Biological Knowledge Discovery Handbook

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).

• PREFACE xiiiCONTRIBUTORS xvSECTION I BIOLOGICAL DATA PREPROCESSING PART A: BIOLOGICAL DATA MANAGEMENT1 GENOME AND TRANSCRIPTOME SEQUENCE DATABASES FOR DISCOVERY, STORAGE, AND REPRESENTATION OF ALTERNATIVE SPLICING EVENTS 5Bahar Taneri and Terry Gaasterland2 CLEANING, INTEGRATING, AND WAREHOUSING GENOMIC DATA FROM BIOMEDICAL RESOURCES 35Fouzia Moussouni and Laure Berti-Equille3 CLEANSING OF MASS SPECTROMETRY DATA FOR PROTEIN IDENTIFICATION AND QUANTIFICATION 59Penghao Wang and Albert Y. Zomaya4 FILTERING PROTEIN–PROTEIN INTERACTIONS BY INTEGRATION OF ONTOLOGY DATA 77Young-Rae ChoPART B: BIOLOGICAL DATA MODELING5 COMPLEXITY AND SYMMETRIES IN DNA SEQUENCES 95Carlo Cattani6 ONTOLOGY-DRIVEN FORMAL CONCEPTUAL DATA MODELING FOR BIOLOGICAL DATA ANALYSIS 129Catharina Maria Keet7 BIOLOGICAL DATA INTEGRATION USING NETWORK MODELS 155Gaurav Kumar and Shoba Ranganathan8 NETWORK MODELING OF STATISTICAL EPISTASIS 175Ting Hu and Jason H. Moore9 GRAPHICAL MODELS FOR PROTEIN FUNCTION AND STRUCTURE PREDICTION 191Mingjie Tang, Kean Ming Tan, Xin Lu Tan, Lee Sael, Meghana Chitale, Juan Esquivel-Rodrýguez, and Daisuke KiharaPART C: BIOLOGICAL FEATURE EXTRACTION10 ALGORITHMS AND DATA STRUCTURES FOR NEXT-GENERATION SEQUENCES 225Francesco Vezzi, Giuseppe Lancia, and Alberto Policriti11 ALGORITHMS FOR NEXT-GENERATION SEQUENCING DATA 251Costas S. Iliopoulos and Solon P. Pissis12 GENE REGULATORY NETWORK IDENTIFICATION WITH QUALITATIVE PROBABILISTIC NETWORKS 281Zina M. Ibrahim, Alioune Ngom, and Ahmed Y. TawfikPART D: BIOLOGICAL FEATURE SELECTION13 COMPARING, RANKING, AND FILTERING MOTIFS WITHCHARACTER CLASSES: APPLICATION TO BIOLOGICAL SEQUENCES ANALYSIS 309Matteo Comin and Davide Verzotto14 STABILITY OF FEATURE SELECTION ALGORITHMS AND ENSEMBLE FEATURE SELECTION METHODS INBIOINFORMATICS 333Pengyi Yang, Bing B. Zhou, Jean Yee-Hwa Yang, and Albert Y. Zomaya15 STATISTICAL SIGNIFICANCE ASSESSMENT FOR BIOLOGICAL FEATURE SELECTION: METHODS AND ISSUES 353Juntao Li, Kwok Pui Choi, Yudi Pawitan, and Radha Krishna Murthy Karuturi16 SURVEY OF NOVEL FEATURE SELECTION METHODS FOR CANCER CLASSIFICATION 379Oleg Okun17 INFORMATION-THEORETIC GENE SELECTION IN EXPRESSION DATA 399Patrick E. Meyer and Gianluca Bontempi18 FEATURE SELECTION AND CLASSIFICATION FOR GENE EXPRESSION DATA USING EVOLUTIONARY COMPUTATION 421Haider Banka, Suresh Dara, and Mourad ElloumiSECTION II BIOLOGICAL DATA MININGPART E: REGRESSION ANALYSIS OF BIOLOGICAL DATA19 BUILDING VALID REGRESSION MODELS FOR BIOLOGICAL DATA USING STATA AND R 445Charles Lindsey and Simon J. Sheather20 LOGISTIC REGRESSION IN GENOMEWIDE ASSOCIATION ANALYSIS 477Wentian Li and Yaning Yang21 SEMIPARAMETRIC REGRESSION METHODS IN LONGITUDINAL DATA: APPLICATIONS TO AIDS CLINICAL TRIAL DATA 501Yehua LiPART F: BIOLOGICAL DATA CLUSTERING22 THE THREE STEPS OF CLUSTERING IN THE POST-GENOMIC ERA 521Raffaele Giancarlo, Giosu´e Lo Bosco, Luca Pinello, and Filippo Utro23 CLUSTERING ALGORITHMS OF MICROARRAY DATA 557Haifa Ben Saber, Mourad Elloumi, and Mohamed Nadif24 SPREAD OF EVALUATION MEASURES FOR MICROARRAY CLUSTERING 569Giulia Bruno and Alessandro Fiori25 SURVEY ON BICLUSTERING OF GENE EXPRESSION DATA 591Adelaide Valente Freitas, Wassim Ayadi, Mourad Elloumi, Jose Luis Oliveira, and Jin-Kao Hao26 MULTIOBJECTIVE BICLUSTERING OF GENE EXPRESSION DATA WITH BIOINSPIRED ALGORITHMS 609Khedidja Seridi, Laetitia Jourdan, and El-Ghazali Talbi27 COCLUSTERING UNDER GENE ONTOLOGY DERIVED CONSTRAINTS FOR PATHWAY IDENTIFICATION 625Alessia Visconti, Francesca Cordero, Dino Ienco, and Ruggero G. PensaPART G: BIOLOGICAL DATA CLASSIFICATION28 SURVEY ON FINGERPRINT CLASSIFICATION METHODS FOR BIOLOGICAL SEQUENCES 645Bhaskar DasGupta and Lakshmi Kaligounder29 MICROARRAY DATA ANALYSIS: FROM PREPARATION TO CLASSIFICATION 657Luciano Cascione, Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, and Alfredo Pulvirenti30 DIVERSIFIED CLASSIFIER FUSION TECHNIQUE FOR GENE EXPRESSION DATA 675Sashikala Mishra, Kailash Shaw, and Debahuti Mishra31 RNA CLASSIFICATION AND STRUCTURE PREDICTION: ALGORITHMS AND CASE STUDIES 685Ling Zhong, Junilda Spirollari, Jason T. L. Wang, and Dongrong Wen32 AB INITIO PROTEIN STRUCTURE PREDICTION: METHODS AND CHALLENGES 703Jad Abbass, Jean-Christophe Nebel, and Nashat Mansour33 OVERVIEW OF CLASSIFICATION METHODS TOSUPPORT HIV/AIDS CLINICAL DECISION MAKING 725Khairul A. Kasmiran, Ali Al Mazari, Albert Y. Zomaya, and Roger J. GarsiaPART H: ASSOCIATION RULES LEARNING FROM BIOLOGICAL DATA34 MINING FREQUENT PATTERNS AND ASSOCIATION RULES FROM BIOLOGICAL DATA 737Ioannis Kavakiotis, George Tzanis, and Ioannis Vlahavas35 GALOIS CLOSURE BASED ASSOCIATION RULE MINING FROM BIOLOGICAL DATA 761Kartick Chandra Mondal and Nicolas Pasquier36 INFERENCE OF GENE REGULATORY NETWORKS BASED ON ASSOCIATION RULES 803Cristian Andres Gallo, Jessica Andrea Carballido, and Ignacio PonzoniPART I: TEXT MINING AND APPLICATION TO BIOLOGICAL DATA37 CURRENT METHODOLOGIES FOR BIOMEDICAL NAMED ENTITY RECOGNITION 841David Campos, Sergio Matos, and José Luýs Oliveira38 AUTOMATED ANNOTATION OF SCIENTIFIC DOCUMENTS: INCREASING ACCESS TO BIOLOGICAL KNOWLEDGE 869Evangelos Pafilis, Heiko Horn, and Nigel P. Brown39 AUGMENTING BIOLOGICAL TEXT MINING WITH SYMBOLIC INFERENCE 901Jong C. Park and Hee-Jin Lee40 WEB CONTENT MINING FOR LEARNING GENERIC RELATIONS AND THEIR ASSOCIATIONS FROM TEXTUAL BIOLOGICAL DATA 919Muhammad Abulaish and Jahiruddin41 PROTEIN–PROTEIN RELATION EXTRACTION FROM BIOMEDICAL ABSTRACTS 943Syed Toufeeq Ahmed, Hasan Davulcu, Sukru Tikves, Radhika Nair, and Chintan PatelPART J: HIGH-PERFORMANCE COMPUTING FOR BIOLOGICAL DATA MINING42 ACCELERATING PAIRWISE ALIGNMENT ALGORITHMS BY USING GRAPHICS PROCESSOR UNITS 971Mourad Elloumi, Mohamed Al Sayed Issa, and Ahmed Mokaddem43 HIGH-PERFORMANCE COMPUTING IN HIGH-THROUGHPUT SEQUENCING 981Kamer Kaya, Ayat Hatem, Hatice Gulcin Ozer, Kun Huang, and Umit V. Catalyurek44 LARGE-SCALE CLUSTERING OF SHORT READS FOR METAGENOMICS ON GPUs 1003Thuy Diem Nguyen, Bertil Schmidt, Zejun Zheng, and Chee Keong KwohSECTION III BIOLOGICAL DATA POSTPROCESSINGPART K: BIOLOGICAL KNOWLEDGE INTEGRATION AND VISUALIZATION45 INTEGRATION OF METABOLIC KNOWLEDGE FOR GENOME-SCALE METABOLIC RECONSTRUCTION 1027Ali Masoudi-Nejad, Ali Salehzadeh-Yazdi, Shiva Akbari-Birgani, and Yazdan Asgari46 INFERRING AND POSTPROCESSING HUGE PHYLOGENIES 1049Stephen A. Smith and Alexandros Stamatakis47 BIOLOGICAL KNOWLEDGE VISUALIZATION 1073Rodrigo Santamarýa48 VISUALIZATION OF BIOLOGICAL KNOWLEDGE BASED ON MULTIMODAL BIOLOGICAL DATA 1109Hendrik Rohn and Falk SchreiberINDEX 1127

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