Bioinformatics Algorithms: Techniques and Applications

Preface ix

Contributors xi

1 Educating Biologists in the 21st Century: Bioinformatics Scientists versus Bioinformatics Technicians 1
Pavel Pevzner

Part I Techniques 7

2 Dynamic Programming Algorithms for Biological Sequence and Structure Comparison 9
Yuzhen Ye and Haixu Tang

3 Graph Theoretical Approaches to Delineate Dynamics of Biological Processes 29
Teresa M. Przytycka and Elena Zotenko

4 Advances in Hidden Markov Models for Sequence Annotation 55
Broňa Brejová, Daniel G. Brown, and Tomáš Vinař

5 Sorting- and FFT-Based Techniques in the Discovery of Biopatterns 93
Sudha Balla, Sanguthevar Rajasekaran, and Jaime Davila

6 A Survey of Seeding for Sequence Alignment 117
Daniel G. Brown

7 The Comparison of Phylogenetic Networks: Algorithms and Complexity 143
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, and Giancarlo Mauri

Part II Genome and Sequence Analysis 175

8 Formal Models of Gene Clusters 177
Anne Bergeron, Cedric Chauve, and Yannick Gingras

9 Integer Linear Programming Techniques for Discovering Approximate Gene Clusters 203
Sven Rahmann and Gunnar W. Klau

10 Efficient Combinatorial Algorithms for DNA Sequence Processing 223
Bhaskar DasGupta and Ming-Yang Kao

11 Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints 241
K.M. Konwar, I.I. Măndoiu, A.C. Russell, and A.A. Shvartsman

12 Recent Developments in Alignment and Motif Finding for Sequences and Networks 259
Sing-Hoi Sze

Part III Microarray Design and Data Analysis 277

13 Algorithms for Oligonucleotide Microarray Layout 279
Sérgio A. De Carvalho Jr. and Sven Rahmann

14 Classification Accuracy Based Microarray Missing Value Imputation 303
Yi Shi, Zhipeng Cai, and Guohui Lin

15 Meta-Analysis of Microarray Data 329
Saumyadipta Pyne, Steve Skiena, and Bruce Futcher

Part IV Genetic Variation Analysis 353

16 Phasing Genotypes Using a Hidden Markov Model 355
P. Rastas, M. Koivisto, H. Mannila, and E. Ukkonen

17 Analytical and Algorithmic Methods for Haplotype Frequency Inference: What Do They Tell Us? 373
Steven Hecht Orzack, Daniel Gusfield, Lakshman Subrahmanyan, Laurent Essioux, and Sebastien Lissarrague

18 Optimization Methods for Genotype Data Analysis in Epidemiological Studies 395
Dumitru Brinza, Jingwu He, and Alexander Zelikovsky

Part V Structural and Systems Biology 417

19 Topological Indices in Combinatorial Chemistry 419
Sergey Bereg

20 Efficient Algorithms for Structural Recall in Databases 439
Hao Wang, Patra Volarath, and Robert W. Harrison

21 Computational Approaches to Predict Protein–Protein and Domain–Domain Interactions 465
Raja Jothi and Teresa M. Przytycka

Index 493