Part I: Constructing Multicellular Systems
1. Recent Progress in Engineering Human-associated Microbiomes
Stephanie J. Yaung, George M. Church, Harris H. Wang
2. Constructing Synthetic Microbial Communities to Explore the Ecology and Evolution of Symbiosis
Adam James Waite and Wenying Shou
3. Combining Engineering and Evolution to Create Novel Metabolic Mutualisms Between Species
Lon Chubiz, Sarah Douglas, and William Harcombe
4. Design, Construction, and Characterization Methodologies for Synthetic Microbial Consortia
Hans C. Bernstein and Ross P. Carlson
5. An Observation Method for Autonomous Signaling-mediated Synthetic Diversification in Escherichia coli
Ryoji Sekine, Shotaro Ayukawa, and Daisuke Kiga
6. Integration-free Reprogramming of Somatic Cells to Induced Pluripotent Stem Cells (iPSCs) without Viral Vectors, Recombinant DNA and Genetic Modification
Boon Chin HENG and Martin FUSSENEGGER
7. Transformation of Bacillus subtilis
Xiao-Zhou Zhang, Chun You and Y.-H. Percival Zhang
8. Culturing Anaerobes to use as a Model System for Studying the Evolution of Syntrophic Mutualism
Sujung Lim, Sergey Syolyar, Kristina Hillesland
9. Therapeutic Microbes for Infectious Disease
Choon Kit Wong, Mui Hua Tan, Bahareh Haji Rasouliha, In Young Hwang, Hua Ling, Chueh Loo Poh, and Matthew Wook Chang
Part II: Analyzing and Modeling Multicellular Systems
10. Quantitative Measurement and Analysis in a Synthetic Pattern Formation Multicellular System
Xiongfei Fu and Wei Huang
11. Transcriptome Analysis of a Microbial Coculture in which the Cell Populations are Separated by a Membrane
Kazufumi Hosoda, Naoaki Ono, Shingo Suzuki, and Tetsuya Yomo
12. Identification of Mutations in Laboratory Evolved Microbes from Next-generation Sequencing data using breseq
Daniel E. Deatherage and Jeffrey E. Barrick
13. 3D-Fluorescence in situ Hybridization of Intact, Anaerobic Biofilm
Kristen A. Brileya, Laura B. Camilleri, and Matthew W. Fields
14. The Characterization of Living Bacterial Colonies Using Nanospray Desorption Electrospray Ionization Mass Spectrometry
Brandi S. Heath, Matthew J. Marshall, Julia Laskin
15. Modeling Community Population Dynamics with the Open-Source Language R
Robin Green and Wenying Shou
16. Simulating Microbial Community Patterning using Biocellion
Seunghwa Kang, Simon Kahan, Babak Momeni
