Microbial Gene Essentiality: Protocols and Bioinformatics

  • Andrei L. Osterman
  • Svetlana Y. Gerdes

Part of the Methods in Molecular Biology™ book series (MIMB, volume 416)

Table of contents

  1. Front Matter
    Pages i-xiv
  2. Introduction

    1. Front Matter
      Pages 1-1
  3. Experimental Protocols

    1. Front Matter
      Pages 9-11
    2. Populational Genome-Wide Essentiality Screens

      1. William S. Reznikoff, Kelly M. Winterberg
        Pages 13-26
      2. Sandy M.S. Wong, Brian J. Akerley
        Pages 27-44
      3. Jeffrey P. Murry, Christopher M. Sassetti, James M. Lane, Zhifang Xie, Eric J. Rubin
        Pages 45-59
      4. François Sanschagrin, Irena Kukavica-Ibrulj, Roger C. Levesque
        Pages 61-82
      5. Taeok Bae, Elizabeth M. Glass, Olaf Schneewind, Dominique Missiakas
        Pages 103-116
    3. Systematic Collections of Knockout Mutants

      1. Nicole T. Liberati, Jonathan M. Urbach, Tara K. Thurber, Gang Wu, Frederick M. Ausubel
        Pages 153-169
      2. Tomoya Baba, Hsuan-Cheng Huan, Kirill Datsenko, Barry L. Wanner, Hirotada Mori
        Pages 183-194
      3. Pamela B. Meluh, Xuewen Pan, Daniel S. Yuan, Carol Tiffany, Ou Chen, Sharon Sookhai-Mahadeo et al.
        Pages 221-247
    4. Genome Minimization

      1. Tamás Fehér, Ildikó Karcagi, Zsuzsa Győrfy, Kinga Umenhoffer, Bálint Csörgő, György Pósfai
        Pages 251-259
    5. Conditional Knockouts

  4. Bioinformatics

    1. Front Matter
      Pages 335-337
    2. Statistics

    3. Data Integration and Modeling

      1. Yukiko Yamazaki, Hironori Niki, Jun-ichi Kato
        Pages 385-389
      2. Isabel Rocha, Jochen Förster, Jens Nielsen
        Pages 409-431
      3. Andrew R. Joyce, Bernhard Ø. Palsson
        Pages 433-457
      4. Andrei L. Osterman, Svetlana Y. Gerdes
        Pages 459-466
  5. Back Matter
    Pages 467-486

About this book


Microbial Gene Essentiality: Protocols and Bioinformatics contains a comprehensive collection of experimental and computational strategies and techniques for microbial genome-scale essentiality studies, developed and presented by the leading groups in the field. In addition to wet-lab protocols, the book describes (i) statistical methods essential for planning successful large-scale essentiality screens, as well for data evaluation and analysis; (ii) in-silico prediction of gene essentiality using genome-scale reconstructed metabolic models; and (iii) data integration and comparative analysis in the context of genomic databases. This volume provides researchers with a first-stop guide for choosing the most appropriate strategy for planned essentiality studies. Experimental and computational aspects are equally important in genome-scale gene essentiality analysis, as in all other genomic technologies, and Microbial Gene Essentiality: Protocols and Bioinformatics reflects both of these aspects. All protocols follow the successful Methods in Molecular Biology™ series format, each offering an introduction outlining the principles behind the techniques, step-by-step instructions, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding pitfalls, and are intended for both novice and expert scientists.


Bur Escherichia coli Genomic databases In-silico prediction Metabolic models Microarray Microbial genome-scale essentiality Mutant Mutation PCR bioinformatics chromosome genes hybridization molecular biology

Editors and affiliations

  • Andrei L. Osterman
    • 1
  • Svetlana Y. Gerdes
    • 2
  1. 1.Burnham Institute for Medical ResearchLa Jolla
  2. 2.Fellowship for Interpretation of Genomes (FIG)Burr Ridge

Bibliographic information

  • DOI
  • Copyright Information Humana Press 2008
  • Publisher Name Humana Press
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-58829-378-7
  • Online ISBN 978-1-59745-321-9
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
Industry Sectors
Chemical Manufacturing
Health & Hospitals
Consumer Packaged Goods