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Microbial Systems Biology

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Ali Navid

    1. Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, USA

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  • 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 2349)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. Parallel Accelerator and Molecular Mass Spectrometry Measurement of Carbon-14-Labeled Analytes

    • Benjamin J. Stewart, Ted J. Ognibene
    Pages 1-10

  3. Fast Sampling of the Cellular Metabolome

    • Walter M. van Gulik, Andre B. Canelas, Hilal Taymaz-Nikerel, Rutger D. Douma, Lodewijk P. de Jonge, Joseph J. Heijnen
    Pages 11-39

  4. Investigation of Protein–Lipid Interactions Using Native Mass Spectrometry

    • Xiao Cong, John W. Patrick, Yang Liu, Xiaowen Liang, Wen Liu, Arthur Laganowsky
    Pages 41-64

  5. Western Blot Processing Optimization: The Perfect Blot

    • Russ Yukhananov, David P. Chimento, Laura A. Marlow
    Pages 65-80

  6. FISHing on a Budget

    • Gable M. Wadsworth, Harold D. Kim
    Pages 81-90

  7. NanoSIP: NanoSIMS Applications for Microbial Biology

    • Jennifer Pett-Ridge, Peter K. Weber
    Pages 91-136

  8. Construction of Metatranscriptomic Libraries for 5′ End Sequencing of rRNAs for Microbiome Research

    • Marja Tiirola, Anita Mäki
    Pages 137-146

  9. Computational Approaches for Designing Highly Specific and Efficient sgRNAs

    • Jaspreet Kaur Dhanjal, Dhvani Vora, Navaneethan Radhakrishnan, Durai Sundar
    Pages 147-166

  10. Complex Network Analysis in Microbial Systems: Theory and Examples

    • André Voigt, Eivind Almaas
    Pages 167-191

  11. Prokaryotic Genome Annotation

    • Jeffrey A. Kimbrel, Brendan M. Jeffrey, Christopher S. Ward
    Pages 193-214

  12. Functional Annotation from Structural Homology

    • Brent W. Segelke
    Pages 215-257

  13. Metabolic Modeling with MetaFlux

    • Mario Latendresse, Wai Kit Ong, Peter D. Karp
    Pages 259-289

  14. Application of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, and Predict Pathways in an Isolate Genome

    • Benjamin H. Allen, Nidhi Gupta, Janaka N. Edirisinghe, José P. Faria, Christopher S. Henry
    Pages 291-320

  15. Curating COBRA Models of Microbial Metabolism

    • Ali Navid
    Pages 321-338

  16. A Beginner’s Guide to the COBRA Toolbox

    • Ali Navid
    Pages 339-365

  17. Rules of Engagement: A Guide to Developing Agent-Based Models

    • Marc Griesemer, Suzanne S. Sindi
    Pages 367-380

  18. Back Matter

    Pages 381-385
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Keywords

About this book

This second edition provides new and updated chapters describing the utility and attributes of different tools that are used for studying microbial systems. Chapters detail a number of methods, including in silico system level analyses by MetaFlux, Kbase genome-scale model builder, COBRA toolbox, NanoSIP, and PAMMS. 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, Microbial Systems Biology: Methods and Protocols, Second Edition aims to introduce and aid scientists in using the various tools that are currently available for analysis, modification, and utilization of microbial organisms.

Editors and Affiliations

  • Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, USA

    Ali Navid

Bibliographic Information

  • Book Title: Microbial Systems Biology

  • Book Subtitle: Methods and Protocols

  • Editors: Ali Navid

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1585-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-1584-3Published: 31 October 2021

  • Softcover ISBN: 978-1-0716-1587-4Published: 31 October 2022

  • eBook ISBN: 978-1-0716-1585-0Published: 30 October 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XII, 385

  • Number of Illustrations: 34 b/w illustrations, 71 illustrations in colour

  • Topics: Microbiology, Bioinformatics

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