Table of Contents
Preface ix
Contributors xi
1 Educating Biologists in the 21st Century: Bioinformatics Scientists versus Bioinformatics Technicians 1Pavel Pevzner
Part I Techniques 7
2 Dynamic Programming Algorithms for Biological Sequence and Structure Comparison 9Yuzhen Ye and Haixu Tang
3 Graph Theoretical Approaches to Delineate Dynamics of Biological Processes 29Teresa M. Przytycka and Elena Zotenko
4 Advances in Hidden Markov Models for Sequence Annotation 55Broňa Brejová, Daniel G. Brown, and Tomáš Vinař
5 Sorting- and FFT-Based Techniques in the Discovery of Biopatterns 93Sudha Balla, Sanguthevar Rajasekaran, and Jaime Davila
6 A Survey of Seeding for Sequence Alignment 117Daniel G. Brown
7 The Comparison of Phylogenetic Networks: Algorithms and Complexity 143Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, and Giancarlo Mauri
Part II Genome and Sequence Analysis 175
8 Formal Models of Gene Clusters 177Anne Bergeron, Cedric Chauve, and Yannick Gingras
9 Integer Linear Programming Techniques for Discovering Approximate Gene Clusters 203Sven Rahmann and Gunnar W. Klau
10 Efficient Combinatorial Algorithms for DNA Sequence Processing 223Bhaskar DasGupta and Ming-Yang Kao
11 Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints 241K.M. Konwar, I.I. Măndoiu, A.C. Russell, and A.A. Shvartsman
12 Recent Developments in Alignment and Motif Finding for Sequences and Networks 259Sing-Hoi Sze
Part III Microarray Design and Data Analysis 277
13 Algorithms for Oligonucleotide Microarray Layout 279Sérgio A. De Carvalho Jr. and Sven Rahmann
14 Classification Accuracy Based Microarray Missing Value Imputation 303Yi Shi, Zhipeng Cai, and Guohui Lin
15 Meta-Analysis of Microarray Data 329Saumyadipta Pyne, Steve Skiena, and Bruce Futcher
Part IV Genetic Variation Analysis 353
16 Phasing Genotypes Using a Hidden Markov Model 355P. Rastas, M. Koivisto, H. Mannila, and E. Ukkonen
17 Analytical and Algorithmic Methods for Haplotype Frequency Inference: What Do They Tell Us? 373Steven Hecht Orzack, Daniel Gusfield, Lakshman Subrahmanyan, Laurent Essioux, and Sebastien Lissarrague
18 Optimization Methods for Genotype Data Analysis in Epidemiological Studies 395Dumitru Brinza, Jingwu He, and Alexander Zelikovsky
Part V Structural and Systems Biology 417
19 Topological Indices in Combinatorial Chemistry 419Sergey Bereg
20 Efficient Algorithms for Structural Recall in Databases 439Hao Wang, Patra Volarath, and Robert W. Harrison
21 Computational Approaches to Predict Protein–Protein and Domain–Domain Interactions 465Raja Jothi and Teresa M. Przytycka
Index 493