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http://dx.doi.org/10.1201/9781420036275
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Front MatterAbstract - Hi-Res PDF (411 KB) - PDF w/links (387 KB)
Chapter 1. Pairwise Sequence AlignmentBenjamin N. JacksonAbstract - Hi-Res PDF (1536 KB) - PDF w/links (805 KB)
Chapter 2. Spliced Alignment and Similarity-based Gene RecognitionAlexei D. Neverov, Andrei A. Mironov, Mikhail S. GelfandAbstract - Hi-Res PDF (1024 KB) - PDF w/links (530 KB)
Chapter 3. Multiple Sequence AlignmentOsamu Gotoh, Shinsuke Yamada, Tetsushi YadaAbstract - Hi-Res PDF (958 KB) - PDF w/links (626 KB)
Chapter 4. Parametric Sequence AlignmentDavid Fernandez-Baca, Balaji VenkatachalamAbstract - Hi-Res PDF (527 KB) - PDF w/links (544 KB)
Chapter 5. Lookup Tables, Suffix Trees and Suffix ArraysPang KoAbstract - Hi-Res PDF (456 KB) - PDF w/links (465 KB)
Chapter 6. Suffix Tree Applications in Computational BiologyPang KoAbstract - Hi-Res PDF (471 KB) - PDF w/links (485 KB)
Chapter 7. Enhanced Suffix Arrays and ApplicationsMohamed I. Abouelhoda, Stefan Kurtz, Enno OhlebuschAbstract - Hi-Res PDF (511 KB) - PDF w/links (515 KB)
Chapter 8. Computational Methods for Genome AssemblyXiaoqiu HuangAbstract - Hi-Res PDF (296 KB) - PDF w/links (308 KB)
Chapter 9. Assembling the Human GenomeRicha AgarwalaAbstract - Hi-Res PDF (525 KB) - PDF w/links (456 KB)
Chapter 10. Comparative Methods for Sequence AssemblyVamsi VeeramachaneniAbstract - Hi-Res PDF (757 KB) - PDF w/links (572 KB)
Chapter 11. Information Theoretic Approach to Genome ReconstructionSuchendra Bhandarkar, Jinling Huang, Jonathan ArnoldAbstract - Hi-Res PDF (410 KB) - PDF w/links (422 KB)
Chapter 12. Expressed Sequence TagsAnantharaman KalyanaramanAbstract - Hi-Res PDF (376 KB) - PDF w/links (422 KB)
Chapter 13. Algorithms for Large-Scale Clustering and Assembly of Biological Sequence DataScott J. Emrich, Anantharaman KalyanaramanAbstract - Hi-Res PDF (1175 KB) - PDF w/links (668 KB)
Chapter 14. Comparisons of Long Genomic SequencesInna Dubchak, Michael BrudnoAbstract - Hi-Res PDF (1340 KB) - PDF w/links (704 KB)
Chapter 15. Chaining Algorithms and Applications in Comparative GenomicsEnno Ohlebusch, Mohamed I. AbouelhodaAbstract - Hi-Res PDF (629 KB) - PDF w/links (649 KB)
Chapter 16. Computational Analysis of Alternative SplicingMikhail S. GelfandAbstract - Hi-Res PDF (412 KB) - PDF w/links (496 KB)
Chapter 17. Human Genetic Linkage AnalysisAlejandro A. SchafferAbstract - Hi-Res PDF (426 KB) - PDF w/links (465 KB)
Chapter 18. Haplotype InferenceDan Gusfield, Steven Hecht OrzackAbstract - Hi-Res PDF (342 KB) - PDF w/links (363 KB)
Chapter 19. An Overview of Phylogeny ReconstructionC. Randal Linder, Tandy WarnowAbstract - Hi-Res PDF (495 KB) - PDF w/links (522 KB)
Chapter 20. Consensus Trees and SupertreesOliver EulensteinAbstract - Hi-Res PDF (3977 KB) - PDF w/links (1534 KB)
Chapter 21. Large-scale Phylogenetic AnalysisTandy WarnowAbstract - Hi-Res PDF (416 KB) - PDF w/links (429 KB)
Chapter 22. High-Performance Algorithms for Phylogeny Reconstruction with Maximum ParsimonyDavid A. Bader, Mi YanAbstract - Hi-Res PDF (349 KB) - PDF w/links (358 KB)
Chapter 23. Microarray DataCatherine A. Ball, Gavin SherlockAbstract - Hi-Res PDF (477 KB) - PDF w/links (354 KB)
Chapter 24. Computational Methods for Microarray DesignHui-Hsien ChouAbstract - Hi-Res PDF (716 KB) - PDF w/links (742 KB)
Chapter 25. Clustering Algorithms for Gene Expression AnalysisPierre Baldi, G. Wesley Hatfield, Li M. FuAbstract - Hi-Res PDF (439 KB) - PDF w/links (409 KB)
Chapter 26. Biclustering AlgorithmsAmos Tanay, Roded Sharan, Ron ShamirAbstract - Hi-Res PDF (330 KB) - PDF w/links (339 KB)
Chapter 27. Identifying Gene Regulatory Networks from Gene Expression DataVladimir FilkovAbstract - Hi-Res PDF (426 KB) - PDF w/links (533 KB)
Chapter 28. Modeling and Analysis of Gene Networks Using Feedback Control TheoryHana El Samad, Mustang RammishAbstract - Hi-Res PDF (628 KB) - PDF w/links (576 KB)
Chapter 29. Predicting Protein Secondary and Supersecondary StructureMona SinghAbstract - Hi-Res PDF (1058 KB) - PDF w/links (1060 KB)
Chapter 30. Protein Structure Prediction with Lattice ModelsWilliam E. Hart, Alantha NewmanAbstract - Hi-Res PDF (1109 KB) - PDF w/links (962 KB)
Chapter 31. Protein Structure Determination via NMR Spectral DataGuohui Lin, Xin Tu, Xiang WanAbstract - Hi-Res PDF (378 KB) - PDF w/links (399 KB)
Chapter 32. Geometric and Signal Processing of Reconstructed 3D Maps of Molecular ComplexesChandrajit Bajaj, Zeyun YuAbstract - Hi-Res PDF (2327 KB) - PDF w/links (663 KB)
Chapter 33. In Search of Remote HomologDong Xu, Ognen Duzlevski, Xii-Fend WanAbstract - Hi-Res PDF (504 KB) - PDF w/links (544 KB)
Chapter 34. Biomolecular Modeling using Parallel SupercomputersLaxmikant V. Kale, Klaus Schulten, Robert D. Skeel, Glenn Martyna, Mark Tuckerman, James C. Phillips, Sameer Kumar, Gengbin ZhengAbstract - Hi-Res PDF (771 KB) - PDF w/links (772 KB)
Chapter 35. String Search in External MemoryPaolo FerraginaAbstract - Hi-Res PDF (728 KB) - PDF w/links (779 KB)
Chapter 36. Index Structures for Approximate Matching in Sequence DatabasesTamer Kahveci, Ambuj K. SinghAbstract - Hi-Res PDF (464 KB) - PDF w/links (486 KB)
Chapter 37. Algorithms for Motif SearchSanguthevar RajasekaranAbstract - Hi-Res PDF (342 KB) - PDF w/links (353 KB)
Chapter 38. Data Mining in Computational BiologyMohammed J. Zaki, Karlton SequeiraAbstract - Hi-Res PDF (1104 KB) - PDF w/links (582 KB)
