Kaufmann M., Klinger C. (Eds.). Functional Genomics: Methods and Protocols

Humana Press, 2012. - 435 p.
Over the last decade Life Science has undergone an accelerated evolution, culminating in the -omics era characterized by the development of a multitude of high throughput methods that are becoming more routinely applied in biochemistry labs. In Functional Genomics: Methods and Protocols, Second Edition expert researchers in the field detail many of the methods which are now commonly used for studies in the life sciences focusing on the dynamic aspects of the transcriptome, proteome and metabolome, respectively.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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Functional Genomics: Methods and Protocols, Second Edition seeks to aid scientists in establishing or extending technologies and techniques in their laboratories.Bioinformatics
Prediction of Protein Tertiary Structures Using MUFOLD
Prediction of Protein Functions
Genome-Wide Screens for Expressed Hypothetical Proteins
Self-Custom-Made SFP Arrays for Nonmodel Organisms
DNA Analysis
Construction and Analysis of Full-Length and Normalized cDNA Libraries from Citrus
Assembling Linear DNA Templates for In Vitro Transcription and Translation
Automated Computational Analysis of Genome-Wide DNA Methylation Profiling Data from HELP-Tagging Assays
RNA Analysis
Detection of RNA Editing Events in Human Cells Using High-Throughput Sequencing
Comparative Study of Differential Gene Expression in Closely Related Bacterial Species by Comparative Hybridization
Whole-Genome RT-qPCR MicroRNA Expression Profiling
Using Quantitative Real-Time Reverse Transcriptase Polymerase Chain Reaction to Validate Gene Regulation by PTTG
FRET-Based Real-Time DNA Microarrays
Protein Analysis I: Quantification and Identification
2-D Gel Electrophoresis: Constructing 2D-Gel Proteome Reference Maps
The Use of Antigen Microarrays in Antibody Profiling
Limited Proteolysis in Proteomics Using Protease-Immobilized Microreactors
Mass Spectrometry for Protein Quantification in Biomarker Discovery
Protein Analysis II: Functional Characterization
High-Throughput Microtitre Plate-Based Assay for DNA Topoisomerases
Microscale Thermophoresis as a Sensitive Method to Quantify Protein: Nucleic Acid Interactions in Solution
Bioluminescence Resonance Energy Transfer: An Emerging Tool for the Detection of Protein–Protein Interaction in Living Cells
LuMPIS: Luciferase-Based MBP-Pull-Down Protein Interaction Screening System
Yeast Two-Hybrid Screens: Improvement of Array-Based Screening Results by N- and C-terminally Tagged Fusion Proteins
Inducible microRNA-Mediated Knockdown of the Endogenous Human Lamin A/C Gene
Multiple-Gene Silencing Using Antisense RNAs in Escherichia coli
Functional Screen of Zebrafish Deubiquitylating Enzymes by Morpholino Knockdown and In Situ Hybridization
Silencing of Gene Expression by Gymnotic Delivery of Antisense Oligonucleotides
Polycistronic Expression of Interfering RNAs from RNA Polymerase III Promoters
Metabolite Analysis
Metabolite Analysis of Cannabis sativa L. by NMR Spectroscopy
Metabolome Analysis of Gram-Positive Bacteria such as Staphylococcus aureus by GC-MS and LC-MS
Metabolic Fingerprinting Using Comprehensive Two-Dimensional Gas Chromatography – Time-of-Flight Mass Spectrometry