Bioinformatics Algorithms (eBook, PDF)

Techniques and Applications
Redaktion: Mandoiu, Ion; Zelikovsky, Alexander

• Format: PDF

Produktbeschreibung

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.

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Produktdetails

• Verlag: John Wiley & Sons
• Seitenzahl: 528
• Erscheinungstermin: 12. März 2008
• Englisch
• ISBN-13: 9780470253427
• Artikelnr.: 37291407

Autorenporträt

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.

Inhaltsangabe

Preface. Contributors. 1. Educating Biologists in the 21st century:
Bioinformatics Scientists versus Bioinformatics Technicians (Pavel
Pevznher) Part I: Techniques. 2. Dynamic Programming Algorithms for
Biological Sequence and Structure Comparison (Yuzhen Ye and Haixu Tang) 3.
Graph Theoretical Approaches to Delineate Dynamics of biological Processes
(Teresa M. Przytycka and Elena Zotenko) 4. Advances in Hidden Markov Models
for Sequence Annotation (Brona Brejova, Daniel G. Brown, and Tomas Vinar)
5. Sorting- and FFT-Based Techniques in the Discovery of Biopatterns (Sudha
Balla, Sanguthevar Rajasekaran, and Jaime Davila) 6. A Survey of Seeding
for Sequence Alignment (Daniel G. Brown) 7. The Comparison of Phylogenetic
Networks: Algorithms and complexity (Paola Bonizzoni, Gianluca Della
Vedova, Riccardo Dondi, and Giancarlo Mauri) Part II: Genome and Sequence
Analysis. 8. Formal Models of Gene Clusters (Anne Bergeron, Cedric
Chauve,and Yannick Gingras) 9. Integer Linear Programming Techniques for
Discovering Approximate gene Clusters (Sven Rahmann and Gunnar W. Klau) 10.
Efficient Combinatorial Algorithms for DNA Sequence Processing (Bhaskar
DasGupta and Ming-Yang Kao) 11. Algorithms for Multiplex PCR Primer Set
Selection with Amplification Length constraints (K.M. Konwar, I.I. Mandoiu,
A.C. Russell, and A.A. Shvartsman) 12. Recent Developments in Alignment and
Motif Finding for Sequences and Networks (Sing-Hoi Sze) Part III:
Microarray Design and Data Analysis. 13. Algorithms for Oligonucleotide
Microarray Layout (Sergio A. De Carvalho Jr. Sven Rahmann) 14.
Classification Accuracy Based Microarray Missing Value Imputation (Yi Shi,
Zhipeng Cai, and Guohui Lin) 15. Meta-Analysis of Microarray Data
(Saumyadipta Pyne, Steve Skiena, and Bruce Futcher) Part IV: Genetic
Variation Analysis. 16. Phasing Genotypes Using a Hidden Markov Model (P.
Rastas, M. Koivisto, H. Mannila, and Ukkonen) 17. Analytical and
Algorithmic Methods for Haplotype Frequency Inference: What Do they Tell
Us? (Steven Hecth Orzack, Daniel Gusfield, Lakshamn Subrahmanyan, Laurent
Essioux, and Sebastein Lissarrague) 18. Optimization Methods for Genotype
Data Analysis in Epidemiological Studies (Dumitru Brinza, Jingwu He, and
Alexander Zelikovsky) Part V: Structural and Systems Biology. 19.
Topological Indices in Combinatorial Chemistry (Sergey Bereg) 20. Efficient
Algorithms for Structural Recall in Databases (Hao Wang, Patra Volarath,
and Robert W. Harrison) 21. Computational Approaches to Predict
Protein-Protein and Domain-Domain Interactions (Raja Jothi and Teresa M.
Przytycka) Index.

Rezensionen

"This clear and approachable presentation makes the book appropriate for researchers, practioners, and graduate students." ( Mathematical Reviews , Issue 2009b) "This volume will be a nice addition to the bioinformatician s bookshelf." ( Quarterly Review of Biology , December 2008)