Biological Data Mining
Edited by Jake Y. Chen & Stefano Lonardi
CRC Press

Contents
Preface ix
Editors xiii
Contributors xv

Part I Sequence, Structure, and Function 1

1 Consensus Structure Prediction for RNA Alignments 3
Junilda Spirollari and Jason T. L. Wang
2 Invariant Geometric Properties of Secondary Structure Elements in Proteins 27
Matteo Comin, Concettina Guerra, and Giuseppe Zanotti
3 Discovering 3D Motifs in RNA 49
Alberto Apostolico, Giovanni Ciriello, Concettina Guerra, and Christine E. Heitsch
4 Protein Structure Classification Using Machine Learning Methods 69
Yazhene Krishnaraj and Chandan Reddy
5 Protein Surface Representation and Comparison: New Approaches in Structural Proteomics 89
Lee Sael and Daisuke Kihara
6 Advanced Graph Mining Methods for Protein Analysis 111
Yi-Ping Phoebe Chen, Jia Rong, and Gang Li
7 Predicting Local Structure and Function of Proteins 137
Huzefa Rangwala and George Karypis

Part II Genomics, Transcriptomics, and Proteomics 161
8 Computational Approaches for Genome Assembly Validation 163
Jeong-Hyeon Choi, Haixu Tang, Sun Kim, and Mihai Pop
9 Mining Patterns of Epistasis in Human Genetics 187
Jason H. Moore
10 Discovery of Regulatory Mechanisms from Gene Expression Variation by eQTL Analysis 205
Yang Huang, Jie Zheng, and Teresa M. Przytycka
11 Statistical Approaches to Gene Expression Microarray Data Preprocessing 229
Megan Kong, Elizabeth McClellan, Richard H. Scheuermann, and Monnie McGee
12 Application of Feature Selection and Classification to Computational Molecular Biology 257
Paola Bertolazzi, Giovanni Felici, and Giuseppe Lancia
13 Statistical Indices for Computational and Data Driven Class Discovery in Microarray Data 295
Raffaele Giancarlo, Davide Scaturro, and Filippo Utro
14 Computational Approaches to Peptide Retention Time Prediction for Proteomics 337
Xiang Zhang, Cheolhwan Oh, Catherine P. Riley, Hyeyoung Cho, and Charles Buck
Part III Functional and Molecular Interaction Networks 351
15 Inferring Protein Functional Linkage Based on Sequence Information and Beyond 353
Li Liao
16 Computational Methods for Unraveling Transcriptional Regulatory Networks in Prokaryotes 377
Dongsheng Che and Guojun Li
17 Computational Methods for Analyzing and Modeling Biological Networks 397
Nataˇsa Prˇzulj and Tijana Milenkovi´c
18 Statistical Analysis of Biomolecular Networks 429
Jing-Dong J. Han and Chris J. Needham

Part IV Literature, Ontology, and Knowledge Integration 447
19 Beyond Information Retrieval: Literature Mining for Biomedical Knowledge Discovery 449
Javed Mostafa, Kazuhiro Seki, and Weimao Ke
20 Mining Biological Interactions from Biomedical Texts for Efficient Query Answering 485
Muhammad Abulaish, Lipika Dey, and Jahiruddin
21 Ontology-Based Knowledge Representation of Experiment Metadata in Biological Data Mining 529
Richard H. Scheuermann, Megan Kong, Carl Dahlke, Jennifer Cai, Jamie Lee, Yu Qian, Burke Squires, Patrick Dunn, Jeff Wiser, Herb Hagler, Barry Smith, and David Karp
22 Redescription Mining and Applications in Bioinformatics 561
Naren Ramakrishnan and Mohammed J. Zaki
Part V Genome Medicine Applications 587
23 Data Mining Tools and Techniques for Identification of Biomarkers for Cancer 589
Mick Correll, Simon Beaulah, Robin Munro, Jonathan Sheldon, Yike Guo, and Hai Hu
24 Cancer Biomarker Prioritization: Assessing the in vivo Impact of in vitro Models by in silico Mining of Microarray Database, Literature, and Gene Annotation 615
Chia-Ju Lee, Zan Huang, Hongmei Jiang, John Crispino, and Simon Lin
25 Biomarker Discovery by Mining Glycomic and Lipidomic Data 627
Haixu Tang, Mehmet Dalkilic, and Yehia Mechref
26 Data Mining Chemical Structures and Biological Data 649
Glenn J. Myatt and Paul E. Blower
Index 689