NYMU Taipei/Paper

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<p><font color="#000000" size="3">[http://www.bioportfolio.com/cgi-bin/acatalog/Synthetic_Biology__A_New_Paradigm_for_Biological_D.html Synthetic Biology: A New Paradigm for Biological Discovery]</font></p>
<p><font color="#000000" size="3">[http://www.bioportfolio.com/cgi-bin/acatalog/Synthetic_Biology__A_New_Paradigm_for_Biological_D.html Synthetic Biology: A New Paradigm for Biological Discovery]</font></p>
<hr />
<hr />
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<p><font color="#0000ff" size="3">Sorted by publication date in descending order</font></p>
+
<p><font color="#0000ff" size="3">Selected References (sorted by publication date in descending order)</font></p>
 +
<p><font size="2">Synthetic biology through the prism of scenarios.<br />
 +
Biotechnol J. 2007 Aug 17; [Epub ahead of print]</font></p>
 +
<p><font size="2">Robustness Analysis and Tuning of Synthetic Gene Networks.<br />
 +
Bioinformatics. 2007 Jul 30; [Epub ahead of print]</font></p>
 +
<p><font size="2">Combinatorial promoter design for engineering noisy gene expression.<br />
 +
Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12726-31.</font></p>
 +
<p><font size="2">Using two-component systems and other bacterial regulatory factors for the fabrication of synthetic genetic devices.<br />
 +
Methods Enzymol. 2007;422:488-512.</font></p>
 +
<p><font size="2">Nano-enabled synthetic biology.<br />
 +
Mol Syst Biol. 2007;3:125. Epub 2007 Jul 10.</font></p>
 +
<p><font size="2">Synthetic biology: designs for life.<br />
 +
Nature. 2007 Jul 5;448(7149):32-33.</font></p> 
 +
<p><font size="2">Bioengineering novel in vitro metabolic pathways using synthetic biology.<br />
 +
Curr Opin Microbiol. 2007 Jun;10(3):246-53.</font></p>
 +
<p><font size="2">The economics of synthetic biology.<br />
 +
Molecular Systems Biology. 3:117-120, 2007.</font></p>
 +
<p><font size="2">Rebuilding microbial genomes.<br />
 +
Bioessays. 29(6):580-590, 2007.</font></p>
 +
<p><font size="2">A synthetic biology challenge: making cells compute.<br />
 +
Molecular BioSystems. 3:343-353, 2007.</font></p>
 +
<p><font size="2">Guiding bacteria with small molecules and RNA.<br />
 +
Journal of the American Chemical Society. 129(21):6807-6811, 2007.</font></p>
 +
<p><font size="2">Designing biological systems.<br />
 +
Genes & Development. 21:242-254, 2007.</font></p>
 +
<p><font size="2">Chemical aspects of synthetic biology.<br />
 +
Chemistry & Biodiversity. 4(4):603-621, 2007.</font></p>  
<p><font size="2">A bottom-up approach to gene regulation.<br />
<p><font size="2">A bottom-up approach to gene regulation.<br />
-
Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC, Collins JJ<br />
+
Nature 30: 979, 2006</font></p>
-
Nature(30.979) , 2006 - USA(Massachusetts)</font></p>
+
<p><font size="2">Regulation of flagella.<br />
<p><font size="2">Regulation of flagella.<br />
-
McCarter LL<br />
+
Curr Opin Microbiol 6: 869, 2006</font></p>
-
Curr Opin Microbiol(6.869) , 2006 - USA(Iowa)</font></p>
+
<p><font size="2">Regulatory dynamics of synthetic gene networks with positive feedback.<br />
<p><font size="2">Regulatory dynamics of synthetic gene networks with positive feedback.<br />
-
Maeda YT, Sano M<br />
+
J Mol Biol 5: 239, 2006</font></p>
-
J Mol Biol(5.239) , 2006 - Japan</font></p>
+
<p><font size="2">Synthetic biology: new engineering rules for an emerging discipline.<br />
<p><font size="2">Synthetic biology: new engineering rules for an emerging discipline.<br />
-
Andrianantoandro E, Basu S, Karig DK, Weiss R<br />
+
Mol Syst Biol, 2006</font></p>
-
Mol Syst Biol(0) , 2006 - USA(New Jersey)</font></p>
+
<p><font size="2">A synthetic multicellular system for programmed pattern formation.<br />
<p><font size="2">A synthetic multicellular system for programmed pattern formation.<br />
-
Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R<br />
+
Nature 30: 979, 2005</font></p>
-
Nature(30.979) , 2005 - USA(New Jersey)</font></p>
+
<p><font size="2">A synthetic gene-metabolic oscillator.<br />
<p><font size="2">A synthetic gene-metabolic oscillator.<br />
-
Fung E, Wong WW, Suen JK, Bulter T, Lee SG, Liao JC<br />
+
Nature 30: 979, 2005</font></p>
-
Nature(30.979) , 2005 - USA(California)</font></p>
+
<p><font size="2">Long-term monitoring of bacteria undergoing programmed population control in a microchemostat.<br />
<p><font size="2">Long-term monitoring of bacteria undergoing programmed population control in a microchemostat.<br />
-
Balagadde FK, You L, Hansen CL, Arnold FH, Quake SR<br />
+
Science 29: 162, 2005</font></p>
-
Science(29.162) , 2005 - USA(California)</font></p>
+
<p><font size="2">Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana.<br />
<p><font size="2">Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana.<br />
-
Chen MT, Weiss R<br />
+
Nat Biotechnol 17: 721, 2005</font></p>
-
Nat Biotechnol(17.721) , 2005 - USA(New Jersey)</font></p>
+
<p><font size="2">Hysteresis in a synthetic mammalian gene network.<br />
<p><font size="2">Hysteresis in a synthetic mammalian gene network.<br />
-
Kramer BP, Fussenegger M<br />
+
Proc Natl Acad Sci U S A 10: 272, 2005</font></p>
-
Proc Natl Acad Sci U S A(10.272) , 2005 - Switzerland</font></p>
+
<p><font size="2">Ultrasensitivity and noise propagation in a synthetic transcriptional cascade.<br />
<p><font size="2">Ultrasensitivity and noise propagation in a synthetic transcriptional cascade.<br />
-
Hooshangi S, Thiberge S, Weiss R<br />
+
Proc Natl Acad Sci U S A 10: 272, 2005</font></p>
-
Proc Natl Acad Sci U S A(10.272) , 2005 - USA(New Jersey)</font></p>
+
<p><font size="2">Semi-synthetic mammalian gene regulatory networks.<br />
<p><font size="2">Semi-synthetic mammalian gene regulatory networks.<br />
-
Kramer BP, Fischer M, Fussenegger M<br />
+
Metab Eng 3: 397, 2005</font></p>
-
Metab Eng(3.397) , 2005 - Switzerland</font></p>
+
<p><font size="2">Transcriptional regulation and metabolism.<br />
<p><font size="2">Transcriptional regulation and metabolism.<br />
-
Brynildsen MP, Wong WW, Liao JC<br />
+
Biochem Soc Trans 2: 579, 2005</font></p>
-
Biochem Soc Trans(2.579) , 2005 - USA(California)</font></p>
+
<p><font size="2">Signal-amplifying genetic circuit enables in vivo observation of weak promoter activation in the Rhl quorum sensing system.<br />
<p><font size="2">Signal-amplifying genetic circuit enables in vivo observation of weak promoter activation in the Rhl quorum sensing system.<br />
-
Karig DK, Weiss R<br />
+
Biotechnol Bioeng 2: 173, 2005</font></p>
-
Biotechnol Bioeng(2.173) , 2005 - USA(New Jersey)</font></p>
+
<p><font size="2">A network of orthogonal ribosome x mRNA pairs.<br />
<p><font size="2">A network of orthogonal ribosome x mRNA pairs.<br />
-
Rackham O, Chin JW<br />
+
Nat Chem Biol, 2005</font></p>
-
Nat Chem Biol(0) , 2005 - UK</font></p>
+
<p><font size="2">Programmed population control by cell-cell communication and regulated killing.<br />
<p><font size="2">Programmed population control by cell-cell communication and regulated killing.<br />
-
You L, Cox RS 3rd, Weiss R, Arnold FH<br />
+
Nature 30: 979, 2004</font></p>
-
Nature(30.979) , 2004 - USA(California)</font></p>
+
<p><font size="2">Using a quantitative blueprint to reprogram the dynamics of the flagella gene network.<br />
<p><font size="2">Using a quantitative blueprint to reprogram the dynamics of the flagella gene network.<br />
-
Kalir S, Alon U<br />
+
Cell 26: 626, 2004</font></p>
-
Cell(26.626) , 2004 - Israel</font></p>
+
<p><font size="2">An engineered epigenetic transgene switch in mammalian cells.<br />
<p><font size="2">An engineered epigenetic transgene switch in mammalian cells.<br />
-
Kramer BP, Viretta AU, Daoud-El-Baba M, Aubel D, Weber W, Fussenegger M<br />
+
Nat Biotechnol 17: 721, 2004</font></p>
-
Nat Biotechnol(17.721) , 2004 - Switzerland</font></p>
+
<p><font size="2">Programmable cells: interfacing natural and engineered gene networks.<br />
<p><font size="2">Programmable cells: interfacing natural and engineered gene networks.<br />
-
Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR, Collins JJ<br />
+
Proc Natl Acad Sci U S A 10: 272, 2004</font></p>
-
Proc Natl Acad Sci U S A(10.272) , 2004 - USA(Massachusetts)</font></p>
+
<p><font size="2">Design of artificial cell-cell communication using gene and metabolic networks.<br />
<p><font size="2">Design of artificial cell-cell communication using gene and metabolic networks.<br />
-
Bulter T, Lee SG, Wong WW, Fung E, Connor MR, Liao JC<br />
+
Proc Natl Acad Sci U S A 101:2299-304, 2004</font></p>
-
Proc Natl Acad Sci U S A(10.272) , 2004 - USA(California)</font></p>
+
<p><font size="2">Spatiotemporal control of gene expression with pulse-generating networks.<br />
<p><font size="2">Spatiotemporal control of gene expression with pulse-generating networks.<br />
-
Basu S, Mehreja R, Thiberge S, Chen MT, Weiss R<br />
+
Proc Natl Acad Sci U S A 10: 272, 2004</font></p>
-
Proc Natl Acad Sci U S A(10.272) , 2004 - USA(New Jersey)</font></p>
+
<p><font size="2">Optimizing genetic circuits by global sensitivity analysis.<br />
<p><font size="2">Optimizing genetic circuits by global sensitivity analysis.<br />
-
Feng XJ, Hooshangi S, Chen D, Li G, Weiss R, Rabitz H<br />
+
Biophys J 4: 463, 2004</font></p>
-
Biophys J(4.463) , 2004 - USA(New Jersey)</font></p>
+
<p><font size="2">Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in ''Escherichia coli''.<br />
-
<p><font size="2">Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli.<br />
+
Cell 26: 626, 2003</font></p>
-
Atkinson MR, Savageau MA, Myers JT, Ninfa AJ<br />
+
-
Cell(26.626) , 2003 - USA(Michigan)</font></p>
+
<p><font size="2">Combinatorial synthesis of genetic networks.<br />
<p><font size="2">Combinatorial synthesis of genetic networks.<br />
-
Guet CC, Elowitz MB, Hsing W, Leibler S<br />
+
Science 29: 162, 2002</font></p>
-
Science(29.162) , 2002 - USA(New Jersey)</font></p>
+
<p><font size="2">Directed evolution of a genetic circuit.<br />
<p><font size="2">Directed evolution of a genetic circuit.<br />
-
Yokobayashi Y, Weiss R, Arnold FH<br />
+
Proc Natl Acad Sci U S A 10: 272, 2002</font></p>
-
Proc Natl Acad Sci U S A(10.272) , 2002 - USA(California)</font></p>
+
<p><font size="2">Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion.<br />
<p><font size="2">Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion.<br />
-
Becskei A, Seraphin B, Serrano L<br />
+
EMBO J 10: 456, 2001</font></p>
-
EMBO J(10.456) , 2001 - Germany</font></p>
+
<p><font size="2">A synthetic oscillatory network of transcriptional regulators.<br />
<p><font size="2">A synthetic oscillatory network of transcriptional regulators.<br />
-
Elowitz MB, Leibler S<br />
+
Nature 30: 979, 2000</font></p>
-
Nature(30.979) , 2000 - USA(New Jersey)</font></p>
+
<p><font size="2">Engineering stability in gene networks by autoregulation.<br />
<p><font size="2">Engineering stability in gene networks by autoregulation.<br />
-
Becskei A, Serrano L<br />
+
Nature 30: 979, 2000</font></p>
-
Nature(30.979) , 2000 - Germany</font></p>
+
<p><font size="2">Construction of a genetic toggle switch in Escherichia coli.<br />
<p><font size="2">Construction of a genetic toggle switch in Escherichia coli.<br />
-
Gardner TS, Cantor CR, Collins JJ<br />
+
Nature 30: 979, 2000</font></p>
-
Nature(30.979) , 2000 - USA(Massachusetts)</font></p>
+
<p>&nbsp;</p>
<p>&nbsp;</p>
<hr />
<hr />
[https://2007.igem.org/Taipei Back]
[https://2007.igem.org/Taipei Back]

Latest revision as of 11:20, 27 October 2007

A very expensive book on Synthetic Biology (US$2700 for single user license edition):

[http://www.bioportfolio.com/cgi-bin/acatalog/Synthetic_Biology__A_New_Paradigm_for_Biological_D.html Synthetic Biology: A New Paradigm for Biological Discovery]

Selected References (sorted by publication date in descending order)

Synthetic biology through the prism of scenarios.
Biotechnol J. 2007 Aug 17; [Epub ahead of print]

Robustness Analysis and Tuning of Synthetic Gene Networks.
Bioinformatics. 2007 Jul 30; [Epub ahead of print]

Combinatorial promoter design for engineering noisy gene expression.
Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12726-31.

Using two-component systems and other bacterial regulatory factors for the fabrication of synthetic genetic devices.
Methods Enzymol. 2007;422:488-512.

Nano-enabled synthetic biology.
Mol Syst Biol. 2007;3:125. Epub 2007 Jul 10.

Synthetic biology: designs for life.
Nature. 2007 Jul 5;448(7149):32-33.

Bioengineering novel in vitro metabolic pathways using synthetic biology.
Curr Opin Microbiol. 2007 Jun;10(3):246-53.

The economics of synthetic biology.
Molecular Systems Biology. 3:117-120, 2007.

Rebuilding microbial genomes.
Bioessays. 29(6):580-590, 2007.

A synthetic biology challenge: making cells compute.
Molecular BioSystems. 3:343-353, 2007.

Guiding bacteria with small molecules and RNA.
Journal of the American Chemical Society. 129(21):6807-6811, 2007.

Designing biological systems.
Genes & Development. 21:242-254, 2007.

Chemical aspects of synthetic biology.
Chemistry & Biodiversity. 4(4):603-621, 2007.

A bottom-up approach to gene regulation.
Nature 30: 979, 2006

Regulation of flagella.
Curr Opin Microbiol 6: 869, 2006

Regulatory dynamics of synthetic gene networks with positive feedback.
J Mol Biol 5: 239, 2006

Synthetic biology: new engineering rules for an emerging discipline.
Mol Syst Biol, 2006

A synthetic multicellular system for programmed pattern formation.
Nature 30: 979, 2005

A synthetic gene-metabolic oscillator.
Nature 30: 979, 2005

Long-term monitoring of bacteria undergoing programmed population control in a microchemostat.
Science 29: 162, 2005

Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana.
Nat Biotechnol 17: 721, 2005

Hysteresis in a synthetic mammalian gene network.
Proc Natl Acad Sci U S A 10: 272, 2005

Ultrasensitivity and noise propagation in a synthetic transcriptional cascade.
Proc Natl Acad Sci U S A 10: 272, 2005

Semi-synthetic mammalian gene regulatory networks.
Metab Eng 3: 397, 2005

Transcriptional regulation and metabolism.
Biochem Soc Trans 2: 579, 2005

Signal-amplifying genetic circuit enables in vivo observation of weak promoter activation in the Rhl quorum sensing system.
Biotechnol Bioeng 2: 173, 2005

A network of orthogonal ribosome x mRNA pairs.
Nat Chem Biol, 2005

Programmed population control by cell-cell communication and regulated killing.
Nature 30: 979, 2004

Using a quantitative blueprint to reprogram the dynamics of the flagella gene network.
Cell 26: 626, 2004

An engineered epigenetic transgene switch in mammalian cells.
Nat Biotechnol 17: 721, 2004

Programmable cells: interfacing natural and engineered gene networks.
Proc Natl Acad Sci U S A 10: 272, 2004

Design of artificial cell-cell communication using gene and metabolic networks.
Proc Natl Acad Sci U S A 101:2299-304, 2004

Spatiotemporal control of gene expression with pulse-generating networks.
Proc Natl Acad Sci U S A 10: 272, 2004

Optimizing genetic circuits by global sensitivity analysis.
Biophys J 4: 463, 2004

Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli.
Cell 26: 626, 2003

Combinatorial synthesis of genetic networks.
Science 29: 162, 2002

Directed evolution of a genetic circuit.
Proc Natl Acad Sci U S A 10: 272, 2002

Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion.
EMBO J 10: 456, 2001

A synthetic oscillatory network of transcriptional regulators.
Nature 30: 979, 2000

Engineering stability in gene networks by autoregulation.
Nature 30: 979, 2000

Construction of a genetic toggle switch in Escherichia coli.
Nature 30: 979, 2000

 

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