Bioinformatics algorithms : techniques and applications /
副标题：无
作 者：edited by Ion I. M鎍ndoiu and Alexander Zelikovsky.
分类号：
ISBN：9780470097731
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简介
Summary:
Publisher Summary 1
This book introduces algorithmic techniques in bioinformatics and shows how they can be used to solve novel problems in post-genomic molecular biology. Beginning with a discussion of the role of algorithms in 21st-century bioinformatics education, the book covers general algorithmic techniques, algorithms and tools for genomic and sequence analysis, microarray design and analysis, algorithmic issues arising in the analysis of genetic variation across human populations, and algorithmic approaches in structural and systems biology. Each chapter begins with a self-contained introduction to a computational problem, continues with a brief review of the existing literature and an in-depth description of recent developments, and concludes with a brief experimental study and a discussion of open research challenges. The book is accessible to researchers, practitioners, and graduate students. Mandoiu teaches in the Department of Computer Science and Engineering at the University of Connecticut. Zelikovsky teaches computer science at Georgia State University. Annotation 漏2008 Book News, Inc., Portland, OR (booknews.com)
Publisher Summary 2
Presents algorithmic techniques for solving problems in bioinformatics, including applications that shed new light on molecular biologyThis 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 algorithmsAlgorithms 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 findingMicroarray design and analysis, including algorithms for microarray physical design, missing value imputation, and meta-analysis of gene expression dataAlgorithmic 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 studiesAlgorithmic approaches in structural and systems biology, including topological and structural classification in biochemistry, and prediction of protein-protein and domain-domain interactionsEach 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.
目录
Preface p. ix
Contributors p. xi
1 Educating Biologists in the 21st Century: Bioinformatics Scientists versus Bioinformatics Technicians Pavel Pevzner p. 1
Part I Techniques p. 7
2 Dynamic Programming Algorithms for Biological Sequence and Structure Comparison Yuzhen Ye and Haixu Tang p. 9
3 Graph Theoretical Approaches to Delineate Dynamics of Biological Processes Teresa M. Przytycka and Elena Zotenko p. 29
4 Advances in Hidden Markov Models for Sequence Annotation Brona Brejova and Daniel G. Brown and Tomas Vinar p. 55
5 Sorting- and FFT-Based Techniques in the Discovery of Biopatterns Sudha Balla and Sanguthevar Rajasekaran and Jaime Davila p. 93
6 A Survey of Seeding for Sequence Alignment Daniel G. Brown p. 117
7 The Comparison of Phylogenetic Networks: Algorithms and Complexity Paola Bonizzoni and Gianluca Della Vedova and Riccardo Dondi and Giancarlo Mauri p. 143
Part II Genome and Sequence Analysis p. 175
8 Formal Models of Gene Clusters Anne Bergeron and Cedric Chauve and Yannick Gingras p. 177
9 Integer Linear Programming Techniques for Discovering Approximate Gene Clusters Sven Rahmann and Gunnar W. Klau p. 203
10 Efficient Combinatorial Algorithms for DNA Sequence Processing Bhaskar DasGupta and Ming-Yang Kao p. 223
11 Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints K.M. Konwar and I.I. Mandoiu and A.C. Russell and A.A. Shvartsman p. 241
12 Recent Developments in Alignment and Motif Finding for Sequences and Networks Sing-Hoi Sze p. 259
Part III Microarray Design and Data Analysis p. 277
13 Algorithms for Oligonucleotide Microarray Layout Sergio A. De Carvalho Jr. and Sven Rahmann p. 279
14 Classification Accuracy Based Microarray Missing Value Imputation Yi Shi and Zhipeng Cai and Guohui Lin p. 303
15 Meta-Analysis of Microarray Data Saumyadipta Pyne and Steve Skiena and Bruce Futcher p. 329
Part IV Genetic Variation Analysis p. 353
16 Phasing Genotypes Using a Hidden Markov Model P. Rastas and M. Koivisto and H. Mannila and E. Ukkonen p. 355
17 Analytical and Algorithmic Methods for Haplotype Frequency Inference: What Do They Tell Us? Steven Hecht Orzack and Daniel Gusfield and Lakshman Subrahmanyan and Laurent Essioux and Sebastien Lissarrague p. 373
18 Optimization Methods for Genotype Data Analysis in Epidemiological Studies Dumitru Brinza and Jingwu He and Alexander Zelikovsky p. 395
Part V Structural and Systems Biology p. 417
19 Topological Indices in Combinatorial Chemistry Sergey Bereg p. 419
20 Efficient Algorithms for Structural Recall in Databases Hao Wang and Patra Volarath and Robert W. Harrison p. 439
21 Computational Approaches to Predict Protein-Protein and Domain-Domain Interactions Raja Jothi and Teresa M. Przytycka p. 465
Index p. 493
Contributors p. xi
1 Educating Biologists in the 21st Century: Bioinformatics Scientists versus Bioinformatics Technicians Pavel Pevzner p. 1
Part I Techniques p. 7
2 Dynamic Programming Algorithms for Biological Sequence and Structure Comparison Yuzhen Ye and Haixu Tang p. 9
3 Graph Theoretical Approaches to Delineate Dynamics of Biological Processes Teresa M. Przytycka and Elena Zotenko p. 29
4 Advances in Hidden Markov Models for Sequence Annotation Brona Brejova and Daniel G. Brown and Tomas Vinar p. 55
5 Sorting- and FFT-Based Techniques in the Discovery of Biopatterns Sudha Balla and Sanguthevar Rajasekaran and Jaime Davila p. 93
6 A Survey of Seeding for Sequence Alignment Daniel G. Brown p. 117
7 The Comparison of Phylogenetic Networks: Algorithms and Complexity Paola Bonizzoni and Gianluca Della Vedova and Riccardo Dondi and Giancarlo Mauri p. 143
Part II Genome and Sequence Analysis p. 175
8 Formal Models of Gene Clusters Anne Bergeron and Cedric Chauve and Yannick Gingras p. 177
9 Integer Linear Programming Techniques for Discovering Approximate Gene Clusters Sven Rahmann and Gunnar W. Klau p. 203
10 Efficient Combinatorial Algorithms for DNA Sequence Processing Bhaskar DasGupta and Ming-Yang Kao p. 223
11 Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints K.M. Konwar and I.I. Mandoiu and A.C. Russell and A.A. Shvartsman p. 241
12 Recent Developments in Alignment and Motif Finding for Sequences and Networks Sing-Hoi Sze p. 259
Part III Microarray Design and Data Analysis p. 277
13 Algorithms for Oligonucleotide Microarray Layout Sergio A. De Carvalho Jr. and Sven Rahmann p. 279
14 Classification Accuracy Based Microarray Missing Value Imputation Yi Shi and Zhipeng Cai and Guohui Lin p. 303
15 Meta-Analysis of Microarray Data Saumyadipta Pyne and Steve Skiena and Bruce Futcher p. 329
Part IV Genetic Variation Analysis p. 353
16 Phasing Genotypes Using a Hidden Markov Model P. Rastas and M. Koivisto and H. Mannila and E. Ukkonen p. 355
17 Analytical and Algorithmic Methods for Haplotype Frequency Inference: What Do They Tell Us? Steven Hecht Orzack and Daniel Gusfield and Lakshman Subrahmanyan and Laurent Essioux and Sebastien Lissarrague p. 373
18 Optimization Methods for Genotype Data Analysis in Epidemiological Studies Dumitru Brinza and Jingwu He and Alexander Zelikovsky p. 395
Part V Structural and Systems Biology p. 417
19 Topological Indices in Combinatorial Chemistry Sergey Bereg p. 419
20 Efficient Algorithms for Structural Recall in Databases Hao Wang and Patra Volarath and Robert W. Harrison p. 439
21 Computational Approaches to Predict Protein-Protein and Domain-Domain Interactions Raja Jothi and Teresa M. Przytycka p. 465
Index p. 493
Bioinformatics algorithms : techniques and applications /
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