Part I: Sample Prepartion and Identification

1. Flow Cytometry in Environmental Microbiology: A Rapid
Approach for the Isolation of Single-Cells for Advanced Molecular Biology Analysis

Ferrari BC., Winsley T., Bergquist PL. and van Dorst, J.

2. Pressure Cycling Technology in Systems Biology

Bradford S. Powell, Alexander V. Lazarev, Greta Carlson, Alexander R. Ivanov, and David A. Rozak

3. Targeted Isolation of Proteins from Natural Microbial Communities Living in an Extreme Environment

Steven W. Singer

4. Bacterial Identification and Subtyping Using DNA Microarray and DNA Sequencing

Sufian F. Al-Khaldi, Magdi M. Mossoba, Marc M. Allard, E. Kurt Lienau, and Eric D. Brown

Part II: Experimental Genomic Analyses

5. Genetic Manipulation of the Obligate Chemolithoautotrophic Bacterium Thiobacillus denitrificans

Harry R. Beller, Tina C. Legler, and Staci R. Kane

6. Genome-wide Mapping of the Binding Sites of Proteins that Interact with DNA

Stephen Spiro

Part III: Protein and Lipid Analyses

7. MICROBIAL PROTEOMICS USING MASS SPECTROMETRY

Harry B. Hines

8. Fourier Transform Infrared Spectroscopy for Molecular Analysis of Microbial Cells

Jesús J. Ojeda

Part IV: Metabolomic Analyses

9. Mass Spectrometry-based Microbial Metabolomics

Edward E. K. Baidoo, Peter I. Benke and Jay D. Keasling

10. Fast Sampling of the Cellular Metabolome

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

Part V: Analyses of Cellular Metabolism

11. Metabolic Pathway Determination and Flux Analysis in Non-model Microorganisms through ¹³C-isotope Labeling

Xueyang Feng, Wei-Qin Zhuang, Peter Colletti, Yinjie J. Tang

12. Biolog Phenotype Microarrays

April Shea, Mark Wolcott, Simon Daefler, and David Rozak

13. NanoSIP: NanoSIMS Applications for Microbial Biology

Jennifer Pett-Ridge and Peter K. Weber

Part VI: Kinetic Modeling of Cellular Processes

14. Electrophysiological-metabolic Modeling of Microbes: Applications in Fuel Cells and Environment Analysis

Max Fontus and Peter Ortoleva

15. Simulating Microbial Systems: Addressing Model Uncertainty/Incompleteness via Multiscale and Entropy Methods

A. Singharoy, H. Joshi, S. Cheluvaraja, Y. Miao, D. Brown and P. Ortoleva

Part VII: Genome-Scale Computational Studies

16. Bacterial Genome Annotation

Nicholas Beckloff, Shawn Starkenburg, Tracey Freitas, and Patrick Chain

17. LeishCyc: a Guide to Building a Metabolic Pathway Database and the Visualization of Metabolic Data

Eleanor C. Saunders, James I. MacRae, Thomas Naderer, Milica Ng, Malcolm J. McConville and Vladimir A. Likic

18. Development of Constraint-base System-level Models of Microbial Metabolism

Ali Navid

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

Zahra Zavareh, Eivind Almaas

20. Modeling a Minimal Cell

Michael L. Shuler, Patricia Foley, Jordan Atlas