Mourad Elloumi, Albert Y. Zomaya

Biological Knowledge Discovery Handbook

Preprocessing, Mining and Postprocessing of Biological Data
Herausgeber: Elloumi, Mourad; Pan, Yi; Zomaya, Albert Y

• Gebundenes Buch

Produktbeschreibung

Molecular biology is undergoing exponential growth in both the volume and complexity of biological data. This book offers the first comprehensive overview of data mining, preprocessing, postprocessing, and storage for biological data. It surveys the latest approaches and techniques in biological KDD, presenting a vast yet detailed view of the most important advances in the field. Combining sound theory, technical depth, and practical applications in molecular biology, Biological Knowledge Discovery is a unique resource for practitioners and researchers in computer science, life science, and mathematics.

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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 Management
Part B: Biological Data Modeling
Part C: Biological Feature Extraction
Part D Biological Feature Selection

BIOLOGICAL DATA MINING
Part E: Regression Analysis of Biological Data
Part F Biological Data Clustering
Part G: Biological Data Classification
Part H: Association Rules Learning from Biological Data
Part I: Text Mining and Application to Biological Data
Part J: High-Performance Computing for Biological Data Mining

Combining sound theory with practical applications in molecular biology, Biological Knowledge Discovery Handbook is ideal for courses in bioinformatics and biological KDD as well as for practitioners and professional researchers in computer science, life science, and mathematics.

Produktdetails

• Wiley Series in Bioinformatics
• Verlag: Wiley & Sons
• 1. Auflage
• Seitenzahl: 1192
• Erscheinungstermin: 16. Dezember 2013
• Englisch
• Abmessung: 259mm x 183mm x 58mm
• Gewicht: 2174g
• ISBN-13: 9781118132739
• ISBN-10: 1118132734
• Artikelnr.: 36731166

Autorenporträt

MOURAD ELLOUMI is a Full Professor in Computer Science at the University of Tunis-El Manar, Tunisia. He is the author/coauthor of more than fifty publications in international journals and conference proceedings and the coeditor, along with Albert Zomaya, of Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications (Wiley). ALBERT Y. ZOMAYA is the Chair Professor of High Performance Computing & Networking at The University of Sydney's School of Information Technologies. He is the author/coauthor of seven books, more than 450 publications in technical journals and conference proceedings, and the editor of fourteen books and nineteen conference volumes. He is a Fellow of the IEEE, the American Association for the Advancement of Science, and IET (UK).

Inhaltsangabe

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-Rodr?guez, 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, Giosüe 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 Lu?s 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 Santamar?a 48 VISUALIZATION OF BIOLOGICAL KNOWLEDGE BASED ON
MULTIMODAL BIOLOGICAL DATA 1109 Hendrik Rohn and Falk Schreiber INDEX 1127