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.

Methods in Molecular Biology Functional Genomics, 2nd Edition   1    Bioinformatics 1.      Prediction of Protein Tertiary Structures using MUFOLD         Jingfen Zhang, Zhiquan He, Qingguo Wang, Bogdan Barz, Ioan Kosztin, Yi Shang, and Dong Xu 2       Prediction of Protein Functions          Roy D. Sleator 3       Genome Wide Screens for Expressed Hypothetical Proteins         Claus Desler, Jon Ambaek Durhuus and Lene Juel Rasmussen 4        Self Custom-Made SFP Arrays for Non-Model Organisms         Ron Ophir and Amir Sherman   2    DNA Analysis 5       Construction and Analysis of Full-length and Normalized cDNA Libraries from Citrus         M Carmen Marques and Miguel A Perez-Amador 6       Assembling Linear DNA Templates for in vitro Transcription and Translation          Viktor Stein, Miriam Kaltenbach and Florian Hollfelder 7       Automated Computational Analysis of Genome-wide DNA Methylation Profiling Data              from HELP-tagging Assays         Qiang Jing, Andrew McLellan, John M. Greally and Masako Suzuki   3    RNA Analysis 8          Detection of RNA Editing Events in Human Cells using High- Throughput    Sequencing         Iouri Chepelev 9          Comparative Study of Differential Gene Expression in Closely Related Bacterial     Species by Comparative Hybridization         Ruisheng An and Parwinder S. Grewal 10        Whole Genome RT-qPCR MicroRNA Expression Profiling Pieter Mestdagh, Stefaan Derveaux, Jo Vandesompele 11        Using Quantitative Real-Time Reverse Transcriptase Polymerase Chain Reaction to     Validate Gene Regulation by PTTG          Siva Kumar Panguluri and Sham S. Kakar 12     FRET-Based Real-Time DNA Microarrays         Arjang Hassibi, Haris Vikalo, Jose Luis Riechmann and Babak Hassibi   4    Protein Analysis I: Quantification and Identification 13        2-D Gel Electrophoresis: Constructing 2D-Gel Proteome Reference Maps         Maria Paola Simula, Agata Notarpietro, Giuseppe Toffoli and Valli De Re 14    The use of Antigen Microarrays in Antibody Profiling          Krisztian Papp and Jozsef Prechl 15     Limited Proteolysis in Proteomics using Protease-immobilized Microreactors         Hiroshi Yamaguchi, Masaya Miyazaki and Hideaki Maeda 16     Mass Spectrometry for Protein Quantification in Biomarker Discovery          Mu Wang and Jinsam You   5    Protein Analysis II: Functional Characterization 17      High-throughput Microtitre Plate-based Assay for DNA Topoisomerases James A Taylor, Nicolas P Burton and Anthony Maxwell 18        Microscale Thermophoresis as a Sensitive Method to Quantify Protein - Nucleic    Acid Interactions in Solution         Karina Zillner, Moran Jerabek-Willemsen, Stefan Duhr, Dieter Braun, Gernot Längst and Philipp Baaske 19    Bioluminescence Resonance Energy Transfer: an Emerging Tool for the Detection of        Protein-protein Interaction in Living Cells          Soren W. Gersting, Amelie S. Lotz-Havla and Ania C. Muntau 20    LuMPIS - Luciferase-based MBP-pull-down Protein Interaction Screening System          María G. Vizoso Pinto and Armin Baiker 21   Yeast Two-Hybrid Screens: Improvement of Array-based Screening Results by N- and    C-terminally Tagged Fusion Proteins          Thorsten Stellberger, Roman Häuser, Peter Uetz and Albrecht von Brunn 22        Inducible microRNA-mediated Knockdown of the Endogenous Human Lamin A/C GeneIna Weidenfeld 23     Multiple-gene Silencing using Antisense RNAs in Escherichia coli Nobutaka Nakashima, Shan Goh, Liam Good and Tomohiro Tamura 24        Functional Screen of Zebrafish Deubiquitylating Enzymes by Morpholino Knockdown     and in situ Hybridization William Ka Fai Tse and Yun-Jin Jiang 25        Silencing of Gene Expression by Gymnotic Delivery of Antisense Oligonucleotides         Harris S. Soifer, Troels Koch, Johnathan Lai, Bo Hansen, Anja Hoeg, ...