Mandoiu / Zelikovsky Bioinformatics Algorithms

Techniques and Applications
1. Auflage 2008
ISBN: 978-0-470-25342-7
Verlag: John Wiley & Sons
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 528 Seiten, E-Book

Reihe: Wiley Series in Bioinformatics

Presents algorithmic techniques for solving problems inbioinformatics, including applications that shed new light onmolecular biology
This book introduces algorithmic techniques in bioinformatics,emphasizing their application to solving novel problems inpost-genomic molecular biology. Beginning with a thought-provokingdiscussion on the role of algorithms in twenty-first-centurybioinformatics education, Bioinformatics Algorithms covers:
* General algorithmic techniques, including dynamic programming,graph-theoretical methods, hidden Markov models, the fast Fouriertransform, seeding, and approximation algorithms
* Algorithms and tools for genome and sequence analysis, includingformal and approximate models for gene clusters, advancedalgorithms for non-overlapping local alignments and genome tilings,multiplex PCR primer set selection, and sequence/network motiffinding
* Microarray design and analysis, including algorithms formicroarray physical design, missing value imputation, andmeta-analysis of gene expression data
* Algorithmic issues arising in the analysis of genetic variationacross human population, including computational inference ofhaplotypes from genotype data and disease association search incase/control epidemiologic studies
* Algorithmic approaches in structural and systems biology,including topological and structural classification inbiochemistry, and prediction of protein-protein and domain-domaininteractions
Each chapter begins with a self-contained introduction to acomputational problem; continues with a brief review of theexisting literature on the subject and an in-depth description ofrecent algorithmic and methodological developments; and concludeswith a brief experimental study and a discussion of open researchchallenges. This clear and approachable presentation makes the bookappropriate for researchers, practitioners, and graduate studentsalike.

Autoren/Hrsg.

Mandoiu, Ion

Zelikovsky, Alexander

Inhaltsverzeichnis

Preface.
Contributors.
1. Educating Biologists in the 21st century: BioinformaticsScientists versus Bioinformatics Technicians (Pavel Pevznher)
Part I: Techniques.
2. Dynamic Programming Algorithms for Biological Sequence andStructure Comparison (Yuzhen Ye and Haixu Tang)
3. Graph Theoretical Approaches to Delineate Dynamics ofbiological 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 ofBiopatterns (Sudha Balla, Sanguthevar Rajasekaran, and JaimeDavila)
6. A Survey of Seeding for Sequence Alignment (Daniel G.Brown)
7. The Comparison of Phylogenetic Networks: Algorithms andcomplexity (Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi,and Giancarlo Mauri)
Part II: Genome and Sequence Analysis.
8. Formal Models of Gene Clusters (Anne Bergeron, CedricChauve,and Yannick Gingras)
9. Integer Linear Programming Techniques for DiscoveringApproximate gene Clusters (Sven Rahmann and Gunnar W. Klau)
10. Efficient Combinatorial Algorithms for DNA SequenceProcessing (Bhaskar DasGupta and Ming-Yang Kao)
11. Algorithms for Multiplex PCR Primer Set Selection withAmplification Length constraints (K.M. Konwar, I.I. Mandoiu, A.C.Russell, and A.A. Shvartsman)
12. Recent Developments in Alignment and Motif Finding forSequences 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 ValueImputation (Yi Shi, Zhipeng Cai, and Guohui Lin)
15. Meta-Analysis of Microarray Data (Saumyadipta Pyne, SteveSkiena, 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 FrequencyInference: What Do they Tell Us? (Steven Hecth Orzack, DanielGusfield, Lakshamn Subrahmanyan, Laurent Essioux, and SebasteinLissarrague)
18. Optimization Methods for Genotype Data Analysis inEpidemiological Studies (Dumitru Brinza, Jingwu He, and AlexanderZelikovsky)
Part V: Structural and Systems Biology.
19. Topological Indices in Combinatorial Chemistry (SergeyBereg)
20. Efficient Algorithms for Structural Recall in Databases (HaoWang, Patra Volarath, and Robert W. Harrison)
21. Computational Approaches to Predict Protein-Protein andDomain-Domain Interactions (Raja Jothi and Teresa M. Przytycka)
Index.

Über Autor(innen)

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.