Alessia Visconti, Francesca Cordero, Dino Ienco, and Ruggero G. Pensa

        PART G: BIOLOGICAL DATA CLASSIFICATION

        28 SURVEY ON FINGERPRINT CLASSIFICATION METHODS FOR BIOLOGICAL SEQUENCES 645
        Bhaskar DasGupta and Lakshmi Kaligounder

        29 MICROARRAY DATA ANALYSIS: FROM PREPARATION TO CLASSIFICATION 657
        Luciano Cascione, Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, and Alfredo Pulvirenti

        30 DIVERSIFIED CLASSIFIER FUSION TECHNIQUE FOR GENE EXPRESSION DATA 675
        Sashikala Mishra, Kailash Shaw, and Debahuti Mishra

        31 RNA CLASSIFICATION AND STRUCTURE PREDICTION: ALGORITHMS AND CASE STUDIES 685
        Ling Zhong, Junilda Spirollari, Jason T. L. Wang, and Dongrong Wen

        32 AB INITIO PROTEIN STRUCTURE PREDICTION: METHODS AND CHALLENGES 703
        Jad Abbass, Jean-Christophe Nebel, and Nashat Mansour

        33 OVERVIEW OF CLASSIFICATION METHODS TO
        SUPPORT HIV/AIDS CLINICAL DECISION MAKING 725
        Khairul A. Kasmiran, Ali Al Mazari, Albert Y. Zomaya, and Roger J. Garsia

        PART H: ASSOCIATION RULES LEARNING FROM BIOLOGICAL DATA

        34 MINING FREQUENT PATTERNS AND ASSOCIATION RULES FROM BIOLOGICAL DATA 737
        Ioannis Kavakiotis, George Tzanis, and Ioannis Vlahavas

        35 GALOIS CLOSURE BASED ASSOCIATION RULE MINING FROM BIOLOGICAL DATA 761
        Kartick Chandra Mondal and Nicolas Pasquier

        36 INFERENCE OF GENE REGULATORY NETWORKS BASED ON ASSOCIATION RULES 803
        Cristian Andres Gallo, Jessica Andrea Carballido, and Ignacio Ponzoni

        PART I: TEXT MINING AND APPLICATION TO BIOLOGICAL DATA

        37 CURRENT METHODOLOGIES FOR BIOMEDICAL NAMED ENTITY RECOGNITION 841
        David Campos, Sergio Matos, and José Luýs Oliveira

        38 AUTOMATED ANNOTATION OF SCIENTIFIC DOCUMENTS: INCREASING ACCESS TO BIOLOGICAL KNOWLEDGE 869
        Evangelos Pafilis, Heiko Horn, and Nigel P. Brown

        39 AUGMENTING BIOLOGICAL TEXT MINING WITH SYMBOLIC INFERENCE 901
        Jong C. Park and Hee-Jin Lee

        40 WEB CONTENT MINING FOR LEARNING GENERIC RELATIONS AND THEIR ASSOCIATIONS FROM TEXTUAL BIOLOGICAL DATA 919
        Muhammad Abulaish and Jahiruddin

        41 PROTEIN–PROTEIN RELATION EXTRACTION FROM BIOMEDICAL ABSTRACTS 943
        Syed Toufeeq Ahmed, Hasan Davulcu, Sukru Tikves, Radhika Nair, and Chintan Patel

        PART J: HIGH-PERFORMANCE COMPUTING FOR BIOLOGICAL DATA MINING

        42 ACCELERATING PAIRWISE ALIGNMENT ALGORITHMS BY USING GRAPHICS PROCESSOR UNITS 971
        Mourad Elloumi, Mohamed Al Sayed Issa, and Ahmed Mokaddem

        43 HIGH-PERFORMANCE COMPUTING IN HIGH-THROUGHPUT SEQUENCING 981
        Kamer Kaya, Ayat Hatem, Hatice Gulcin Ozer, Kun Huang, and Umit V. Catalyurek

        44 LARGE-SCALE CLUSTERING OF SHORT READS FOR METAGENOMICS ON GPUs 1003
        Thuy Diem Nguyen, Bertil Schmidt, Zejun Zheng, and Chee Keong Kwoh

        SECTION III BIOLOGICAL DATA POSTPROCESSING

        PART K: BIOLOGICAL KNOWLEDGE INTEGRATION AND VISUALIZATION

        45 INTEGRATION OF METABOLIC KNOWLEDGE FOR GENOME-SCALE METABOLIC RECONSTRUCTION 1027
        Ali Masoudi-Nejad, Ali Salehzadeh-Yazdi, Shiva Akbari-Birgani, and Yazdan Asgari

        46 INFERRING AND POSTPROCESSING HUGE PHYLOGENIES 1049
        Stephen A. Smith and Alexandros Stamatakis

        47 BIOLOGICAL KNOWLEDGE VISUALIZATION 1073
        Rodrigo Santamarýa

        48 VISUALIZATION OF BIOLOGICAL KNOWLEDGE BASED ON MULTIMODAL BIOLOGICAL DATA 1109
        Hendrik Rohn and Falk Schreiber

        INDEX 1127

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