Biological data mining /

Preface p. ix
Editors p. xiii
Contributors p. xv
Part I Sequence, Structure, and Function p. 1
1 Consensus Structure Prediction for RNA Alignments Junilda Spirollari and Jason T. L. Wang p. 3
2 Invariant Geometric Properties of Secondary Structure Elements in Proteins Matteo Comin and Concettina Guerra and Giuseppe Zanotti p. 27
3 Discovering 3D Motifs in RNA Alberto Apostolico and Giovanni Ciriello and Concettina Guerra and Christine E. Heitsch p. 49
4 Protein Structure Classification Using Machine Learning Methods Yazhene Krishnaraj and Chandan Reddy p. 69
5 Protein Surface Representation and Comparison: New Approaches in Structural Proteomics Lee Sael and Daisuke Kihara p. 89
6 Advanced Graph Mining Methods for Protein Analysis Yi-Ping Phoebe Chen and Jia Rong and Gang Li p. 111
7 Predicting Local Structure and Function of Proteins Huzefa Rangwala and George Karypis p. 137
Part II Genomics, Transcriptomics, and Proteomics p. 161
8 Computational Approaches for Genome Assembly Validation Jeong-Hyeon Choi and Haixu Tang and Sun Kim and Mihai Pop p. 163
9 Mining Patterns of Epistasis in Human Genetics Jason H. Moore p. 187
10 Discovery of Regulatory Mechanisms from Gene Expression Variation by eQTL Analysis Yang Huang and Jie Zheng and Teresa M. Przytycka p. 205
11 Statistical Approaches to Gene Expression Microarray Data Preprocessing Megan Kong and Elizabeth McClellan and Richard H. Scheuermann and Monnie McGee p. 229
12 Application of Feature Selection and Classification to Computational Molecular Biology Paola Bertolazzi and Giovanni Felici and Giuseppe Lancia p. 257
13 Statistical Indices for Computational and Data Driven Class Discovery in Microarray Data Raffaele Giancarlo and Davide Scaturro and Filippo Utro p. 295
14 Computational Approaches to Peptide Retention Time Prediction for Proteomics Xiang Zhang and Cheolhwan Oh and Catherine P. Riley and Hyeyoung Cho and Charles Buck p. 337
Part III Functional and Molecular Interaction Networks p. 351
15 Inferring Protein Functional Linkage Based on Sequence Information and Beyond Li Liao p. 353
16 Computational Methods for Unraveling Transcriptional Regulatory Networks in Prokaryotes Dongsheng Che and Guojun Li p. 377
17 Computational Methods for Analyzing and Modeling Biological Networks Natasa Przulj and Tijana Milenkovic p. 397
18 Statistical Analysis of Biomolecular Networks Jing-Dong J. Han and Chris J. Needham p. 429
Part IV Literature, Ontology, and Knowledge Integration p. 447
19 Beyond Information Retrieval: Literature Mining for Biomedical Knowledge Discovery Javed Mostafa and Kazuhiro Seki and Weimao Ke p. 449
20 Mining Biological Interactions from Biomedical Texts for Efficient Query Answering Muhammad Abulaish and Lipika Dey and Jahiruddin p. 485
21 Ontology-Based Knowledge Representation of Experiment Metadata in Biological Data Mining Richard H. Scheuermann and Megan Kong and Carl Dahlke and Jennifer Cai and Jamie Lee and Yu Qian and Burke Squires and Patrick Dunn and Jeff Wiser and Herb Hagler and Barry Smith and David Karp p. 529
22 Redescription Mining and Applications in Bioinformatics Naren Ramakrishnan and Mohammed J. Zaki p. 561
Part V Genome Medicine Applications p. 587
23 Data Mining Tools and Techniques for Identification of Biomarkers for Cancer Mick Correll and Simon Beaulah and Robin Munro and Jonathan Sheldon and Yike Guo and Hai Hu p. 589
24 Cancer Biomarker Prioritization: Assessing the in vivo Impact of in vitro Models by in silico Mining of Microarray Database, Literature, and Gene Annotation Chia-Ju Lee and Zan Huang and Hongmei Jiang and John Crispino and Simon Lin p. 615
25 Biomarker Discovery by Mining Glycomic and Lipidomic Data Haixu Tang and Mehmet Dalkilic and Yehia Mechref p. 627
26 Data Mining Chemical Structures and Biological Data Glenn J. Myatt and Paul E. Blower p. 649
Index p. 689