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Modeling Transcriptional Regulation

Methods and Protocols

Editors:

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2328)

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-xi
  2. Co-expression Networks in Predicting Transcriptional Gene Regulation

    • Synan F. AbuQamar, Khaled A. El-Tarabily, Arjun Sham
    Pages 1-11
  3. Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks

    • Tomás C. Moyano, Rodrigo A. Gutiérrez, José M. Alvarez
    Pages 25-46
  4. Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap for Analysis, Visualization, and Key Gene Identification

    • Ryan Spurney, Michael Schwartz, Mariah Gobble, Rosangela Sozzani, Lisa Van den Broeck
    Pages 47-65
  5. Dynamic Modeling of Transcriptional Gene Regulatory Networks

    • Joanna E. Handzlik, Yen Lee Loh, Manu
    Pages 67-97
  6. Multiscale Modeling of Cross-Regulatory Transcript and Protein Influences

    • Megan L. Matthews, Cranos M. Williams
    Pages 115-138
  7. Biological Network Mining

    • Zongliang Yue, Da Yan, Guimu Guo, Jake Y. Chen
    Pages 139-151
  8. Identification of Gene Regulatory Networks from Single-Cell Expression Data

    • Song Li, Haidong Yan, Jiyoung Lee
    Pages 153-170
  9. Inference of Gene Regulatory Network from Single-Cell Transcriptomic Data Using pySCENIC

    • Nilesh Kumar, Bharat Mishra, Mohammad Athar, Shahid Mukhtar
    Pages 171-182
  10. Modeling Immune Dynamics in Plants Using JIMENA-Package

    • Özge Osmanoglu, Shabana Shams, Thomas Dandekar, Muhammad Naseem
    Pages 183-189
  11. Dynamic Regulatory Event Mining by iDREM in Large-Scale Multi-omics Datasets During Biotic and Abiotic Stress in Plants

    • Bharat Mishra, Nilesh Kumar, Jinbao Liu, Karolina M. Pajerowska-Mukhtar
    Pages 191-202
  12. A Semi-In Vivo Transcriptional Assay to Dissect Plant Defense Regulatory Modules

    • Fatimah Aljedaani, Naganand Rayapuram, Ikram Blilou
    Pages 203-214
  13. Assessing Global Circadian Rhythm Through Single-Time-Point Transcriptomic Analysis

    • Xingwei Wang, Yufeng Xu, Mian Zhou, Wei Wang
    Pages 215-225
  14. In Silico Prediction for ncRNAs in Prokaryotes

    • Amanda Carvalho Garcia
    Pages 277-285

About this book

This book provides methods and techniques used in construction of global transcriptional regulatory networks in diverse systems, various layers of gene regulation and mathematical as well as computational modeling of transcriptional gene regulation. 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.

 

Authoritative and cutting-edge, Modeling Transcriptional Regulation: Methods and Protocols aims to provide an in depth understanding of new techniques in transcriptional gene regulation for specialized audience.

Editors and Affiliations

  • Department of Biology, University of Alabama, Birmingham, USA

    SHAHID MUKHTAR

Bibliographic Information

  • Book Title: Modeling Transcriptional Regulation

  • Book Subtitle: Methods and Protocols

  • Editors: SHAHID MUKHTAR

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1534-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-1533-1Published: 13 July 2021

  • Softcover ISBN: 978-1-0716-1536-2Published: 14 July 2022

  • eBook ISBN: 978-1-0716-1534-8Published: 12 July 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 307

  • Number of Illustrations: 45 b/w illustrations, 59 illustrations in colour

  • Topics: Genetics and Genomics

Buy it now

Buying options

eBook USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access