20.109 | Fall 2007 | Undergraduate

Laboratory Fundamentals in Biological Engineering


List of Papers for Module 1 Presentations


Dwyer, M. A., L. L. Looger, and H. W. Hellinga. “Computational Design of a Biologically Active Enzyme.” Science 304 (2004): 1967-1971.

Knight, T. “Idempotent Vector Design for Standard Assembly of Biobricks.” Massachussetts Institute of Technology Artificial Intelligence Laboratory, MIT Synthetic Biology Working Group, 2004.

Phillips, I., and P. A. Silver. “A New Biobrick Assembly Strategy Designed for Facile Protein Engineering.” Massachussetts Institute of Technology Artificial Intelligence Laboratory, MIT Synthetic Biology Working Group, 2003.


Fields, S., and O. K. Song. “A Novel Genetic System to Detect Protein-Protein Interactions.” Nature 340 (1989): 245-246.

Hasty, J., D. McMillen, and J. J. Collins. “Engineered Gene Circuits.” Nature 420 (2002): 224-230.

Elowitz, M. B., and S. Leibler. “A Synthetic Oscillatory Network of Transcriptional Regulators.” Nature 403 (2000): 335-338.

Bayer, T. S., and C. D. Smolke. “Programmable Ligand-controlled Riboregulators of Eukaryotic Gene Expression.” Nat Biotechnol 23 (2005): 337-343.

Atsumi, S., and J. W. Little. “Regulatory Circuit Design and Evolution Using Phage {Lambda}.” Genes & Dev 18 (2004): 2086-2094.

Gardner, T. S., C. R. Cantor, and J. J. Collins. “Construction of a Genetic Toggle Switch in Escherichia coli.” Nature 403 (2000): 339-342.

Anderson, J. C., C. Voigt, and A. P. Arkin. “Environmental Signal Integration by a Modular AND Gate.” Molecular Systems Biology 3 (2007): 133.

Win, M. N., and C. D. Smolke. “A Modular and Extensible RNA-based Gene-regulatory Platform for Engineering Cellular Function.” Proc Natl Acad Sci USA (August 20, 2007).


Basu, S., Y. Gerchman, C. H. Collins, F. H. Arnold, and R. Weiss. “A Synthetic Multicellular System for Programmed Pattern Formation.” Nature 434 (2005): 1130-1134.

Anderson, J. C., E. J. Clarke, A. P. Arkin, and C. A. Voigt. “Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria.” J Mol Biol 355 (2006): 619-627.

Dejong, J. M., Y. Liu, A. P. Bollon, R. M. Long, S. Jennewein, D. Williams, and R. B. Croteau. “Genetic Engineering of Taxol Biosynthetic Genes in Saccharomyces Cerevisiae.” Biotechnol Bioeng 93 (2006): 212-224.

Levskaya, A., A. A. Chevalier, J. J. Tabor, Z. B. Simpson, L. A. Lavery, M. Levy, E. A. Davidson, A. Scouras, A. D. Ellington, and E. M. Marcotte, et al. “Synthetic Biology: Engineering Escherichia coli to See Light.” Nature 438 (2005): 441-442.

Martin, V. J., D. J. Pitera, S. T. Withers, J. D. Newman, and J. D. Keasling. “Engineering a Mevalonate Pathway in Escherichia coli for Production of Terpenoids.” Nat Biotechnol 21 (2003): 796-802.

Noireaux, V., and A. Libchaber. “A Vesicle Bioreactor as a Step Toward an Artificial Cell Assembly.” Proc Natl Acad Sci USA 101 (2004): 17669-17674.

Wang, L., J. Xie, and P. G. Schultz. “Expanding the Genetic Code.” Annu Rev Biophys Biomol Struct 35 (2006): 225-249.

Yeh, B. J., R. J. Rutigliano, A. Deb, D. Bar-Sagi, and W. A. Lim. “Rewiring Cellular Morphology Pathways with Synthetic Guanine Nucleotide Exchange Factors.” Nature 447, no. 7144 (2007): 596-600.

Dueber, J. E., E. A. Mirsky, and W. A. Lim. “Engineering Synthetic Signaling Proteins with Ultrasensitive Input/Output Control.” Nat Biotechnol 25, no. 6 (2007): 660-662.

Artificial Life

Glass, J. I., N. Assad-Garcia, N. Alperovich, S. Yooseph, M. R. Lewis, M. Maruf, C. A. Hutchison III, H. O. Smith, and J. C. Venter. “Essential Genes of a Minimal Bacterium.” Proc Natl Acad Sci 103 (2006): 425-430.

Ishikawa, K., K. Sato, Y. Shima, I. Urabe, and T. Yomo. “Expression of a Cascading Genetic Network within Liposomes.” FEBS Lett 576 (2004): 387-390.

Smith, H. O., C. A. Hutchison III, C. Pfannkoch, and J. C. Venter. “Generating a Synthetic Genome by Whole Genome Assembly: {Phi}X174 Bacteriophage from Synthetic Oligonucleotides.” Proc Natl Acad Sci USA 100 (2003): 15440-15445.

Tumpey, T. M., C. F. Basler, P. V. Aguilar, H. Zeng, A. Solorzano, D. E. Swayne, N. J. Cox, J. M. Katz, J. K. Taubenberger, and P. Palese, et al. “Characterization of the Reconstructed 1918 Spanish Influenza Pandemic Virus.” Science 310 (2005): 77-80.

Itaya, M., K. Tsuge, M. Koizumi, and K. Fujita. “Combining Two Genomes in One Cell: Stable Cloning of the Synechocystis PCC6803 Genome in the Bacillus Subtilis 168 Genome.” Proc Natl Acad Sci USA 102, no. 44 (November 1, 2005): 15971-6.

Lartigue, C., J. I. Glass, N. Alperovich, R. Pieper, P. P. Parmar, C. A. Hutchison 3rd, H. O. Smith, and J. C. Venter. “Genome Transplantation in Bacteria: Changing One Species to Another.” Science 317, no. 5838: 632-8.


Haywood, Annika F. M., and Brian E. Staveley. “Parkin Counteracts Symptoms in a Drosophila Model of Parkinson’s Disease.” BMC Neuroscience. 5 (2004): 14.

Learning Resource Types
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