Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications

Copyright © 2011 John Wiley & Sons, Inc.

Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications

Editor(s): Mourad Elloumi, Albert Y. Zomaya

Published Online: 23 DEC 2010 02:09PM EST

Print ISBN: 9780470505199

Online ISBN: 9780470892107

DOI: 10.1002/9780470892107

About this Book

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, Algorithms in Computational Molecular Biology 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.

Table of contents

    1. You have free access to this content
      Frontmatter (pages i–xxxvii)

  2. Part I: Strings Processing and Application to Biological Sequences

    1. Chapter 1

      String Data Structures for Computational Molecular Biology (pages 1–25)

      Christos Makris and Evangelos Theodoridis

    2. Chapter 2

      Efficient Restricted-Case Algorithms for Problems in Computational Biology (pages 27–49)

      Patricia A. Evans and H. Todd Wareham

    3. Chapter 3

      Finite Automata in Pattern Matching (pages 51–71)

      Jan Holub

    4. Chapter 4

      New Developments in Processing of Degenerate Sequences (pages 73–90)

      Pavlos Antoniou and Costas S. Iliopoulos

    5. Chapter 5

      Exact Search Algorithms for Biological Sequences (pages 91–111)

      Eric Rivals, Leena Salmela and Jorma Tarhio

    6. Chapter 6

      Algorithmic Aspects of ARC-Annotated Sequences (pages 113–127)

      Guillaume Blin, Maxime Crochemore and Stéphane Vialette

    7. Chapter 7

      Algorithmic Issues in DNA Barcoding Problems (pages 129–142)

      Bhaskar DasGupta, Ming-Yang Kao and Ion Măndoiu

    8. Chapter 8

      Recent Advances in Weighted DNA Sequences (pages 143–169)

      Manolis Christodoulakis and Costas S. Iliopoulos

    9. Chapter 9

      DNA Computing for Subgraph Isomorphism Problem and Related Problems (pages 171–190)

      Sun-Yuan Hsieh, Chao-Wen Huang and Hsin-Hung Chou

  3. Part II: Analysis of Biological Sequences

    1. Chapter 10

      Graphs in Bioinformatics (pages 191–219)

      Elsa Chacko and Shoba Ranganathan

    2. Chapter 11

      A Flexible Data Store for Managing Bioinformatics Data (pages 221–239)

      Bassam A. Alqaralleh, Chen Wang, Bing Bing Zhou and Albert Y. Zomaya

    3. Chapter 12

      Algorithms for the Alignment of Biological Sequences (pages 241–260)

      Ahmed Mokaddem and Mourad Elloumi

    4. Chapter 13

      Algorithms for Local Structural Alignment and Structural Motif Identification (pages 261–276)

      Sanguthevar Rajasekaran, Vamsi Kundeti and Martin Schiller

    5. Chapter 14

      Evolution of the Clustal Family of Multiple Sequence Alignment Programs (pages 277–298)

      Mohamed Radhouene Aniba and Julie Thompson

    6. Chapter 15

      Filters and Seeds Approaches for Fast Homology Searches in Large Datasets (pages 299–319)

      Nadia Pisanti, Mathieu Giraud and Pierre Peterlongo

    7. Chapter 16

      Novel Combinatorial and Information-Theoretic Alignment-Free Distances for Biological Data Mining (pages 321–359)

      Chiara Epifanio, Alessandra Gabriele, Raffaele Giancarlo and Marinella Sciortino

    8. Chapter 17

      In Silico Methods for the Analysis of Metabolites and Drug Molecules (pages 361–381)

      Varun Khanna and Shoba Ranganathan

  4. Part III: Motif Finding and Structure Prediction

    1. Chapter 18

      Motif Finding Algorithms in Biological Sequences (pages 383–396)

      Tarek El Falah, Mourad Elloumi and Thierry Lecroq

    2. Chapter 19

      Computational Characterization of Regulatory Regions (pages 397–424)

      Enrique Blanco

    3. Chapter 20

      Algorithmic Issues in the Analysis of Chip-Seq Data (pages 425–448)

      Federico Zambelli and Giulio Pavesi

    4. Chapter 21

      Approaches and Methods for Operon Prediction based on Machine Learning Techniques (pages 449–477)

      Yan Wang, You Zhou, Chunguang Zhou, Shuqin Wang, Wei Du, Chen Zhang and Yanchun Liang

    5. Chapter 22

      Protein Function Prediction with Data-Mining Techniques (pages 479–499)

      Xing-Ming Zhao and Luonan Chen

    6. Chapter 23

      Protein Domain Boundary Prediction (pages 501–519)

      Paul D. Yoo, Bing Bing Zhou and Albert Y. Zomaya

    7. Chapter 24

      An Introduction to RNA Structure and Pseudoknot Prediction (pages 521–546)

      Jana Sperschneider and Amitava Datta

  5. Part IV: Phylogeny Reconstruction

    1. Chapter 25

      Phylogenetic Search Algorithms for Maximum Likelihood (pages 547–577)

      Alexandros Stamatakis

    2. Chapter 26

      Heuristic Methods for Phylogenetic Reconstruction with Maximum Parsimony (pages 579–597)

      Adrien Goëffon, Jean-Michel Richer and Jin-Kao Hao

    3. Chapter 27

      Maximum Entropy Method for Composition Vector Method (pages 599–622)

      Raymond H.-F. Chan, Roger W. Wang and Jeff C.-F. Wong

  6. Part V: Microarray Data Analysis

    1. Chapter 28

      Microarray Gene Expression Data Analysis (pages 623–650)

      Alan Wee-Chung Liew and Xiangchao Gan

    2. Chapter 29

      Biclustering of Microarray Data (pages 651–663)

      Wassim Ayadi and Mourad Elloumi

    3. Chapter 30

      Computational Models for Condition-Specific Gene and Pathway Inference (pages 665–689)

      Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen

    4. Chapter 31

      Heterogeneity of Differential Expression in Cancer Studies: Algorithms and Methods (pages 691–722)

      Radha Krishna and Murthy Karuturi

  7. Part VI: Analysis of Genomes

    1. Chapter 32

      Comparative Genomics: Algorithms and Applications (pages 723–747)

      Xiao Yang and Srinivas Aluru

    2. Chapter 33

      Advances in Genome Rearrangement Algorithms (pages 749–772)

      Masud Hasan and Sohel Rahman

    3. Chapter 34

      Computing Genomic Distances: An Algorithmic Viewpoint (pages 773–797)

      Guillaume Fertin and Irena Rusu

    4. Chapter 35

      Wavelet Algorithms for DNA Analysis (pages 799–841)

      Carlo Cattani

    5. Chapter 36

      Haplotype Inference Models and Algorithms (pages 843–864)

      Ling-Yun Wu

  8. Part VII: Analysis of Biological Networks

    1. Chapter 37

      Untangling Biological Networks Using Bioinformatics (pages 865–892)

      Gaurav Kumar, Adrian P. Cootes and Shoba Ranganathan

    2. Chapter 38

      Probabilistic Approaches for Investigating Biological Networks (pages 893–913)

      Jérémie Bourdon and Damien Eveillard

    3. Chapter 39

      Modeling and Analysis of Biological Networks with Model Checking (pages 915–940)

      Dragan Bošnački and Ronny S. Mans

    4. Chapter 40

      Reverse Engineering of Molecular Networks from a Common Combinatorial Approach (pages 941–953)

      Bhaskar Dasgupta, Paola Vera-licona and Eduardo Sontag

    5. Chapter 41

      Unsupervised Learning for Gene Regulation Network Inference from Expression Data: A Review (pages 955–978)

      Mohamed Elati and Céline Rouveirol

    6. Chapter 42

      Approaches to Construction and Analysis of Microrna-Mediated Networks (pages 979–1006)

      Ilana Lichtenstein, Albert Zomaya, Jennifer Gamble and Mathew Vadas

    1. You have free access to this content
      Index (pages 1007–1044)

    1. You have free access to this content
      Wiley Series on Bioinformatics: Computational Techniques and Engineering (page 1045)

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