Part I: Bioinformatics 1. Predicting RNA Structure with Vfold Chenhan Zhao, Xiaojun Xu, and Shi-Jie Chen 2. RNA Function Prediction Yongsheng Li, Juan Xu, Tingting Shao, Yunpeng Zhang, Hong Chen, and Xia Li 3. Computational Prediction of Novel miRNAs from Genome-Wide Data Georgina Stegmayer, Cristian Yones, Laura Kamenetzky, Natalia Macchiaroli, and Diego H. Milone 4. Protein Structure Modeling with MODELLER Benjamin Webb and Andrej Sali 5. Protein Function Prediction Leonardo Magalhaes Cruz, Sheyla Trefflich, Vinicius Almir Weiss, and Mauro Antonio Alves Castro Part II: DNA Analysis 6. Capturing Three-Dimensional Genome Organization in Individual Cells by Single-Cell Hi-C Takashi Nagano, Steven W. Wingett, and Peter Fraser 7. Genome-Wide Cell Type-Specific Mapping of In Vivo Chromatin Protein Binding Using an FLP-Inducible DamID System in Drosophila Alexey V. Pindyurin 8. DNA Methylation Profiling Using Long-Read Single-Molecule Real-Time Bisulfite Sequencing (SMRT-BS) Yao Yang and Stuart A. Scott 9. Copy Number Variation Analysis by Droplet Digital PCR Suvi K. Harmala, Robert Butcher, and Chrissy H. Roberts 10. MicroScale Thermophoresis: A Rapid and Precise Method to Quantify Protein-Nucleic Acid Interactions in Solution Adrian Michael Muller, Dennis Breitsprecher, Stefan Duhr, Philipp Baaske, Thomas Schubert, and Gernot Langst 11. Establishment of the CRISPR/Cas9 System for Targeted Gene Disruption and Gene Tagging Eric Ehrke-Schulz, Maren Schiwon, Claudia Hagedorn, and Anja Ehrhardt Part III: RNA Analysis 12. Holistic and Affordable Analyses of MicroRNA Expression Profiles Using Tagged cDNA Libraries and a Multiplex Sequencing Strategy Patrick P. Weil, Yan Jaszczyszyn, Anne Baroin-Tourancheau, Jan Postberg, and Laurence Amar 13. MicroRNA Expression Analysis Using Small RNA Sequencing Discovery and RT-qPCR-Based Validation Alan Van Goethem, Pieter Mestdagh, Tom Van Maerken, and Jo Vandesompele 14. Using Firefly(R) Particle Technology for Multiplex MicroRNA Profiling Without RNA Purification Michael R. Tackett and Izzudin Diwan 15. Multiplex Real-Time PCR Using Encoded Microparticles for MicroRNA Profiling Seungwon Jung and Sang Kyung Kim 16. Optimized Whole Transcriptome Profiling of Motor Axons Lena Saal, Michael Briese, and Michael Sendtner Part IV: Protein Analysis 17. 2D-DIGE in Proteomics Matias Pasquali, Tommaso Serchi, Sebastien Planchon, and Jenny Renaut 18. STAGE-Diging in Proteomics Paolo Soffientini and Angela Bachi 19. Protein Arrays I: Antibody Arrays Yulin Yuan, Zuan-Tao Lin, Hongting Wang, Xia Hong, Mikala Heon, and Tianfu Wu 20. Protein Arrays II: Antigen Arrays Yulin Yuan, Hongting Wang, Zuan-Tao Lin, Xia Hong, Mikala Heon, and Tianfu Wu 21. Protein Arrays III: Reverse-Phase Protein Arrays Yulin Yuan, Xia Hong, Zuan-Tao Lin, Hongting Wang, Mikala Heon, and Tianfu Wu 22. Isolation of Exosomes for the Purpose of Protein Cargo Analysis with the Use of Mass Spectrometry Monika Pietrowska, Sonja Funk, Marta Gawin, Lukasz Marczak, Agata Abramowicz, Piotr Widlak, and Theresa Whiteside Part V: From Genotype to Phenotype 23. Virus-Induced Gene Silencing (VIGS) and Foreign Gene Expression in Pisum sativum L. Using the 'One-Step' Bean pod mottle virus (BPMV) Viral Vector Chouaib Meziadi, Sophie Blanchet, Valerie Geffroy, and Stephanie Pflieger 24. Re-Expressing Epigenetically Silenced Genes by Inducing DNA Demethylation through Targeting of Ten-Eleven Translocation 2 to Any Given Genomic Locus Julio Cesar Rendon, David Cano-Rodriguez, and Marianne G. Rots 25. Knockdown of Rice MicroRNA166 by Short Tandem Target Mimic (STTM) Sachin Teotia, Dabing Zhang, and Guiliang Tang 26. RNAi-Mediated Knockdown of Protein Expression Volker Baumann, Cornelia Lorenzer, Michael Thell, Anna-Maria Winkler, and Johannes Winkler 27. Engineered Zinc Finger DNA-Binding Domains: Synthesis, Assessment of DNA-Binding Affinity, and Direct Protein Delivery to Mammalian Cells Mir A. Hossain, Isaac J. Knudson, Shaleen Thakur, Yong Shen, Jared R. Stees, Joeva J. Barrow, and Jorg Bungert 28. Production, Purification, and Titration of First-Generation Adenovirus Vectors Ramona F. Kratzer and Florian Kreppel
