Data Mining Techniques for the Life Sciences (2^nd Ed., Softcover reprint of the original 2nd ed. 2016) Methods in Molecular Biology Series, Vol. 1415

This volume details several important databases and data mining tools. Data Mining Techniques for the Life Sciences, Second Edition guides readers through archives of macromolecular three-dimensional structures, databases of protein-protein interactions, thermodynamics information on protein and mutant stability, ?Kbdock? protein domain structure database, PDB_REDO databank, erroneous sequences, substitution matrices, tools to align RNA sequences, interesting procedures for kinase family/subfamily classifications, new tools to predict protein crystallizability, metabolomics data, drug-target interaction predictions, and a recipe for protein-sequence-based function prediction and its implementation in the latest version of the ANNOTATOR software suite. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Data Mining Techniques for the Life Sciences, Second Editionaims to ensure successful results in the further study of this vital field.

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

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

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

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

Chintalapati Janaki,Narayanaswamy Srinivasan, MaliniManoharan

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  

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

Badri Adhikari and Jianlin Cheng

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 Fabijanić and Kristian Vlahoviček

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

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts

Includes supplementary material: sn.pub/extras