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Modeling transcriptional regulation : methods and protocols Cover Image Book Book

Modeling transcriptional regulation : methods and protocols

Mukhtar, Shahid M. (Added Author).

Summary: 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.

Record details

  • ISBN: 9781071615331 (hardcover)
  • Physical Description: print
    xi, 307 pages : illustrations (some color), charts (some color) ; 27 cm.
  • Publisher: New York, NY : Humana Press, [2021]

Content descriptions

General Note:
Includes index.
Formatted Contents Note: Co-expression Networks in Predicting Transcriptional Gene Regulation -- Inference of Gene Coexpression Networks from Bulk-based RNA-Sequencing Data -- Genomic Footprinting Analyses from DNase-seq data to Construct Gene Regulatory Networks -- Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap For Analysis, Visualization, and Key Gene Identification -- Dynamic Modeling of Transcriptional Gene Regulatory Networks -- Mathematical Programming for Modelling Expression of a Gene using Gurobi Optimizer to Identify its Transcriptional Regulators -- Multiscale Modeling of Cross-Regulatory Transcript and Protein Influences -- Biological Network Mining -- Identification of Gene Regulatory Networks from Single-Cell Expression Data -- Inference of Gene Regulatory Network From Single-Cell Transcriptomic Data using pySCENIC -- Modeling Immune Dynamics in Plants using JIMENA-package -- Dynamic Regulatory Event Mining by iDREM in Large Scale Multi-Omics Datasets during Biotic and Abiotic Stress in Plants -- A semi-in vivo Transcriptional Assay to Dissect Plant Defense Regulatory Modules -- Assessing Global Circadian Rhythm through Single-Time-Point Transcriptomic Analysis -- High-throughput Targeted Transcriptional Profiling of Defense Genes using RNA-mediated oligonucleotide Annealing, Selection, and Ligation with next-generation sequencing in Arabidopsi -- Rapid Validation of Transcriptional Enhancers Using a Transient Reporter Assay -- Computational Identification of ceRNA and Reconstruction of ceRNA Regulatory Network Based on RNA-seq and Small RNA-seq Data in Plants -- In Silico Prediction for ncRNAs in Prokaryotes -- Mathematical Linear Programming to Model MicroRNAs-Mediated Gene Regulation Using Gurobi Optimizer.

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Subject: Genetic transcription -- Regulation
Genetic regulation -- Mathematical models
Genre: Laboratory manuals.

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Available copies

  • 2 of 2 copies available at University College of the North Libraries.

Holds

  • 0 current holds with 2 total copies.
Show Only Available Copies
Location Call Number / Copy Notes Barcode Shelving Location Holdable? Status Due Date
The Pas Campus Library QH 450.2 .M63 2021 (Text) 58500001128032 Stacks Volume hold Available -
UCN/Norway House Public Library QH450.2.M63 2021 (Text) 58500001128024 Stacks Volume hold Available -
► Summaries & More
▼ Additional Content
Preface v
Contributors ix
1 Co-expression Networks in Predicting Transcriptional Gene Regulation
1(12)
Synan F. AbuQamar
Khaled A. El-Tarabily
Arjun Sham
2 Inference of Gene Coexpression Networks from Bulk-Based RNA-Sequencing Data
13(12)
Alicia T. Lamere
3 Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks
25(22)
Tomds C. Moyano
Rodrigo A. Gutierrez
Jose M. Alvarez
4 Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap for Analysis, Visualization, and Key Gene Identification
47(20)
Ryan Spurney
Michael Schwartz
Mariah Gobble
Rosangela Sozzani
Lisa Van den Broeck
5 Dynamic Modeling of Transcriptional Gene Regulatory Networks
67(32)
Joanna E. Handzlik
Yen Lee Loh
Manu
6 Mathematical Programming for Modeling Expression of a Gene Using Gurobi Optimizer to Identify Its Transcriptional Regulators
99(16)
Vijaykumar Yogesh Muley
7 Multiscale Modeling of Cross-Regulatory Transcript and Protein Influences
115(24)
Megan L. Matthews
Cranos M. Williams
8 Biological Network Mining
139(14)
Zongliang Yue
Da Yan
Guimu Guo
Jake T. Chen
9 Identification of Gene Regulatory Networks from Single-Cell Expression Data
153(18)
Song Li
Haidong Tan
Jiyoung Lee
10 Inference of Gene Regulatory Network from Single-Cell Transcriptomic Data Using pySCENIC
171(12)
Nilesh Kumar
Bharat Mishra
Mohammad Athar
Shahid Mukhtar
11 Modeling Immune Dynamics in Plants Using JIMENA-Package
183(8)
Ozge Osmanoglu
Shabana Shams
Thomas Dandekar
Muhammad Naseem
12 Dynamic Regulatory Event Mining by iDREM in Large-Scale Multi-omics Datasets During Biotic and Abiotic Stress in Plants
191(12)
Bharat Mishra
Nilesh Kumar
Jinbao Liu
Karolina M. Pajerowska-Mukhtar
13 A Semi-In Vivo Transcriptional Assay to Dissect Plant Defense Regulatory Modules
203(12)
Fatimah Aljedaani
Naganand Rayapuram
Ikram Blilou
14 Assessing Global Circadian Rhythm Through Single-Time-Point Transcriptomic Analysis
215(12)
Xingwei Wang
Yufeng Xu
Mian Zhou
Wei Wang
15 High-Throughput Targeted Transcriptional Profiling of Defense Genes Using RNA-Mediated Oligonucleotide Annealing, Selection, and Ligation with Next-Generation Sequencing in Arabidopsis
227(26)
Sung-Il Kim
Togendra Bordiya
Ji-Chul Nam
Jose Mayorga
Hong-Gu Rang
16 Rapid Validation of Transcriptional Enhancers Using a Transient Reporter Assay
253(8)
Yuan Lin
Jiming Jiang
17 Computational Identification of ceRNA and Reconstruction of ceRNA Regulatory Network Based on RNA-seq and Small RNA-seq Data in Plants
261(16)
Xiangyuan Wan
Ziwen Li
18 In Silico Prediction for ncRNAs in Prokaryotes
277(10)
Amanda Carvalho Garcia
19 Mathematical Linear Programming to Model MicroRNAs-Mediated Gene Regulation Using Gurobi Optimizer
287
Vijaykumar Yogesh Muley
Correction to: Inference of Gene Regulatory Network from Single-Cell Transcriptomic Data Using pySCENIC 1(302)
Index 303

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