Data Mining Techniques for the Life Sciences

Part I: Data Basses 1. Update on Genomic Databases and Resources at the National Center for Biotechnology Information Tatiana Tatusova 2. Protein Structure Databases Roman A. Laskowski 3. The MIntAct Project and Molecular Interaction Databases Luana Licata and Sandra Orchard 4. Applications of Protein Thermodynamic Database for Understanding Protein Mutant Stability and Designing Stable Mutants M. Michael Gromiha, P. Anoosha, and Liang-Tsung Huang 5. Classification and Exploration of 3D Protein Domain Interactions using Kbdock Anisah W. Ghoorah, Marie-Dominique Devignes, Malika Smail-Tabbone, David W. Ritchie 6. Data Mining of Macromolecular Structures Bart van Beusekom, Anastassis Perrakis, and Robbie P. Joosten 7. Criteria to Extract High Quality Protein Data Bank Subsets for Structure Users Oliviero Carugo and Kristina Djinovic-Carugo 8. Homology-based Annotation of Large Protein Datasets Marco Punta and Jaina Mistry PART II: Computational Techniques 9. Identification and Correction Of Erroneous Protein Sequences in Public Databases Laszlo Patthy 10. Improving the Accuracy of Fitted Atomic Models in Cryo-EM Density Maps Of Protein Assemblies Using Evolutionary Information From Aligned Homologous Proteins Ramachandran Rakesh and Narayanaswamy Srinivasan 11. Systematic Exploration of an Efficient Amino Acid Substitution Matrix, MIQS Kentaro Tomii and Kazunori Yamada 12. Promises and Pitfalls of High Throughput Biological Assays"/p> Greg Finak and Raphael Gottardo 13. Optimizing RNA-seq Mapping with STAR Alexander Dobin and Thomas R. Gingeras PART III: Prediction Methods 14. Predicting Conformational Disorder Philippe Lieutaud, Francois Ferron, and Sonia Longhi 15. Classification of Protein Kinases Influenced By Conservation of Substrate Binding Residues Chintalapati Janaki, Narayanaswamy Srinivasan, Malini Manoharan 16. Spectral-Statistical Approach for Revealing Latent Regular Structures in DNA Sequence Maria Chaley and Vladimir Kutyrkin 17.Protein Crystallizability Pawel Smialowski and Philip Wong 18. Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments using ngs.plot Yong-Hwee Eddie Loh, and Li Shen 19. Dataming with ontologies Robert Hoehndorft, Georgios V. Gkoutos, and Paul N. Schofield 20. Functional Analysis of Metabolomics Data Monica Chagoyen, Javier Lopez-Ibanez, and Florencio Pazos < 21. Bacterial Genomics Data Analysis in the Next-Generation Sequencing Era Massimiliano Orsini, Gianmauro Cuccuru, Paolo Uva, and Giorgio Fotia 22. A Broad Overview of Computational Methods for Predicting the Pathophysiological Effects of Non-Synonymous Variants Stefano Castellana, Caterina Fusilli, and Tommaso Mazza 23. Recommendation Techniques for Drug-Target Interaction Prediction and Drug-Repositioning Salvatore Alaimo, Rosalba Giugno, and Alfredo Pulvirenti 24. Protein Residue Contacts and Prediction Methods Badri Adhikari and Jianlin Cheng 25. The Recipe for Protein Sequence-Based Function Prediction and its Implementation in the Annotator Software Environment Birgit Eisenhaber, Durga Kuchibhatla, Westley Sherman, Fernanda L. Sirota, Igor N. Berezovsky, Wing-Cheong Wong, and Frank Eisenhaber Part IV: Big Data 26. Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles Maja Fabijanic and Kristian Vlahovicek 27. Big Data in Plant Science: Resources and Data Mining Tools for Plant Genomics and Proteomics George V. Popescu, Christos Noutsos, and Sorina C. Popescu