Handbook of Computational Molecular Biology

The Handbook of Computational Molecular Biology offers a comprehensive, systematic treatment of computational biology, from the most basic concepts to advanced applications. Algorithmic in nature, the handbook highlights applications to molecular biology through every topic covered. In addition, many of the newer topics in the field are covered in depth, like microarrays, comparative genomics and external memory algorithms, and parallel methods. Written by experts in the field, it covers problems related to understanding genetic diseases, the design of drugs tailored to the individual, deciphering the genomes of specific organisms, and understanding the process of evolution.

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.

Sequence Alignments Pairwise Sequence Alignments; Benjamin N. Jackson and Srinivas Aluru Spliced Alignment and Similarity-Based Gene Recognition; Alexey D. Neverov, Andrey A. Mironov, and Mikhail S. Gelfand Multiple Sequence Alignment; Osamu Gotoh, Shinsuke Yamada, and Tetsushi Yada Parametric Sequence Alignment; David Fernández-Baca and Balaji Venkatachalam String Data Structures Lookup Tables, Suffix Trees and Suffix Arrays; Srinivas Aluru Suffix Tree Applications in Computational Biology; Pang Ko and Srinivas Aluru Enhanced Suffix Arrays and Applications; Mohamed I. Abouelhoda, Stefan Kurtz, and Enno Ohlebusch Genome Assembly and EST Clustering 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, and Jonathan Arnold Expressed Sequence Tags: Clustering and Applications; Anantharaman Kalyanaraman and Srinivas Aluru Algorithms for Large-Scale Clustering and Assembly of Biological Sequence Data; Scott J. Emrich, Anantharaman Kalyanaraman, and Srinivas Aluru Genome-Scale Computational Methods Comparisons of Long Genomic Sequences: Algorithms and Applications; Michael Brudno and Inna Dubchak Chaining Algorithms and Applications in Comparative Genomics; Enno Ohlebusch and Mohamed I. Abouelhoda Computational Analysis of Alternative Splicing; Mikhail S. Gelfand Human Genetic Linkage Analysis; Alejandro A. Schäffer Combinatorial Methods for Haplotype Inference; Dan Gusfield and Steven Hecht Orzack Phylogenetics An Overview of Phylogeny Reconstruction; C. Randal Linder and Tandy Warnow Consensus Trees and Supertrees; Oliver Eulenstein Large-Scale Phylogenetic Analysis; Tandy Warnow High-Performance Phylogeny Reconstruction; David A. Bader and Mi Yan Microarrays and Gene Expression Analysis Microarray Data: Annotation, Storage, Retrieval and Communication; Catherine A. Ball and Gavin Sherlock Computational Methods for Microarray Design; Hui-Hsien Chou Clustering Algorithms for Gene Expression Analysis; Pierre Baldi, G. Wesley Hatfield, and Li M. Fu Biclustering Algorithms: A Survey; Amos Tanay, Roded Sharan, and 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 and Mustafa Khammash Computational Structural Biology Predicting Protein Secondary and Supersecondary Structure; Mona Singh Protein Structure Prediction with Lattice Models; William E. Hart and Alantha Newman Protein Structure Determination via NMR Spectral Data; Guohui Lin, Xin Tu, and Xiang Wan Geometric Processing of Reconstructed 3D Maps of Molecular Complexes; Chandrajit Bajaj and Zeyun Yu In Search of Remote Homolog; Dong Xu, Ognen Duzlevski, and Xiu-Feng Wan Biomolecular Modeling using Parallel Supercomputers; Laxmikant V. Kalé, Klaus Schulten, Robert D. Skeel, Glenn Martyna, Mark Tuckerman, James C. Phillips, Sameer Kumar, and Gengbin Zheng Bioinformatic Databases and Data Mining String Search in External Memory: Data Structures and Algorithms; Paolo Ferragina Index Structures for Approximate Matching in Sequence Databases; Tamer Kahveci and Ambuj K. Singh Algorithms for Motif Search; Sanguthevar Rajasekaran Data Mining in Computational Biology; Mohammed J. Zaki and Karlton Sequeira Index

Srinivas Aluru