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.

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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-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, 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 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