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Current Topics in Computational Molecular Biology - Tao Jiang , Ying Xu , Michael Q. Zhang

Contents


I INTRODUCTION 1
1 The Challenges Facing Genomic Informatics 3
Temple F. Smith
II COMPARATIVE SEQUENCE AND GENOME ANALYSIS 9
2 Bayesian Modeling and Computation in Bioinformatics Research 11
Jun S. Liu
3 Bio-Sequence Comparison and Applications 45
Xiaoqiu Huang
4 Algorithmic Methods for Multiple Sequence Alignment 71
Tao Jiang and Lusheng Wang
5 Phylogenetics and the Quartet Method 111
Paul Kearney
6 Genome Rearrangement 135
David Sanko¤ and Nadia El-Mabrouk
7 Compressing DNA Sequences 157
Ming Li

III DATA MINING AND PATTERN DISCOVERY 173
8 Linkage Analysis of Quantitative Traits 175
Shizhong Xu
9 Finding Genes by Computer: Probabilistic and Discriminative
Approaches 201
Victor V. Solovyev
10 Computational Methods for Promoter Recognition 249
Michael Q. Zhang
11 Algorithmic Approaches to Clustering Gene Expression Data 269
Ron Shamir and Roded Sharan
12 KEGG for Computational Genomics 301
Minoru Kanehisa and Susumu Goto

13 Datamining: Discovering Information from Bio-Data 317
Limsoon Wong
IV COMPUTATIONAL STRUCTURAL BIOLOGY 343
14 RNA Secondary Structure Prediction 345
Zhuozhi Wang and Kaizhong Zhang
15 Properties and Prediction of Protein Secondary Structure 365
Victor V. Solovyev and Ilya N. Shindyalov
16 Computational Methods for Protein Folding: Scaling a Hierarchy of
Complexities 403
Hue Sun Chan, Hu¨seyin Kaya, and Seishi Shimizu
17 Protein Structure Prediction by Comparison: Homology-Based
Modeling 449
Manuel C. Peitsch, Torsten Schwede, Alexander Diemand, and
Nicolas Guex
18 Protein Structure Prediction by Protein Threading and Partial
Experimental Data 467
Ying Xu and Dong Xu
19 Computational Methods for Docking and Applications to Drug Design:
Functional Epitopes and Combinatorial Libraries 503
Ruth Nussinov, Buyong Ma, and Haim J. Wolfson

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