Reading List : Intro. to Synthetic Biology, Fall 2011
9/28 : Introduction
- Special Issue of Science on Synthetic Biology: Read the introduction, news, reviews and perspectives sections.
- Five hard truths: http://www.nature.com/news/2010/100120/pdf/463288a.pdf
- Andrianantoandro, Basu, Karig and Ron Weiss, Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology 2, 2006.
- Arkin and Fletcher, Fast, Cheap and Somewhat in Control. Genome Biology 7(8), 114, 2006.
- Basu, Karig and Weiss, Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology 2, 2006.
- Caleb J. Bashor, Andrew A. Horwitz, Sergio G. Peisajovich, and Wendell A. Lim, Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. Annual Review of Biophysics 39, 515-537 (2010).
- Guillaume, Mutalik, and Arkin, Toward rational design of bacterial genomes. Current Opinion in Microbiology, 2011.
- Smith, Bacterial Growth, unpublished?
- Chaitanya A. Athale and Hemangi Chaudhari, Population Length Variability and Nucleoid Numbers in E. coli, Bioinformatics, 2011.
- The yeast life cycle: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/Y/Yeast.html
- The gro documentation.
- The Wikipedia entry on Euler integration
- Ratkowsky, Olley, McMeekin, and Ball, Relationship between temperature and growth rate of bacterial cultures, J. Bacteriology, 1982.
- Dijkstra, Guarded commands, nondeterminacy and formal derivation of programs, CACM, 1975.
- Elowitz, Levine, Siggia, and Swain. Stochastic Gene Expression in a Single Cell, Science, 2006.
- Swain, Elowitz, Siggia. Intrinsic and Extrinsic Contributions to Stochasticity in Gene Expression, PNAS, 2002.
- Raj and van Oudenaarden, Single-molecule approaches to stochastic gene expression, Annual Review of Biophysics, 2009.
- Thattai and van Oudenaarden, Intrinsic noise in gene regulatory networks. PNAS, 2001.
- Lestas, Vinnecombe, and Paullson, Fundamental limits on the suppression of molecular fluctuations, Nature, 2010.
- Go look up all the definitions in today's lecture on Wikipedia or Planet Math.
- Feller, An Introduction to Probability Theory and its Applications. This is simply the best book out there on probability.
- Wilkinsen, Stochastic Modelling for Systems Biology. This is a good book for how probability is used in biology. Also covers the basic definitions.
10/10: The Biology of Gene Expression
- A good overview.
- A Youtube video on transcription and translation.
- Transcribe and translate a gene -- interactive! (somewhat misleading in the translation step, as the code seems not complimented like it should be).
- A good text on biochemistry is essential. I like Lehninger Principles of Biochemistry, Fourth Edition, 2004.
- Raser and O'Shea, Noise in Gene Expression: Origins, Consequences, and Control, Science 2005.
- McAdams and Arkin. Stochastic mechanisms in gene expression, PNAS, 1997.
10/12: Project Ideas
- Check out the iGEM projects for 2011.
10/14: The Math of Gene Expression
- Klavins, 2009 Course Notes on Stochasticity, 2009.
- Ozbudak, Thattai, Kurtser, Grossman and van Oudenaarden, Regulation of noise in the expression of a single gene, Nature Genetics 2002.
10/17: Engineering Gene Expression
- Lu, Khalil, and Collins. Next-generation synthetic gene networks. Nat. Biotechnol 2009.
- Alper, Fischer, Nevoigt, and Stephanopoulos. Tuning genetic control through promoter engineering. PNAS 2005.
- Pfleger, Douglas, Smolke, and Keasling. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotechnol 2006.
- Salis, Mirsky, Voigt. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol 2009.
- Yokobayashi, Weiss, and Arnold. Directed Evolution of a Genetic Circuit. PNAS 2002.
- Andersen, Sternberg, Poulsen, Bjorn, Givskov, and Molin. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl Environ Microbiol 1998.
10/19: Gene Regulation
- Cox, Surette, and Elowitz, Programming gene expression with combinatorial promoters, MSB, 2007.
- N Rosenfeld, M Elowitz & U Alon, Negative Autoregulation Speeds the Response Times of Transcription Networks JMB, 323:785-793 (2002).
- Attila Becskei & Luis Serrano, Engineering stability in gene networks by autoregulation, Nature 405, 590-593, 2000.
- Eric Klavins, Proportional-Integral Control of Stochastic Gene Regulatory Networks, Conference on Decision and Control, 2010.
- Daniel Madar, Erez Dekel, Anat Bren and Uri Alon, Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli, BMC System Biology, 5:111 (2011).
- Timothy S. Gardner, Charles R. Cantor, and James J. Collins, Construction of a genetic toggle switch in Escherichia coli, Nature 403, 339-342, 2000.
- Brian Munsky and Mustafa Khammash, Transient analysis of stochastic switches and trajectories with applications to gene regulatory networks, IET Systems Biology, September 2008 Volume: 2 Issue, 323 - 333.
- Joshua Cherry and Frederick Adler, How to make a Biological Switch, Journal of Theoretical Biology, Volume 203, Issue 2, 21 March 2000, Pages 117-133.
10/22: Feedback and Noise
- Lestas, Vinnecombe, and Paulsson, Fundamental Limits on the Suppression of Molecular Fluctuations, Nature, 2010.
- Singh and Hespanha, Optimal feedback strength for noise suppression in auto-regulatory gene networks.
- N. Napp, S. Burden, and E. Klavins, Setpoint Regulation for Stochastically Interacting Robots, Autonomous Robotics, Vol. 30, No. 1. Sep. 2010. pp. 57--71. url
10/28: Biowarfare, safety, ethics
- American experience material on biowarfare: http://www.pbs.org/wgbh/americanexperience/features/timeline/weapon-timeline/
- Video on polio reconstruction: http://www.youtube.com/watch_popup?v=hfElVabRh2Y&vq=medium#t=31.
- The CDC's biosafety guidlines: http://www.cdc.gov/biosafety/publications/bmbl5/index.htm
- Presidential commission on synthetic biology: http://www.bioethics.gov/documents/synthetic-biology/PCSBI-Synthetic-Biology-Report-12.16.10.pdf
- Elowitz and Leibler, A synthetic oscillatory network of transcriptional regulators, Nature, 2000.
- The BZ Reaction: http://en.wikipedia.org/wiki/Belousov%E2%80%93Zhabotinsky_reaction.
- The Brusselator: http://en.wikipedia.org/wiki/Brusselator
- Predator prey: http://en.wikipedia.org/wiki/Lotka-Volterra
- The Oregonator: http://en.wikipedia.org/wiki/Oregonator
- Nakajima et al., Reconstitution of Circadian Oscillation of Cyanobacterial KaiC Phosphorylation in Vitro, Science 2005.
- Stricker et al., A fast, robust and tunable synthetic gene oscillator, Nature 2008.
- Danino et al., A synchronized quorum of genetic clocks, Nature, 2010.
- Kim and Winfree, Synthetic in vitro transcriptional oscillators, Molecular Systems Biology, 2011.
- You, Cox, Weiss and Arnold, Programmed population control by cell–cell communication and regulated killing, Nature, 2004.
- Basu, Gerchman, Collins, Arnold and Weiss, A synthetic multicellular system for programmed pattern formation. Nature 434, 1130-1134, 2005.
- Stewart and Nemhauser, Do Trees Grow on Money? Auxin as the Currency of the Cellular Economy, CSHL Perspectives on Biology, 2011.
- Zhao Y., Auxin biosynthesis and its role in plant development., Annu Rev Plant Biol. 2010 Jun 2;61:49-64.
- Chen and Weiss, Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana, Nature, 2005.
- Juan M. Pedraza and Alexander van Oudenaarden, Noise Propagation in Gene Networks, Science 2005.
- Mukund Thattai, Alexander van Oudenaarden, http://www.sciencedirect.com/science/article/pii/S000634950275635X, Biophysical Journal, 2002.
- Kuo-Chen Yeh, Shu-Hsing Wu, John T. Murphy and J. Clark Lagarias, A Cyanobacterial Phytochrome Two-Component Light Sensory System, Science 1997.
- J.J. Tabor, H. Salis, Z.B. Simpson, A.A. Chevalier, A. Levskaya, E.M.Marcotte, C.A. Voigt and A.D. Ellington, A Synthetic Genetic Edge Detection Program, Cell, 137 (7) 1272-81 (2009).
- A. Levskaya, A.A. Chevalier, J.J. Tabor, Z.B. Simpson, L.A. Lavery, M.Levy, E.A. Davidson, A.Scouras, A.D. Ellington, E.M. Marcotte, and C.A. Voigt, Engineering Escherichia coli to see light Nature, 438 (7067), 441-442, (2005).
11/16: Cellular Automata
- Howard Gutowitz, Cellular Automata, 1991.
- Stephen Wolfram, A New Kind of Science, 2002.
- Daniel Yamins, Radhika Nagpal, Automated Global-to-Local Programming in 1-D Spatial Multi-Agent Systems, AAMAS, 2008.
- Nelson, Cox, Principles of Biochemistry, 4th Edition, Section II, Freeman, 2005.
- The Kegg Database.
11/23: Evolution I
- Araya CL, Payen C, Dunham MJ, Fields S, Whole-genome sequencing of a laboratory-evolved yeast strain, BMC Genomics, 2010.
- Svend K. Petersen-Mahrt, Reuben S. Harris & Michael S. Neuberger, AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification, Nature, 2002.
- Wang et al, Programming cells by multiplex genome engineering and accelerated evolution, Nature 2009.
- Sleight SC, Bartley BA, Lieviant JA and Sauro HM, Designing and engineering evolutionary robust genetic circuits, JBE 2010.
- Lenski, The Long Term Experimental Evolution Project, ongoing.
11/28: Evolution II
- Dekel and Alon, Optimality and evolutionary tuning of the expression level of a protein, Nature, 2005.
- Tuck Seng Wong, Daria Zhurina and Ulrich Schwaneberg, The Diversity Challenge in Directed Protein Evolution, Comb. Chem, 2006.
- Padilla, Colovos, and Yeates, Nanohedra: Using symmetry to design self assembling protein cages, layers, crystals, and filaments, PNAS 2001.
- Zhang, Fabrication of novel biomaterials through molecular self-assembly, Nature Biotech, 2003.