Latest revision as of 21:17, 17 October 2014

iGEM ETH Zurich 2014

References

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[2] [http://dx.doi.org/10.1016/j.molcel.2014.06.007 Ausländer, D. et al., A Synthetic Multifunctional Mammalian pH Sensor and CO₂ Transgene-Control Device, Molecular Cell, 55, 2014]

[3] [http://dx.doi.org/10.1016/j.cbpa.2012.04.009 Bugaj, L. J., Schaffer, D. V., Bringing next-generation therapeutics to the clinic through synthetic biology, Current Opinion in Chemical Biology, 16, 2012]

[4] [http://dx.doi.org/10.1021/bi00512a013 Eberhard, A. et al., Structural identification of autoinducer of Photobacterium fischeri luciferase, Biochemistry, 20, 1981]

[5] [http://dx.doi.org/10.1098/rstb.2007.2039 Williams, P. et al., Look who's talking: communication and quorum sensing in the bacterial world, Philosophical Transactions of the Royal Society B: Biological Sciences, 362.1483, 2007]

[6] [http://dx.doi.org/10.1146/annurev.bioeng.10.061807.160536 Jayaraman, A., Wood, T. K. Bacterial quorum sensing: signals, circuits, and implications for biofilms and disease, Annual Review of Biomedical Engineering, 10, 2008]

[7] [http://dx.doi.org/10.1126/science.1237738 Benenson, Y., Recombinatorial Logic, Science, 340, 2013]

[8] [http://dx.doi.org/10.1038/nbt.2510 Siuti, P. et al., Synthetic circuits integrating logic and memory in living cells, Nature Biotechnology, 31.5, 2013]

[9] [http://dx.doi.org/10.1126/science.1232758 Bonnet, J. et al., Amplifying genetic logic gates, Science, 340.6132, 2013]

[10] [http://dx.doi.org/10.1038/nbt986 Collins, J. et al., Engineered riboregulators enable post-transcriptional control of gene expression, Nature Biotechnology, 22, 2004]

[11] [http://www.wolframscience.com/nksonline/toc.html Stephen, W., A new kind of science, Vol. 5, Champaign: Wolfram media, 2002]

[12][http://www.plluisi.org/emergence.html Luisi, P. L., The emergence of life: from chemical origins to synthetic biology, Chapter 6. Cambridge University Press, 2006]

[13][http://www.nature.com/nbt/journal/v27/n10/full/nbt.1568.html Salis, H. M., Mirsky, E. A., Voigt, C. A., Automated design of synthetic ribosome binding sites to control protein expression, Nature Biotechnology, 27, 2009]

[14][http://www.sciencedirect.com/science/article/pii/S1046202310003142 Brown, W. R. A. et al., Serine recombinases as tools for genome engineering, Methods 53.4: 372-379, 2011]

[15][http://www.sciencedirect.com/science/article/pii/0378111977900002 Bolivar, F. et al., Construction and characterization of new cloning vehicles. II. A multipurpose cloning system, Gene 2.2: 95-113, 1977]

[16][http://onlinelibrary.wiley.com/store/10.1002/bit.22660/asset/22660_ftp.pdf?v=1&t=i16i1rwr&s=2e51942db05c273bde36a22670b3baa138f7faf7 Lennen, R. M. et al., A Process for Microbial Hydrocarbon Synthesis: Overproduction of Fatty Acids in Escherichia coli and Catalytic Conversion to Alkanes Biotechnology and Bioengineering 106.2: 193-202, 2010]

[17] [http://kirschner.med.harvard.edu/files/bionumbers/Protein%20half-lives%20in%20E.%20coli.pdf Maurizi M. R., Proteases and protein degradation in Escherichia coli, Experientia. 1992 Feb 15 48(2):178-201. p.181 table 2]

[18] [http://www.pnas.org/content/109/15/5850.abstract Callura, J. M., Cantor, C. R., Collins, J. J., Genetic switchboard for synthetic biology applications, PNAS, 2012]

[19] [http://www.biomedcentral.com/1752-0509/7/6.abstract Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013]

[20] [http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html.abstract Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R., A synthetic multicellular system for programmed pattern formation, Nature, 2005]

[21] Team MIT 2010

[22] [http://www.ncbi.nlm.nih.gov/pubmed/10329160, Liang S. T., Ehrenberg M., Dennis P., Bremer H.,Decay of rplN and lacZ mRNA in Escherichia coli, Journal of molecular biology, 1999]

[23] [http://www.hbcpnetbase.com/ Haynes, W. M., ed. CRC handbook of chemistry and physics, CRC press, 2012]

[24] [http://onlinelibrary.wiley.com/doi/10.1002/3527600035.bpol6008/full Draget, K. I., Smidsrød, O., Skjåk-Bræk, G., Alginates from Algae, Biopolymers Online, 6, 2005]

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[26] [http://www.biomedcentral.com/1471-2105/15/136, O., Egea, J.A et. al, "MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics ", BMC Bioinformatics, 15:136, 2014]

[27] [http://jb.asm.org/content/185/5/1485.full Stewart, Philip S. "Diffusion in biofilms." Journal of bacteriology 185.5 : 1485-1491, 2003]

[28] [http://jb.asm.org/content/163/3/1210.short Kaplan, HEIDI B., and E. P. Greenberg. "Diffusion of autoinducer is involved in regulation of the Vibrio fischeri luminescence system." Journal of Bacteriology 163.3 : 1210-1214, 1985]

[29] [http://www.sabrinaandlars.ch/download/scientific/MasterThesis.pdf Lars Müller, "Growing of encapsulated Escherichia coli in picolitre sized calcium alginate beads", Master Thesis, Supervisor: Dr. Rene Pellaux, Bioprocess Laboratory ETH Zürich, 2008]

[30] [http://onlinelibrary.wiley.com/doi/10.1002/bit.260280609/pdf Hannoun, Betty JM, and Gregory Stephanopoulos. "Diffusion coefficients of glucose and ethanol in cell‐free and cell‐occupied calcium alginate membranes." Biotechnology and bioengineering 28.6 : 829-835, 1986]

[31] [http://dx.doi.org/10.1039/C2LC40761B Kitson, P.J., Rosnes, M. H., Sans, V., Dragone, V., Cronin, L., Configurable 3D-Printed millifluidic and microfluidic ‘lab on a chip’ reactionware devices, Lab on a Chip, 12, 2012]

[32] [http://dx.doi.org/10.1038/nbt986 Isaacs, F. J., Dwyer, D. J., Ding, C, Pervouchine, D. D., Cantor, C. R., Collins, J. J., Engineered riboregulators enable post-transcriptional control of gene expression, Nature Biotechnology, 22, 2004]

[33] [http://aem.asm.org/content/65/6/2324 Panke, S., Meyer, S., Huber, C. M., Witholt, B., Wubbolts, M.G., An alkane-responsive expression system for the production of fine chemicals, Applied and environmental microbiology, 65,1999]

[34] [http://pubs.acs.org/doi/abs/10.1021/sb4001323 Casini, A., Christodoulou, G., Freemont, P. S., Baldwin, G. S., Ellis, T., MacDonald, J. T. , R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences, ACS Synthetic Biology, 2013]

[35] [http://jb.asm.org/content/134/3/1141.full.pdf Chang, A. C. and Cohen, S. N., Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid, Journal of Bacteriology, 1978]

[36] [http://spectrum.ieee.org/robotics/diy/3d-printing-takes-shape Wallich, P., 3D-Printing takes shape, IEEE Spectrum, 2011]

@@ Line 2: / Line 2: @@
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-<div id="refEberhard" align="left"></html>[4] [http://dx.doi.org/10.1021/bi00512a013 Eberhard, A., ''et al''., Structural identification of autoinducer of ''Photobacterium fischeri'' luciferase, Biochemistry, 20, 1981]<html></div>
+<div id="refEberhard" align="left"></html>[4] [http://dx.doi.org/10.1021/bi00512a013 Eberhard, A. ''et al.'', Structural identification of autoinducer of ''Photobacterium fischeri'' luciferase, Biochemistry, 20, 1981]<html></div>
-<div id="refWilliams" align="left"></html>[5] [http://dx.doi.org/10.1098/rstb.2007.2039 Williams, P., ''et al''. Look who's talking: communication and quorum sensing in the bacterial world, Philosophical Transactions of the Royal Society B: Biological Sciences, 362.1483, 2007]<html></div>
+<div id="refWilliams" align="left"></html>[5] [http://dx.doi.org/10.1098/rstb.2007.2039 Williams, P. ''et al.'', Look who's talking: communication and quorum sensing in the bacterial world, Philosophical Transactions of the Royal Society B: Biological Sciences, 362.1483, 2007]<html></div>
-<div id="refJayaraman" align="left"></html>[6] [http://dx.doi.org/10.1146/annurev.bioeng.10.061807.160536 Jayaraman, A., and Wood, TK. Bacterial quorum sensing: signals, circuits, and implications for biofilms and disease, Annual Review of Biomedical Engineering, 10, 2008]<html></div>
+<div id="refJayaraman" align="left"></html>[6] [http://dx.doi.org/10.1146/annurev.bioeng.10.061807.160536 Jayaraman, A., Wood, T. K. Bacterial quorum sensing: signals, circuits, and implications for biofilms and disease, Annual Review of Biomedical Engineering, 10, 2008]<html></div>
 <div id="refKobi" align="left"></html>[7] [http://dx.doi.org/10.1126/science.1237738  Benenson, Y., Recombinatorial Logic, Science, 340, 2013]<html></div>
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-<div id="refBonnet" align="left"></html>[9] [http://dx.doi.org/10.1126/science.1232758 Bonnet, J., ''et al''., Amplifying genetic logic gates, Science, 340.6132, 2013]<html></div>
+<div id="refBonnet" align="left"></html>[9] [http://dx.doi.org/10.1126/science.1232758 Bonnet, J. ''et al.'', Amplifying genetic logic gates, Science, 340.6132, 2013]<html></div>
-<div id="refCollins" align="left"></html>[10] [http://dx.doi.org/10.1038/nbt986 Collins, J., ''et al''., Engineered riboregulators enable post-transcriptional control of gene expression, Nature Biotechnology, 22, 2004]<html></div>
+<div id="refCollins" align="left"></html>[10] [http://dx.doi.org/10.1038/nbt986 Collins, J. ''et al.'', Engineered riboregulators enable post-transcriptional control of gene expression, Nature Biotechnology, 22, 2004]<html></div>
-<div id="refWolfram" align="left"></html>[11] [http://www.wolframscience.com/nksonline/toc.html Wolfram, Stephen. A new kind of science. Vol. 5. Champaign: Wolfram media, 2002] <html></div>
+<div id="refWolfram" align="left"></html>[11] [http://www.wolframscience.com/nksonline/toc.html Stephen, W., A new kind of science, Vol. 5, Champaign: Wolfram media, 2002] <html></div>
-<div id="refEmergence" align="left"></html>[12][http://www.plluisi.org/emergence.html Luisi, Pier Luigi. The emergence of life: from chemical origins to synthetic biology. ''Chapter 6''. Cambridge University Press, 2006]<html></div>
+<div id="refEmergence" align="left"></html>[12][http://www.plluisi.org/emergence.html Luisi, P. L., The emergence of life: from chemical origins to synthetic biology, ''Chapter 6''. Cambridge University Press, 2006]<html></div>
-<div id="refSalis" align="left"></html>[13][http://www.nature.com/nbt/journal/v27/n10/full/nbt.1568.html Salis, H. M., Mirsky, E. A. & Voigt, C. A., Automated design of synthetic ribosome binding sites to control protein expression, Nature Biotechnology, 27, 2009]<html></div>
+<div id="refSalis" align="left"></html>[13][http://www.nature.com/nbt/journal/v27/n10/full/nbt.1568.html Salis, H. M., Mirsky, E. A., Voigt, C. A., Automated design of synthetic ribosome binding sites to control protein expression, Nature Biotechnology, 27, 2009]<html></div>
-<div id="refBrown" align="left"></html>[14][http://www.sciencedirect.com/science/article/pii/S1046202310003142 Brown, William RA, et al. Serine recombinases as tools for genome engineering, Methods 53.4: 372-379, 2011]<html></div>
+<div id="refBrown" align="left"></html>[14][http://www.sciencedirect.com/science/article/pii/S1046202310003142 Brown, W. R. A. ''et al.'', Serine recombinases as tools for genome engineering, Methods 53.4: 372-379, 2011]<html></div>
-<div id="refBolivar" align="left"></html>[15][http://www.sciencedirect.com/science/article/pii/0378111977900002 Bolivar, F. et al. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system, Gene 2.2: 95-113, 1977]<html></div>
+<div id="refBolivar" align="left"></html>[15][http://www.sciencedirect.com/science/article/pii/0378111977900002 Bolivar, F. ''et al.'', Construction and characterization of new cloning vehicles. II. A multipurpose cloning system, Gene 2.2: 95-113, 1977]<html></div>
-<div id="refLennen" align="left"></html>[16][http://onlinelibrary.wiley.com/store/10.1002/bit.22660/asset/22660_ftp.pdf?v=1&t=i16i1rwr&s=2e51942db05c273bde36a22670b3baa138f7faf7 Lennen, R. M. et al., A Process for Microbial Hydrocarbon Synthesis: Overproduction of Fatty Acids in ''Escherichia coli'' and Catalytic Conversion to Alkanes Biotechnology and Bioengineering 106.2: 193-202, 2010]<html></div>
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 <div id="refDegProt" align="left"></html>[17]
-[http://kirschner.med.harvard.edu/files/bionumbers/Protein%20half-lives%20in%20E.%20coli.pdf Maurizi MR., Proteases and protein degradation in ''Escherichia coli'', Experientia. 1992 Feb 15 48(2):178-201. p.181 table 2]<html></div>
+[http://kirschner.med.harvard.edu/files/bionumbers/Protein%20half-lives%20in%20E.%20coli.pdf Maurizi M. R., Proteases and protein degradation in ''Escherichia coli'', Experientia. 1992 Feb 15 48(2):178-201. p.181 table 2]<html></div>
 <div id="refCallura" align="left"></html>[18] [http://www.pnas.org/content/109/15/5850.abstract Callura, J. M., Cantor, C. R., Collins, J. J., Genetic switchboard for synthetic biology applications, PNAS, 2012]<html></div>
 <div id="Weber" align="left"></html>[19] [http://www.biomedcentral.com/1752-0509/7/6.abstract Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013]<html></div>
 <div id="Basu" align="left"></html>[20] [http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html.abstract Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R., A synthetic multicellular system for programmed pattern formation, Nature, 2005]<html></div>
-<div id="MIT" align="left"></html>[21] [https://2010.igem.org/Team:MIT_tmodel, Team MIT 2010]<html></div>
+<div id="MIT" align="left"></html>[21] [https://2010.igem.org/Team:MIT_tmodel Team MIT 2010]<html></div>
-<div id="refCRC" align="left"></html>[21] [http://www.hbcpnetbase.com/ Haynes, W.M., ed. CRC handbook of chemistry and physics, CRC press, 2012]<html></div>
+<div id="refCRC" align="left"></html>[22] [http://www.ncbi.nlm.nih.gov/pubmed/10329160, Liang S. T., Ehrenberg M., Dennis P., Bremer H.,Decay of rplN and lacZ mRNA in ''Escherichia coli'', Journal of molecular biology, 1999] <html></div>
-<div id="refCRC" align="left"></html>[22] [http://www.ncbi.nlm.nih.gov/pubmed/10329160, Liang S.T., Ehrenberg M., Dennis P., Bremer H., Journal of molecular biology, 1999] <html></div>
+<div id="refCRC" align="left"></html>[23] [http://www.hbcpnetbase.com/ Haynes, W. M., ed. CRC handbook of chemistry and physics, CRC press, 2012]<html></div>
+<div id="refCRC" align="left"></html>[24] [http://onlinelibrary.wiley.com/doi/10.1002/3527600035.bpol6008/full Draget, K. I.,  Smidsrød, O., Skjåk-Bræk, G., Alginates from Algae, Biopolymers Online, 6, 2005]<html></div>
+<div id="refCRC" align="left"></html>[25] [http://ac.els-cdn.com/016777999090139O/1-s2.0-016777999090139O-main.pdf?_tid=ae84eb60-54a0-11e4-b254-00000aab0f6c&acdnat=1413401162_64b33e6ee56a40fe717b500d16a4db15 Smidsrød, O., Skjåk-Bræk, G., Alginate as immobilization matrix for cells, Trends in Biotechnology, 8, 1990]<html></div>
+<div id="Meigo" align="left"></html>[26] [http://www.biomedcentral.com/1471-2105/15/136, O., Egea, J.A et. al, "MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics ", BMC Bioinformatics, 15:136, 2014]<html></div>
+<div id="Stewart" align='left'> </html>[27] [http://jb.asm.org/content/185/5/1485.full Stewart, Philip S. "Diffusion in biofilms." Journal of bacteriology 185.5 : 1485-1491, 2003]<html></div>
+<div id="Kaplan" align='left'> </html>[28] [http://jb.asm.org/content/163/3/1210.short Kaplan, HEIDI B., and E. P. Greenberg. "Diffusion of autoinducer is involved in regulation of the Vibrio fischeri luminescence system." Journal of Bacteriology 163.3 : 1210-1214, 1985]<html></div>
+<div id="Lars" align='left'> </html>[29] [http://www.sabrinaandlars.ch/download/scientific/MasterThesis.pdf Lars Müller, "Growing of encapsulated Escherichia coli in picolitre sized calcium alginate beads", Master Thesis, Supervisor: Dr. Rene Pellaux, Bioprocess Laboratory ETH Zürich, 2008]<html></div>
+<div id="Hannoun" align='left'> </html>[30] [http://onlinelibrary.wiley.com/doi/10.1002/bit.260280609/pdf Hannoun, Betty JM, and Gregory Stephanopoulos. "Diffusion coefficients of glucose and ethanol in cell‐free and cell‐occupied calcium alginate membranes." Biotechnology and bioengineering 28.6 : 829-835, 1986]<html></div>
+<div id="refKitson" align='left'> </html>[31] [http://dx.doi.org/10.1039/C2LC40761B Kitson, P.J., Rosnes, M. H., Sans, V., Dragone, V., Cronin, L., Configurable 3D-Printed millifluidic and microfluidic ‘lab on a chip’ reactionware devices, Lab on a Chip, 12, 2012]<html></div>
+<div id="refIsaacs" align='left'> </html>[32] [http://dx.doi.org/10.1038/nbt986 Isaacs, F. J., Dwyer, D. J., Ding, C, Pervouchine, D. D., Cantor, C. R., Collins, J. J., Engineered riboregulators enable post-transcriptional control of gene expression, Nature Biotechnology, 22, 2004]<html></div>
+<div id="refPanke" align='left'> </html>[33] [http://aem.asm.org/content/65/6/2324 Panke, S., Meyer, S., Huber, C. M., Witholt, B., Wubbolts, M.G., An alkane-responsive expression system for the production of fine chemicals, Applied and environmental microbiology, 65,1999]<html></div>
+<div id="refR2oDNA" align='left'> </html>[34] [http://pubs.acs.org/doi/abs/10.1021/sb4001323 Casini, A., Christodoulou, G., Freemont, P. S., Baldwin, G. S., Ellis, T., MacDonald, J. T. , R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences, ACS Synthetic Biology, 2013]<html></div>
+<div id="refChang" align='left'> </html>[35] [http://jb.asm.org/content/134/3/1141.full.pdf Chang, A. C. and Cohen, S. N., Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid, Journal of Bacteriology, 1978]<html></div>
+<div id="refWallich" align='left'> </html>[36] [http://spectrum.ieee.org/robotics/diy/3d-printing-takes-shape Wallich, P., 3D-Printing takes shape, IEEE Spectrum, 2011]<html></div>
 </article>
 </html>
 {{:Team:ETH Zurich/tpl/foot}}

Team:ETH Zurich/project/references

From 2014.igem.org

Latest revision as of 21:17, 17 October 2014

References

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