PREFACE xxxi CONTRIBUTORS xxxiii I STRINGS PROCESSING AND APPLICATION TO BIOLOGICAL SEQUENCES 1 1 STRING DATA STRUCTURES FOR COMPUTATIONAL MOLECULAR BIOLOGY 3 Christos Makris and Evangelos Theodoridis 2 EFFICIENT RESTRICTED-CASE ALGORITHMS FOR PROBLEMS IN COMPUTATIONAL BIOLOGY 27 Patricia A. Evans and H. Todd Wareham 3 FINITE AUTOMATA IN PATTERN MATCHING 51 Jan Holub 4 NEW DEVELOPMENTS IN PROCESSING OF DEGENERATE SEQUENCES 73 Pavlos Antoniou and Costas S. Iliopoulos 5 EXACT SEARCH ALGORITHMS FOR BIOLOGICAL SEQUENCES 91 Eric Rivals, Leena Salmela, and Jorma Tarhio 6 ALGORITHMIC ASPECTS OF ARC-ANNOTATED SEQUENCES 113 Guillaume Blin, Maxime Crochemore, and Stéphane Vialette 7 ALGORITHMIC ISSUES IN DNA BARCODING PROBLEMS 129 Bhaskar DasGupta, Ming-Yang Kao, and Ion Mandoiu 8 RECENT ADVANCES IN WEIGHTED DNA SEQUENCES 143 Manolis Christodoulakis and Costas S. Iliopoulos 9 DNA COMPUTING FOR SUBGRAPH ISOMORPHISM PROBLEM AND RELATED PROBLEMS 171 Sun-Yuan Hsieh, Chao-Wen Huang, and Hsin-Hung Chou II ANALYSIS OF BIOLOGICAL SEQUENCES 191 10 GRAPHS IN BIOINFORMATICS 193 Elsa Chacko and Shoba Ranganathan 11 A FLEXIBLE DATA STORE FOR MANAGING BIOINFORMATICS DATA 221 Bassam A. Alqaralleh, Chen Wang, Bing Bing Zhou, and Albert Y. Zomaya 12 ALGORITHMS FOR THE ALIGNMENT OF BIOLOGICAL SEQUENCES 241 Ahmed Mokaddem and Mourad Elloumi 13 ALGORITHMS FOR LOCAL STRUCTURAL ALIGNMENT AND STRUCTURAL MOTIF IDENTIFICATION 261 Sanguthevar Rajasekaran, Vamsi Kundeti, and Martin Schiller 14 EVOLUTION OF THE CLUSTAL FAMILY OF MULTIPLE SEQUENCE ALIGNMENT PROGRAMS 277 Mohamed Radhouene Aniba and Julie Thompson 15 FILTERS AND SEEDS APPROACHES FOR FAST HOMOLOGY SEARCHES IN LARGE DATASETS 299 Nadia Pisanti, Mathieu Giraud, and Pierre Peterlongo 16 NOVEL COMBINATORIAL AND INFORMATION-THEORETIC ALIGNMENT-FREE DISTANCES FOR BIOLOGICAL DATA MINING 321 Chiara Epifanio, Alessandra Gabriele, Raffaele Giancarlo, and Marinella Sciortino 17 IN SILICO METHODS FOR THE ANALYSIS OF METABOLITES AND DRUG MOLECULES 361 Varun Khanna and Shoba Ranganathan III MOTIF FINDING AND STRUCTURE PREDICTION 383 18 MOTIF FINDING ALGORITHMS IN BIOLOGICAL SEQUENCES 385 Tarek El Falah, Mourad Elloumi, and Thierry Lecroq 19 COMPUTATIONAL CHARACTERIZATION OF REGULATORY REGIONS 397 Enrique Blanco 20 ALGORITHMIC ISSUES IN THE ANALYSIS OF CHIP-SEQ DATA 425 Federico Zambelli and Giulio Pavesi 21 APPROACHES AND METHODS FOR OPERON PREDICTION BASED ON MACHINE LEARNING TECHNIQUES 449 Yan Wang, You Zhou, Chunguang Zhou, Shuqin Wang, Wei Du, Chen Zhang, and Yanchun Liang 22 PROTEIN FUNCTION PREDICTION WITH DATA-MINING TECHNIQUES 479 Xing-Ming Zhao and Luonan Chen 23 PROTEIN DOMAIN BOUNDARY PREDICTION 501 Paul D. Yoo, Bing Bing Zhou, and Albert Y.

Zomaya 24 AN INTRODUCTION TO RNA STRUCTURE AND PSEUDOKNOT PREDICTION 521 Jana Sperschneider and Amitava Datta IV PHYLOGENY RECONSTRUCTION 547 25 PHYLOGENETIC SEARCH ALGORITHMS FOR MAXIMUM LIKELIHOOD 549 Alexandros Stamatakis 26 HEURISTIC METHODS FOR PHYLOGENETIC RECONSTRUCTION WITH MAXIMUM PARSIMONY 579 Adrien Goëffon, Jean-Michel Richer, and Jin-Kao Hao 27 MAXIMUM ENTROPY METHOD FOR COMPOSITION VECTOR METHOD 599 Raymond H.-F. Chan, Roger W. Wang, and Jeff C.-F. Wong V MICROARRAY DATA ANALYSIS 623 28 MICROARRAY GENE EXPRESSION DATA ANALYSIS 625 Alan Wee-Chung Liew and Xiangchao Gan 29 BICLUSTERING OF MICROARRAY DATA 651 Wassim Ayadi and Mourad Elloumi 30 COMPUTATIONAL MODELS FOR CONDITION-SPECIFIC GENE AND PATHWAY INFERENCE 665 Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang, and Luonan Chen 31 HETEROGENEITY OF DIFFERENTIAL EXPRESSION IN CANCER STUDIES: ALGORITHMS AND METHODS 691 Radha Krishna Murthy Karuturi VI ANALYSIS OF GENOMES 723 32 COMPARATIVE GENOMICS: ALGORITHMS AND APPLICATIONS 725 Xiao Yang and Srinivas Aluru 33 ADVANCES IN GENOME REARRANGEMENT ALGORITHMS 749 Masud Hasan and M. Sohel Rahman 34 COMPUTING GENOMIC DISTANCES: AN ALGORITHMIC VIEWPOINT 773 Guillaume Fertin and Irena Rusu 35 WAVELET ALGORITHMS FOR DNA ANALYSIS 799 Carlo Cattani 36 HAPLOTYPE INFERENCE MODELS AND ALGORITHMS 843 Ling-Yun Wu VII ANALYSIS OF BIOLOGICAL NETWORKS 865 37 UNTANGLING BIOLOGICAL NETWORKS USING BIOINFORMATICS 867 Gaurav Kumar, Adrian P. Cootes, and Shoba Ranganathan 38 PROBABILISTIC APPROACHES FOR INVESTIGATING BIOLOGICAL NETWORKS 893 Jérémie Bourdon and Damien Eveillard 39 MODELING AND ANALYSIS OF BIOLOGICAL NETWORKS WITH MODEL CHECKING 915 Dragan Bosnacki, Peter A.

J. Hilbers, Ronny S. Mans, and Erik P. de Vink 40 REVERSE ENGINEERING OF MOLECULAR NETWORKS FROM A COMMON COMBINATORIAL APPROACH 941 Bhaskar DasGupta, Paola Vera-Licona, and Eduardo Sontag 41 UNSUPERVISED LEARNING FOR GENE REGULATION NETWORK INFERENCE FROM EXPRESSION DATA: A REVIEW 955 Mohamed Elati and Céline Rouveirol 42 APPROACHES TO CONSTRUCTION AND ANALYSIS OF MICRORNA-MEDIATED NETWORKS 979 Ilana Lichtenstein, Albert Zomaya, Jennifer Gamble, and Mathew Vadas INDEX 1007.