Bioinformatics Algorithms : Techniques and Applications

Presents algorithmic techniques for solving problems in bioinformatics, including applications that shed new light on molecular biology

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, Bioinformatics Algorithms covers:

• General algorithmic techniques, including dynamic programming, graph-theoretical methods, hidden Markov models, the fast Fourier transform, seeding, and approximation algorithms
• Algorithms and tools for genome and sequence analysis, including formal and approximate models for gene clusters, advanced algorithms for non-overlapping local alignments and genome tilings, multiplex PCR primer set selection, and sequence/network motif finding
• Microarray design and analysis, including algorithms for microarray physical design, missing value imputation, and meta-analysis of gene expression data
• Algorithmic issues arising in the analysis of genetic variation across human population, including computational inference of haplotypes from genotype data and disease association search in case/control epidemiologic studies
• Algorithmic approaches in structural and systems biology, including topological and structural classification in biochemistry, and prediction of protein-protein and domain-domain interactions

Each chapter begins with a self-contained introduction to a computational problem; continues with a brief review of the existing literature on the subject and an in-depth description of recent algorithmic and methodological developments; and concludes with a brief experimental study and a discussion of open research challenges. This clear and approachable presentation makes the book appropriate for researchers, practitioners, and graduate students alike.

Ion Mandoiu received the M.S. degree from Bucharest University in 1992 and the Ph.D. degree from Georgia Institute of Technology in 2000, both in Computer Science. He is now an Assistant Professor with the Computer Science and Engineering Department at the University of Connecticut. His research focuses on the design and analysis of exact and approximation algorithms for NP-hard optimization problems, particularly in the areas of bioinformatics and computational molecular biology, VLSI computer aided design, and ad-hoc wireless networks. He has authored over 60 refereed scientific publications in these areas Dr. Mandoiu has served as Program Committee Chair for the 2006 International Workshop on Bioinformatics Research and Applications; Co-Chair of the ACIS International Workshop on Self-Assembling Wireless Networks (2005 and 2006) and other current efforts tied to IEEE and ACM publications.

Alexander Zelikovsky received the M.S. degree from Moldova University in 1982 and the Ph.D. degree Byelorussia Academy of Sciences in 1989, both in Computer Science. He is now an Associate Professor with the Computer Science Department at the Georgia State University. His research focuses on discrete algorithms and their applications in computational biotechnology and biology, bioinformatics, VLSI CAD, and wireless networks. He has authored over 120-refereed scientific publications in these areas. Dr. Zelikovsky has served as co-Chair for the 2005 and 2006 International Workshop on Bioinformatics Research and Applications; Co-Chair of the 2005 and 2006 ACIS International Workshop on Self-Assembling Wireless Networks; Poster Chair of the Second SECABC Fall Workshop on Biocomputing (2005) and others.