20.20(S10):Advanced topics: Difference between revisions
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|'''Rewiring the specificity of two-component signal transduction systems.''' <br>Skerker JM, et al. ''Cell'' (2008)133(6):1043-54.<br>[[DOI: 10.1016/j.cell.2008.04.040]] | |'''Rewiring the specificity of two-component signal transduction systems.''' <br>Skerker JM, et al. ''Cell'' (2008)133(6):1043-54.<br>[[DOI: 10.1016/j.cell.2008.04.040]] | ||
|'''Synthetic biology: engineering Escherichia coli to see light | |'''Synthetic biology: engineering Escherichia coli to see light'''<br>Levskaya A, et al. ''Nature'' (2005) 438(7067):441-2.<br> [[PMID: 16306980]] | ||
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| '''Controlling System Dynamics''' <br> | | '''Controlling System Dynamics''' <br> | ||
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|'''Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics''' <br>Bashor CJ, et al. ''Science'' (2008)319: 1539-1543 <br> [[DOI: 10.1126/science.1151153]] | |'''Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics''' <br>Bashor CJ, et al. ''Science'' (2008)319: 1539-1543 <br> [[DOI: 10.1126/science.1151153]] | ||
| '''Synthetic protein scaffolds provide modular control over metabolic flux | | '''Synthetic protein scaffolds provide modular control over metabolic flux'''<br> Dueber JE, et al. ''Nat Biotech'' 2009 27(8):753-9.<br>[[PMID: 19648908]] | ||
|-- | |-- | ||
| '''Functional Network Composition'''<br> | | '''Functional Network Composition'''<br> | ||
| <font color = blue> Thursday Mar 11</font color> | | <font color = blue> Thursday Mar 11</font color> | ||
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| '''Diversity-based, model-guided construction of synthetic gene networks with predicted functions''' <br>Ellis T, Wang X, and Collins JJ. ''Nat Biotech'' | | '''Diversity-based, model-guided construction of synthetic gene networks with predicted functions''' <br>Ellis T, Wang X, and Collins JJ. ''Nat Biotech'' (2009) 27(5):465-71<br>[[PMID: 19377462]] | ||
| '''A synthetic genetic edge detection program'''<br>Tabor JJ et al. <br>[[PMID: 19563759]] | | '''A synthetic genetic edge detection program'''<br>Tabor JJ et al. ''Cell'' (2009) 137(7):1272-81 <br>[[PMID: 19563759]] | ||
|-- | |-- | ||
| '''Tuning the system: directed evolution''' <br> | | '''Tuning the system: directed evolution''' <br> | ||
| Wed Mar 17 | | Wed Mar 17 | ||
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| '''A fast, robust and tunable synthetic gene oscillator''' <br>Stricker, J. et al. ''Nature'' 456, 516–519 | | '''A fast, robust and tunable synthetic gene oscillator''' <br>Stricker, J. et al. ''Nature'' (2008) 456, 516–519<br>[[PMID: 18971928]] | ||
| '''Directed evolution of a genetic circuit''' <br>Yokobayashi, Y, et al.''Proc. Natl Acad. Sci. USA'' 99, 16587–16591 | | '''Directed evolution of a genetic circuit''' <br>Yokobayashi, Y, et al.''Proc. Natl Acad. Sci. USA'' (2002) 99, 16587–16591 <br>[[PMID: 12451174]] | ||
|-- | |-- | ||
! colspan="3" | Spring Break Mar 22-26 | ! colspan="3" | Spring Break Mar 22-26 | ||
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| Wed Mar 31 | | Wed Mar 31 | ||
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| '''Article 1:''' <br>'''Programming cells by multiplex genome engineering and accelerated evolution | | '''Article 1:''' <br>'''Programming cells by multiplex genome engineering and accelerated evolution'''<br>Wang HH, et al. ''Nature'' (2009) Aug 13;460(7257):894-8. <br>[[PMID: 19633652 ]]<br>'''Article 2:''' <br> '''Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.'''Gibson DG, et al. Science. 2008 Feb 29;319(5867):1215-20. <br>[[PMID: 18218864]] | ||
| | | '''Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides'''<br>Stemmer WP, et al. ''Gene'' (1995) 164(1):49-53 <br>[[PMID: 7590320]] <br> | ||
[[PMID: 7590320]] <br> | |||
|-- | |-- | ||
| '''Chassis''' <br> | | '''Chassis''' <br> | ||
| <font color = blue> Thursday Apr 8 </font color> | | <font color = blue> Thursday Apr 8 </font color> | ||
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| '''Article 1: Towards synthesis of a minimal cell'''<br>Forster, A. C. & Church, G. M. <br> ''Mol. Syst. Biol.'' 2, 45 | | '''Article 1: <br>Towards synthesis of a minimal cell'''<br>Forster, A. C. & Church, G. M. <br> ''Mol. Syst. Biol.'' (2006) 2, 45<br>[[PMID: 16924266]] <br> '''alternative Article 1? Emergent properties of reduced-genome Escherichia coli.''' <br> Pósfai G, et al. ''Science.''(2006)312(5776):1044-6.<br> [[PMID: 16645050]] <br> '''Article 2:<br> Genome transplantation in bacteria:changing one species to another'''<br>Lartigue C, et al. ''Science'' 2007, 317:632-638.<br>[[PMID: 17600181]] | ||
changing one species to another | |||
|'''Reconstitution of contractile FtsZ rings in liposomes.''' Osawa M, Anderson DE, Erickson HP.''Science'' (2008)320(5877):792-4.<br>[[DOI: 10.1126/science.1154520]] | |'''Reconstitution of contractile FtsZ rings in liposomes.''' Osawa M, Anderson DE, Erickson HP.''Science'' (2008)320(5877):792-4.<br>[[DOI: 10.1126/science.1154520]] | ||
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| Wed Apr 14 | | Wed Apr 14 | ||
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|'''Article 1: | |'''Article 1:<br>Design of genetic networks with specified functions by evolution in silico'''<br> Francois, P. & Hakim, V. ''Proc. Natl Acad. Sci. USA'' 101, 580–585 (2004). <br> [[PMID: 14704282]]<br>'''Article 2:<br>Engineering transcription factors with novel DNA-binding specificity using comparative genomics''' <br> Desai TA, et al. ''Nucleic Acids Res'' (2009) 37(8): 2493-503<br>[[PMID: 19264798]] | ||
| '''Design of multi-specificity in protein interfaces'''Humphris, EL; Kortemme, T. ''PLoS computational biology'' (2007) 3(8):e164<br>[[DOI : 10.1371/journal.pcbi.0030164]] | | '''Design of multi-specificity in protein interfaces'''Humphris, EL; Kortemme, T. ''PLoS computational biology'' (2007) 3(8):e164<br>[[DOI : 10.1371/journal.pcbi.0030164]] | ||
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| Wed Apr 21 | | Wed Apr 21 | ||
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|'''Article 1: Gene regulation at the single-cell level'''<br>Rosenfeld N, et al. ''Science'' 307, 1962–1965 (2005) | |'''Article 1: <br>Gene regulation at the single-cell level'''<br>Rosenfeld N, et al. ''Science'' 307, 1962–1965 (2005)<br>[[PMID: 15790856]]<br> '''Article 2: <br>Stochastic switching as a survival strategy in fluctuating environments'''<br> Acar M. et al. ''Nature Genetics'' 40, 471 – 475 (2008) <br>[[PMID: 18362885]] | ||
|'''Phenotypic consequences of promoter-mediated transcriptional noise.''' <br>Blake WJ, et al. ''Molecular Cell''(2006) 24(6):853-65<br>[[DOI : 10.1016/j.molcel.2006.11.003]] | |'''Phenotypic consequences of promoter-mediated transcriptional noise.''' <br>Blake WJ, et al. ''Molecular Cell''(2006) 24(6):853-65<br>[[DOI : 10.1016/j.molcel.2006.11.003]] | ||
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| Wed Apr 28 | | Wed Apr 28 | ||
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|'''Article 1: Production of the antimalarial drug precursor artemisinic acid in engineered yeast'''<br>Ro DK, et al. ''Nature'' (2006) 440, 940–943 <br>[[PMID: 16612385]]<br> '''Article 2: Synthesis of methyl halides from biomass using engineered microbes''' <br> Bayer TS, et al. ''J Am Chem Soc'' 2009, 131:6508-6515.<br>[[PMID: 19378995]] | |'''Article 1:<br> Production of the antimalarial drug precursor artemisinic acid in engineered yeast'''<br>Ro DK, et al. ''Nature'' (2006) 440, 940–943 <br>[[PMID: 16612385]]<br> '''Article 2: <br>Synthesis of methyl halides from biomass using engineered microbes''' <br> Bayer TS, et al. ''J Am Chem Soc'' 2009, 131:6508-6515.<br>[[PMID: 19378995]] | ||
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| <font color = blue>Tue May 4</font color> | | <font color = blue>Tue May 4</font color> | ||
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|'''Article 1: A synthetic Escherichia coli predator-prey ecosystem'''<br> Balagaddé FK, et al. ''Mol Syst Biol.'' 2008;4:187. <br>[[PMID: 18414488]] '''Article 2: Synthetic ecosystems based on airborne inter- and intrakingdom communication''' <br> Weber, W., Daoud-El Baba, M. & Fussenegger, M. ''Proc. Natl Acad. Sci. USA'' (2007) 104, 10435–10440 <br>[[PMID: 17551014]] | |'''Article 1: <br>A synthetic Escherichia coli predator-prey ecosystem'''<br> Balagaddé FK, et al. ''Mol Syst Biol.'' 2008;4:187. <br>[[PMID: 18414488]]<br> '''Article 2:<br> Synthetic ecosystems based on airborne inter- and intrakingdom communication''' <br> Weber, W., Daoud-El Baba, M. & Fussenegger, M. ''Proc. Natl Acad. Sci. USA'' (2007) 104, 10435–10440 <br>[[PMID: 17551014]] | ||
| '''Synthetic cooperation in engineered yeast populations'''<br> Shou W, Ram S, Vilar JM. ''Proc Natl Acad Sci U S A.'' (2007) Feb 6;104(6):1877-82. <br>[[PMID: 17267602]] | | '''Synthetic cooperation in engineered yeast populations'''<br> Shou W, Ram S, Vilar JM. ''Proc Natl Acad Sci U S A.'' (2007) Feb 6;104(6):1877-82. <br>[[PMID: 17267602]] | ||
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| <font color = blue> Tue May 11? </font color> | | <font color = blue> Tue May 11? </font color> | ||
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|''' Article 1: Synthetic biology: caught between property rights, the public domain, and the commons''' <br>Rai A, Boyle ''J. PLoS Biol.'' (2007)5(3):e58<br>[[PMID: 17355173]] <br> | |''' Article 1: <br>Synthetic biology: caught between property rights, the public domain, and the commons''' <br>Rai A, Boyle ''J. PLoS Biol.'' (2007)5(3):e58<br>[[PMID: 17355173]] <br> | ||
|'''Article 2: Patents and Translational Research in Genomics'''<br>Kaye J, Hawkins N, and Taylor J. ''Nature Biotech'' (2007) 25(7): 739–741.[[doi: 10.1038/nbt0707-739.]] | |'''Article 2: <br>Patents and Translational Research in Genomics'''<br>Kaye J, Hawkins N, and Taylor J. ''Nature Biotech'' (2007) 25(7): 739–741.[[doi: 10.1038/nbt0707-739.]] | ||
|-- | |-- | ||
|'''Safety!''' | |'''Safety!''' | ||
| <font color = blue> Tue May 11? </font color> | | <font color = blue> Tue May 11? </font color> | ||
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| '''Article 1: Managing the unimaginable. Regulatory responses to the challenges posed by synthetic biology and synthetic genomics.''' <br>Samuel GN, Selgelid MJ, Kerridge I. ''EMBO reports'' (2009) 10(1):7-11.<br>[[DOI: 10.1038/embor.2008.232]]<br> | | '''Article 1:<br> Managing the unimaginable. Regulatory responses to the challenges posed by synthetic biology and synthetic genomics.''' <br>Samuel GN, Selgelid MJ, Kerridge I. ''EMBO reports'' (2009) 10(1):7-11.<br>[[DOI: 10.1038/embor.2008.232]]<br> | ||
|'''Article 2: Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses?''' <br>Michael Specter [http://www.newyorker.com/reporting/2007/12/03/071203fa_fact_specter New Yorker article] | |'''Article 2: <br>Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses?''' <br>Michael Specter [http://www.newyorker.com/reporting/2007/12/03/071203fa_fact_specter New Yorker article] | ||
|-- | |-- | ||
|'''Programming Languages''' | |'''Programming Languages''' | ||
| <font color = blue> Tue May 11? </font color> | | <font color = blue> Tue May 11? </font color> | ||
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| '''Article 1: Towards programming languages for genetic engineering of living cells'''<br> Pedersen M, Phillips A ''J R Soc Interface'' 2009, 6(Suppl 4):S437-S450.<br>[[PMID: 19369220]]<br> | | '''Article 1: <br>Towards programming languages for genetic engineering of living cells'''<br> Pedersen M, Phillips A ''J R Soc Interface'' 2009, 6(Suppl 4):S437-S450.<br>[[PMID: 19369220]]<br> | ||
|'''Article 2: Cells Are Plausible Targets for High-Level Spatial Languages'''<br> Beal J, and Bachrach, J. Spatial Computing Workshop, October 2008. | |'''Article 2: <br>Cells Are Plausible Targets for High-Level Spatial Languages'''<br> Beal J, and Bachrach, J. Spatial Computing Workshop, October 2008. | ||
|-- | |-- | ||
|'''Molecular and Cellular Computing''' | |'''Molecular and Cellular Computing''' | ||
| <font color = blue> Tue May 11? </font color> | | <font color = blue> Tue May 11? </font color> | ||
| | | | ||
|'''Article 1: An autonomous molecular computer for logical control of gene expression'''<br>Benenson Y, et al. ''Nature'' 2004 May 27;429(6990):423-9. Epub 2004 Apr 28.<br>[[PMID: 15116117]] | |'''Article 1: <br>An autonomous molecular computer for logical control of gene expression'''<br>Benenson Y, et al. ''Nature'' 2004 May 27;429(6990):423-9. Epub 2004 Apr 28.<br>[[PMID: 15116117]] | ||
|'''Article 2: Engineering bacteria to solve the Burnt Pancake Problem''' <br>Haynes KA, et al. ''J Biol Eng.'' 2008 May 20;2:8.<br>[[PMID: 18492232]] | |'''Article 2: <br>Engineering bacteria to solve the Burnt Pancake Problem''' <br>Haynes KA, et al. ''J Biol Eng.'' 2008 May 20;2:8.<br>[[PMID: 18492232]] | ||
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Revision as of 14:08, 18 January 2010
20.385: Advanced Topics in Synthetic Biology
Assignments
Homework dropbox is here
Part 1: Readings
Instructions for these assignment are here |
Part 2: Team Mentoring
Instructions for these assignments are here |
Reading Schedule
Discussions will be 1 hour long during Wednesday 2-5 studio block
26-152
TOPIC | DATE | Discussion leader(s) | Discussion paper(s) | Related paper(s) to enjoy | |
Preview of 20.385 | Wed Feb 3 | Natalie Kuldell Ron Weiss |
before next week read
| ||
Parts™ | Wed Feb 10 | Natalie Kuldell Ron Weiss |
A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor.
Brent R, Ptashne M.Cell. 1985 Dec;43(3 Pt 2):729-36. |
Activation of prokaryotic transcription through arbitrary protein-protein contacts Dove SL, et al. Nature. 1997 Apr 10;386(6625):627-30. PMID: 9121589 | |
Logic Modules |
Wed Feb 17 (RW OoT) | Environmental signal integration by a modular AND gate. Anderson JC, Voigt C, Arkin, AP Molecular systems biology3 133 2007 DOI : 10.1038/msb4100173 |
A synthetic oscillatory network of transcriptional regulators. Elowitz, MB, and Leibler, S. Nature 403, 335–338 (2000) | ||
Signal Specificity |
Wed Feb 24 | Rewiring the specificity of two-component signal transduction systems. Skerker JM, et al. Cell (2008)133(6):1043-54. DOI: 10.1016/j.cell.2008.04.040 |
Synthetic biology: engineering Escherichia coli to see light Levskaya A, et al. Nature (2005) 438(7067):441-2. PMID: 16306980 | ||
Controlling System Dynamics |
Wed Mar 3 (RW OoT) | Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics Bashor CJ, et al. Science (2008)319: 1539-1543 DOI: 10.1126/science.1151153 |
Synthetic protein scaffolds provide modular control over metabolic flux Dueber JE, et al. Nat Biotech 2009 27(8):753-9. PMID: 19648908 | ||
Functional Network Composition |
Thursday Mar 11 | Diversity-based, model-guided construction of synthetic gene networks with predicted functions Ellis T, Wang X, and Collins JJ. Nat Biotech (2009) 27(5):465-71 PMID: 19377462 |
A synthetic genetic edge detection program Tabor JJ et al. Cell (2009) 137(7):1272-81 PMID: 19563759 | ||
Tuning the system: directed evolution |
Wed Mar 17 | A fast, robust and tunable synthetic gene oscillator Stricker, J. et al. Nature (2008) 456, 516–519 PMID: 18971928 |
Directed evolution of a genetic circuit Yokobayashi, Y, et al.Proc. Natl Acad. Sci. USA (2002) 99, 16587–16591 PMID: 12451174 | ||
Spring Break Mar 22-26 | No class all week | ||||
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DNA construction and editing technologies |
Wed Mar 31 | Article 1: Programming cells by multiplex genome engineering and accelerated evolution Wang HH, et al. Nature (2009) Aug 13;460(7257):894-8. PMID: 19633652 Article 2: Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.Gibson DG, et al. Science. 2008 Feb 29;319(5867):1215-20. PMID: 18218864 |
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides Stemmer WP, et al. Gene (1995) 164(1):49-53 PMID: 7590320 | ||
Chassis |
Thursday Apr 8 | Article 1: Towards synthesis of a minimal cell Forster, A. C. & Church, G. M. Mol. Syst. Biol. (2006) 2, 45 PMID: 16924266 alternative Article 1? Emergent properties of reduced-genome Escherichia coli. Pósfai G, et al. Science.(2006)312(5776):1044-6. PMID: 16645050 Article 2: Genome transplantation in bacteria:changing one species to another Lartigue C, et al. Science 2007, 317:632-638. PMID: 17600181 |
Reconstitution of contractile FtsZ rings in liposomes. Osawa M, Anderson DE, Erickson HP.Science (2008)320(5877):792-4. DOI: 10.1126/science.1154520 | ||
In silico and -omics |
Wed Apr 14 | Article 1: Design of genetic networks with specified functions by evolution in silico Francois, P. & Hakim, V. Proc. Natl Acad. Sci. USA 101, 580–585 (2004). PMID: 14704282 Article 2: Engineering transcription factors with novel DNA-binding specificity using comparative genomics Desai TA, et al. Nucleic Acids Res (2009) 37(8): 2493-503 PMID: 19264798 |
Design of multi-specificity in protein interfacesHumphris, EL; Kortemme, T. PLoS computational biology (2007) 3(8):e164 DOI : 10.1371/journal.pcbi.0030164 | ||
Noise |
Wed Apr 21 | Article 1: Gene regulation at the single-cell level Rosenfeld N, et al. Science 307, 1962–1965 (2005) PMID: 15790856 Article 2: Stochastic switching as a survival strategy in fluctuating environments Acar M. et al. Nature Genetics 40, 471 – 475 (2008) PMID: 18362885 |
Phenotypic consequences of promoter-mediated transcriptional noise. Blake WJ, et al. Molecular Cell(2006) 24(6):853-65 DOI : 10.1016/j.molcel.2006.11.003 | ||
Metabolic Engineering | Wed Apr 28 | Article 1: Production of the antimalarial drug precursor artemisinic acid in engineered yeast Ro DK, et al. Nature (2006) 440, 940–943 PMID: 16612385 Article 2: Synthesis of methyl halides from biomass using engineered microbes Bayer TS, et al. J Am Chem Soc 2009, 131:6508-6515. PMID: 19378995 |
|||
Cell Cell Communication/System Ecology | Tue May 4 | Article 1: A synthetic Escherichia coli predator-prey ecosystem Balagaddé FK, et al. Mol Syst Biol. 2008;4:187. PMID: 18414488 Article 2: Synthetic ecosystems based on airborne inter- and intrakingdom communication Weber, W., Daoud-El Baba, M. & Fussenegger, M. Proc. Natl Acad. Sci. USA (2007) 104, 10435–10440 PMID: 17551014 |
Synthetic cooperation in engineered yeast populations Shou W, Ram S, Vilar JM. Proc Natl Acad Sci U S A. (2007) Feb 6;104(6):1877-82. PMID: 17267602 | ||
Property rights in synthetic biology | Tue May 11? | Article 1: Synthetic biology: caught between property rights, the public domain, and the commons Rai A, Boyle J. PLoS Biol. (2007)5(3):e58 PMID: 17355173 |
Article 2: Patents and Translational Research in Genomics Kaye J, Hawkins N, and Taylor J. Nature Biotech (2007) 25(7): 739–741.doi: 10.1038/nbt0707-739. | ||
Safety! | Tue May 11? | Article 1: Managing the unimaginable. Regulatory responses to the challenges posed by synthetic biology and synthetic genomics. Samuel GN, Selgelid MJ, Kerridge I. EMBO reports (2009) 10(1):7-11. DOI: 10.1038/embor.2008.232 |
Article 2: Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses? Michael Specter New Yorker article | ||
Programming Languages | Tue May 11? | Article 1: Towards programming languages for genetic engineering of living cells Pedersen M, Phillips A J R Soc Interface 2009, 6(Suppl 4):S437-S450. PMID: 19369220 |
Article 2: Cells Are Plausible Targets for High-Level Spatial Languages Beal J, and Bachrach, J. Spatial Computing Workshop, October 2008. | ||
Molecular and Cellular Computing | Tue May 11? | Article 1: An autonomous molecular computer for logical control of gene expression Benenson Y, et al. Nature 2004 May 27;429(6990):423-9. Epub 2004 Apr 28. PMID: 15116117 |
Article 2: Engineering bacteria to solve the Burnt Pancake Problem Haynes KA, et al. J Biol Eng. 2008 May 20;2:8. PMID: 18492232 |