Bioinformatics Algorithms

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.

• Preface ixContributors xi1 Educating Biologists in the 21st Century: Bioinformatics Scientists versus Bioinformatics Technicians 1Pavel PevznerPart I Techniques 72 Dynamic Programming Algorithms for Biological Sequence and Structure Comparison 9Yuzhen Ye and Haixu Tang3 Graph Theoretical Approaches to Delineate Dynamics of Biological Processes 29Teresa M. Przytycka and Elena Zotenko4 Advances in Hidden Markov Models for Sequence Annotation 55Broňa Brejová, Daniel G. Brown, and Tomáš Vinař5 Sorting- and FFT-Based Techniques in the Discovery of Biopatterns 93Sudha Balla, Sanguthevar Rajasekaran, and Jaime Davila6 A Survey of Seeding for Sequence Alignment 117Daniel G. Brown7 The Comparison of Phylogenetic Networks: Algorithms and Complexity 143Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, and Giancarlo MauriPart II Genome and Sequence Analysis 1758 Formal Models of Gene Clusters 177Anne Bergeron, Cedric Chauve, and Yannick Gingras9 Integer Linear Programming Techniques for Discovering Approximate Gene Clusters 203Sven Rahmann and Gunnar W. Klau10 Efficient Combinatorial Algorithms for DNA Sequence Processing 223Bhaskar DasGupta and Ming-Yang Kao11 Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints 241K.M. Konwar, I.I. Măndoiu, A.C. Russell, and A.A. Shvartsman12 Recent Developments in Alignment and Motif Finding for Sequences and Networks 259Sing-Hoi SzePart III Microarray Design and Data Analysis 27713 Algorithms for Oligonucleotide Microarray Layout 279Sérgio A. De Carvalho Jr. and Sven Rahmann14 Classification Accuracy Based Microarray Missing Value Imputation 303Yi Shi, Zhipeng Cai, and Guohui Lin15 Meta-Analysis of Microarray Data 329Saumyadipta Pyne, Steve Skiena, and Bruce FutcherPart IV Genetic Variation Analysis 35316 Phasing Genotypes Using a Hidden Markov Model 355P. Rastas, M. Koivisto, H. Mannila, and E. Ukkonen17 Analytical and Algorithmic Methods for Haplotype Frequency Inference: What Do They Tell Us? 373Steven Hecht Orzack, Daniel Gusfield, Lakshman Subrahmanyan, Laurent Essioux, and Sebastien Lissarrague18 Optimization Methods for Genotype Data Analysis in Epidemiological Studies 395Dumitru Brinza, Jingwu He, and Alexander ZelikovskyPart V Structural and Systems Biology 41719 Topological Indices in Combinatorial Chemistry 419Sergey Bereg20 Efficient Algorithms for Structural Recall in Databases 439Hao Wang, Patra Volarath, and Robert W. Harrison21 Computational Approaches to Predict Protein–Protein and Domain–Domain Interactions 465Raja Jothi and Teresa M. PrzytyckaIndex 493

"This clear and approachable presentation makes the book appropriate for researchers, practioners, and graduate students." (Mathematical Reviews, Issue 2009b)"This volume will be a nice addition to the bioinformatician's bookshelf." (Quarterly Review of Biology, December 2008)