Bioinformatics Algorithms Techniques and Applications

by Mandoiu, Ion; Zelikovsky, Alexander

• ISBN13: 9780470097731
• ISBN10: 0470097736
• Edition: 1st
• Format: Hardcover
• Copyright: 2008-02-25
• Publisher: Wiley-Interscience

Summary

This book introduces algorithmic techniques in bioinformatics, emphasizing their application to solving novel problems in post-genomic molecular biology. Beginning with a thought-provoking discussion on the role of algorithms in twenty-first-century bioinformatics education, the book covers: general algorithmic techniques, algorithms and tools for genome and sequence analysis, microarray design and analysis, algorithmic issues arising in the analysis of genetic variation across human population, and algorithmic approaches in structural and systems biology.

Author Biography

Alexander Zelikovsky, PhD, is Associate Professor in the Computer Science Department at Georgia State University. His research focuses on discrete algorithms and their applications in bio-technology, bioinformatics, VLSI computer-aided design, and wireless networks.

Table of Contents

Preface	p. ix
Contributors	p. xi
Educating Biologists in the 21st Century: Bioinformatics Scientists versus Bioinformatics Technicians	p. 1
Techniques	p. 7
Dynamic Programming Algorithms for Biological Sequence and Structure Comparison	p. 9
Graph Theoretical Approaches to Delineate Dynamics of Biological Processes	p. 29
Advances in Hidden Markov Models for Sequence Annotation	p. 55
Sorting- and FFT-Based Techniques in the Discovery of Biopatterns	p. 93
A Survey of Seeding for Sequence Alignment	p. 117
The Comparison of Phylogenetic Networks: Algorithms and Complexity	p. 143
Genome and Sequence Analysis	p. 175
Formal Models of Gene Clusters	p. 177
Integer Linear Programming Techniques for Discovering Approximate Gene Clusters	p. 203
Efficient Combinatorial Algorithms for DNA Sequence Processing	p. 223
Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints	p. 241
Recent Developments in Alignment and Motif Finding for Sequences and Networks	p. 259
Microarray Design and Data Analysis	p. 277
Algorithms for Oligonucleotide Microarray Layout	p. 279
Classification Accuracy Based Microarray Missing Value Imputation	p. 303
Meta-Analysis of Microarray Data	p. 329
Genetic Variation Analysis	p. 353
Phasing Genotypes Using a Hidden Markov Model	p. 355
Analytical and Algorithmic Methods for Haplotype Frequency Inference: What Do They Tell Us?	p. 373
Optimization Methods for Genotype Data Analysis in Epidemiological Studies	p. 395
Structural and Systems Biology	p. 417
Topological Indices in Combinatorial Chemistry	p. 419
Efficient Algorithms for Structural Recall in Databases	p. 439
Computational Approaches to Predict Protein-Protein and Domain-Domain Interactions	p. 465
Index	p. 493
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