Handbook Of Computational Molecular Biology

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 Fernandez-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. Schaffer 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. Kale, 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