Contents:

Preface ix Contributors xi 1 Educating Biologists in the 21st Century: Bioinformatics Scientists versus Bioinformatics Technicians Pavel Pevzner 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 Bro?na Brejov´a, Daniel G. Brown, and Tom´a?s Vina?r 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. M?andoiu, 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 S´ergio A. De Carvalho Jr. and 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 E. Ukkonen 17 Analytical and Algorithmic Methods for Haplotype Frequency Inference: What Do They Tell Us? Steven Hecht Orzack, Daniel Gusfield, Lakshman Subrahmanyan, Laurent Essioux, and Sebastien 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