Pairwise Sequence Alignment / Benjamin N. Jackson, Srinivas Aluru -- Spliced Alignment and Similarity-based Gene Recognition / Alexei D. Neverov, Andrei A. Mironov, Mikhail S. Gelfand -- Multiple Sequence Alignment / Osamu Gotoh, Shinsuke Yamada, Tetsushi Yada -- Parametric Sequence Alignment / David Fernandez-Baca, Balaji Venkatachalam -- Lookup Tables, Suffix Trees and Suffix Arrays / Srinivas Aluru, Pang Ko -- Suffix Tree Applications in Computational Biology / Pang Ko, Srinivas Aluru -- Enhanced Suffix Arrays and Applications / Mohamed I. Abouelhoda, Stefan Kurtz, Enno Ohlebusch -- Computational Methods for Genome Assembly / Xiaoqiu Huang -- Assembling the Human Genome / Richa Agarwala -- Comparative Methods for Sequence Assembly / Vamsi Veeramachaneni -- Information Theoretic Approach to Genome Reconstruction / Suchendra Bhandarkar, Jinling Huang, Jonathan Arnold -- Expressed Sequence Tags: Clustering and Applications / Anantharaman Kalyanaraman, Srinivas Aluru. Algorithms for Large-Scale Clustering and Assembly of Biological Sequence Data / Scott J. Emrich, Anantharaman Kalyanaraman, Srinivas Aluru -- Comparisons of Long Genomic Sequences: Algorithms and Applications / Michael Brudno, Inna Dubchak -- Chaining Algorithms and Applications in Comparative Genomics / Enno Ohlebusch, Mohamed I. Abouelhoda -- Computational Analysis of Alternative Splicing / Mikhail S. Gelfand -- Human Genetic Linkage Analysis / Alejandro A. Schaffer -- Haplotype Inference / Dan Gusfield, Steven Hecht Orzack -- An Overview of Phylogeny Reconstruction / C. Randal Linder, Tandy Warnow -- Consensus Trees and Supertrees / Oliver Eulenstein -- Large-scale Phylogenetic Analysis / Tandy Warnow -- High-Performance Phylogeny Reconstruction / David A. Bader, Mi Yan -- Microarray Data: Annotation, Storage, Retrieval and Communication / Catherine A. Ball, Gavin Sherlock -- Computational Methods for Microarray Design / Hui-Hsien Chou -- Clustering Algorithms for Gene Expression Analysis / Pierre Baldi, G. Wesley Hatfield, Li M. Fu -- Biclustering Algorithms: A Survey / Amos Tanay, Roded Sharan, Ron Shamir. Identifying Gene Regulatory Networks from Gene Expression Data / Vladimir Filkov -- Modeling and Analysis of Gene Networks Using Feedback Control Theory / Hana El Samad, Mustang Rammish -- Predicting Protein Secondary and Supersecondary Structure / Mona Singh -- Protein Structure Prediction with Lattice Models / William E. Hart, Alantha Newman -- Protein Structure Determination via NMR Spectral Data / Guohui Lin, Xin Tu, Xiang Wan -- Geometric and Signal Processing of Reconstructed D Maps of Molecular Complexes / Chandrajit Bajaj, Zeyun Yu -- In Search of Remote Homolog / Dong Xu, Ognen Duzlevski, Xii-Fend Wan -- Biomolecular Modeling using Parallel Supercomputers / Laxmikant V. Kale [and others] -- String Search in External Memory: Data Structures and Algorithms / Paolo Ferragina -- Index Structures for Approximate Matching in Sequence Databases / Tamer Kahveci, Ambuj K. Singh -- Algorithms for Motif Search / Sanguthevar Rajasekaran -- Data Mining in Computational Biology / Mohammed J. Zaki, Karlton Sequeira. "The enormous complexity of biological systems at the molecular level must be answered with powerful computational methods. Computational biology is a young field, but has seen rapid growth and advancement over the past few decades. Surveying the progress made in this multidisciplinary field, the Handbook of Computational Molecular Biology offers comprehensive, systematic coverage of the various techniques and methodologies currently available. Accomplished researcher Srinivas Aluru leads a team of experts from around the world to produce this groundbreaking, authoritative reference. With discussions ranging from fundamental concepts to practical applications, this book details the algorithms necessary to solve novel problems and manage the massive amounts of data housed in biological databases throughout the world. Divided into eight sections for convenient searching, the handbook covers methods and algorithms for sequence alignment, string data structures, sequence assembly and clustering, genome-scale computational methods in comparative genomics, evolutionary and phylogenetic trees, microarrays and gene expression analysis, computational methods in structural biology, and bioinformatics databases and data mining. The Handbook of Computational Molecular Biology is the first resource to integrate coverage of the broad spectrum of topics in computational biology and bioinformatics. It supplies a quick-reference guide for easy implementation and provides a strong foundation for future discoveries in the field."--Publisher's website.