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 Smaïl-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
László Patthy10. 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
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, François 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
Mónica Chagoyen, Javier López-Ibáñez, 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 Vlahoviček
27. Big Data in Plant Science: Resources and Data Mining Tools for Plant Genomics and Prote
