Handbook of Computational Molecular Biology Book

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