Current Topics in Computational Molecular Biology Edited by Tao Jiang Ying Xu Michael Q. Zhang a Bradford Book the MIT Press

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Current Topics in Computational Molecular Biology edited by Tao Jiang Ying Xu Michael Q. Zhang A Bradford Book The MIT Press Cambridge, Massachusetts London, England Contents Preface vii I INTRODUCTION 1 1 The Challenges Facing Genomic Informatics 3 Temple F. Smith H 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 Sankoff and Nadia El-Mabrouk 7 Compressing DNA Sequences 157 Ming Li HI 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 vi Contents 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, Huseyin 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 Contributors 525 Index 527.

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Bonnie Berger Named ISCB 2019 ISCB Accomplishments by a Senior
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