Details

Algorithms in Computational Molecular Biology


Algorithms in Computational Molecular Biology

Techniques, Approaches and Applications
Wiley Series in Bioinformatics, Band 16 1. Aufl.

von: Mourad Elloumi, Albert Y. Zomaya, Yi Pan

160,99 €

Verlag: Wiley
Format: PDF
Veröffentl.: 07.12.2010
ISBN/EAN: 9780470892091
Sprache: englisch
Anzahl Seiten: 1080

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Beschreibungen

This book represents the most comprehensive and up-to-date collection of information on the topic of computational molecular biology. Bringing the most recent research into the forefront of discussion, <i>Algorithms in Computational Molecular Biology</i> studies the most important and useful algorithms currently being used in the field, and provides related problems. It also succeeds where other titles have failed, in offering a wide range of information from the introductory fundamentals right up to the latest, most advanced levels of study.
<p>PREFACE xxxi</p> <p>CONTRIBUTORS xxxiii</p> <p>I STRINGS PROCESSING AND APPLICATION TO BIOLOGICAL SEQUENCES 1</p> <p>1 STRING DATA STRUCTURES FOR COMPUTATIONAL MOLECULAR BIOLOGY 3<br /><i>Christos Makris and Evangelos Theodoridis</i></p> <p>2 EFFICIENT RESTRICTED-CASE ALGORITHMS FOR PROBLEMS IN COMPUTATIONAL BIOLOGY 27<br /><i>Patricia A. Evans and H. Todd Wareham</i></p> <p>3 FINITE AUTOMATA IN PATTERN MATCHING 51<br /><i>Jan Holub</i></p> <p>4 NEW DEVELOPMENTS IN PROCESSING OF DEGENERATE SEQUENCES 73<br /><i>Pavlos Antoniou and Costas S. Iliopoulos</i></p> <p>5 EXACT SEARCH ALGORITHMS FOR BIOLOGICAL SEQUENCES 91<br /><i>Eric Rivals, Leena Salmela, and Jorma Tarhio</i></p> <p>6 ALGORITHMIC ASPECTS OF ARC-ANNOTATED SEQUENCES 113<br /><i>Guillaume Blin, Maxime Crochemore, and Stéphane Vialette</i></p> <p>7 ALGORITHMIC ISSUES IN DNA BARCODING PROBLEMS 129<br /><i>Bhaskar DasGupta, Ming-Yang Kao, and Ion Mandoiu</i></p> <p>8 RECENT ADVANCES IN WEIGHTED DNA SEQUENCES 143<br /><i>Manolis Christodoulakis and Costas S. Iliopoulos</i></p> <p>9 DNA COMPUTING FOR SUBGRAPH ISOMORPHISM PROBLEM AND RELATED PROBLEMS 171<br /><i>Sun-Yuan Hsieh, Chao-Wen Huang, and Hsin-Hung Chou</i></p> <p><b>II ANALYSIS OF BIOLOGICAL SEQUENCES 191</b></p> <p>10 GRAPHS IN BIOINFORMATICS 193<br /><i>Elsa Chacko and Shoba Ranganathan</i></p> <p>11 A FLEXIBLE DATA STORE FOR MANAGING BIOINFORMATICS DATA 221<br /><i>Bassam A. Alqaralleh, Chen Wang, Bing Bing Zhou, and Albert Y. Zomaya</i></p> <p>12 ALGORITHMS FOR THE ALIGNMENT OF BIOLOGICAL SEQUENCES 241<br /><i>Ahmed Mokaddem and Mourad Elloumi</i></p> <p>13 ALGORITHMS FOR LOCAL STRUCTURAL ALIGNMENT AND STRUCTURAL MOTIF IDENTIFICATION 261<br /><i>Sanguthevar Rajasekaran, Vamsi Kundeti, and Martin Schiller</i></p> <p>14 EVOLUTION OF THE CLUSTAL FAMILY OF MULTIPLE SEQUENCE ALIGNMENT PROGRAMS 277<br /><i>Mohamed Radhouene Aniba and Julie Thompson</i></p> <p>15 FILTERS AND SEEDS APPROACHES FOR FAST HOMOLOGY SEARCHES IN LARGE DATASETS 299<br /><i>Nadia Pisanti, Mathieu Giraud, and Pierre Peterlongo</i></p> <p>16 NOVEL COMBINATORIAL AND INFORMATION-THEORETIC ALIGNMENT-FREE DISTANCES FOR BIOLOGICAL DATA MINING 321<br /><i>Chiara Epifanio, Alessandra Gabriele, Raffaele Giancarlo, and Marinella Sciortino</i></p> <p>17 IN SILICO METHODS FOR THE ANALYSIS OF METABOLITES AND DRUG MOLECULES 361<br /><i>Varun Khanna and Shoba Ranganathan</i></p> <p><b>III MOTIF FINDING AND STRUCTURE PREDICTION 383</b></p> <p>18 MOTIF FINDING ALGORITHMS IN BIOLOGICAL SEQUENCES 385<br /><i>Tarek El Falah, Mourad Elloumi, and Thierry Lecroq</i></p> <p>19 COMPUTATIONAL CHARACTERIZATION OF REGULATORY REGIONS 397<br /><i>Enrique Blanco</i></p> <p>20 ALGORITHMIC ISSUES IN THE ANALYSIS OF CHIP-SEQ DATA 425<br /><i>Federico Zambelli and Giulio Pavesi</i></p> <p>21 APPROACHES AND METHODS FOR OPERON PREDICTION BASED ON MACHINE LEARNING TECHNIQUES 449<br /><i>Yan Wang, You Zhou, Chunguang Zhou, Shuqin Wang, Wei Du, Chen Zhang, and Yanchun Liang</i></p> <p>22 PROTEIN FUNCTION PREDICTION WITH DATA-MINING TECHNIQUES 479<br /><i>Xing-Ming Zhao and Luonan Chen</i></p> <p>23 PROTEIN DOMAIN BOUNDARY PREDICTION 501<br /><i>Paul D. Yoo, Bing Bing Zhou, and Albert Y. Zomaya</i></p> <p>24 AN INTRODUCTION TO RNA STRUCTURE AND PSEUDOKNOT PREDICTION 521<br /><i>Jana Sperschneider and Amitava Datta</i></p> <p><b>IV PHYLOGENY RECONSTRUCTION 547</b></p> <p>25 PHYLOGENETIC SEARCH ALGORITHMS FOR MAXIMUM LIKELIHOOD 549<br /><i>Alexandros Stamatakis</i></p> <p>26 HEURISTIC METHODS FOR PHYLOGENETIC RECONSTRUCTION WITH MAXIMUM PARSIMONY 579<br /><i>Adrien Goëffon, Jean-Michel Richer, and Jin-Kao Hao</i></p> <p>27 MAXIMUM ENTROPY METHOD FOR COMPOSITION VECTOR METHOD 599<br /><i>Raymond H.-F. Chan, Roger W. Wang, and Jeff C.-F. Wong</i></p> <p><b>V MICROARRAY DATA ANALYSIS 623</b></p> <p>28 MICROARRAY GENE EXPRESSION DATA ANALYSIS 625<br /><i>Alan Wee-Chung Liew and Xiangchao Gan</i></p> <p>29 BICLUSTERING OF MICROARRAY DATA 651<br /><i>Wassim Ayadi and Mourad Elloumi</i></p> <p>30 COMPUTATIONAL MODELS FOR CONDITION-SPECIFIC GENE AND PATHWAY INFERENCE 665<br /><i>Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang, and Luonan Chen</i></p> <p>31 HETEROGENEITY OF DIFFERENTIAL EXPRESSION IN CANCER STUDIES: ALGORITHMS AND METHODS 691<br /><i>Radha Krishna Murthy Karuturi</i></p> <p><b>VI ANALYSIS OF GENOMES 723</b></p> <p>32 COMPARATIVE GENOMICS: ALGORITHMS AND APPLICATIONS 725<br /><i>Xiao Yang and Srinivas Aluru</i></p> <p>33 ADVANCES IN GENOME REARRANGEMENT ALGORITHMS 749<br /><i>Masud Hasan and M. Sohel Rahman</i></p> <p>34 COMPUTING GENOMIC DISTANCES: AN ALGORITHMIC VIEWPOINT 773<br /><i>Guillaume Fertin and Irena Rusu</i></p> <p>35 WAVELET ALGORITHMS FOR DNA ANALYSIS 799<br /><i>Carlo Cattani</i></p> <p>36 HAPLOTYPE INFERENCE MODELS AND ALGORITHMS 843<br /><i>Ling-Yun Wu</i></p> <p><b>VII ANALYSIS OF BIOLOGICAL NETWORKS 865</b></p> <p>37 UNTANGLING BIOLOGICAL NETWORKS USING BIOINFORMATICS 867<br /><i>Gaurav Kumar, Adrian P. Cootes, and Shoba Ranganathan</i></p> <p>38 PROBABILISTIC APPROACHES FOR INVESTIGATING BIOLOGICAL NETWORKS 893<br /><i>Jérémie Bourdon and Damien Eveillard</i></p> <p>39 MODELING AND ANALYSIS OF BIOLOGICAL NETWORKS WITH MODEL CHECKING 915<br /><i>Dragan Bosnacki, Peter A.J. Hilbers, Ronny S. Mans, and Erik P. de Vink</i></p> <p>40 REVERSE ENGINEERING OF MOLECULAR NETWORKS FROM A COMMON COMBINATORIAL APPROACH 941<br /><i>Bhaskar DasGupta, Paola Vera-Licona, and Eduardo Sontag</i></p> <p>41 UNSUPERVISED LEARNING FOR GENE REGULATION NETWORK INFERENCE FROM EXPRESSION DATA: A REVIEW 955<br /><i>Mohamed Elati and Céline Rouveirol</i></p> <p>42 APPROACHES TO CONSTRUCTION AND ANALYSIS OF MICRORNA-MEDIATED NETWORKS 979<br /><i>Ilana Lichtenstein, Albert Zomaya, Jennifer Gamble, and Mathew Vadas</i></p> <p>INDEX 1007</p>
<p><b>Mourad Elloumi</b>, PhD, is Associate Professor in Computer Science, Faculty of Economic Sciences and Management of Tunis (Tunisia), and member of the Unit of Technologies of Information and Communication (UTIC). He is the author/coauthor of more than forty publications in international journals and conferences. Professor Elloumi was the guest editor of a special issue on biological knowledge discovery and data mining in Knowledge-Based Systems and the coeditor of the proceedings of two international conferences.</p> <p><b>Albert Y. Zomaya</b>, PhD, is the Chair Professor of High Performance Computing and Networking in the School of Information Technologies at The University of Sydney (Australia). He is the author/coauthor of eight books and more than 400 publications in technical journals and conferences, and the editor of eight books and eight conference volumes. Professor Zomaya is currently an associate editor for twenty journals, the Founding Editor of the Wiley Series on Parallel and Distributed Computing, and a Founding Coeditor of the Wiley Series in Bioinformatics.</p>
<p><b>The most comprehensive, practical overview of algorithms in computational molecular biology</b></p> <p>Computational molecular biology has emerged from the Human Genome Project as an important discipline for academic research and industrial application. Due to the exponential growth?in the size of biological databases and the increasing intricacy of biological problems, high-performance algorithms are now necessary to deal with errors in biological sequences.?Bringing the most recent research into the forefront of discussion, Algorithms in Computational Molecular Biology is the first in-depth examination of these important algorithms, which are based on the newest and most improved approaches and techniques in the field.</p> <p>The book's unique coverage offers both a wide range of information—from theintroductory fundamentals right up to the latest, most advanced levels of study—and enough technical depth to be of practical use to working professionals. Organized into seven parts, it addresses:</p> <ul> <li>Strings processing and application to biological sequences</li> <li>Analysis of biological sequences</li> <li>Motif finding and structure prediction</li> <li>Phylogeny reconstruction</li> <li>Microarray data analysis</li> <li>Analysis of genomes</li> <li>Analysis of biological networks</li> </ul> <p>Also featured are a combination of experiments and simulations that provide not only qualitative but also quantitative insights into this rich field. By covering a wide range of combinatorial problems that arise in computational molecular biology, this book enables researchers, computer scientists, life scientists, mathematicians, graduate students, and senior undergraduates to deal with more complex issues and richer data sets.</p>

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