Synthetic Biology, Part A

Section I. Measuring and Engineering Central Dogma Processes
Sequence-specificity and Energy Landscapes of DNA-binding Molecules
Joshua R. Tietjen, Leslie J. Donato, Devesh Bhimisaria and Aseem Z. Ansari
Promoter Reliability in Modular Transcriptional Networks
Rajat Anand, Navneet Rai and Mukund Thattai
The Analysis of ChIP-seq Data
Wenxiu Ma and Wing Hung Wong
Using DNA Microarrays to Assay Part Function
Virgil A. Rhodius and Carol A. Gross
Orthogonal gene expression in Escherichia coli
Wenlin An and Jason Chin
Directed evolution of promoters and tandem gene arrays for customizing RNA synthesis rates and regulation
Keith E.J. Tyo, Elke Nevoigt and Gregory StephanopoulosSection II. Device and System Design, Optimization, and Debugging
Design and Connection of Robust Genetic Circuits
Ron Weiss
Engineering RNAi circuits
Yaakov Benenson
From SELEX to cell: Dual selections for synthetic riboswitches
Joy Sinha, Shana Topp, and Justin P. Gallivan
Using noisy gene expression mediated by engineered adenovirus to probe signaling dynamics in mammalian cells
Jeffrey V. Wong, Guang Yao, Joseph R. Nevins and Lingchong You
De novo design and construction of an inducible gene expression system in mammalian cells
Maria Karlsson, Wilfried Weber and Martin Fussenegger
BioBuilding: Using banana-scented bacteria to teach synthetic biology
James Dixon and Natalie KuldellSection III. Device Measurement, Optimization, and Debugging
Use of Fluorescence Microscopy to Analyze Genetic Circuit Dynamics
Gürol Süel
Microfluidics for synthetic biology: From design to execution
M. S. Ferry, I. A. Razinkov, J. Hasty
Plate-based assays for light-regulated gene expression systems
Jeffrey J. Tabor
Spatiotemporal control of small GTPases with light using the LOV domain
Yi I. Wu, Xiaobo Wang, Li He, Denise Montell and Klaus M. Hahn
Light Control of Plasma Membrane Recruitment using the Phy-PIF system
Jared E. Toettcher, Delquin Gong,