Handbook of computational molecular biology /

Part I Sequence Alignments
1 Pairwise Sequence Alignment Benjamin N. Jackson and Srinivas Aluru p. 1
2 Spliced Alignment and Similarity-based Gene Recognition Alexei D. Neverov and Andrei A. Mironov and Mikhail S. Gelfand p. 2
3 Multiple Sequence Alignment Osamu Gotoh and Shinsuke Yamada and Tetsushi Yada p. 3
4 Parametric Sequence Alignment David Fernandez-Baca and Balaji Venkatachalam p. 4
Part II String Data Structures
5 Lookup Tables, Suffix Trees and Suffix Arrays Srinivas Aluru and Pang Ko p. 5
6 Suffix Tree Applications in Computational Biology Pang Ko and Srinivas Aluru p. 6
7 Enhanced Suffix Arrays and Applications Mohamed I. Abouelhoda and Stefan Kurtz and Enno Ohlebusch p. 7
Part III Genome Assembly and EST Clustering
8 Computational Methods for Genome Assembly Xiaoqiu Huang p. 8
9 Assembling the Human Genome Richa Agarwala p. 9
10 Comparative Methods for Sequence Assembly Vamsi Veeramachaneni p. 10
11 Information Theoretic Approach to Genome Reconstruction Suchendra Bhandarkar and Jinling Huang and Jonathan Arnold p. 11
12 Expressed Sequence Tags: Clustering and Applications Anantharaman Kalyanaraman and Srinivas Aluru p. 12
13 Algorithms for Large-Scale Clustering and Assembly of Biological Sequence Data Scott J. Emrich and Anantharaman Kalyanaraman and Srinivas Aluru p. 13
Part IV Genome-Scale Computational Methods
14 Comparisons of Long Genomic Sequences: Algorithms and Applications Michael Brudno and Inna Dubchak p. 14
15 Chaining Algorithms and Applications in Comparative Genomics Enno Ohlebusch and Mohamed I. Abouelhoda p. 15
16 Computational Analysis of Alternative Splicing Mikhail S. Gelfand p. 16
17 Human Genetic Linkage Analysis Alejandro A. Schaffer p. 17
18 Haplotype Inference Dan Gusfield and Steven Hecht Orzack p. 18
Part V Phylogenetics
19 An Overview of Phylogeny Reconstruction C. Randal Linder and Tandy Warnow p. 19
20 Consensus Trees and Supertrees Oliver Eulenstein p. 20
21 Large-scale Phylogenetic Analysis Tandy Warnow p. 21
22 High-Performance Phylogeny Reconstruction David A. Bader and Mi Yan p. 22
Part VI Microarrays and Gene Expression Analysis
23 Microarray Data: Annotation, Storage, Retrieval and Communication Catherine A. Ball and Gavin Sherlock p. 23
24 Computational Methods for Microarray Design Hui-Hsien Chou p. 24
25 Clustering Algorithms for Gene Expression Analysis Pierre Baldi and G. Wesley Hatfield and Li M. Fu p. 25
26 Biclustering Algorithms: A Survey Amos Tanay and Roded Sharan and Ron Shamir p. 26
27 Identifying Gene Regulatory Networks from Gene Expression Data Vladimir Filkov p. 27
28 Modeling and Analysis of Gene Networks Using Feedback Control Theory Hana El Samad and Mustang Rammish p. 28
Part VII Computational Structural Biology
29 Predicting Protein Secondary and Supersecondary Structure Mona Singh p. 29
30 Protein Structure Prediction with Lattice Models William E. Hart and Alantha Newman p. 30
31 Protein Structure Determination via NMR Spectral Data Guohui Lin and Xin Tu and Xiang Wan p. 31
32 Geometric and Signal Processing of Reconstructed 3D Maps of Molecular Complexes Chandrajit Bajaj and Zeyun Yu p. 32
33 In Search of Remote Homolog Dong Xu and Ognen Duzlevski and Xii-Fend Wan p. 33
34 Biomolecular Modeling using Parallel Supercomputers Laxmikant V. Kale and Klaus Schulten and Robert D. Skeel and Glenn Martyna and Mark Tuckerman and James C. Phillips and Sameer Kumar and Gengbin Zheng p. 34
Part VIII Bioinformatic Databases and Data Mining
35 String Search in External Memory: Data Structures and Algorithms Paolo Ferragina p. 35
36 Index Structures for Approximate Matching in Sequence Databases Tamer Kahveci and Ambuj K. Singh p. 36
37 Algorithms for Motif Search Sanguthevar Rajasekaran p. 37
38 Data Mining in Computational Biology Mohammed J. Zaki and Karlton Sequeira p. 38
Index p. 1