Handbook of Computational Molecular Biology

Contents: I. Sequence alignments: 1. Pairwise sequence alignment/Benjamin N. Jackson and Srinivas Aluru. 2. Spliced alignment and similarity - based gene recognition/Alexi D. Neverov, Andrei A. Mironov and Mikhail S. Gelfand. 3. Multiple sequence alignment/Osamu Gotoh, Shinsuke Yamada and Tetsushi Yada. 4. Parametric sequence alignment/David Fernandez-Baca and Balaji Venkatachalam. II. String data structures: 5. Lookup tables, suffix trees and suffix arrays/Srinivas Aluru and Pang Ko. 6. Suffix tree applications in computational biology/Pang Ko and Srinivas Aluru. 7. Enhanced suffix arrays and applications/Mohamed I. Abouelhoda, Stefan Kurtz and Enno Ohlebusch. III. Genome assembly and EST clustering: 8. Computational methods for genome assembly/Xiaoqiu Huang. 9. Assembling the human genome/Richa Agarwala. 10. Comparative methods for sequence assembly/Vamsi Veeramachaneni. 11. Information theoretic approach to genome reconstruction/Suchendra Bhandarkar, Jinling Huang and Jonathan Arnold. 12. Expressed sequence tags: clustering and applications/Anantharaman Kalyanaraman and Srinivas Aluru. 13. Algorithms for large-scale clustering and assembly of biological sequence data/Scott J. Emrich, Anantharaman Kalyanaraman and Srinivas Aluru. IV. Genome-scale computational methods: 14. Comparisons of long genomic sequences: algorithms and applications/Michael Brudno and Inna Dubchak. 15. Chaining algorithms and applications in comparative genomics/Enno Ohlebusch and Mohamed I. Abouelhoda. 16. Computational analysis of alternative splicing/Mikhail S. Gelfand. 17. Human genetic linkage analysis/Alejandro A. Schaffer. 18. Haplotype inference/Dan Gusfield and Steven Hecht Orzack. V. Phylogenetics: 19. An overview of phylogeny reconstruction/C. Randal Linder and Tandy Warnow. 20. Consensus trees and supertrees/Oliver Eulenstein. 21. Large-scale phylogenetic analysis/Tandy Warnow. 22. High-performance phylogeny reconstruction/David A. Bader and Mi Yan. VI. Microarrays and gene expression analysis: 23. Microarray data: annotation, storage, retrieval and communication/Catherine A. Ball and Gavin Sherlock. 24. Computational methods for microarray design/Hui-Hsien Chou. 25. Clustering algorithms for gene expression analysis/Pierre Baldi, G. Wesley Hatfield and Li M. Fu. 26. Biclustering algorithms: a survey/Amos Tanay, Roded Sharan and Ron Shamir. 27. Identifying gene regulatory networks from gene expression data/Vladimir Filkov. 28. Modeling and analysis of gene networks using feedback control theory/Hana EI Samad and Mustang Rammish. VII. Computational structural biology: 29. Predicting protein secondary and supersecondary structure/Mona Singh. 30. Protein structure prediction with Lattice models/William E. Hart and Alantha Newman. 31. Protein structure determination via NMR spectral data/Guohui Lin, Xin Tu and Xiang Wan. 32. Geometric and signal processing of reconstructed 3D maps of molecular complexes/Chandrajit Bajaj and Zeyun Yu. 33. In search of Remote Homolog/Dong Xu, Ognen Duzlevski and Xii-Fend Wan. 34. 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. VIII. Bioinformatic databases and data mining: 35. String search in external memory: data structures and algorithms/Paolo Ferragina. 36. Index structures for approximate matching in sequence databases/Tamer Kahveci and Ambuj K. Singh. 37. Algorithms for motif search/Sanguthevar Rajasekaran. 38. Data mining in computational biology/Mohammed J. Zaki and Karlton Sequeira. Index.

"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. 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.

Ranging from fundamental concepts to practical applications, this book...

• Presents the first comprehensive distillation of accumulated knowledge in computational biology.
  
• Links each topic to applications in molecular biology while building on fundamental concepts.
  
• Takes an algorithmic point of view for immediate implementation and easy reference.
  
• Includes numerous illustrations to highlight the discussion as well as references to more in-depth information."