Functional Genomics

Part I: Bioinformatics1. Prediction of Protein Tertiary Structures using MUFOLDJingfen Zhang, Zhiquan He, Qingguo Wang, Bogdan Barz, Ioan Kosztin, Yi Shang, and Dong Xu2. Prediction of Protein Functions Roy D. Sleator3. Genome Wide Screens for Expressed Hypothetical ProteinsClaus Desler, Jon Ambaek Durhuus and Lene Juel Rasmussen4. Self Custom-Made SFP Arrays for Non-Model OrganismsRon Ophir and Amir ShermanPart II: DNA Analysis5. Construction and Analysis of Full-length and Normalized cDNA Libraries from CitrusM Carmen Marques and Miguel A Perez-Amador 6. Assembling Linear DNA Templates for In vitro Transcription and TranslationViktor Stein, Miriam Kaltenbach and Florian Hollfelder7. Automated Computational Analysis of Genome-wide DNA Methylation Profiling Data from HELP-tagging AssaysQiang Jing, Andrew McLellan, John M. Greally and Masako SuzukiPart III: RNA Analysis 8. Detecting of RNA Editing Events in Human Cells using High-Throughput SequencingIouri Chepelev9. Comparative Study of Differential Gene Expression in Closely Related Bacterial Species by Comparative HybridizationRuisheng An and Parwinder S. Grewal10. Whole Genome RT-qPCR MicroRNA Expression ProfilingPieter Mestdagh, Stefaan Derveaux, Jo Vandesompele11. Using Quantitative Real-Time Reverse Transcriptase Polymerase Chain Reaction to Validate Gene Regulation by PTTGSiva Kumar Panguluri and Sham S. Kakar12. FRET-Based Real-Time DNA MicroarraysArjang Hassibi, Haris Vikalo, Jose Riechmann and Babak HassibiPart IV: Protein Analysis I: Quantification and Indentification 13. 2-D Gel Electrophoresis: Constructing 2D-Gel Proteome Reference MapsMaria Paola Simula, Agata Notarpietro, Giuseppe Toffoli, and Valli De Re14. The Use of Antigen Microarrays in Antibody Profiling Krisztian Papp and Jozsef Prechl15. Limited Proteolysis in Proteomics using Protease-immobilized Microreactors Hiroshi Yamaguchi, Masaya Miyazaki and Hideaki Maeda16. Mass Spectrometry for Protein Quantification in Biomarker DiscoveryMu Wang and Jinsam YouPart V: Protein Analysis II: Functional Characterization17. High-throughput Microtitre Plate-based Assay for DNA TopoisomerasesJames A Taylor, Nicolas P Burton and Anthony Maxwell18. Microscale Thermophoresis as a Sensitive Method to Quantify Protein-Nucleic Acid Interactions in SolutionsKarina Zillner, Moran Jerabek-Willemsen, Stefan Duhr, Dieter Braun, Gernot Langst and Philipp Baaske19 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. Muntau20 LuMPIS - Luciferase-based MBP-pull-down Protein Interaction Screening System Maria G. Vizoso Pinto and Armin Baiker21 Yeast Two-Hybrid Screens: Improvement of Array-based Screening Results by N- and C-terminally Tagged Fusion ProteinsThorsten Stellberger, Roman Hauser, Peter Uetz, and Albrecht von Brunn22. Inducible microRNA-mediated Knockdown of the Endogenous Human Lamin A/C GeneIna Weidenfeld23. Multiple-gene Silencing using Antisense RNAs in Escherichia ColiNobutaka Nakashima, Shan Goh, Liam Good and Tomohiro Tamura24. Functional Screen of Zebrafish Deubiquitylating Enzymes by Morpholino Knockdown and in Situ HybridizationWilliam Ka Fai Tse and Yun-Jin Jiang25. Silencing of Gene Expression by Gymnotic Delivery of Antisense OligonucleotidesHarris S. Soifer, Troels Koch, Johnathan Lai, Bo Hansen, Anja Hoeg, Henrik Oerum and C.A. Stein26. Polycistronic Expression of Interfering RNAs and RNA Plymerase III PromotersLaura F. Steel and Viraj R. SanghviPart VI: Metabolite Analysis27. Metabolite Analysis of Cannabis sativa L. by NMR SpectroscopyIsvett Josefina Flores-Sanchez, Young Hae Choi and Robert Verpoorte28. Metabolome Analysis of Grame-positive Bacteria such as Staphylococcus aureus by GC-MS and LC MSManuel Liebeke, Kirsten Dorries, Hanna Meyer and Micheal Lalk29. Metabolic Fingerprinting Using Comprehensive Two-dimensional Gas Chromatography-Time-of-Flight Mass Spectrometry(GCxGX-TOF-MS)Martin F. Almstetter, Peter J. Oefner, and Katja Dettmer