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Functional Genomics

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Michael Kaufmann

    1. Chair of Biochemistry and Molecular Medicine, Division of Functional Genomics, Faculty of Health, School of Medicine, Center for Biochemical Research and Education ZBAF, Witten/Herdecke University, Witten, Germany

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  2. Claudia Klinger

    1. Chair of Biochemistry and Molecular Medicine, Division of Functional Genomics, Faculty of Health, School of Medicine, Center for Biochemical Research and Education ZBAF, Witten/Herdecke University, Witten, Germany

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    You can also search for this editor in PubMed   Google Scholar

  3. Andreas Savelsbergh

    1. Chair of Biochemistry and Molecular Medicine, Division of Functional Genomics, Faculty of Health, School of Medicine, Center for Biochemical Research and Education ZBAF, Witten/Herdecke University, Witten, Germany

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    You can also search for this editor in PubMed   Google Scholar

  • Includes fully updated, cutting-edge techniques for the study of functional genomics
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1654)

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Table of contents (28 protocols)

  1. Front Matter

    Pages i-xv
    Download chapter PDF

  2. Bioinformatics

    1. Front Matter

      Pages 1-1
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    2. Predicting RNA Structure with Vfold

      • Chenhan Zhao, Xiaojun Xu, Shi-Jie Chen
      Pages 3-15

    3. RNA Function Prediction

      • Yongsheng Li, Juan Xu, Tingting Shao, Yunpeng Zhang, Hong Chen, Xia Li
      Pages 17-28

    4. Computational Prediction of Novel miRNAs from Genome-Wide Data

      • Georgina Stegmayer, Cristian Yones, Laura Kamenetzky, Natalia Macchiaroli, Diego H. Milone
      Pages 29-37

    5. Protein Structure Modeling with MODELLER

      • Benjamin Webb, Andrej Sali
      Pages 39-54

    6. Protein Function Prediction

      • Leonardo Magalhães Cruz, Sheyla Trefflich, Vinícius Almir Weiss, Mauro Antônio Alves Castro
      Pages 55-75

  3. DNA Analysis

    1. Front Matter

      Pages 77-77
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    2. Capturing Three-Dimensional Genome Organization in Individual Cells by Single-Cell Hi-C

      • Takashi Nagano, Steven W. Wingett, Peter Fraser
      Pages 79-97

    3. Genome-Wide Cell Type-Specific Mapping of In Vivo Chromatin Protein Binding Using an FLP-Inducible DamID System in Drosophila

      • Alexey V. Pindyurin
      Pages 99-124

    4. DNA Methylation Profiling Using Long-Read Single Molecule Real-Time Bisulfite Sequencing (SMRT-BS)

      • Yao Yang, Stuart A. Scott
      Pages 125-134

    5. Copy Number Variation Analysis by Droplet Digital PCR

      • Suvi K. Härmälä, Robert Butcher, Chrissy H. Roberts
      Pages 135-149

    6. MicroScale Thermophoresis: A Rapid and Precise Method to Quantify Protein–Nucleic Acid Interactions in Solution

      • Adrian Michael Mueller, Dennis Breitsprecher, Stefan Duhr, Philipp Baaske, Thomas Schubert, Gernot Längst
      Pages 151-164

    7. Establishment of the CRISPR/Cas9 System for Targeted Gene Disruption and Gene Tagging

      • Eric Ehrke-Schulz, Maren Schiwon, Claudia Hagedorn, Anja Ehrhardt
      Pages 165-176

  4. RNA Analysis

    1. Front Matter

      Pages 177-177
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    2. 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, Laurence Amar
      Pages 179-196

    3. MicroRNA Expression Analysis Using Small RNA Sequencing Discovery and RT-qPCR-Based Validation

      • Alan Van Goethem, Pieter Mestdagh, Tom Van Maerken, Jo Vandesompele
      Pages 197-208

    4. Using FirePlex™ Particle Technology for Multiplex MicroRNA Profiling Without RNA Purification

      • Michael R. Tackett, Izzuddin Diwan
      Pages 209-219

    5. Multiplex Real-Time PCR Using Encoded Microparticles for MicroRNA Profiling

      • Seungwon Jung, Sang Kyung Kim
      Pages 221-230

    6. Optimized Whole Transcriptome Profiling of Motor Axons

      • Lena Saal-Bauernschubert, Michael Briese, Michael Sendtner
      Pages 231-241
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Keywords

About this book

Reflecting developments in genome editing, this third edition volume fully updates a collection of key techniques for the study of functional genomics. The book is broken up into sections on bioinformatics, DNA, RNA, and protein analysis, as well as a closing section entitled “From Genotype to Phenotype.” 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.

Updated and authoritative, Functional Genomics: Methods and Protocols, Third Edition seeks to aid scientists in establishing or extending technologies and techniques in their laboratories.

Editors and Affiliations

  • Chair of Biochemistry and Molecular Medicine, Division of Functional Genomics, Faculty of Health, School of Medicine, Center for Biochemical Research and Education ZBAF, Witten/Herdecke University, Witten, Germany

    Michael Kaufmann, Claudia Klinger, Andreas Savelsbergh

Bibliographic Information

  • Book Title: Functional Genomics

  • Book Subtitle: Methods and Protocols

  • Editors: Michael Kaufmann, Claudia Klinger, Andreas Savelsbergh

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7231-9

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2017

  • Hardcover ISBN: 978-1-4939-7230-2Published: 07 October 2017

  • Softcover ISBN: 978-1-4939-8424-4Published: 14 August 2018

  • eBook ISBN: 978-1-4939-7231-9Published: 07 October 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 3

  • Number of Pages: XV, 392

  • Number of Illustrations: 23 b/w illustrations, 51 illustrations in colour

  • Topics: Human Genetics

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